CifFile.CifFile API documentation

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# CifFile.CifFile module

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    # To maximize python3/python2 compatibility
    from __future__ import print_function
    from __future__ import unicode_literals
    from __future__ import division
    from __future__ import absolute_import

    try:
        from cStringIO import StringIO
    except ImportError:
        from io import StringIO

    # Python 2,3 compatibility
    try:
        from urllib import urlopen         # for arbitrary opening
        from urlparse import urlparse, urlunparse,urljoin
    except:
        from urllib.request import urlopen
        from urllib.parse import urlparse,urlunparse,urljoin

    # The unicode type does not exist in Python3 as the str type
    # encompasses unicode.  PyCIFRW tests for 'unicode' would fail
    # Suggestions for a better approach welcome.

    if isinstance(u"abc",str):   #Python3
        unicode = str

    __copyright = """
    PYCIFRW License Agreement (Python License, Version 2)
    -----------------------------------------------------

    1. This LICENSE AGREEMENT is between the Australian Nuclear Science
    and Technology Organisation ("ANSTO"), and the Individual or
    Organization ("Licensee") accessing and otherwise using this software
    ("PyCIFRW") in source or binary form and its associated documentation.

    2. Subject to the terms and conditions of this License Agreement,
    ANSTO hereby grants Licensee a nonexclusive, royalty-free, world-wide
    license to reproduce, analyze, test, perform and/or display publicly,
    prepare derivative works, distribute, and otherwise use PyCIFRW alone
    or in any derivative version, provided, however, that this License
    Agreement and ANSTO's notice of copyright, i.e., "Copyright (c)
    2001-2014 ANSTO; All Rights Reserved" are retained in PyCIFRW alone or
    in any derivative version prepared by Licensee.

    3. In the event Licensee prepares a derivative work that is based on
    or incorporates PyCIFRW or any part thereof, and wants to make the
    derivative work available to others as provided herein, then Licensee
    hereby agrees to include in any such work a brief summary of the
    changes made to PyCIFRW.

    4. ANSTO is making PyCIFRW available to Licensee on an "AS IS"
    basis. ANSTO MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
    IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, ANSTO MAKES NO AND
    DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
    FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYCIFRW WILL NOT
    INFRINGE ANY THIRD PARTY RIGHTS.

    5. ANSTO SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYCIFRW
    FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS A
    RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYCIFRW, OR ANY
    DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.

    6. This License Agreement will automatically terminate upon a material
    breach of its terms and conditions.

    7. Nothing in this License Agreement shall be deemed to create any
    relationship of agency, partnership, or joint venture between ANSTO
    and Licensee. This License Agreement does not grant permission to use
    ANSTO trademarks or trade name in a trademark sense to endorse or
    promote products or services of Licensee, or any third party.

    8. By copying, installing or otherwise using PyCIFRW, Licensee agrees
    to be bound by the terms and conditions of this License Agreement.

    """

    import re,sys
    from . import StarFile
    from .StarFile import StarList  #put in global scope for exec statement
    try:
        import numpy                   #put in global scope for exec statement
        from .drel import drel_runtime  #put in global scope for exec statement
    except ImportError:
        pass                       #will fail when using dictionaries for calcs
    from copy import copy          #must be in global scope for exec statement

    def track_recursion(in_this_func):
        """Keep an eye on a function call to make sure that the key argument hasn't been
        seen before"""
        def wrapper(*args,**kwargs):
            key_arg = args[1]
            if key_arg in wrapper.called_list:
                print('Recursion watch: %s already called %d times' % (key_arg,wrapper.called_list.count(key_arg)))
                raise CifRecursionError( key_arg,wrapper.called_list[:])    #failure
            if len(wrapper.called_list) == 0:   #first time
                wrapper.stored_use_defaults = kwargs.get("allow_defaults",False)
                print('All recursive calls will set allow_defaults to ' + repr(wrapper.stored_use_defaults))
            else:
                kwargs["allow_defaults"] = wrapper.stored_use_defaults
            wrapper.called_list.append(key_arg)
            print('Recursion watch: call stack: ' + repr(wrapper.called_list))
            try:
                result = in_this_func(*args,**kwargs)
            except StarFile.StarDerivationError as s:
                if len(wrapper.called_list) == 1: #no more
                    raise StarFile.StarDerivationFailure(wrapper.called_list[0])
                else:
                    raise
            finally:
                wrapper.called_list.pop()
                if len(wrapper.called_list) == 0:
                    wrapper.stored_used_defaults = 'error'
            return result
        wrapper.called_list = []
        return wrapper

    class CifBlock(StarFile.StarBlock):
        """
        A class to hold a single block of a CIF file.  A `CifBlock` object can be treated as
        a Python dictionary, in particular, individual items can be accessed using square
        brackets e.g. `b['_a_dataname']`.  All other Python dictionary methods are also
        available (e.g. `keys()`, `values()`).  Looped datanames will return a list of values.

        ## Initialisation

        When provided, `data` should be another `CifBlock` whose contents will be copied to
        this block.

        * if `strict` is set, maximum name lengths will be enforced

        * `maxoutlength` is the maximum length for output lines

        * `wraplength` is the ideal length to make output lines

        * When set, `overwrite` allows the values of datanames to be changed (otherwise an error
        is raised).

        * `compat_mode` will allow deprecated behaviour of creating single-dataname loops using
        the syntax `a[_dataname] = [1,2,3,4]`.  This should now be done by calling `CreateLoop`
        after setting the dataitem value.
        """
        def __init__(self,data = (), strict = 1, compat_mode=False, **kwargs):
            """When provided, `data` should be another CifBlock whose contents will be copied to
            this block.

            * if `strict` is set, maximum name lengths will be enforced

            * `maxoutlength` is the maximum length for output lines

            * `wraplength` is the ideal length to make output lines

            * When set, `overwrite` allows the values of datanames to be changed (otherwise an error
            is raised).

            * `compat_mode` will allow deprecated behaviour of creating single-dataname loops using
            the syntax `a[_dataname] = [1,2,3,4]`.  This should now be done by calling `CreateLoop`
            after setting the dataitem value.
            """
            if strict: maxnamelength=75
            else:
               maxnamelength=-1
            super(CifBlock,self).__init__(data=data,maxnamelength=maxnamelength,**kwargs)
            self.dictionary = None   #DDL dictionary referring to this block
            self.compat_mode = compat_mode   #old-style behaviour of setitem

        def RemoveCifItem(self,itemname):
            """Remove `itemname` from the CifBlock"""
            self.RemoveItem(itemname)

        def __setitem__(self,key,value):
            self.AddItem(key,value)
            # for backwards compatibility make a single-element loop
            if self.compat_mode:
                if isinstance(value,(tuple,list)) and not isinstance(value,StarFile.StarList):
                     # single element loop
                     self.CreateLoop([key])

        def copy(self):
            newblock = super(CifBlock,self).copy()
            return self.copy.im_class(newblock)   #catch inheritance

        def AddCifItem(self,data):
            """ *DEPRECATED*. Use `AddItem` instead."""
            # we accept only tuples, strings and lists!!
            if not (isinstance(data[0],(unicode,tuple,list,str))):
                      raise TypeError('Cif datanames are either a string, tuple or list')
            # we catch single item loops as well...
            if isinstance(data[0],(unicode,str)):
                self.AddSingleCifItem(data[0],list(data[1]))
                if isinstance(data[1],(tuple,list)) and not isinstance(data[1],StarFile.StarList):  # a single element loop
                    self.CreateLoop([data[0]])
                return
            # otherwise, we loop over the datanames
            keyvals = zip(data[0][0],[list(a) for a in data[1][0]])
            [self.AddSingleCifItem(a,b) for a,b in keyvals]
            # and create the loop
            self.CreateLoop(data[0][0])

        def AddSingleCifItem(self,key,value):
            """*Deprecated*. Use `AddItem` instead"""
            """Add a single data item. If it is part of a loop, a separate call should be made"""
            self.AddItem(key,value)

        def loopnames(self):
            return [self.loops[a] for a in self.loops]

    class CifFile(StarFile.StarFile):
        def __init__(self,datasource=None,strict=1,standard='CIF',**kwargs):
            super(CifFile,self).__init__(datasource=datasource,standard=standard, **kwargs)
            self.strict = strict
            self.header_comment = \
    """
    ##########################################################################
    #               Crystallographic Information Format file
    #               Produced by PyCifRW module
    #
    #  This is a CIF file.  CIF has been adopted by the International
    #  Union of Crystallography as the standard for data archiving and
    #  transmission.
    #
    #  For information on this file format, follow the CIF links at
    #  http://www.iucr.org
    ##########################################################################
    """

    class CifError(Exception):
        def __init__(self,value):
            self.value = value
        def __str__(self):
            return '\nCif Format error: '+ self.value

    class ValidCifError(Exception):
        def __init__(self,value):
            self.value = value
        def __str__(self):
            return '\nCif Validity error: ' + self.value

    class CifRecursionError(Exception):
        def __init__(self,key_value,call_stack):
            self.key_value = key_value
            self.call_stack = call_stack
        def __str__(self):
            return "Derivation has recursed, %s seen twice (call stack %s)" % (self.key_value,repr(self.call_stack))

    class CifDic(StarFile.StarFile):
        """Create a Cif Dictionary object from the provided source, which can
        be a filename/URL or a CifFile.  Optional arguments (relevant to DDLm
        only):

        * do_minimum (Boolean):
             Do not set up the dREL system for auto-calculation or perform
             imports.  This implies do_imports=False and do_dREL=False

        * do_imports = No/Full/Contents/All:
             If not 'No', replace _import.get statements with the imported contents for
             Full mode/Contents mode/Both respectively.

        * do_dREL = True/False:
             Parse and convert all dREL methods to Python. Implies do_imports=All

        """
        def __init__(self,dic,do_minimum=False,do_imports='All', do_dREL=True,
                                                                 grammar='auto',**kwargs):
            self.do_minimum = do_minimum
            if do_minimum:
                do_imports = 'No'
                do_dREL = False
            if do_dREL: do_imports = 'All'
            self.template_cache = {}    #for DDLm imports
            self.ddlm_functions = {}    #for DDLm functions
            self.switch_numpy(False)    #no Numpy arrays returned
            super(CifDic,self).__init__(datasource=dic,grammar=grammar,**kwargs)
            self.standard = 'Dic'    #for correct output order
            self.scoping = 'dictionary'
            (self.dicname,self.diclang) = self.dic_determine()
            print('%s is a %s dictionary' % (self.dicname,self.diclang))
            self.scopes_mandatory = {}
            self.scopes_naughty = {}
            # rename and expand out definitions using "_name" in DDL dictionaries
            if self.diclang == "DDL1":
                self.DDL1_normalise()   #this removes any non-definition entries
            self.create_def_block_table() #From now on, [] uses definition_id
            if self.diclang == "DDL1":
                self.ddl1_cat_load()
            elif self.diclang == "DDL2":
                self.DDL2_normalise()   #iron out some DDL2 tricky bits
            elif self.diclang == "DDLm":
                self.scoping = 'dictionary'   #expose all save frames
                if do_imports is not 'No':
                   self.ddlm_import(import_mode=do_imports)#recursively calls this routine
                self.create_alias_table()
                self.create_cat_obj_table()
                self.create_cat_key_table()
                if do_dREL:
                    print('Doing full dictionary initialisation')
                    self.initialise_drel()
            self.add_category_info(full=do_dREL)
            # initialise type information
            self.typedic={}
            self.primdic = {}   #typecode<->primitive type translation
            self.add_type_info()
            self.install_validation_functions()

        def dic_determine(self):
            if "on_this_dictionary" in self:
                self.master_block = super(CifDic,self).__getitem__("on_this_dictionary")
                self.def_id_spec = "_name"
                self.cat_id_spec = "_category.id"   #we add this ourselves
                self.type_spec = "_type"
                self.enum_spec = "_enumeration"
                self.cat_spec = "_category"
                self.esd_spec = "_type_conditions"
                self.must_loop_spec = "_list"
                self.must_exist_spec = "_list_mandatory"
                self.list_ref_spec = "_list_reference"
                self.key_spec = "_list_mandatory"
                self.unique_spec = "_list_uniqueness"
                self.child_spec = "_list_link_child"
                self.parent_spec = "_list_link_parent"
                self.related_func = "_related_function"
                self.related_item = "_related_item"
                self.primitive_type = "_type"
                self.dep_spec = "xxx"
                self.cat_list = []   #to save searching all the time
                name = super(CifDic,self).__getitem__("on_this_dictionary")["_dictionary_name"]
                version = super(CifDic,self).__getitem__("on_this_dictionary")["_dictionary_version"]
                return (name+version,"DDL1")
            elif len(self.get_roots()) == 1:              # DDL2/DDLm
                self.master_block = super(CifDic,self).__getitem__(self.get_roots()[0][0])
                # now change to dictionary scoping
                self.scoping = 'dictionary'
                name = self.master_block["_dictionary.title"]
                version = self.master_block["_dictionary.version"]
                if self.master_block.has_key("_dictionary.class"):   #DDLm
                    self.enum_spec = '_enumeration_set.state'
                    self.key_spec = '_category.key_id'
                    self.must_exist_spec = None
                    self.cat_spec = '_name.category_id'
                    self.primitive_type = '_type.contents'
                    self.cat_id_spec = "_definition.id"
                    self.def_id_spec = "_definition.id"
                    return(name+version,"DDLm")
                else:   #DDL2
                    self.cat_id_spec = "_category.id"
                    self.def_id_spec = "_item.name"
                    self.key_spec = "_category_mandatory.name"
                    self.type_spec = "_item_type.code"
                    self.enum_spec = "_item_enumeration.value"
                    self.esd_spec = "_item_type_conditions.code"
                    self.cat_spec = "_item.category_id"
                    self.loop_spec = "there_is_no_loop_spec!"
                    self.must_loop_spec = "xxx"
                    self.must_exist_spec = "_item.mandatory_code"
                    self.child_spec = "_item_linked.child_name"
                    self.parent_spec = "_item_linked.parent_name"
                    self.related_func = "_item_related.function_code"
                    self.related_item = "_item_related.related_name"
                    self.unique_spec = "_category_key.name"
                    self.list_ref_spec = "xxx"
                    self.primitive_type = "_type"
                    self.dep_spec = "_item_dependent.dependent_name"
                    return (name+version,"DDL2")
            else:
                raise CifError("Unable to determine dictionary DDL version")

        def DDL1_normalise(self):
            # switch off block name collision checks
            self.standard = None
            # add default type information in DDL2 style
            # initial types and constructs
            base_types = ["char","numb","null"]
            prim_types = base_types[:]
            base_constructs = [".*",
                '(-?(([0-9]*[.][0-9]+)|([0-9]+)[.]?)([(][0-9]+[)])?([eEdD][+-]?[0-9]+)?)|\?|\.',
                "\"\" "]
            for key,value in self.items():
               newnames = [key]  #keep by default
               if "_name" in value:
                   real_name = value["_name"]
                   if isinstance(real_name,list):        #looped values
                       for looped_name in real_name:
                          new_value = value.copy()
                          new_value["_name"] = looped_name  #only looped name
                          self[looped_name] = new_value
                       newnames = real_name
                   else:
                          self[real_name] = value
                          newnames = [real_name]
               # delete the old one
               if key not in newnames:
                  del self[key]
            # loop again to normalise the contents of each definition
            for key,value in self.items():
               #unlock the block
               save_overwrite = value.overwrite
               value.overwrite = True
               # deal with a missing _list, _type_conditions
               if "_list" not in value: value["_list"] = 'no'
               if "_type_conditions" not in value: value["_type_conditions"] = 'none'
               # deal with enumeration ranges
               if "_enumeration_range" in value:
                   max,min = self.getmaxmin(value["_enumeration_range"])
                   if min == ".":
                       self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,max),(max,min))))
                   elif max == ".":
                       self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,min),(min,min))))
                   else:
                       self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,max,min),(max,min,min))))
               #add any type construct information
               if "_type_construct" in value:
                   base_types.append(value["_name"]+"_type")   #ie dataname_type
                   base_constructs.append(value["_type_construct"]+"$")
                   prim_types.append(value["_type"])     #keep a record
                   value["_type"] = base_types[-1]   #the new type name

            #make categories conform with ddl2
            #note that we must remove everything from the last underscore
               if value.get("_category",None) == "category_overview":
                    last_under = value["_name"].rindex("_")
                    catid = value["_name"][1:last_under]
                    value["_category.id"] = catid  #remove square bracks
                    if catid not in self.cat_list: self.cat_list.append(catid)
               value.overwrite = save_overwrite
            # we now add any missing categories before filling in the rest of the
            # information
            for key,value in self.items():
                #print('processing ddl1 definition %s' % key)
                if "_category" in self[key]:
                    if self[key]["_category"] not in self.cat_list:
                        # rogue category, add it in
                        newcat = self[key]["_category"]
                        fake_name = "_" + newcat + "_[]"
                        newcatdata = CifBlock()
                        newcatdata["_category"] = "category_overview"
                        newcatdata["_category.id"] = newcat
                        newcatdata["_type"] = "null"
                        self[fake_name] = newcatdata
                        self.cat_list.append(newcat)
            # write out the type information in DDL2 style
            self.master_block.AddLoopItem((
                ("_item_type_list.code","_item_type_list.construct",
                  "_item_type_list.primitive_code"),
                (base_types,base_constructs,prim_types)
                ))

        def ddl1_cat_load(self):
            deflist = self.keys()       #slight optimization
            cat_mand_dic = {}
            cat_unique_dic = {}
            # a function to extract any necessary information from each definition
            def get_cat_info(single_def):
                if self[single_def].get(self.must_exist_spec)=='yes':
                    thiscat = self[single_def]["_category"]
                    curval = cat_mand_dic.get(thiscat,[])
                    curval.append(single_def)
                    cat_mand_dic[thiscat] = curval
                # now the unique items...
                # cif_core.dic throws us a curly one: the value of list_uniqueness is
                # not the same as the defined item for publ_body_label, so we have
                # to collect both together.  We assume a non-listed entry, which
                # is true for all current (May 2005) ddl1 dictionaries.
                if self[single_def].get(self.unique_spec,None)!=None:
                    thiscat = self[single_def]["_category"]
                    new_unique = self[single_def][self.unique_spec]
                    uis = cat_unique_dic.get(thiscat,[])
                    if single_def not in uis: uis.append(single_def)
                    if new_unique not in uis: uis.append(new_unique)
                    cat_unique_dic[thiscat] = uis

            [get_cat_info(a) for a in deflist] # apply the above function
            for cat in cat_mand_dic.keys():
                self[cat]["_category_mandatory.name"] = cat_mand_dic[cat]
            for cat in cat_unique_dic.keys():
                self[cat]["_category_key.name"] = cat_unique_dic[cat]

        def create_pcloop(self,definition):
            old_children = self[definition].get('_item_linked.child_name',[])
            old_parents = self[definition].get('_item_linked.parent_name',[])
            if isinstance(old_children,unicode):
                 old_children = [old_children]
            if isinstance(old_parents,unicode):
                 old_parents = [old_parents]
            if (len(old_children)==0 and len(old_parents)==0) or \
               (len(old_children) > 1 and len(old_parents)>1):
                 return
            if len(old_children)==0:
                 old_children = [definition]*len(old_parents)
            if len(old_parents)==0:
                 old_parents = [definition]*len(old_children)
            newloop = CifLoopBlock(dimension=1)
            newloop.AddLoopItem(('_item_linked.parent_name',old_parents))
            newloop.AddLoopItem(('_item_linked.child_name',old_children))
            try:
                del self[definition]['_item_linked.parent_name']
                del self[definition]['_item_linked.child_name']
            except KeyError:
                pass
            self[definition].insert_loop(newloop)

        def DDL2_normalise(self):
           listed_defs = filter(lambda a:isinstance(self[a].get('_item.name'),list),self.keys())
           # now filter out all the single element lists!
           dodgy_defs = filter(lambda a:len(self[a]['_item.name']) > 1, listed_defs)
           for item_def in dodgy_defs:
                    # print("DDL2 norm: processing %s" % item_def)
                    thisdef = self[item_def]
                    packet_no = thisdef['_item.name'].index(item_def)
                    realcat = thisdef['_item.category_id'][packet_no]
                    realmand = thisdef['_item.mandatory_code'][packet_no]
                    # first add in all the missing categories
                    # we don't replace the entry in the list corresponding to the
                    # current item, as that would wipe out the information we want
                    for child_no in range(len(thisdef['_item.name'])):
                        if child_no == packet_no: continue
                        child_name = thisdef['_item.name'][child_no]
                        child_cat = thisdef['_item.category_id'][child_no]
                        child_mand = thisdef['_item.mandatory_code'][child_no]
                        if child_name not in self:
                            self[child_name] = CifBlock()
                            self[child_name]['_item.name'] = child_name
                        self[child_name]['_item.category_id'] = child_cat
                        self[child_name]['_item.mandatory_code'] = child_mand
                    self[item_def]['_item.name'] = item_def
                    self[item_def]['_item.category_id'] = realcat
                    self[item_def]['_item.mandatory_code'] = realmand

           target_defs = [a for a in self.keys() if '_item_linked.child_name' in self[a] or \
                                         '_item_linked.parent_name' in self[a]]
           # now dodgy_defs contains all definition blocks with more than one child/parent link
           for item_def in dodgy_defs: self.create_pcloop(item_def)           #regularise appearance
           for item_def in dodgy_defs:
                 print('Processing %s' % item_def)
                 thisdef = self[item_def]
                 child_list = thisdef['_item_linked.child_name']
                 parents = thisdef['_item_linked.parent_name']
                 # for each parent, find the list of children.
                 family = list(zip(parents,child_list))
                 notmychildren = family         #We aim to remove non-children
                 # Loop over the parents, relocating as necessary
                 while len(notmychildren):
                    # get all children of first entry
                    mychildren = [a for a in family if a[0]==notmychildren[0][0]]
                    print("Parent %s: %d children" % (notmychildren[0][0],len(mychildren)))
                    for parent,child in mychildren:   #parent is the same for all
                             # Make sure that we simply add in the new entry for the child, not replace it,
                             # otherwise we might spoil the child entry loop structure
                             try:
                                 childloop = self[child].GetLoop('_item_linked.parent_name')
                             except KeyError:
                                 print('Creating new parent entry %s for definition %s' % (parent,child))
                                 self[child]['_item_linked.parent_name'] = [parent]
                                 childloop = self[child].GetLoop('_item_linked.parent_name')
                                 childloop.AddLoopItem(('_item_linked.child_name',[child]))
                                 continue
                             else:
                                 # A parent loop already exists and so will a child loop due to the
                                 # call to create_pcloop above
                                 pars = [a for a in childloop if getattr(a,'_item_linked.child_name','')==child]
                                 goodpars = [a for a in pars if getattr(a,'_item_linked.parent_name','')==parent]
                                 if len(goodpars)>0:   #no need to add it
                                     print('Skipping duplicated parent - child entry in %s: %s - %s' % (child,parent,child))
                                     continue
                                 print('Adding %s to %s entry' % (parent,child))
                                 newpacket = childloop.GetPacket(0)   #essentially a copy, I hope
                                 setattr(newpacket,'_item_linked.child_name',child)
                                 setattr(newpacket,'_item_linked.parent_name',parent)
                                 childloop.AddPacket(newpacket)
                    #
                    # Make sure the parent also points to the children.  We get
                    # the current entry, then add our
                    # new values if they are not there already
                    #
                    parent_name = mychildren[0][0]
                    old_children = self[parent_name].get('_item_linked.child_name',[])
                    old_parents = self[parent_name].get('_item_linked.parent_name',[])
                    oldfamily = zip(old_parents,old_children)
                    newfamily = []
                    print('Old parents -> %s' % repr(old_parents))
                    for jj, childname in mychildren:
                        alreadythere = [a for a in oldfamily if a[0]==parent_name and a[1] ==childname]
                        if len(alreadythere)>0: continue
                        'Adding new child %s to parent definition at %s' % (childname,parent_name)
                        old_children.append(childname)
                        old_parents.append(parent_name)
                    # Now output the loop, blowing away previous definitions.  If there is something
                    # else in this category, we are destroying it.
                    newloop = CifLoopBlock(dimension=1)
                    newloop.AddLoopItem(('_item_linked.parent_name',old_parents))
                    newloop.AddLoopItem(('_item_linked.child_name',old_children))
                    del self[parent_name]['_item_linked.parent_name']
                    del self[parent_name]['_item_linked.child_name']
                    self[parent_name].insert_loop(newloop)
                    print('New parents -> %s' % repr(self[parent_name]['_item_linked.parent_name']))
                    # now make a new,smaller list
                    notmychildren = [a for a in notmychildren if a[0]!=mychildren[0][0]]

           # now flatten any single element lists
           single_defs = filter(lambda a:len(self[a]['_item.name'])==1,listed_defs)
           for flat_def in single_defs:
               flat_keys = self[flat_def].GetLoop('_item.name').keys()
               for flat_key in flat_keys: self[flat_def][flat_key] = self[flat_def][flat_key][0]
           # now deal with the multiple lists
           # next we do aliases
           all_aliases = [a for a in self.keys() if self[a].has_key('_item_aliases.alias_name')]
           for aliased in all_aliases:
              my_aliases = listify(self[aliased]['_item_aliases.alias_name'])
              for alias in my_aliases:
                  self[alias] = self[aliased].copy()   #we are going to delete stuff...
                  del self[alias]["_item_aliases.alias_name"]

        def ddlm_parse_valid(self):
            if "_dictionary_valid.application" not in self.master_block:
                return
            for scope_pack in self.master_block.GetLoop("_dictionary_valid.application"):
                scope = getattr(scope_pack,"_dictionary_valid.application")
                valid_info = getattr(scope_pack,"_dictionary_valid.attributes")
                if scope[1] == "Mandatory":
                    self.scopes_mandatory[scope[0]] = self.expand_category_opt(valid_info)
                elif scope[1] == "Prohibited":
                    self.scopes_naughty[scope[0]] = self.expand_category_opt(valid_info)

        def ddlm_import(self,import_mode='All'):
            import_frames = list([(a,self[a]['_import.get']) for a in self.keys() if '_import.get' in self[a]])
            print ('Import mode %s applied to following frames' % import_mode)
            print (str([a[0] for a in import_frames]))
            if import_mode != 'All':
               for i in range(len(import_frames)):
                    import_frames[i] = (import_frames[i][0],[a for a in import_frames[i][1] if a.get('mode','Contents') == import_mode])
               print('Importing following frames in mode %s' % import_mode)
               print(str(import_frames))
            #resolve all references
            for parent_block,import_list in import_frames:
              for import_ref in import_list:
                file_loc = import_ref["file"]
                full_uri = self.resolve_path(file_loc)
                if full_uri not in self.template_cache:
                    dic_as_cif = CifFile(urlopen(full_uri),grammar=self.grammar)
                    self.template_cache[full_uri] = CifDic(dic_as_cif,do_imports=import_mode,do_dREL=False)  #this will recurse internal imports
                    print('Added %s to cached dictionaries' % full_uri)
                import_from = self.template_cache[full_uri]
                dupl = import_ref.get('dupl','Exit')
                miss = import_ref.get('miss','Exit')
                target_key = import_ref["save"]
                try:
                    import_target = import_from[target_key]
                except KeyError:
                    if miss == 'Exit':
                       raise CifError('Import frame %s not found in %s' % (target_key,full_uri))
                    else: continue
                # now import appropriately
                mode = import_ref.get("mode",'Contents').lower()
                if target_key in self and mode=='full':  #so blockname will be duplicated
                    if dupl == 'Exit':
                        raise CifError('Import frame %s already in dictionary' % target_key)
                    elif dupl == 'Ignore':
                        continue
                if mode == 'contents':   #merge attributes only
                    self[parent_block].merge(import_target)
                elif mode =="full":
                    # Do the syntactic merge
                    syntactic_head = self[self.get_parent(parent_block)] #root frame if no nesting
                    from_cat_head = import_target['_name.object_id']
                    child_frames = import_from.ddlm_all_children(from_cat_head)
                     # Check for Head merging Head
                    if self[parent_block].get('_definition.class','Datum')=='Head' and \
                       import_target.get('_definition.class','Datum')=='Head':
                          head_to_head = True
                    else:
                          head_to_head = False
                          child_frames.remove(from_cat_head)
                    # As we are in syntax land, we call the CifFile methods
                    child_blocks = list([import_from.block_id_table[a.lower()] for a in child_frames])
                    child_blocks = super(CifDic,import_from).makebc(child_blocks)
                    # Prune out any datablocks that have identical definitions
                    from_defs = dict([(a,child_blocks[a].get('_definition.id','').lower()) for a in child_blocks.keys()])
                    double_defs = list([b for b in from_defs.items() if self.has_key(b[1])])
                    print ('Definitions for %s superseded' % repr(double_defs))
                    for b in double_defs:
                        del child_blocks[b[0]]
                    super(CifDic,self).merge_fast(child_blocks,parent=syntactic_head)      #
                    print('Syntactic merge of %s (%d defs) in %s mode, now have %d defs' % (target_key,len(child_frames),
                       mode,len(self)))
                    # Now the semantic merge
                    # First expand our definition <-> blockname tree
                    self.create_def_block_table()
                    merging_cat = self[parent_block]['_name.object_id']      #new parent
                    if head_to_head:
                        child_frames = self.ddlm_immediate_children(from_cat_head)    #old children
                        #the new parent is the importing category for all old children
                        for f in child_frames:
                            self[f].overwrite = True
                            self[f]['_name.category_id'] = merging_cat
                            self[f].overwrite = False
                        # remove the old head
                        del self[from_cat_head]
                        print('Semantic merge: %d defs reparented from %s to %s' % (len(child_frames),from_cat_head,merging_cat))
                    else:  #imported category is only child
                        from_frame = import_from[target_key]['_definition.id'] #so we can find it
                        child_frame = [d for d in self.keys() if self[d]['_definition.id']==from_frame][0]
                        self[child_frame]['_name.category_id'] = merging_cat
                        print('Semantic merge: category for %s : now %s' % (from_frame,merging_cat))
                # it will never happen again...
                del self[parent_block]["_import.get"]

        def resolve_path(self,file_loc):
            url_comps = urlparse(file_loc)
            if url_comps[0]: return file_loc    #already full URI
            new_url = urljoin(self.my_uri,file_loc)
            #print("Transformed %s to %s for import " % (file_loc,new_url))
            return new_url

        def create_def_block_table(self):
            """ Create an internal table matching definition to block id """
            proto_table = [(super(CifDic,self).__getitem__(a),a) for a in super(CifDic,self).keys()]
            # now get the actual ids instead of blocks
            proto_table = list([(a[0].get(self.cat_id_spec,a[0].get(self.def_id_spec,a[1])),a[1]) for a in proto_table])
            # remove non-definitions
            if self.diclang != "DDL1":
                top_blocks = list([a[0].lower() for a in self.get_roots()])
            else:
                top_blocks = ["on_this_dictionary"]
            # catch dodgy duplicates
            uniques = set([a[0] for a in proto_table])
            if len(uniques)<len(proto_table):
                def_names = list([a[0] for a in proto_table])
                dodgy = [a for a in def_names if def_names.count(a)>1]
                raise CifError('Duplicate definitions in dictionary:' + repr(dodgy))
            self.block_id_table = dict([(a[0].lower(),a[1].lower()) for a in proto_table if a[1].lower() not in top_blocks])

        def __getitem__(self,key):
            """Access a datablock by definition id, after the lookup has been created"""
            try:
                return super(CifDic,self).__getitem__(self.block_id_table[key.lower()])
            except AttributeError:   #block_id_table not present yet
                return super(CifDic,self).__getitem__(key)
            except KeyError: # key is missing
                # print(Definition for %s not found, reverting to CifFile' % key)
                return super(CifDic,self).__getitem__(key)

        def __setitem__(self,key,value):
            """Add a new definition block"""
            super(CifDic,self).__setitem__(key,value)
            try:
                self.block_id_table[value['_definition.id']]=key
            except AttributeError:   #does not exist yet
                pass

        def __delitem__(self,key):
            """Remove a definition"""
            try:
                super(CifDic,self).__delitem__(self.block_id_table[key.lower()])
                del self.block_id_table[key.lower()]
            except (AttributeError,KeyError):   #block_id_table not present yet
                super(CifDic,self).__delitem__(key)
                return
            # fix other datastructures
            # cat_obj table

        def keys(self):
            """Return all definitions"""
            try:
                return self.block_id_table.keys()
            except AttributeError:
                return super(CifDic,self).keys()

        def has_key(self,key):
            return key in self

        def __contains__(self,key):
            try:
                return key.lower() in self.block_id_table
            except AttributeError:
                return super(CifDic,self).__contains__(key)

        def items(self):
            """Return (key,value) pairs"""
            return list([(a,self[a]) for a in self.keys()])

        def unlock(self):
            """Allow overwriting of all definitions in this collection"""
            for a in self.keys():
                self[a].overwrite=True

        def lock(self):
            """Disallow changes in definitions"""
            for a in self.keys():
                self[a].overwrite=False

        def rename(self,oldname,newname,blockname_as_well=True):
            """Change a _definition.id from oldname to newname, and if `blockname_as_well` is True,
            change the underlying blockname too."""
            if blockname_as_well:
                super(CifDic,self).rename(self.block_id_table[oldname.lower()],newname)
                self.block_id_table[newname.lower()]=newname
                if oldname.lower() in self.block_id_table: #not removed
                   del self.block_id_table[oldname.lower()]
            else:
                self.block_id_table[newname.lower()]=self.block_id_table[oldname.lower()]
                del self.block_id_table[oldname.lower()]
                return

        def get_root_category(self):
            """Get the single 'Head' category of this dictionary"""
            root_cats = [r for r in self.keys() if self[r].get('_definition.class','Datum')=='Head']
            if len(root_cats)>1 or len(root_cats)==0:
                raise CifError("Cannot determine a unique Head category, got" % repr(root_cats))
            return root_cats[0]

        def ddlm_immediate_children(self,catname):
            """Return a list of datanames for the immediate children of catname.  These are
            semantic children (i.e. based on _name.category_id), not structural children as
            in the case of StarFile.get_immediate_children"""

            straight_children = [a for a in self.keys() if self[a].get('_name.category_id','').lower() == catname.lower()]
            return list(straight_children)

        def ddlm_all_children(self,catname):
            """Return a list of all children, including the `catname`"""
            all_children = self.ddlm_immediate_children(catname)
            cat_children = [a for a in all_children if self[a].get('_definition.scope','Item') == 'Category']
            for c in cat_children:
                all_children.remove(c)
                all_children += self.ddlm_all_children(c)
            return all_children + [catname]

        def is_semantic_child(self,parent,maybe_child):
            """Return true if `maybe_child` is a child of `parent`"""
            all_children = self.ddlm_all_children(parent)
            return maybe_child in all_children

        def ddlm_danglers(self):
            """Return a list of definitions that do not have a category defined
            for them, or are children of an unattached category"""
            top_block = self.get_root_category()
            connected = set(self.ddlm_all_children(top_block))
            all_keys = set(self.keys())
            unconnected = all_keys - connected
            return list(unconnected)

        def get_ddlm_parent(self,itemname):
            """Get the parent category of itemname"""
            parent = self[itemname].get('_name.category_id','')
            if parent == '':  # use the top block by default
                raise CifError("%s has no parent" % itemname)
            return parent

        def expand_category_opt(self,name_list):
            """Return a list of all non-category items in a category or return the name
               if the name is not a category"""
            new_list = []
            for name in name_list:
              if self.get(name,{}).get('_definition.scope','Item') == 'Category':
                new_list += self.expand_category_opt([a for a in self.keys() if \
                         self[a].get('_name.category_id','').lower() == name.lower()])
              else:
                new_list.append(name)
            return new_list

        def get_categories(self):
            """Return a list of category names"""
            return list([c for c in self.keys() if self[c].get("_definition.scope")=='Category'])

        def names_in_cat(self,cat,names_only=False):
            names = [a for a in self.keys() if self[a].get('_name.category_id','').lower()==cat.lower()]
            if not names_only:
                return list([a for a in names if self[a].get('_definition.scope','Item')=='Item'])
            else:
                return list([self[a]["_name.object_id"] for a in names])

        def create_alias_table(self):
            """Populate an alias table that we can look up when searching for a dataname"""
            all_aliases = [a for a in self.keys() if '_alias.definition_id' in self[a]]
            self.alias_table = dict([[a,self[a]['_alias.definition_id']] for a in all_aliases])

        def create_cat_obj_table(self):
            """Populate a table indexed by (cat,obj) and returning the correct dataname"""
            base_table = dict([((self[a].get('_name.category_id','').lower(),self[a].get('_name.object_id','').lower()),[self[a].get('_definition.id','')]) \
                               for a in self.keys() if self[a].get('_definition.scope','Item')=='Item'])
            loopable = self.get_loopable_cats()
            loopers = [self.ddlm_immediate_children(a) for a in loopable]
            print('Loopable cats:' + repr(loopable))
            loop_children = [[b for b in a if b.lower() in loopable ] for a in loopers]
            expand_list = dict([(a,b) for a,b in zip(loopable,loop_children) if len(b)>0])
            print("Expansion list:" + repr(expand_list))
            extra_table = {}   #for debugging we keep it separate from base_table until the end
            def expand_base_table(parent_cat,child_cats):
                extra_names = []
                # first deal with all the child categories
                for child_cat in child_cats:
                  nn = []
                  if child_cat in expand_list:  # a nested category: grab its names
                    nn = expand_base_table(child_cat,expand_list[child_cat])
                    # store child names
                    extra_names += nn
                  # add all child names to the table
                  child_names = [(self[n]['_name.object_id'].lower(),self[n]['_definition.id']) \
                                 for n in self.names_in_cat(child_cat) if self[n].get('_type.purpose','') != 'Key']
                  child_names += extra_names
                  extra_table.update(dict([((parent_cat,obj),[name]) for obj,name in child_names if (parent_cat,name) not in extra_table]))
                # and the repeated ones get appended instead
                repeats = [a for a in child_names if a in extra_table]
                for obj,name in repeats:
                    extra_table[(parent_cat,obj)] += [name]
                # and finally, add our own names to the return list
                child_names += [(self[n]['_name.object_id'].lower(),self[n]['_definition.id']) \
                                for n in self.names_in_cat(parent_cat) if self[n].get('_type.purpose','')!='Key']
                return child_names
            [expand_base_table(parent,child) for parent,child in expand_list.items()]
            print('Expansion cat/obj values: ' + repr(extra_table))
            # append repeated ones
            non_repeats = dict([a for a in extra_table.items() if a[0] not in base_table])
            repeats = [a for a in extra_table.keys() if a in base_table]
            base_table.update(non_repeats)
            for k in repeats:
                base_table[k] += extra_table[k]
            self.cat_obj_lookup_table = base_table
            self.loop_expand_list = expand_list

        def get_loopable_cats(self):
            """A short utility function which returns a list of looped categories. This
            is preferred to a fixed attribute as that fixed attribute would need to be
            updated after any edits"""
            return [a.lower() for a in self.keys() if self[a].get('_definition.class','')=='Loop']

        def create_cat_key_table(self):
            """Create a utility table with a list of keys applicable to each category. A key is
            a compound key, that is, it is a list"""
            self.cat_key_table = dict([(c,[listify(self[c].get("_category_key.name",
                [self[c].get("_category.key_id")]))]) for c in self.get_loopable_cats()])
            def collect_keys(parent_cat,child_cats):
                    kk = []
                    for child_cat in child_cats:
                        if child_cat in self.loop_expand_list:
                            kk += collect_keys(child_cat)
                        # add these keys to our list
                        kk += [listify(self[child_cat].get('_category_key.name',[self[child_cat].get('_category.key_id')]))]
                    self.cat_key_table[parent_cat] = self.cat_key_table[parent_cat] + kk
                    return kk
            for k,v in self.loop_expand_list.items():
                collect_keys(k,v)
            print('Keys for categories' + repr(self.cat_key_table))

        def add_type_info(self):
            if "_item_type_list.construct" in self.master_block:
                types = self.master_block["_item_type_list.code"]
                prim_types = self.master_block["_item_type_list.primitive_code"]
                constructs = list([a + "$" for a in self.master_block["_item_type_list.construct"]])
                # add in \r wherever we see \n, and change \{ to \\{
                def regex_fiddle(mm_regex):
                    brack_match = r"((.*\[.+)(\\{)(.*\].*))"
                    ret_match = r"((.*\[.+)(\\n)(.*\].*))"
                    fixed_regexp = mm_regex[:]  #copy
                    # fix the brackets
                    bm = re.match(brack_match,mm_regex)
                    if bm != None:
                        fixed_regexp = bm.expand(r"\2\\\\{\4")
                    # fix missing \r
                    rm = re.match(ret_match,fixed_regexp)
                    if rm != None:
                        fixed_regexp = rm.expand(r"\2\3\\r\4")
                    #print("Regexp %s becomes %s" % (mm_regex,fixed_regexp))
                    return fixed_regexp
                constructs = map(regex_fiddle,constructs)
                for typecode,construct in zip(types,constructs):
                    self.typedic[typecode] = re.compile(construct,re.MULTILINE|re.DOTALL)
                # now make a primitive <-> type construct mapping
                for typecode,primtype in zip(types,prim_types):
                    self.primdic[typecode] = primtype

        def add_category_info(self,full=True):
            if self.diclang == "DDLm":
                catblocks = [c for c in self.keys() if self[c].get('_definition.scope')=='Category']
                looped_cats = [a for a in catblocks if self[a].get('_definition.class','Set') == 'Loop']
                self.parent_lookup = {}
                for one_cat in looped_cats:
                    parent_cat = one_cat
                    parent_def = self[parent_cat]
                    next_up = parent_def['_name.category_id'].lower()
                    while next_up in self and self[next_up].get('_definition.class','Set') == 'Loop':
                        parent_def = self[next_up]
                        parent_cat = next_up
                        next_up = parent_def['_name.category_id'].lower()
                    self.parent_lookup[one_cat] = parent_cat

                if full:
                    self.key_equivs = {}
                    for one_cat in looped_cats:   #follow them up
                        lower_keys = listify(self[one_cat]['_category_key.name'])
                        start_keys = lower_keys[:]
                        while len(lower_keys)>0:
                            this_cat = self[lower_keys[0]]['_name.category_id']
                            parent = [a for a in looped_cats if self[this_cat]['_name.category_id'].lower()==a]
                            #print(Processing %s, keys %s, parent %s" % (this_cat,repr(lower_keys),repr(parent)))
                            if len(parent)>1:
                                raise CifError("Category %s has more than one parent: %s" % (one_cat,repr(parent)))
                            if len(parent)==0: break
                            parent = parent[0]
                            parent_keys = listify(self[parent]['_category_key.name'])
                            linked_keys = [self[l]["_name.linked_item_id"] for l in lower_keys]
                            # sanity check
                            if set(parent_keys) != set(linked_keys):
                                raise CifError("Parent keys and linked keys are different! %s/%s" % (parent_keys,linked_keys))
                                # now add in our information
                            for parent,child in zip(linked_keys,start_keys):
                                self.key_equivs[child] = self.key_equivs.get(child,[])+[parent]
                            lower_keys = linked_keys  #preserves order of start keys

            else:
                self.parent_lookup = {}
                self.key_equivs = {}

        def change_category_name(self,oldname,newname):
            self.unlock()
            """Change the category name from [[oldname]] to [[newname]]"""
            if oldname not in self:
                raise KeyError('Cannot rename non-existent category %s to %s' % (oldname,newname))
            if newname in self:
                raise KeyError('Cannot rename %s to %s as %s already exists' % (oldname,newname,oldname))
            child_defs = self.ddlm_immediate_children(oldname)
            self.rename(oldname,newname)   #NB no name integrity checks
            self[newname]['_name.object_id']=newname
            self[newname]['_definition.id']=newname
            for child_def in child_defs:
                self[child_def]['_name.category_id'] = newname
                if self[child_def].get('_definition.scope','Item')=='Item':
                    newid = self.create_catobj_name(newname,self[child_def]['_name.object_id'])
                    self[child_def]['_definition.id']=newid
                    self.rename(child_def,newid[1:])  #no underscore at the beginning
            self.lock()

        def create_catobj_name(self,cat,obj):
            """Combine category and object in approved fashion to create id"""
            return ('_'+cat+'.'+obj)

        def change_category(self,itemname,catname):
            """Move itemname into catname, return new handle"""
            defid = self[itemname]
            if defid['_name.category_id'].lower()==catname.lower():
                print('Already in category, no change')
                return itemname
            if catname not in self:    #don't have it
                print('No such category %s' % catname)
                return itemname
            self.unlock()
            objid = defid['_name.object_id']
            defid['_name.category_id'] = catname
            newid = itemname # stays the same for categories
            if defid.get('_definition.scope','Item') == 'Item':
                newid = self.create_catobj_name(catname,objid)
                defid['_definition.id']= newid
                self.rename(itemname,newid)
            self.set_parent(catname,newid)
            self.lock()
            return newid

        def change_name(self,one_def,newobj):
            """Change the object_id of one_def to newobj. This is not used for
            categories, but can be used for dictionaries"""
            if '_dictionary.title' not in self[one_def]:  #a dictionary block
                newid = self.create_catobj_name(self[one_def]['_name.category_id'],newobj)
                self.unlock()
                self.rename(one_def,newid)
                self[newid]['_definition.id']=newid
                self[newid]['_name.object_id']=newobj
            else:
                self.unlock()
                newid = newobj
                self.rename(one_def,newobj)
                self[newid]['_dictionary.title'] = newid
            self.lock()
            return newid

        # Note that our semantic parent is given by catparent, but our syntactic parent is
        # always just the root block
        def add_category(self,catname,catparent=None,is_loop=True,allow_dangler=False):
            """Add a new category to the dictionary with name [[catname]].
               If [[catparent]] is None, the category will be a child of
               the topmost 'Head' category or else the top data block. If
               [[is_loop]] is false, a Set category is created. If [[allow_dangler]]
               is true, the parent category does not have to exist."""
            if catname in self:
                raise CifError('Attempt to add existing category %s' % catname)
            self.unlock()
            syntactic_root = self.get_roots()[0][0]
            if catparent is None:
                semantic_root = [a for a in self.keys() if self[a].get('_definition.class',None)=='Head']
                if len(semantic_root)>0:
                    semantic_root = semantic_root[0]
                else:
                    semantic_root = syntactic_root
            else:
                semantic_root = catparent
            realname = super(CifDic,self).NewBlock(catname,parent=syntactic_root)
            self.block_id_table[catname.lower()]=realname
            self[catname]['_name.object_id'] = catname
            if not allow_dangler or catparent is None:
                self[catname]['_name.category_id'] = self[semantic_root]['_name.object_id']
            else:
                self[catname]['_name.category_id'] = catparent
            self[catname]['_definition.id'] = catname
            self[catname]['_definition.scope'] = 'Category'
            if is_loop:
                self[catname]['_definition.class'] = 'Loop'
            else:
                self[catname]['_definition.class'] = 'Set'
            self[catname]['_description.text'] = 'No definition provided'
            self.lock()
            return catname

        def add_definition(self,itemname,catparent,def_text='PLEASE DEFINE ME',allow_dangler=False):
            """Add itemname to category [[catparent]]. If itemname contains periods,
            all text before the final period is ignored. If [[allow_dangler]] is True,
            no check for a parent category is made."""
            self.unlock()
            if '.' in itemname:
                objname = itemname.split('.')[-1]
            else:
                objname = itemname
            objname = objname.strip('_')
            if not allow_dangler and (catparent not in self or self[catparent]['_definition.scope']!='Category'):
                raise CifError('No category %s in dictionary' % catparent)
            fullname = '_'+catparent.lower()+'.'+objname
            print('New name: %s' % fullname)
            syntactic_root = self.get_roots()[0][0]
            realname = super(CifDic,self).NewBlock(fullname, fix=False, parent=syntactic_root) #low-level change
            # update our dictionary structures
            self.block_id_table[fullname]=realname
            self[fullname]['_definition.id']=fullname
            self[fullname]['_name.object_id']=objname
            self[fullname]['_name.category_id']=catparent
            self[fullname]['_definition.class']='Datum'
            self[fullname]['_description.text']=def_text

        def remove_definition(self,defname):
            """Remove a definition from the dictionary."""
            if defname not in self:
                return
            if self[defname].get('_definition.scope')=='Category':
                children = self.ddlm_immediate_children(defname)
                [self.remove_definition(a) for a in children]
                cat_id = self[defname]['_definition.id'].lower()
            del self[defname]

        def get_cat_obj(self,name):
            """Return (cat,obj) tuple. [[name]] must contain only a single period"""
            cat,obj = name.split('.')
            return (cat.strip('_'),obj)

        def get_name_by_cat_obj(self,category,object,give_default=False):
            """Return the dataname corresponding to the given category and object"""
            if category[0] == '_':    #accidentally left in
               true_cat = category[1:].lower()
            else:
               true_cat = category.lower()
            try:
                return self.cat_obj_lookup_table[(true_cat,object.lower())][0]
            except KeyError:
                if give_default:
                   return '_'+true_cat+'.'+object
            raise KeyError('No such category,object in the dictionary: %s %s' % (true_cat,object))

        def WriteOut(self,**kwargs):
            myblockorder = self.get_full_child_list()
            self.set_grammar(self.grammar)
            self.standard = 'Dic'
            return super(CifDic,self).WriteOut(blockorder = myblockorder,**kwargs)

        def get_full_child_list(self):
            """Return a list of definition blocks in order parent-child-child-child-parent-child..."""
            top_block = self.get_roots()[0][0]
            root_cat = [a for a in self.keys() if self[a].get('_definition.class','Datum')=='Head']
            if len(root_cat) == 1:
                all_names = [top_block] + self.recurse_child_list(root_cat[0])
                unrooted = self.ddlm_danglers()
                double_names =  set(unrooted).intersection(set(all_names))
                if len(double_names)>0:
                    raise CifError('Names are children of internal and external categories:%s' % repr(double_names))
                remaining = unrooted[:]
                for no_root in unrooted:
                    if self[no_root].get('_definition.scope','Item')=='Category':
                        all_names += [no_root]
                        remaining.remove(no_root)
                        these_children = [n for n in unrooted if self[n]['_name.category_id'].lower()==no_root.lower()]
                        all_names += these_children
                        [remaining.remove(n) for n in these_children]
                # now sort by category
                ext_cats = set([self[r].get('_name.category_id',self.cat_from_name(r)).lower() for r in remaining])
                for e in ext_cats:
                    cat_items = [r for r in remaining if self[r].get('_name.category_id',self.cat_from_name(r)).lower() == e]
                    [remaining.remove(n) for n in cat_items]
                    all_names += cat_items
                if len(remaining)>0:
                    print('WARNING: following items do not seem to belong to a category??')
                    print(repr(remaining))
                    all_names += remaining
                print('Final block order: ' + repr(all_names))
                return all_names
            raise ValueError('Dictionary contains no/multiple Head categories, please print as plain CIF instead')

        def cat_from_name(self,one_name):
            """Guess the category from the name. This should be used only when this is not important semantic information,
            for example, when printing out"""
            (cat,obj) = one_name.split(".")
            if cat[0] == "_": cat = cat[1:]
            return cat

        def recurse_child_list(self,parentname):
            """Recursively expand the logical child list of [[parentname]]"""
            final_list = [parentname]
            child_blocks = [a for a in self.child_table.keys() if self[a].get('_name.category_id','').lower() == parentname.lower()]
            child_blocks.sort()    #we love alphabetical order
            child_items = [a for a in child_blocks if self[a].get('_definition.scope','Item') == 'Item']
            final_list += child_items
            child_cats = [a for a in child_blocks if self[a].get('_definition.scope','Item') == 'Category']
            for child_cat in child_cats:
                final_list += self.recurse_child_list(child_cat)
            return final_list

        def get_key_pack(self,category,value,data):
            keyname = self[category][self.unique_spec]
            onepack = data.GetPackKey(keyname,value)
            return onepack

        def get_number_with_esd(numstring):
            import string
            numb_re = '((-?(([0-9]*[.]([0-9]+))|([0-9]+)[.]?))([(][0-9]+[)])?([eEdD][+-]?[0-9]+)?)|(\?)|(\.)'
            our_match = re.match(numb_re,numstring)
            if our_match:
                a,base_num,b,c,dad,dbd,esd,exp,q,dot = our_match.groups()
                # print("Debug: {} -> {!r}".format(numstring, our_match.groups()))
            else:
                return None,None
            if dot or q: return None,None     #a dot or question mark
            if exp:          #has exponent
               exp = exp.replace("d","e")     # mop up old fashioned numbers
               exp = exp.replace("D","e")
               base_num = base_num + exp
            # print("Debug: have %s for base_num from %s" % (base_num,numstring))
            base_num = float(base_num)
            # work out esd, if present.
            if esd:
                esd = float(esd[1:-1])    # no brackets
                if dad:                   # decimal point + digits
                    esd = esd * (10 ** (-1* len(dad)))
                if exp:
                    esd = esd * (10 ** (float(exp[1:])))
            return base_num,esd

        def getmaxmin(self,rangeexp):
            regexp = '(-?(([0-9]*[.]([0-9]+))|([0-9]+)[.]?)([eEdD][+-]?[0-9]+)?)*'
            regexp = regexp + ":" + regexp
            regexp = re.match(regexp,rangeexp)
            try:
                minimum = regexp.group(1)
                maximum = regexp.group(7)
            except AttributeError:
                print("Can't match %s" % rangeexp)
            if minimum == None: minimum = "."
            else: minimum = float(minimum)
            if maximum == None: maximum = "."
            else: maximum = float(maximum)
            return maximum,minimum

        def initialise_drel(self):
            """Parse drel functions and prepare data structures in dictionary"""
            self.ddlm_parse_valid() #extract validity information from data block
            self.transform_drel()   #parse the drel functions
            self.add_drel_funcs()   #put the drel functions into the namespace

        def transform_drel(self):
            from .drel import drel_ast_yacc
            from .drel import py_from_ast
            import traceback
            parser = drel_ast_yacc.parser
            lexer = drel_ast_yacc.lexer
            my_namespace = self.keys()
            my_namespace = dict(zip(my_namespace,my_namespace))
            # we provide a table of loopable categories {cat_name:((key1,key2..),[item_name,...]),...})
            loopable_cats = self.get_loopable_cats()
            loop_keys = [listify(self[a]["_category_key.name"]) for a in loopable_cats]
            loop_keys = [[self[a]['_name.object_id'] for a in b] for b in loop_keys]
            cat_names = [self.names_in_cat(a,names_only=True) for a in loopable_cats]
            loop_info = dict(zip(loopable_cats,zip(loop_keys,cat_names)))
            # parser.listable_items = [a for a in self.keys() if "*" in self[a].get("_type.dimension","")]
            derivable_list = [a for a in self.keys() if "_method.expression" in self[a] \
                                  and self[a].get("_name.category_id","")!= "function"]
            for derivable in derivable_list:
                target_id = derivable
                # reset the list of visible names for parser
                special_ids = [dict(zip(self.keys(),self.keys()))]
                print("Target id: %s" % derivable)
                drel_exprs = self[derivable]["_method.expression"]
                drel_purposes = self[derivable]["_method.purpose"]
                all_methods = []
                if not isinstance(drel_exprs,list):
                    drel_exprs = [drel_exprs]
                    drel_purposes = [drel_purposes]
                for drel_purpose,drel_expr in zip(drel_purposes,drel_exprs):
                    if drel_purpose != 'Evaluation':
                        continue
                    drel_expr = "\n".join(drel_expr.splitlines())
                    # print("Transforming %s" % drel_expr)
                    # List categories are treated differently...
                    try:
                        meth_ast = parser.parse(drel_expr+"\n",lexer=lexer)
                    except:
                        print('Syntax error in method for %s; leaving as is' % derivable)
                        a,b = sys.exc_info()[:2]
                        print((repr(a),repr(b)))
                        print(traceback.print_tb(sys.exc_info()[-1],None,sys.stdout))
                        # reset the lexer
                        lexer.begin('INITIAL')
                        continue
                    # Construct the python method
                    cat_meth = False
                    if self[derivable].get('_definition.scope','Item') == 'Category':
                        cat_meth = True
                    pyth_meth = py_from_ast.make_python_function(meth_ast,"pyfunc",target_id,
                                                                               loopable=loop_info,
                                                                 cif_dic = self,cat_meth=cat_meth)
                    all_methods.append(pyth_meth)
                if len(all_methods)>0:
                    save_overwrite = self[derivable].overwrite
                    self[derivable].overwrite = True
                    self[derivable]["_method.py_expression"] = all_methods
                    self[derivable].overwrite = save_overwrite
                #print("Final result:\n " + repr(self[derivable]["_method.py_expression"]))

        def add_drel_funcs(self):
            from .drel import drel_ast_yacc
            from .drel import py_from_ast
            funclist = [a for a in self.keys() if self[a].get("_name.category_id","")=='function']
            funcnames = [(self[a]["_name.object_id"],
                          getattr(self[a].GetKeyedPacket("_method.purpose","Evaluation"),"_method.expression")) for a in funclist]
            # create executable python code...
            parser = drel_ast_yacc.parser
            # we provide a table of loopable categories {cat_name:(key,[item_name,...]),...})
            loopable_cats = self.get_loopable_cats()
            loop_keys = [listify(self[a]["_category_key.name"]) for a in loopable_cats]
            loop_keys = [[self[a]['_name.object_id'] for a in b] for b in loop_keys]
            cat_names = [self.names_in_cat(a,names_only=True) for a in loopable_cats]
            loop_info = dict(zip(loopable_cats,zip(loop_keys,cat_names)))
            for funcname,funcbody in funcnames:
                newline_body = "\n".join(funcbody.splitlines())
                parser.target_id = funcname
                res_ast = parser.parse(newline_body)
                py_function = py_from_ast.make_python_function(res_ast,None,targetname=funcname,func_def=True,loopable=loop_info,cif_dic = self)
                #print('dREL library function ->\n' + py_function)
                global_table = globals()
                exec(py_function, global_table)    #add to namespace
            #print('Globals after dREL functions added:' + repr(globals()))
            self.ddlm_functions = globals()  #for outside access

        @track_recursion
        def derive_item(self,start_key,cifdata,store_value = False,allow_defaults=True):
            key = start_key   #starting value
            result = None     #success is a non-None value
            default_result = False #we have not used a default value
            # check for aliases
            # check for an older form of a new value
            found_it = [k for k in self.alias_table.get(key,[]) if k in cifdata]
            if len(found_it)>0:
                corrected_type = self.change_type(key,cifdata[found_it[0]])
                return corrected_type
            # now do the reverse check - any alternative form
            alias_name = [a for a in self.alias_table.items() if key in a[1]]
            print('Aliases for %s: %s' % (key,repr(alias_name)))
            if len(alias_name)==1:
                key = alias_name[0][0]   #actual definition name
                if key in cifdata: return self.change_type(key,cifdata[key])
                found_it = [k for k in alias_name[0][1] if k in cifdata]
                if len(found_it)>0:
                    return self.change_type(key,cifdata[found_it[0]])
            elif len(alias_name)>1:
                raise CifError('Dictionary error: dataname alias appears in different definitions: ' + repr(alias_name))

            the_category = self[key]["_name.category_id"]
            cat_names = [a for a in self.keys() if self[a].get("_name.category_id",None)==the_category]
            has_cat_names = [a for a in cat_names if cifdata.has_key_or_alias(a)]
            # store any default value in case we have a problem
            def_val = self[key].get("_enumeration.default","")
            def_index_val = self[key].get("_enumeration.def_index_id","")
            if len(has_cat_names)==0: # try category method
                cat_result = {}
                pulled_from_cats = [k for k in self.keys() if '_category_construct_local.components' in self[k]]
                pulled_from_cats = [(k,[
                                      self[n]['_name.category_id'] for n in self[k]['_category_construct_local.components']]
                                   ) for k in pulled_from_cats]
                pulled_to_cats = [k[0] for k in pulled_from_cats if the_category in k[1]]
                if '_category_construct_local.type' in self[the_category]:
                    print("**Now constructing category %s using DDLm attributes**" % the_category)
                    try:
                        cat_result = self.construct_category(the_category,cifdata,store_value=True)
                    except (CifRecursionError,StarFile.StarDerivationError):
                        print('** Failed to construct category %s (error)' % the_category)
                # Trying a pull-back when the category is partially populated
                # will not work, hence we test that cat_result has no keys
                if len(pulled_to_cats)>0 and len(cat_result)==0:
                    print("**Now populating category %s from pulled-back category %s" % (the_category,repr(pulled_to_cats)))
                    try:
                        cat_result = self.push_from_pullback(the_category,pulled_to_cats,cifdata,store_value=True)
                    except (CifRecursionError,StarFile.StarDerivationError):
                        print('** Failed to construct category %s from pullback information (error)' % the_category)
                if '_method.py_expression' in self[the_category] and key not in cat_result:
                    print("**Now applying category method for %s in search of %s**" % (the_category,key))
                    cat_result = self.derive_item(the_category,cifdata,store_value=True)
                print("**Tried pullbacks, obtained for %s " % the_category + repr(cat_result))
                # do we now have our value?
                if key in cat_result:
                    return cat_result[key]

            # Recalculate in case it actually worked
            has_cat_names = [a for a in cat_names if cifdata.has_key_or_alias(a)]
            the_funcs = self[key].get('_method.py_expression',"")
            if the_funcs:   #attempt to calculate it
                #global_table = globals()
                #global_table.update(self.ddlm_functions)
                for one_func in the_funcs:
                    print('Executing function for %s:' % key)
                    #print(one_func)
                    exec(one_func, globals())  #will access dREL functions, puts "pyfunc" in scope
                    # print('in following global environment: ' + repr(global_table))
                    stored_setting = cifdata.provide_value
                    cifdata.provide_value = True
                    try:
                        result = pyfunc(cifdata)
                    except CifRecursionError as s:
                        print(s)
                        result = None
                    except StarFile.StarDerivationError as s:
                        print(s)
                        result = None
                    finally:
                        cifdata.provide_value = stored_setting
                    if result is not None:
                        break
                    #print("Function returned {!r}".format(result))

            if result is None and allow_defaults:   # try defaults
                if def_val:
                    result = self.change_type(key,def_val)
                    default_result = True
                elif def_index_val:            #derive a default value
                    index_vals = self[key]["_enumeration_default.index"]
                    val_to_index = cifdata[def_index_val]     #what we are keying on
                    if self[def_index_val]['_type.contents'] in ['Code','Name','Tag']:
                        lcase_comp = True
                        index_vals = [a.lower() for a in index_vals]
                    # Handle loops
                    if isinstance(val_to_index,list):
                        if lcase_comp:
                            val_to_index = [a.lower() for a in val_to_index]
                        keypos = [index_vals.index(a) for a in val_to_index]
                        result = [self[key]["_enumeration_default.value"][a]  for a in keypos]
                    else:
                        if lcase_comp:
                            val_to_index = val_to_index.lower()
                        keypos = index_vals.index(val_to_index)   #value error if no such value available
                        result = self[key]["_enumeration_default.value"][keypos]
                        default_result = True   #flag that it must be extended
                    result = self.change_type(key,result)
                    print("Indexed on %s to get %s for %s" % (def_index_val,repr(result),repr(val_to_index)))

            # read it in
            if result is None:   #can't do anything else
                print('Warning: no way of deriving item %s, allow_defaults is %s' % (key,repr(allow_defaults)))
                raise StarFile.StarDerivationError(start_key)
            is_looped = False
            if self[the_category].get('_definition.class','Set')=='Loop':
                is_looped = True
                if len(has_cat_names)>0:   #this category already exists
                    if result is None or default_result: #need to create a list of values
                        loop_len = len(cifdata[has_cat_names[0]])
                        out_result = [result]*loop_len
                        result = out_result
                else:   #nothing exists in this category, we can't store this at all
                    print('Resetting result %s for %s to null list as category is empty' % (key,result))
                    result = []

            # now try to insert the new information into the right place
            # find if items of this category already appear...
            # Never cache empty values
            if not (isinstance(result,list) and len(result)==0) and\
              store_value:
                if self[key].get("_definition.scope","Item")=='Item':
                    if is_looped:
                        result = self.store_new_looped_value(key,cifdata,result,default_result)
                    else:
                        result = self.store_new_unlooped_value(key,cifdata,result)
                else:
                    self.store_new_cat_values(cifdata,result,the_category)
            return result

        def store_new_looped_value(self,key,cifdata,result,default_result):
              """Store a looped value from the dREL system into a CifFile"""
              # try to change any matrices etc. to lists
              the_category = self[key]["_name.category_id"]
              out_result = result
              if result is not None and not default_result:
                      # find any numpy arrays
                      def conv_from_numpy(one_elem):
                          if not hasattr(one_elem,'dtype'):
                             if isinstance(one_elem,(list,tuple)):
                                return StarFile.StarList([conv_from_numpy(a) for a in one_elem])
                             return one_elem
                          if one_elem.size > 1:   #so is not a float
                             return StarFile.StarList([conv_from_numpy(a) for a in one_elem.tolist()])
                          else:
                              try:
                                return one_elem.item(0)
                              except:
                                return one_elem
                      out_result = [conv_from_numpy(a) for a in result]
              # so out_result now contains a value suitable for storage
              cat_names = [a for a in self.keys() if self[a].get("_name.category_id",None)==the_category]
              has_cat_names = [a for a in cat_names if a in cifdata]
              print('Adding {}, found pre-existing names: '.format(key) + repr(has_cat_names))
              if len(has_cat_names)>0:   #this category already exists
                  cifdata[key] = out_result      #lengths must match or else!!
                  cifdata.AddLoopName(has_cat_names[0],key)
              else:
                  cifdata[key] = out_result
                  cifdata.CreateLoop([key])
              print('Loop info:' + repr(cifdata.loops))
              return out_result

        def store_new_unlooped_value(self,key,cifdata,result):
              """Store a single value from the dREL system"""
              if result is not None and hasattr(result,'dtype'):
                  if result.size > 1:
                      out_result = StarFile.StarList(result.tolist())
                      cifdata[key] = out_result
                  else:
                      cifdata[key] = result.item(0)
              else:
                  cifdata[key] = result
              return result

        def construct_category(self,category,cifdata,store_value=True):
            """Construct a category using DDLm attributes"""
            con_type = self[category].get('_category_construct_local.type',None)
            if con_type == None:
                return {}
            if con_type == 'Pullback' or con_type == 'Filter':
                morphisms  = self[category]['_category_construct_local.components']
                morph_values = [cifdata[a] for a in morphisms] # the mapped values for each cat
                cats = [self[a]['_name.category_id'] for a in morphisms]
                cat_keys = [self[a]['_category.key_id'] for a in cats]
                cat_values = [list(cifdata[a]) for a in cat_keys] #the category key values for each cat
                if con_type == 'Filter':
                    int_filter = self[category].get('_category_construct_local.integer_filter',None)
                    text_filter = self[category].get('_category_construct_local.text_filter',None)
                    if int_filter is not None:
                        morph_values.append([int(a) for a in int_filter])
                    if text_filter is not None:
                        morph_values.append(text_filter)
                    cat_values.append(range(len(morph_values[-1])))
                # create the mathematical product filtered by equality of dataname values
                pullback_ids = [(x,y) for x in cat_values[0] for y in cat_values[1] \
                                if morph_values[0][cat_values[0].index(x)]==morph_values[1][cat_values[1].index(y)]]
                # now prepare for return
                if len(pullback_ids)==0:
                    return {}
                newids = self[category]['_category_construct_local.new_ids']
                fullnewids = [self.cat_obj_lookup_table[(category,n)][0] for n in newids]
                if con_type == 'Pullback':
                    final_results = {fullnewids[0]:[x[0] for x in pullback_ids],fullnewids[1]:[x[1] for x in pullback_ids]}
                    final_results.update(self.duplicate_datanames(cifdata,cats[0],category,key_vals = final_results[fullnewids[0]],skip_names=newids))
                    final_results.update(self.duplicate_datanames(cifdata,cats[1],category,key_vals = final_results[fullnewids[1]],skip_names=newids))
                elif con_type == 'Filter':   #simple filter
                    final_results = {fullnewids[0]:[x[0] for x in pullback_ids]}
                    final_results.update(self.duplicate_datanames(cifdata,cats[0],category,key_vals = final_results[fullnewids[0]],skip_names=newids))
                if store_value:
                    self.store_new_cat_values(cifdata,final_results,category)
                return final_results

        def push_from_pullback(self,target_category,source_categories,cifdata,store_value=True):
            """Each of the categories in source_categories are pullbacks that include
            the target_category"""
            target_key = self[target_category]['_category.key_id']
            result = {target_key:[]}
            first_time = True
            # for each source category, determine which element goes to the target
            for sc in source_categories:
                components = self[sc]['_category_construct_local.components']
                comp_cats = [self[c]['_name.category_id'] for c in components]
                new_ids = self[sc]['_category_construct_local.new_ids']
                source_ids = [self.cat_obj_lookup_table[(sc,n)][0] for n in new_ids]
                if len(components) == 2:  # not a filter
                    element_pos = comp_cats.index(target_category)
                    old_id = source_ids[element_pos]
                    print('Using %s to populate %s' % (old_id,target_key))
                    result[target_key].extend(cifdata[old_id])
                    # project through all identical names
                    extra_result = self.duplicate_datanames(cifdata,sc,target_category,skip_names=new_ids+[target_key])
                    # we only include keys that are common to all categories
                    if first_time:
                        result.update(extra_result)
                    else:
                        for k in extra_result.keys():
                            if k in result:
                                print('Updating %s: was %s' % (k,repr(result[k])))
                                result[k].extend(extra_result[k])
                else:
                    extra_result = self.duplicate_datanames(cifdata,sc,target_category,skip_names=new_ids)
                    if len(extra_result)>0 or source_ids[0] in cifdata:  #something is present
                        result[target_key].extend(cifdata[source_ids[0]])
                        for k in extra_result.keys():
                            if k in result:
                                print('Reverse filter: Updating %s: was %s' % (k,repr(result[k])))
                                result[k].extend(extra_result[k])
                            else:
                                result[k]=extra_result[k]
        # Bonus derivation if there is a singleton filter
                        if self[sc]['_category_construct_local.type'] == 'Filter':
                            int_filter = self[sc].get('_category_construct_local.integer_filter',None)
                            text_filter = self[sc].get('_category_construct_local.text_filter',None)
                            if int_filter is not None:
                                filter_values = int_filter
                            else:
                                filter_values = text_filter
                            if len(filter_values)==1:    #a singleton
                                extra_dataname = self[sc]['_category_construct_local.components'][0]
                                if int_filter is not None:
                                    new_value = [int(filter_values[0])] * len(cifdata[source_ids[0]])
                                else:
                                    new_value = filter_values * len(cifdata[source_ids[0]])
                                if extra_dataname not in result:
                                    result[extra_dataname] = new_value
                                else:
                                    result[extra_dataname].extend(new_value)
                        else:
                            raise ValueError('Unexpected category construct type' + self[sc]['_category_construct_local.type'])
                first_time = False
            # check for sanity - all dataname lengths must be identical
            datalen = len(set([len(a) for a in result.values()]))
            if datalen != 1:
                raise AssertionError('Failed to construct equal-length category items,'+ repr(result))
            if store_value:
                print('Now storing ' + repr(result))
                self.store_new_cat_values(cifdata,result,target_category)
            return result

        def duplicate_datanames(self,cifdata,from_category,to_category,key_vals=None,skip_names=[]):
            """Copy across datanames for which the from_category key equals [[key_vals]]"""
            result = {}
            s_names_in_cat = set(self.names_in_cat(from_category,names_only=True))
            t_names_in_cat = set(self.names_in_cat(to_category,names_only=True))
            can_project = s_names_in_cat & t_names_in_cat
            can_project -= set(skip_names)  #already dealt with
            source_key = self[from_category]['_category.key_id']
            print('Source dataname set: ' + repr(s_names_in_cat))
            print('Target dataname set: ' + repr(t_names_in_cat))
            print('Projecting through following datanames from %s to %s' % (from_category,to_category) + repr(can_project))
            for project_name in can_project:
                full_from_name = self.cat_obj_lookup_table[(from_category.lower(),project_name.lower())][0]
                full_to_name = self.cat_obj_lookup_table[(to_category.lower(),project_name.lower())][0]
                if key_vals is None:
                    try:
                        result[full_to_name] = cifdata[full_from_name]
                    except StarFile.StarDerivationError:
                        pass
                else:
                    all_key_vals = cifdata[source_key]
                    filter_pos = [all_key_vals.index(a) for a in key_vals]
                    try:
                        all_data_vals = cifdata[full_from_name]
                    except StarFile.StarDerivationError:
                        pass
                    result[full_to_name] = [all_data_vals[i] for i in filter_pos]
            return result

        def store_new_cat_values(self,cifdata,result,the_category):
            """Store the values in [[result]] into [[cifdata]]"""
            the_key = [a for a in result.keys() if self[a].get('_type.purpose','')=='Key']
            double_names = [a for a in result.keys() if a in cifdata]
            if len(double_names)>0:
                already_present = [a for a in self.names_in_cat(the_category) if a in cifdata]
                if set(already_present) != set(result.keys()):
                    print("Category %s not updated, mismatched datanames: %s" % (the_category, repr(set(already_present)^set(result.keys()))))
                    return
                #check key values
                old_keys = set(cifdata[the_key])
                common_keys = old_keys & set(result[the_key])
                if len(common_keys)>0:
                    print("Category %s not updated, key values in common:" % (common_keys))
                    return
                #extend result values with old values
                for one_name,one_value in result.items():
                    result[one_name].extend(cifdata[one_name])
            for one_name, one_value in result.items():
                try:
                    self.store_new_looped_value(one_name,cifdata,one_value,False)
                except StarFile.StarError:
                    print('%s: Not replacing %s with calculated %s' % (one_name,repr(cifdata[one_name]),repr(one_value)))
            #put the key as the first item
            print('Fixing item order for {}'.format(repr(the_key)))
            for one_key in the_key:  #should only be one
                cifdata.ChangeItemOrder(one_key,0)

        def generate_default_packet(self,catname,catkey,keyvalue):
            """Return a StarPacket with items from ``catname`` and a key value
            of ``keyvalue``"""
            newpack = StarPacket()
            for na in self.names_in_cat(catname):
                def_val = self[na].get("_enumeration.default","")
                if def_val:
                    final_val = self.change_type(na,def_val)
                    newpack.extend(final_val)
                    setattr(newpack,na,final_val)
            if len(newpack)>0:
                newpack.extend(keyvalue)
                setattr(newpack,catkey,keyvalue)
            return newpack

        def switch_numpy(self,to_val):
            pass

        def change_type(self,itemname,inval):
            import numpy
            if inval == "?": return inval
            change_function = convert_type(self[itemname])
            if isinstance(inval,list) and not isinstance(inval,StarFile.StarList):   #from a loop
                newval = list([change_function(a) for a in inval])
            else:
                newval = change_function(inval)
            return newval

        def install_validation_functions(self):
            """Install the DDL-appropriate validation checks"""
            if self.diclang != 'DDLm':
              self.item_validation_funs = [
                self.validate_item_type,
                self.validate_item_esd,
                self.validate_item_enum,   # functions which check conformance
                self.validate_enum_range,
                self.validate_looping]
              self.loop_validation_funs = [
                self.validate_loop_membership,
                self.validate_loop_key,
                self.validate_loop_references]    # functions checking loop values
              self.global_validation_funs = [
                self.validate_exclusion,
                self.validate_parent,
                self.validate_child,
                self.validate_dependents,
                self.validate_uniqueness] # where we need to look at other values
              self.block_validation_funs = [  # where only a full block will do
                self.validate_mandatory_category]
              self.global_remove_validation_funs = [
                self.validate_remove_parent_child] # removal is quicker with special checks
            elif self.diclang == 'DDLm':
                self.item_validation_funs = [
                    self.validate_item_enum,
                    self.validate_item_esd_ddlm,
                    ]
                self.loop_validation_funs = [
                    self.validate_looping_ddlm,
                    self.validate_loop_key_ddlm,
                    self.validate_loop_membership
                    ]
                self.global_validation_funs = []
                self.block_validation_funs = [
                    self.check_mandatory_items,
                    self.check_prohibited_items
                    ]
                self.global_remove_validation_funs = []
            self.optimize = False        # default value
            self.done_parents = []
            self.done_children = []
            self.done_keys = []

        def validate_item_type(self,item_name,item_value):
            def mymatch(m,a):
                res = m.match(a)
                if res != None: return res.group()
                else: return ""
            target_type = self[item_name].get(self.type_spec)
            if target_type == None:          # e.g. a category definition
                return {"result":True}                  # not restricted in any way
            matchexpr = self.typedic[target_type]
            item_values = listify(item_value)
            #for item in item_values:
                #print("Type match " + item_name + " " + item + ":",)
            #skip dots and question marks
            check_all = [a for a in item_values if a !="." and a != "?"]
            check_all = [a for a in check_all if mymatch(matchexpr,a) != a]
            if len(check_all)>0: return {"result":False,"bad_values":check_all}
            else: return {"result":True}

        def decide(self,result_list):
            """Construct the return list"""
            if len(result_list)==0:
                   return {"result":True}
            else:
                   return {"result":False,"bad_values":result_list}

        def validate_item_container(self, item_name,item_value):
            container_type = self[item_name]['_type.container']
            item_values = listify(item_value)
            if container_type == 'Single':
               okcheck = [a for a in item_values if not isinstance(a,(int,float,long,unicode))]
               return decide(okcheck)
            if container_type in ('Multiple','List'):
               okcheck = [a for a in item_values if not isinstance(a,StarList)]
               return decide(okcheck)
            if container_type == 'Array':    #A list with numerical values
               okcheck = [a for a in item_values if not isinstance(a,StarList)]
               first_check = decide(okcheck)
               if not first_check['result']: return first_check
               #num_check = [a for a in item_values if len([b for b in a if not isinstance

        def validate_item_esd(self,item_name,item_value):
            if self[item_name].get(self.primitive_type) != 'numb':
                return {"result":None}
            can_esd = self[item_name].get(self.esd_spec,"none") == "esd"
            if can_esd: return {"result":True}         #must be OK!
            item_values = listify(item_value)
            check_all = list([a for a in item_values if get_number_with_esd(a)[1] != None])
            if len(check_all)>0: return {"result":False,"bad_values":check_all}
            return {"result":True}

        def validate_item_esd_ddlm(self,item_name,item_value):
            if self[item_name].get('self.primitive_type') not in \
            ['Count','Index','Integer','Real','Imag','Complex','Binary','Hexadecimal','Octal']:
                return {"result":None}
            can_esd = True
            if self[item_name].get('_type.purpose') != 'Measurand':
                can_esd = False
            item_values = listify(item_value)
            check_all = [get_number_with_esd(a)[1] for a in item_values]
            check_all = [v for v in check_all if (can_esd and v == None) or \
                     (not can_esd and v != None)]
            if len(check_all)>0: return {"result":False,"bad_values":check_all}
            return {"result":True}

        def validate_enum_range(self,item_name,item_value):
            if "_item_range.minimum" not in self[item_name] and \
               "_item_range.maximum" not in self[item_name]:
                return {"result":None}
            minvals = self[item_name].get("_item_range.minimum",default = ["."])
            maxvals = self[item_name].get("_item_range.maximum",default = ["."])
            def makefloat(a):
                if a == ".": return a
                else: return float(a)
            maxvals = map(makefloat, maxvals)
            minvals = map(makefloat, minvals)
            rangelist = list(zip(minvals,maxvals))
            item_values = listify(item_value)
            def map_check(rangelist,item_value):
                if item_value == "?" or item_value == ".": return True
                iv,esd = get_number_with_esd(item_value)
                if iv==None: return None  #shouldn't happen as is numb type
                for lower,upper in rangelist:
                    #check the minima
                    if lower == ".": lower = iv - 1
                    if upper == ".": upper = iv + 1
                    if iv > lower and iv < upper: return True
                    if upper == lower and iv == upper: return True
                # debug
                # print("Value %s fails range check %d < x < %d" % (item_value,lower,upper))
                return False
            check_all = [a for a in item_values if map_check(rangelist,a) != True]
            if len(check_all)>0: return {"result":False,"bad_values":check_all}
            else: return {"result":True}

        def validate_item_enum(self,item_name,item_value):
            try:
                enum_list = self[item_name][self.enum_spec][:]
            except KeyError:
                return {"result":None}
            enum_list.append(".")   #default value
            enum_list.append("?")   #unknown
            item_values = listify(item_value)
            #print("Enum check: {!r} in {!r}".format(item_values, enum_list))
            check_all = [a for a in item_values if a not in enum_list]
            if len(check_all)>0: return {"result":False,"bad_values":check_all}
            else: return {"result":True}

        def validate_looping(self,item_name,item_value):
            try:
                must_loop = self[item_name][self.must_loop_spec]
            except KeyError:
                return {"result":None}
            if must_loop == 'yes' and isinstance(item_value,(unicode,str)): # not looped
                return {"result":False}      #this could be triggered
            if must_loop == 'no' and not isinstance(item_value,(unicode,str)):
                return {"result":False}
            return {"result":True}

        def validate_looping_ddlm(self,loop_names):
            """Check that all names are loopable"""
            truly_loopy = self.get_final_cats(loop_names)
            if len(truly_loopy)<len(loop_names):  #some are bad
                categories = [(a,self[a][self.cat_spec].lower()) for a in loop_names]
                not_looped = [a[0] for a in categories if a[1] not in self.parent_lookup.keys()]
                return {"result":False,"bad_items":not_looped}
            return {"result":True}

        def validate_loop_membership(self,loop_names):
            final_cat = self.get_final_cats(loop_names)
            bad_items =  [a for a in final_cat if a != final_cat[0]]
            if len(bad_items)>0:
                return {"result":False,"bad_items":bad_items}
            else: return {"result":True}

        def get_final_cats(self,loop_names):
            """Return a list of the uppermost parent categories for the loop_names. Names
            that are not from loopable categories are ignored."""
            try:
                categories = [self[a][self.cat_spec].lower() for a in loop_names]
            except KeyError:       #category is mandatory
                raise ValidCifError( "%s missing from dictionary %s for item in loop containing %s" % (self.cat_spec,self.dicname,loop_names[0]))
            truly_looped = [a for a in categories if a in self.parent_lookup.keys()]
            return [self.parent_lookup[a] for a in truly_looped]

        def validate_loop_key(self,loop_names):
            category = self[loop_names[0]][self.cat_spec]
            # find any unique values which must be present
            key_spec = self[category].get(self.key_spec,[])
            for names_to_check in key_spec:
                if isinstance(names_to_check,unicode):   #only one
                    names_to_check = [names_to_check]
                for loop_key in names_to_check:
                    if loop_key not in loop_names:
                        #is this one of those dang implicit items?
                        if self[loop_key].get(self.must_exist_spec,None) == "implicit":
                            continue          #it is virtually there...
                        alternates = self.get_alternates(loop_key)
                        if alternates == []:
                            return {"result":False,"bad_items":loop_key}
                        for alt_names in alternates:
                            alt = [a for a in alt_names if a in loop_names]
                            if len(alt) == 0:
                                return {"result":False,"bad_items":loop_key}  # no alternates
            return {"result":True}

        def validate_loop_key_ddlm(self,loop_names):
            """Make sure at least one of the necessary keys are available"""
            final_cats = self.get_final_cats(loop_names)
            if len(final_cats)>0:
                poss_keys = self.cat_key_table[final_cats[0]]
                found_keys = [a for a in poss_keys if a in loop_names]
                if len(found_keys)>0:
                    return {"result":True}
                else:
                    return {"result":False,"bad_items":poss_keys}
            else:
                return {"result":True}

        def validate_loop_references(self,loop_names):
            must_haves = [self[a].get(self.list_ref_spec,None) for a in loop_names]
            must_haves = [a for a in must_haves if a != None]
            # build a flat list.  For efficiency we don't remove duplicates,as
            # we expect no more than the order of 10 or 20 looped names.
            def flat_func(a,b):
                if isinstance(b,unicode):
                   a.append(b)       #single name
                else:
                   a.extend(b)       #list of names
                return a
            flat_mh = []
            [flat_func(flat_mh,a) for a in must_haves]
            group_mh = filter(lambda a:a[-1]=="_",flat_mh)
            single_mh = filter(lambda a:a[-1]!="_",flat_mh)
            res = [a for a in single_mh if a not in loop_names]
            def check_gr(s_item, name_list):
                nl = map(lambda a:a[:len(s_item)],name_list)
                if s_item in nl: return True
                return False
            res_g = [a for a in group_mh if check_gr(a,loop_names)]
            if len(res) == 0 and len(res_g) == 0: return {"result":True}
            # construct alternate list
            alternates = map(lambda a: (a,self.get_alternates(a)),res)
            alternates = [a for a in alternates if a[1] != []]
            # next line purely for error reporting
            missing_alts = [a[0] for a in alternates if a[1] == []]
            if len(alternates) != len(res):
               return {"result":False,"bad_items":missing_alts}   #short cut; at least one
                                                           #doesn't have an altern
            #loop over alternates
            for orig_name,alt_names in alternates:
                 alt = [a for a in alt_names if a in loop_names]
                 if len(alt) == 0: return {"result":False,"bad_items":orig_name}# no alternates
            return {"result":True}        #found alternates

        def get_alternates(self,main_name,exclusive_only=False):
            alternates = self[main_name].get(self.related_func,None)
            alt_names = []
            if alternates != None:
                alt_names =  self[main_name].get(self.related_item,None)
                if isinstance(alt_names,unicode):
                    alt_names = [alt_names]
                    alternates = [alternates]
                together = zip(alt_names,alternates)
                if exclusive_only:
                    alt_names = [a for a in together if a[1]=="alternate_exclusive" \
                                                 or a[1]=="replace"]
                else:
                    alt_names = [a for a in together if a[1]=="alternate" or a[1]=="replace"]
                alt_names = list([a[0] for a in alt_names])
            # now do the alias thing
            alias_names = listify(self[main_name].get("_item_aliases.alias_name",[]))
            alt_names.extend(alias_names)
            # print("Alternates for {}: {!r}".format(main_name, alt_names))
            return alt_names

        def validate_exclusion(self,item_name,item_value,whole_block,provisional_items={},globals={}):
           alternates = [a.lower() for a in self.get_alternates(item_name,exclusive_only=True)]
           item_name_list = [a.lower() for a in whole_block.keys()]
           item_name_list.extend([a.lower() for a in provisional_items.keys()])
           bad = [a for a in alternates if a in item_name_list]
           if len(bad)>0:
               print("Bad: %s, alternates %s" % (repr(bad),repr(alternates)))
               return {"result":False,"bad_items":bad}
           else: return {"result":True}

        # validate that parent exists and contains matching values
        def validate_parent(self,item_name,item_value,whole_block,provisional_items={},globals={}):
            parent_item = self[item_name].get(self.parent_spec)
            if not parent_item: return {"result":None}   #no parent specified
            if isinstance(parent_item,list):
                parent_item = parent_item[0]
            if self.optimize:
                if parent_item in self.done_parents:
                    return {"result":None}
                else:
                    self.done_parents.append(parent_item)
                    print("Done parents %s" % repr(self.done_parents))
            # initialise parent/child values
            if isinstance(item_value,unicode):
                child_values = [item_value]
            else: child_values = item_value[:]    #copy for safety
            # track down the parent
            # print("Looking for {} parent item {} in {!r}".format(item_name, parent_item, whole_block))
            # if globals contains the parent values, we are doing a DDL2 dictionary, and so
            # we have collected all parent values into the global block - so no need to search
            # for them elsewhere.
            # print("Looking for {!r}".format(parent_item))
            parent_values = globals.get(parent_item)
            if not parent_values:
                parent_values = provisional_items.get(parent_item,whole_block.get(parent_item))
            if not parent_values:
                # go for alternates
                namespace = whole_block.keys()
                namespace.extend(provisional_items.keys())
                namespace.extend(globals.keys())
                alt_names = filter_present(self.get_alternates(parent_item),namespace)
                if len(alt_names) == 0:
                    if len([a for a in child_values if a != "." and a != "?"])>0:
                        return {"result":False,"parent":parent_item}#no parent available -> error
                    else:
                        return {"result":None}       #maybe True is more appropriate??
                parent_item = alt_names[0]           #should never be more than one??
                parent_values = provisional_items.get(parent_item,whole_block.get(parent_item))
                if not parent_values:   # check global block
                    parent_values = globals.get(parent_item)
            if isinstance(parent_values,unicode):
                parent_values = [parent_values]
            #print("Checking parent %s against %s, values %r/%r" % (parent_item,
            #                                          item_name, parent_values, child_values))
            missing = self.check_parent_child(parent_values,child_values)
            if len(missing) > 0:
                return {"result":False,"bad_values":missing,"parent":parent_item}
            return {"result":True}

        def validate_child(self,item_name,item_value,whole_block,provisional_items={},globals={}):
            try:
                child_items = self[item_name][self.child_spec][:]  #copy
            except KeyError:
                return {"result":None}    #not relevant
            # special case for dictionaries  -> we check parents of children only
            if item_name in globals:  #dictionary so skip
                return {"result":None}
            if isinstance(child_items,unicode): # only one child
                child_items = [child_items]
            if isinstance(item_value,unicode): # single value
                parent_values = [item_value]
            else: parent_values = item_value[:]
            # expand child list with list of alternates
            for child_item in child_items[:]:
                child_items.extend(self.get_alternates(child_item))
            # now loop over the children
            for child_item in child_items:
                if self.optimize:
                    if child_item in self.done_children:
                        return {"result":None}
                    else:
                        self.done_children.append(child_item)
                        print("Done children %s" % repr(self.done_children))
                if child_item in provisional_items:
                    child_values = provisional_items[child_item][:]
                elif child_item in whole_block:
                    child_values = whole_block[child_item][:]
                else:  continue
                if isinstance(child_values,unicode):
                    child_values = [child_values]
                    # print("Checking child %s against %s, values %r/%r" % (child_item,
                    #       item_name, child_values, parent_values))
                missing = self.check_parent_child(parent_values,child_values)
                if len(missing)>0:
                    return {"result":False,"bad_values":missing,"child":child_item}
            return {"result":True}       #could mean that no child items present

        #a generic checker: all child vals should appear in parent_vals
        def check_parent_child(self,parent_vals,child_vals):
            # shield ourselves from dots and question marks
            pv = parent_vals[:]
            pv.extend([".","?"])
            res =  [a for a in child_vals if a not in pv]
            #print("Missing: %s" % res)
            return res

        def validate_remove_parent_child(self,item_name,whole_block):
            try:
                child_items = self[item_name][self.child_spec]
            except KeyError:
                return {"result":None}
            if isinstance(child_items,unicode): # only one child
                child_items = [child_items]
            for child_item in child_items:
                if child_item in whole_block:
                    return {"result":False,"child":child_item}
            return {"result":True}

        def validate_dependents(self,item_name,item_value,whole_block,prov={},globals={}):
            try:
                dep_items = self[item_name][self.dep_spec][:]
            except KeyError:
                return {"result":None}    #not relevant
            if isinstance(dep_items,unicode):
                dep_items = [dep_items]
            actual_names = whole_block.keys()
            actual_names.extend(prov.keys())
            actual_names.extend(globals.keys())
            missing = [a for a in dep_items if a not in actual_names]
            if len(missing) > 0:
                alternates = map(lambda a:[self.get_alternates(a),a],missing)
                # compact way to get a list of alternative items which are
                # present
                have_check = [(filter_present(b[0],actual_names),
                                           b[1]) for b in alternates]
                have_check = list([a for a in have_check if len(a[0])==0])
                if len(have_check) > 0:
                    have_check = [a[1] for a in have_check]
                    return {"result":False,"bad_items":have_check}
            return {"result":True}

        def validate_uniqueness(self,item_name,item_value,whole_block,provisional_items={},
                                                                      globals={}):
            category = self[item_name].get(self.cat_spec)
            if category == None:
                print("No category found for %s" % item_name)
                return {"result":None}
            # print("Category {!r} for item {}".format(category, item_name))
            # we make a copy in the following as we will be removing stuff later!
            unique_i = self[category].get("_category_key.name",[])[:]
            if isinstance(unique_i,unicode):
                unique_i = [unique_i]
            if item_name not in unique_i:       #no need to verify
                return {"result":None}
            if isinstance(item_value,unicode):  #not looped
                return {"result":None}
            # print("Checking %s -> %s -> %s ->Unique: %r" % (item_name,category,catentry, unique_i))
            # check that we can't optimize by not doing this check
            if self.optimize:
                if unique_i in self.done_keys:
                    return {"result":None}
                else:
                    self.done_keys.append(unique_i)
            val_list = []
            # get the matching data from any other data items
            unique_i.remove(item_name)
            other_data = []
            if len(unique_i) > 0:            # i.e. do have others to think about
               for other_name in unique_i:
               # we look for the value first in the provisional dict, then the main block
               # the logic being that anything in the provisional dict overrides the
               # main block
                   if other_name in provisional_items:
                       other_data.append(provisional_items[other_name])
                   elif other_name in whole_block:
                       other_data.append(whole_block[other_name])
                   elif self[other_name].get(self.must_exist_spec)=="implicit":
                       other_data.append([item_name]*len(item_value))  #placeholder
                   else:
                       return {"result":False,"bad_items":other_name}#missing data name
            # ok, so we go through all of our values
            # this works by comparing lists of strings to one other, and
            # so could be fooled if you think that '1.' and '1' are
            # identical
            for i in range(len(item_value)):
                #print("Value no. %d" % i, end=" ")
                this_entry = item_value[i]
                for j in range(len(other_data)):
                    this_entry = " ".join([this_entry,other_data[j][i]])
                #print("Looking for {!r} in {!r}: ".format(this_entry, val_list))
                if this_entry in val_list:
                    return {"result":False,"bad_values":this_entry}
                val_list.append(this_entry)
            return {"result":True}

        def validate_mandatory_category(self,whole_block):
            mand_cats = [self[a]['_category.id'] for a in self.keys() if self[a].get("_category.mandatory_code","no")=="yes"]
            if len(mand_cats) == 0:
                return {"result":True}
            # print("Mandatory categories - {!r}".format(mand_cats)
            # find which categories each of our datanames belongs to
            all_cats = [self[a].get(self.cat_spec) for a in whole_block.keys()]
            missing = set(mand_cats) - set(all_cats)
            if len(missing) > 0:
                return {"result":False,"bad_items":repr(missing)}
            return {"result":True}

        def check_mandatory_items(self,whole_block,default_scope='Item'):
            """Return an error if any mandatory items are missing"""
            if len(self.scopes_mandatory)== 0: return {"result":True}
            if default_scope == 'Datablock':
                return {"result":True}     #is a data file
            scope = whole_block.get('_definition.scope',default_scope)
            if '_dictionary.title' in whole_block:
               scope = 'Dictionary'
            missing = list([a for a in self.scopes_mandatory[scope] if a not in whole_block])
            if len(missing)==0:
                return {"result":True}
            else:
                return {"result":False,"bad_items":missing}

        def check_prohibited_items(self,whole_block,default_scope='Item'):
            """Return an error if any prohibited items are present"""
            if len(self.scopes_naughty)== 0: return {"result":True}
            if default_scope == 'Datablock':
                return {"result":True}     #is a data file
            scope = whole_block.get('_definition.scope',default_scope)
            if '_dictionary.title' in whole_block:
               scope = 'Dictionary'
            present = list([a for a in self.scopes_naughty[scope] if a in whole_block])
            if len(present)==0:
                return {"result":True}
            else:
                return {"result":False,"bad_items":present}

        def run_item_validation(self,item_name,item_value):
            return {item_name:list([(f.__name__,f(item_name,item_value)) for f in self.item_validation_funs])}

        def run_loop_validation(self,loop_names):
            return {loop_names[0]:list([(f.__name__,f(loop_names)) for f in self.loop_validation_funs])}

        def run_global_validation(self,item_name,item_value,data_block,provisional_items={},globals={}):
            results = list([(f.__name__,f(item_name,item_value,data_block,provisional_items,globals)) for f in self.global_validation_funs])
            return {item_name:results}

        def run_block_validation(self,whole_block,block_scope='Item'):
            results = list([(f.__name__,f(whole_block)) for f in self.block_validation_funs])
            # fix up the return values
            return {"whole_block":results}

        def optimize_on(self):
            self.optimize = True
            self.done_keys = []
            self.done_children = []
            self.done_parents = []

        def optimize_off(self):
            self.optimize = False
            self.done_keys = []
            self.done_children = []
            self.done_parents = []

    class ValidCifBlock(CifBlock):
        """A `CifBlock` that is valid with respect to a given CIF dictionary.  Methods
        of `CifBlock` are overridden where necessary to disallow addition of invalid items to the
        `CifBlock`.

        ## Initialisation

        * `dic` is a `CifDic` object to be used for validation.

        """
        def __init__(self,dic = None, diclist=[], mergemode = "replace",*args,**kwords):
            CifBlock.__init__(self,*args,**kwords)
            if dic and diclist:
                print("Warning: diclist argument ignored when initialising ValidCifBlock")
            if isinstance(dic,CifDic):
                self.fulldic = dic
            else:
                raise TypeError( "ValidCifBlock passed non-CifDic type in dic argument")
            if len(diclist)==0 and not dic:
                raise ValidCifError( "At least one dictionary must be specified")
            if diclist and not dic:
                self.fulldic = merge_dic(diclist,mergemode)
            if not self.run_data_checks()[0]:
                raise ValidCifError( self.report())

        def run_data_checks(self,verbose=False):
            self.v_result = {}
            self.fulldic.optimize_on()
            for dataname in self.keys():
                update_value(self.v_result,self.fulldic.run_item_validation(dataname,self[dataname]))
                update_value(self.v_result,self.fulldic.run_global_validation(dataname,self[dataname],self))
            for loop_names in self.loops.values():
                update_value(self.v_result,self.fulldic.run_loop_validation(loop_names))
            # now run block-level checks
            update_value(self.v_result,self.fulldic.run_block_validation(self))
            # return false and list of baddies if anything didn't match
            self.fulldic.optimize_off()
            all_keys = list(self.v_result.keys()) #dictionary will change
            for test_key in all_keys:
                #print("%s: %r" % (test_key, self.v_result[test_key]))
                self.v_result[test_key] = [a for a in self.v_result[test_key] if a[1]["result"]==False]
                if len(self.v_result[test_key]) == 0:
                    del self.v_result[test_key]
            isvalid = len(self.v_result)==0
            #if not isvalid:
            #    print("Baddies: {!r}".format(self.v_result))
            return isvalid,self.v_result

        def single_item_check(self,item_name,item_value):
            #self.match_single_item(item_name)
            if item_name not in self.fulldic:
                result = {item_name:[]}
            else:
                result = self.fulldic.run_item_validation(item_name,item_value)
            baddies = list([a for a in result[item_name] if a[1]["result"]==False])
            # if even one false one is found, this should trigger
            isvalid = (len(baddies) == 0)
            # if not isvalid: print("Failures for {}: {!r}".format(item_name, baddies))
            return isvalid,baddies

        def loop_item_check(self,loop_names):
            in_dic_names = list([a for a in loop_names if a in self.fulldic])
            if len(in_dic_names)==0:
                result = {loop_names[0]:[]}
            else:
                result = self.fulldic.run_loop_validation(in_dic_names)
            baddies = list([a for a in result[in_dic_names[0]] if a[1]["result"]==False])
            # if even one false one is found, this should trigger
            isvalid = (len(baddies) == 0)
            # if not isvalid: print("Failures for {}: {!r}".format(loop_names, baddies))
            return isvalid,baddies

        def global_item_check(self,item_name,item_value,provisional_items={}):
            if item_name not in self.fulldic:
                result = {item_name:[]}
            else:
                result = self.fulldic.run_global_validation(item_name,
                   item_value,self,provisional_items = provisional_items)
            baddies = list([a for a in result[item_name] if a[1]["result"] is False])
            # if even one false one is found, this should trigger
            isvalid = (len(baddies) == 0)
            # if not isvalid: print("Failures for {}: {!r}".format(item_name, baddies))
            return isvalid,baddies

        def remove_global_item_check(self,item_name):
            if item_name not in self.fulldic:
                result = {item_name:[]}
            else:
                result = self.fulldic.run_remove_global_validation(item_name,self,False)
            baddies = list([a for a in result[item_name] if a[1]["result"]==False])
            # if even one false one is found, this should trigger
            isvalid = (len(baddies) == 0)
            # if not isvalid: print("Failures for {}: {!r}".format(item_name, baddies))
            return isvalid,baddies

        def AddToLoop(self,dataname,loopdata):
            # single item checks
            paired_data = loopdata.items()
            for name,value in paired_data:
                valid,problems = self.single_item_check(name,value)
                self.report_if_invalid(valid,problems)
            # loop item checks; merge with current loop
            found = 0
            for aloop in self.block["loops"]:
                if dataname in aloop:
                    loopnames = aloop.keys()
                    for new_name in loopdata.keys():
                        if new_name not in loopnames: loopnames.append(new_name)
                    valid,problems = self.looped_item_check(loopnames)
                    self.report_if_invalid(valid,problems)
            prov_dict = loopdata.copy()
            for name,value in paired_data:
                del prov_dict[name]   # remove temporarily
                valid,problems = self.global_item_check(name,value,prov_dict)
                prov_dict[name] = value  # add back in
                self.report_if_invalid(valid,problems)
            CifBlock.AddToLoop(self,dataname,loopdata)

        def AddCifItem(self,data):
            if isinstance(data[0],(unicode,str)):   # single item
                valid,problems = self.single_item_check(data[0],data[1])
                self.report_if_invalid(valid,problems,data[0])
                valid,problems = self.global_item_check(data[0],data[1])
                self.report_if_invalid(valid,problems,data[0])
            elif isinstance(data[0],tuple) or isinstance(data[0],list):
                paired_data = list(zip(data[0],data[1]))
                for name,value in paired_data:
                    valid,problems = self.single_item_check(name,value)
                    self.report_if_invalid(valid,problems,name)
                valid,problems = self.loop_item_check(data[0])
                self.report_if_invalid(valid,problems,data[0])
                prov_dict = {}            # for storing temporary items
                for name,value in paired_data: prov_dict[name]=value
                for name,value in paired_data:
                    del prov_dict[name]   # remove temporarily
                    valid,problems = self.global_item_check(name,value,prov_dict)
                    prov_dict[name] = value  # add back in
                    self.report_if_invalid(valid,problems,name)
            else:
                raise ValueError("Programming error: AddCifItem passed non-tuple,non-string item")
            super(ValidCifBlock,self).AddCifItem(data)

        def AddItem(self,key,value,**kwargs):
            """Set value of dataname `key` to `value` after checking for conformance with CIF dictionary"""
            valid,problems = self.single_item_check(key,value)
            self.report_if_invalid(valid,problems,key)
            valid,problems = self.global_item_check(key,value)
            self.report_if_invalid(valid,problems,key)
            super(ValidCifBlock,self).AddItem(key,value,**kwargs)

        # utility function
        def report_if_invalid(self,valid,bad_list,data_name):
            if not valid:
                bad_tests = [a[0] for a in bad_list]
                error_string = ",".join(bad_tests)
                error_string = repr(data_name) + " fails following validity checks: "  + error_string
                raise ValidCifError( error_string)

        def __delitem__(self,key):
            # we don't need to run single item checks; we do need to run loop and
            # global checks.
            if key in self:
                try:
                    loop_items = self.GetLoop(key)
                except TypeError:
                    loop_items = []
                if loop_items:             #need to check loop conformance
                    loop_names = [a[0] for a in loop_items if a[0] != key]
                    valid,problems = self.loop_item_check(loop_names)
                    self.report_if_invalid(valid,problems)
                valid,problems = self.remove_global_item_check(key)
                self.report_if_invalid(valid,problems)
            self.RemoveCifItem(key)

        def report(self):
           outstr = StringIO()
           outstr.write( "Validation results\n")
           outstr.write( "------------------\n")
           print("%d invalid items found\n" % len(self.v_result))
           for item_name,val_func_list in self.v_result.items():
               outstr.write("%s fails following tests:\n" % item_name)
               for val_func in val_func_list:
                   outstr.write("\t%s\n")
           return outstr.getvalue()

    class ValidCifFile(CifFile):
        """A CIF file for which all datablocks are valid.  Argument `dic` to
        initialisation specifies a `CifDic` object to use for validation."""
        def __init__(self,dic=None,diclist=[],mergemode="replace",*args,**kwargs):
            if not diclist and not dic and not hasattr(self,'bigdic'):
                raise ValidCifError( "At least one dictionary is required to create a ValidCifFile object")
            if not dic and diclist:     #merge here for speed
                self.bigdic = merge_dic(diclist,mergemode)
            elif dic and not diclist:
                self.bigdic = dic
            CifFile.__init__(self,*args,**kwargs)
            for blockname in self.keys():
                self.dictionary[blockname]=ValidCifBlock(data=self.dictionary[blockname],dic=self.bigdic)

        def NewBlock(self,blockname,blockcontents,**kwargs):
            CifFile.NewBlock(self,blockname,blockcontents,**kwargs)
            # dictionary[blockname] is now a CifBlock object.  We
            # turn it into a ValidCifBlock object
            self.dictionary[blockname] = ValidCifBlock(dic=self.bigdic,
                                             data=self.dictionary[blockname])

    class ValidationResult:
        """Represents validation result. It is initialised with """
        def __init__(self,results):
            """results is return value of validate function"""
            self.valid_result, self.no_matches = results

        def report(self,use_html):
            """Return string with human-readable description of validation result"""
            return validate_report((self.valid_result, self.no_matches),use_html)

        def is_valid(self,block_name=None):
            """Return True for valid CIF file, otherwise False"""
            if block_name is not None:
                block_names = [block_name]
            else:
                block_names = self.valid_result.iterkeys()
            for block_name in block_names:
                if not self.valid_result[block_name] == (True,{}):
                    valid = False
                    break
                else:
                    valid = True
            return valid

        def has_no_match_items(self,block_name=None):
            """Return true if some items are not found in dictionary"""
            if block_name is not None:
                block_names = [block_name]
            else:
                block_names = self.no_matches.iter_keys()
            for block_name in block_names:
                if self.no_matches[block_name]:
                    has_no_match_items = True
                    break
                else:
                    has_no_match_items = False
            return has_no_match_items

    def Validate(ciffile,dic = "", diclist=[],mergemode="replace",isdic=False):
        """Validate the `ciffile` conforms to the definitions in `CifDic` object `dic`, or if `dic` is missing,
        to the results of merging the `CifDic` objects in `diclist` according to `mergemode`.  Flag
        `isdic` indicates that `ciffile` is a CIF dictionary meaning that save frames should be
        accessed for validation and that mandatory_category should be interpreted differently for DDL2."""
        if not isinstance(ciffile,CifFile):
            check_file = CifFile(ciffile)
        else:
            check_file = ciffile
        if not dic:
            fulldic = merge_dic(diclist,mergemode)
        else:
            fulldic = dic
        no_matches = {}
        valid_result = {}
        if isdic:          #assume one block only
            check_file.scoping = 'instance' #only data blocks visible
            top_level = check_file.keys()[0]
            check_file.scoping = 'dictionary'   #all blocks visible
            # collect a list of parents for speed
            if fulldic.diclang == 'DDL2':
                poss_parents = fulldic.get_all("_item_linked.parent_name")
                for parent in poss_parents:
                    curr_parent = listify(check_file.get(parent,[]))
                    new_vals = check_file.get_all(parent)
                    new_vals.extend(curr_parent)
                    if len(new_vals)>0:
                        check_file[parent] = new_vals
                    print("Added %s (len %d)" % (parent,len(check_file[parent])))
        # now run the validations
        for block in check_file.keys():
            if isdic and block == top_level:
               block_scope = 'Dictionary'
            elif isdic:
               block_scope = 'Item'
            else:
               block_scope = 'Datablock'
            no_matches[block] = [a for a in check_file[block].keys() if a not in fulldic]
            # remove non-matching items
            print("Not matched: " + repr(no_matches[block]))
            for nogood in no_matches[block]:
                 del check_file[block][nogood]
            print("Validating block %s, scope %s" % (block,block_scope))
            valid_result[block] = run_data_checks(check_file[block],fulldic,block_scope=block_scope)
        return valid_result,no_matches

    def validate_report(val_result,use_html=False):
        valid_result,no_matches = val_result
        outstr = StringIO()
        if use_html:
            outstr.write("<h2>Validation results</h2>")
        else:
            outstr.write( "Validation results\n")
            outstr.write( "------------------\n")
        if len(valid_result) > 10:
            suppress_valid = True         #don't clutter with valid messages
            if use_html:
               outstr.write("<p>For brevity, valid blocks are not reported in the output.</p>")
        else:
            suppress_valid = False
        for block in valid_result.keys():
            block_result = valid_result[block]
            if block_result[0]:
                out_line = "Block '%s' is VALID" % block
            else:
                out_line = "Block '%s' is INVALID" % block
            if use_html:
                if (block_result[0] and (not suppress_valid or len(no_matches[block])>0)) or not block_result[0]:
                    outstr.write( "<h3>%s</h3><p>" % out_line)
            else:
                    outstr.write( "\n %s\n" % out_line)
            if len(no_matches[block])!= 0:
                if use_html:
                    outstr.write( "<p>The following items were not found in the dictionary")
                    outstr.write(" (note that this does not invalidate the data block):</p>")
                    outstr.write("<p><table>\n")
                    [outstr.write("<tr><td>%s</td></tr>" % it) for it in no_matches[block]]
                    outstr.write("</table>\n")
                else:
                    outstr.write( "\n The following items were not found in the dictionary:\n")
                    outstr.write("Note that this does not invalidate the data block\n")
                    [outstr.write("%s\n" % it) for it in no_matches[block]]
            # now organise our results by type of error, not data item...
            error_type_dic = {}
            for error_item, error_list in block_result[1].items():
                for func_name,bad_result in error_list:
                    bad_result.update({"item_name":error_item})
                    try:
                        error_type_dic[func_name].append(bad_result)
                    except KeyError:
                        error_type_dic[func_name] = [bad_result]
            # make a table of test name, test message
            info_table = {\
            'validate_item_type':\
                "The following data items had badly formed values",
            'validate_item_esd':\
                "The following data items should not have esds appended",
            'validate_enum_range':\
                "The following data items have values outside permitted range",
            'validate_item_enum':\
                "The following data items have values outside permitted set",
            'validate_looping':\
                "The following data items violate looping constraints",
            'validate_loop_membership':\
                "The following looped data names are of different categories to the first looped data name",
            'validate_loop_key':\
                "A required dataname for this category is missing from the loop\n containing the dataname",
            'validate_loop_key_ddlm':\
                "A loop key is missing for the category containing the dataname",
            'validate_loop_references':\
                "A dataname required by the item is missing from the loop",
            'validate_parent':\
                "A parent dataname is missing or contains different values",
            'validate_child':\
                "A child dataname contains different values to the parent",
            'validate_uniqueness':\
                "One or more data items do not take unique values",
            'validate_dependents':\
                "A dataname required by the item is missing from the data block",
            'validate_exclusion': \
                "Both dataname and exclusive alternates or aliases are present in data block",
            'validate_mandatory_category':\
                "A required category is missing from this block",
            'check_mandatory_items':\
                "A required data attribute is missing from this block",
            'check_prohibited_items':\
                "A prohibited data attribute is present in this block"}

            for test_name,test_results in error_type_dic.items():
               if use_html:
                   outstr.write(html_error_report(test_name,info_table[test_name],test_results))
               else:
                   outstr.write(error_report(test_name,info_table[test_name],test_results))
                   outstr.write("\n\n")
        return outstr.getvalue()

    # A function to lay out a single error report.  We are passed
    # the name of the error (one of our validation functions), the
    # explanation to print out, and a dictionary with the error
    # information.  We print no more than 50 characters of the item

    def error_report(error_name,error_explanation,error_dics):
       retstring = "\n\n " + error_explanation + ":\n\n"
       headstring = "%-32s" % "Item name"
       bodystring = ""
       if "bad_values" in error_dics[0]:
          headstring += "%-20s" % "Bad value(s)"
       if "bad_items" in error_dics[0]:
          headstring += "%-20s" % "Bad dataname(s)"
       if "child" in error_dics[0]:
          headstring += "%-20s" % "Child"
       if "parent" in error_dics[0]:
          headstring += "%-20s" % "Parent"
       headstring +="\n"
       for error in error_dics:
          bodystring += "\n%-32s" % error["item_name"]
          if "bad_values" in error:
              out_vals = [repr(a)[:50] for a in error["bad_values"]]
              bodystring += "%-20s" % out_vals
          if "bad_items" in error:
              bodystring += "%-20s" % repr(error["bad_items"])
          if "child" in error:
              bodystring += "%-20s" % repr(error["child"])
          if "parent" in error:
              bodystring += "%-20s" % repr(error["parent"])
       return retstring + headstring + bodystring

    #  This lays out an HTML error report

    def html_error_report(error_name,error_explanation,error_dics,annotate=[]):
       retstring = "<h4>" + error_explanation + ":</h4>"
       retstring = retstring + "<table cellpadding=5><tr>"
       headstring = "<th>Item name</th>"
       bodystring = ""
       if "bad_values" in error_dics[0]:
          headstring += "<th>Bad value(s)</th>"
       if "bad_items" in error_dics[0]:
          headstring += "<th>Bad dataname(s)</th>"
       if "child" in error_dics[0]:
          headstring += "<th>Child</th>"
       if "parent" in error_dics[0]:
          headstring += "<th>Parent</th>"
       headstring +="</tr>\n"
       for error in error_dics:
          bodystring += "<tr><td><tt>%s</tt></td>" % error["item_name"]
          if "bad_values" in error:
              bodystring += "<td>%s</td>" % error["bad_values"]
          if "bad_items" in error:
              bodystring += "<td><tt>%s</tt></td>" % error["bad_items"]
          if "child" in error:
              bodystring += "<td><tt>%s</tt></td>" % error["child"]
          if "parent" in error:
              bodystring += "<td><tt>%s</tt></td>" % error["parent"]
          bodystring += "</tr>\n"
       return retstring + headstring + bodystring + "</table>\n"

    def run_data_checks(check_block,fulldic,block_scope='Item'):
        v_result = {}
        for key in check_block.keys():
            update_value(v_result, fulldic.run_item_validation(key,check_block[key]))
            update_value(v_result, fulldic.run_global_validation(key,check_block[key],check_block))
        for loopnames in check_block.loops.values():
            update_value(v_result, fulldic.run_loop_validation(loopnames))
        update_value(v_result,fulldic.run_block_validation(check_block,block_scope=block_scope))
        # return false and list of baddies if anything didn't match
        all_keys = list(v_result.keys())
        for test_key in all_keys:
            v_result[test_key] = [a for a in v_result[test_key] if a[1]["result"]==False]
            if len(v_result[test_key]) == 0:
                del v_result[test_key]
        # if even one false one is found, this should trigger
        # print("Baddies: {!r}".format(v_result))
        isvalid = len(v_result)==0
        return isvalid,v_result

    def get_number_with_esd(numstring):
        import string
        numb_re = '((-?(([0-9]*[.]([0-9]+))|([0-9]+)[.]?))([(][0-9]+[)])?([eEdD][+-]?[0-9]+)?)|(\?)|(\.)'
        our_match = re.match(numb_re,numstring)
        if our_match:
            a,base_num,b,c,dad,dbd,esd,exp,q,dot = our_match.groups()
            # print("Debug: {} -> {!r}".format(numstring, our_match.groups()))
        else:
            return None,None
        if dot or q: return None,None     #a dot or question mark
        if exp:          #has exponent
           exp = exp.replace("d","e")     # mop up old fashioned numbers
           exp = exp.replace("D","e")
           base_num = base_num + exp
        # print("Debug: have %s for base_num from %s" % (base_num,numstring))
        base_num = float(base_num)
        # work out esd, if present.
        if esd:
            esd = float(esd[1:-1])    # no brackets
            if dad:                   # decimal point + digits
                esd = esd * (10 ** (-1* len(dad)))
            if exp:
                esd = esd * (10 ** (float(exp[1:])))
        return base_num,esd

    def float_with_esd(inval):
        if isinstance(inval,unicode):
            j = inval.find("(")
            if j>=0:  return float(inval[:j])
        return float(inval)

    def convert_type(definition):
        """Convert value to have the type given by definition"""
        #extract the actual required type information
        container = definition['_type.container']
        dimension = definition.get('_type.dimension',StarFile.StarList([]))
        structure = interpret_structure(definition['_type.contents'])
        if container == 'Single':   #a single value to convert
            return convert_single_value(structure)
        elif container == 'List':   #lots of the same value
            return convert_list_values(structure,dimension)
        elif container == 'Multiple': #no idea
            return None
        elif container in ('Array','Matrix'): #numpy array
            return convert_matrix_values(structure)
        return lambda a:a    #unable to convert

    def convert_single_value(type_spec):
        """Convert a single item according to type_spec"""
        if type_spec == 'Real':
            return float_with_esd
        if type_spec in ('Count','Integer','Index','Binary','Hexadecimal','Octal'):
            return int
        if type_spec == 'Complex':
            return complex
        if type_spec == 'Imag':
            return lambda a:complex(0,a)
        if type_spec in ('Code','Name','Tag'):  #case-insensitive -> lowercase
            return lambda a:a.lower()
        return lambda a:a   #can't do anything numeric

    def convert_list_values(structure,dimension):
        """Convert the values according to the element
           structure given in [[structure]]"""
        if isinstance(structure,(unicode,str)):   #simple repetition
            func_def =  "element_convert = convert_single_value('%s')" % structure
        else:
            func_def =       "def element_convert(element):\n"
            func_def +=      "   final_val = []\n"
            for pos_no in range(len(structure)):
                func_def +=  "   final_val.append("
                type_spec = structure[pos_no]
                if type_spec == 'Real':
                    cf = "float_with_esd("
                elif type_spec in ('Count','Integer','Index','Binary','Hexadecimal','Octal'):
                    cf = 'int('
                elif type_spec == 'Complex':
                    cf = 'complex('
                elif type_spec == 'Imag':
                    cf = 'complex(0,'
                elif type_spec in ('Code','Name','Tag'):
                    cf = '('
                else: cf = ''
                func_def += cf
                func_def += "element[%d]" % pos_no
                if "(" in cf: func_def +=")"
                if type_spec in ('Code','Name','Tag'):
                    func_def +=".lower()"
                func_def +=")\n"  # close append
            func_def +=      "   return final_val\n"
        print(func_def)
        exec(func_def, globals()) #(re)defines element_convert in global namespace
        if len(dimension)> 0 and int(dimension[0]) != 1:
            return lambda a: list(map(element_convert,a))
        else: return element_convert

    def convert_matrix_values(valtype):
        """Convert a dREL String or Float valued List structure to a numpy matrix structure"""
        # first convert to numpy array, then let numpy do the work
        try: import numpy
        except:
            return lambda a:a   #cannot do it
        func_def =     "def matrix_convert(a):\n"
        func_def +=    "    import numpy\n"
        func_def +=    "    p = numpy.array(a)\n"
        if valtype == 'Real':
            func_def+= "    return p.astype('float')\n"
        elif valtype == 'Integer':
            func_def +="    return p.astype('int')\n"
        elif valtype == 'Complex':
            func_def +="    return p.astype('complex')\n"
        else:
            raise ValueError('Unknown matrix value type')
        exec(func_def,globals())  #matrix convert is defined
        return matrix_convert

    def interpret_structure(struc_spec):
        """Interpret a DDLm structure specification"""
        from . import TypeContentsParser as t
        p = t.TypeParser(t.TypeParserScanner(struc_spec))
        return getattr(p,"input")()

    # A utility function to append to item values rather than replace them
    def update_value(base_dict,new_items):
        for new_key in new_items.keys():
            if new_key in base_dict:
                base_dict[new_key].extend(new_items[new_key])
            else:
                base_dict[new_key] = new_items[new_key]

    #Transpose the list of lists passed to us
    def transpose(base_list):
        new_lofl = []
        full_length = len(base_list)
        opt_range = range(full_length)
        for i in range(len(base_list[0])):
           new_packet = []
           for j in opt_range:
              new_packet.append(base_list[j][i])
           new_lofl.append(new_packet)
        return new_lofl

    # listify strings - used surprisingly often
    def listify(item):
        if isinstance(item,(unicode,str)): return [item]
        else: return item

    # given a list of search items, return a list of items
    # actually contained in the given data block
    def filter_present(namelist,datablocknames):
        return [a for a in namelist if a in datablocknames]

    # Make an item immutable, used if we want a list to be a key
    def make_immutable(values):
        """Turn list of StarList values into a list of immutable items"""
        if not isinstance(values[0],StarList):
            return values
        else:
            return [tuple(a) for a in values]

    # merge ddl dictionaries.  We should be passed filenames or CifFile
    # objects
    def merge_dic(diclist,mergemode="replace",ddlspec=None):
        dic_as_cif_list = []
        for dic in diclist:
            if not isinstance(dic,CifFile) and \
               not isinstance(dic,(unicode,str)):
                   raise TypeError("Require list of CifFile names/objects for dictionary merging")
            if not isinstance(dic,CifFile): dic_as_cif_list.append(CifFile(dic))
            else: dic_as_cif_list.append(dic)
        # we now merge left to right
        basedic = dic_as_cif_list[0]
        if "on_this_dictionary" in basedic:   #DDL1 style only
            for dic in dic_as_cif_list[1:]:
               basedic.merge(dic,mode=mergemode,match_att=["_name"])
        elif len(basedic.keys()) == 1:                     #One block: DDL2/m style
            old_block = basedic[basedic.keys()[0]]
            for dic in dic_as_cif_list[1:]:
               new_block = dic[dic.keys()[0]]
               basedic.merge(dic,mode=mergemode,
                             single_block=[basedic.keys()[0],dic.keys()[0]],
                             match_att=["_item.name"],match_function=find_parent)
        return CifDic(basedic)

    def find_parent(ddl2_def):
        if "_item.name" not in ddl2_def:
           return None
        if isinstance(ddl2_def["_item.name"],unicode):
            return ddl2_def["_item.name"]
        if "_item_linked.child_name" not in ddl2_def:
            raise CifError("Asked to find parent in block with no child_names")
        if "_item_linked.parent_name" not in ddl2_def:
            raise CifError("Asked to find parent in block with no parent_names")
        result = list([a for a in ddl2_def["_item.name"] if a not in ddl2_def["_item_linked.child_name"]])
        if len(result)>1 or len(result)==0:
            raise CifError("Unable to find single unique parent data item")
        return result[0]

    def ReadCif(filename,grammar='auto',scantype='standard',scoping='instance',standard='CIF'):
        """ Read in a CIF file, returning a `CifFile` object.

        * `filename` may be a URL, a file
        path on the local system, or any object with a `read` method.

        * `grammar` chooses the CIF grammar variant. `1.0` is the original 1992 grammar and `1.1`
        is identical except for the exclusion of square brackets as the first characters in
        undelimited datanames. `2.0` will read files in the CIF2.0 standard, and `STAR2` will
        read files according to the STAR2 publication.  If grammar is `None`, autodetection
        will be attempted in the order `2.0`, `1.1` and `1.0`. This will always succeed for
        properly-formed CIF2.0 files.  Note that only Unicode characters in the basic multilingual
        plane are recognised (this will be fixed when PyCIFRW is ported to Python 3).

        * `scantype` can be `standard` or `flex`.  `standard` provides pure Python parsing at the
        cost of a factor of 10 or so in speed.  `flex` will tokenise the input CIF file using
        fast C routines, but is not available for CIF2/STAR2 files.  Note that running PyCIFRW in
        Jython uses native Java regular expressions
        to provide a speedup regardless of this argument (and does not yet support CIF2).

        * `scoping` is only relevant where nested save frames are expected (STAR2 only).
        `instance` scoping makes nested save frames
        invisible outside their hierarchy, allowing duplicate save frame names in separate
        hierarchies. `dictionary` scoping makes all save frames within a data block visible to each
        other, thereby restricting all save frames to have unique names.
        Currently the only recognised value for `standard` is `CIF`, which when set enforces a
        maximum length of 75 characters for datanames and has no other effect. """

        finalcif = CifFile(scoping=scoping,standard=standard)
        return StarFile.ReadStar(filename,prepared=finalcif,grammar=grammar,scantype=scantype)
        #return StarFile.StarFile(filename,maxlength,scantype=scantype,grammar=grammar,**kwargs)

    class CifLoopBlock(StarFile.LoopBlock):
        def __init__(self,data=(),**kwargs):
            super(CifLoopBlock,self).__init__(data,**kwargs)

    #No documentation flags

## Functions

def ReadCif(

filename, grammar=u'auto', scantype=u'standard', scoping=u'instance', standard=u'CIF')

Read in a CIF file, returning a `CifFile` object.

- `filename` may be a URL, a file path on the local system, or any object with a `read` method.

- `grammar` chooses the CIF grammar variant. `1.0` is the original 1992 grammar and `1.1` is identical except for the exclusion of square brackets as the first characters in undelimited datanames. `2.0` will read files in the CIF2.0 standard, and `STAR2` will read files according to the STAR2 publication. If grammar is `None`, autodetection will be attempted in the order `2.0`, `1.1` and `1.0`. This will always succeed for properly-formed CIF2.0 files. Note that only Unicode characters in the basic multilingual plane are recognised (this will be fixed when PyCIFRW is ported to Python 3).

- `scantype` can be `standard` or `flex`. `standard` provides pure Python parsing at the cost of a factor of 10 or so in speed. `flex` will tokenise the input CIF file using fast C routines, but is not available for CIF2/STAR2 files. Note that running PyCIFRW in Jython uses native Java regular expressions to provide a speedup regardless of this argument (and does not yet support CIF2).

- `scoping` is only relevant where nested save frames are expected (STAR2 only). `instance` scoping makes nested save frames invisible outside their hierarchy, allowing duplicate save frame names in separate hierarchies. `dictionary` scoping makes all save frames within a data block visible to each other, thereby restricting all save frames to have unique names. Currently the only recognised value for `standard` is `CIF`, which when set enforces a maximum length of 75 characters for datanames and has no other effect.

Show source ≡

    def ReadCif(filename,grammar='auto',scantype='standard',scoping='instance',standard='CIF'):
        """ Read in a CIF file, returning a `CifFile` object.

        * `filename` may be a URL, a file
        path on the local system, or any object with a `read` method.

        * `grammar` chooses the CIF grammar variant. `1.0` is the original 1992 grammar and `1.1`
        is identical except for the exclusion of square brackets as the first characters in
        undelimited datanames. `2.0` will read files in the CIF2.0 standard, and `STAR2` will
        read files according to the STAR2 publication.  If grammar is `None`, autodetection
        will be attempted in the order `2.0`, `1.1` and `1.0`. This will always succeed for
        properly-formed CIF2.0 files.  Note that only Unicode characters in the basic multilingual
        plane are recognised (this will be fixed when PyCIFRW is ported to Python 3).

        * `scantype` can be `standard` or `flex`.  `standard` provides pure Python parsing at the
        cost of a factor of 10 or so in speed.  `flex` will tokenise the input CIF file using
        fast C routines, but is not available for CIF2/STAR2 files.  Note that running PyCIFRW in
        Jython uses native Java regular expressions
        to provide a speedup regardless of this argument (and does not yet support CIF2).

        * `scoping` is only relevant where nested save frames are expected (STAR2 only).
        `instance` scoping makes nested save frames
        invisible outside their hierarchy, allowing duplicate save frame names in separate
        hierarchies. `dictionary` scoping makes all save frames within a data block visible to each
        other, thereby restricting all save frames to have unique names.
        Currently the only recognised value for `standard` is `CIF`, which when set enforces a
        maximum length of 75 characters for datanames and has no other effect. """

        finalcif = CifFile(scoping=scoping,standard=standard)
        return StarFile.ReadStar(filename,prepared=finalcif,grammar=grammar,scantype=scantype)

def Validate(

ciffile, dic=u'', diclist=[], mergemode=u'replace', isdic=False)

Validate the `ciffile` conforms to the definitions in `CifDic` object `dic`, or if `dic` is missing, to the results of merging the `CifDic` objects in `diclist` according to `mergemode`. Flag `isdic` indicates that `ciffile` is a CIF dictionary meaning that save frames should be accessed for validation and that mandatory_category should be interpreted differently for DDL2.

Show source ≡

    def Validate(ciffile,dic = "", diclist=[],mergemode="replace",isdic=False):
        """Validate the `ciffile` conforms to the definitions in `CifDic` object `dic`, or if `dic` is missing,
        to the results of merging the `CifDic` objects in `diclist` according to `mergemode`.  Flag
        `isdic` indicates that `ciffile` is a CIF dictionary meaning that save frames should be
        accessed for validation and that mandatory_category should be interpreted differently for DDL2."""
        if not isinstance(ciffile,CifFile):
            check_file = CifFile(ciffile)
        else:
            check_file = ciffile
        if not dic:
            fulldic = merge_dic(diclist,mergemode)
        else:
            fulldic = dic
        no_matches = {}
        valid_result = {}
        if isdic:          #assume one block only
            check_file.scoping = 'instance' #only data blocks visible
            top_level = check_file.keys()[0]
            check_file.scoping = 'dictionary'   #all blocks visible
            # collect a list of parents for speed
            if fulldic.diclang == 'DDL2':
                poss_parents = fulldic.get_all("_item_linked.parent_name")
                for parent in poss_parents:
                    curr_parent = listify(check_file.get(parent,[]))
                    new_vals = check_file.get_all(parent)
                    new_vals.extend(curr_parent)
                    if len(new_vals)>0:
                        check_file[parent] = new_vals
                    print("Added %s (len %d)" % (parent,len(check_file[parent])))
        # now run the validations
        for block in check_file.keys():
            if isdic and block == top_level:
               block_scope = 'Dictionary'
            elif isdic:
               block_scope = 'Item'
            else:
               block_scope = 'Datablock'
            no_matches[block] = [a for a in check_file[block].keys() if a not in fulldic]
            # remove non-matching items
            print("Not matched: " + repr(no_matches[block]))
            for nogood in no_matches[block]:
                 del check_file[block][nogood]
            print("Validating block %s, scope %s" % (block,block_scope))
            valid_result[block] = run_data_checks(check_file[block],fulldic,block_scope=block_scope)
        return valid_result,no_matches

## Classes

class CifBlock

A class to hold a single block of a CIF file. A `CifBlock` object can be treated as a Python dictionary, in particular, individual items can be accessed using square brackets e.g. `b['_a_dataname']`. All other Python dictionary methods are also available (e.g. `keys()`, `values()`). Looped datanames will return a list of values.

## Initialisation

When provided, `data` should be another `CifBlock` whose contents will be copied to this block.

- if `strict` is set, maximum name lengths will be enforced

- `maxoutlength` is the maximum length for output lines

- `wraplength` is the ideal length to make output lines

- When set, `overwrite` allows the values of datanames to be changed (otherwise an error is raised).

- `compat_mode` will allow deprecated behaviour of creating single-dataname loops using the syntax `a[_dataname] = [1,2,3,4]`. This should now be done by calling `CreateLoop` after setting the dataitem value.

Show source ≡

    class CifBlock(StarFile.StarBlock):
        """
        A class to hold a single block of a CIF file.  A `CifBlock` object can be treated as
        a Python dictionary, in particular, individual items can be accessed using square
        brackets e.g. `b['_a_dataname']`.  All other Python dictionary methods are also
        available (e.g. `keys()`, `values()`).  Looped datanames will return a list of values.

        ## Initialisation

        When provided, `data` should be another `CifBlock` whose contents will be copied to
        this block.

        * if `strict` is set, maximum name lengths will be enforced

        * `maxoutlength` is the maximum length for output lines

        * `wraplength` is the ideal length to make output lines

        * When set, `overwrite` allows the values of datanames to be changed (otherwise an error
        is raised).

        * `compat_mode` will allow deprecated behaviour of creating single-dataname loops using
        the syntax `a[_dataname] = [1,2,3,4]`.  This should now be done by calling `CreateLoop`
        after setting the dataitem value.
        """
        def __init__(self,data = (), strict = 1, compat_mode=False, **kwargs):
            """When provided, `data` should be another CifBlock whose contents will be copied to
            this block.

            * if `strict` is set, maximum name lengths will be enforced

            * `maxoutlength` is the maximum length for output lines

            * `wraplength` is the ideal length to make output lines

            * When set, `overwrite` allows the values of datanames to be changed (otherwise an error
            is raised).

            * `compat_mode` will allow deprecated behaviour of creating single-dataname loops using
            the syntax `a[_dataname] = [1,2,3,4]`.  This should now be done by calling `CreateLoop`
            after setting the dataitem value.
            """
            if strict: maxnamelength=75
            else:
               maxnamelength=-1
            super(CifBlock,self).__init__(data=data,maxnamelength=maxnamelength,**kwargs)
            self.dictionary = None   #DDL dictionary referring to this block
            self.compat_mode = compat_mode   #old-style behaviour of setitem

        def RemoveCifItem(self,itemname):
            """Remove `itemname` from the CifBlock"""
            self.RemoveItem(itemname)

        def __setitem__(self,key,value):
            self.AddItem(key,value)
            # for backwards compatibility make a single-element loop
            if self.compat_mode:
                if isinstance(value,(tuple,list)) and not isinstance(value,StarFile.StarList):
                     # single element loop
                     self.CreateLoop([key])

        def copy(self):
            newblock = super(CifBlock,self).copy()
            return self.copy.im_class(newblock)   #catch inheritance

        def AddCifItem(self,data):
            """ *DEPRECATED*. Use `AddItem` instead."""
            # we accept only tuples, strings and lists!!
            if not (isinstance(data[0],(unicode,tuple,list,str))):
                      raise TypeError('Cif datanames are either a string, tuple or list')
            # we catch single item loops as well...
            if isinstance(data[0],(unicode,str)):
                self.AddSingleCifItem(data[0],list(data[1]))
                if isinstance(data[1],(tuple,list)) and not isinstance(data[1],StarFile.StarList):  # a single element loop
                    self.CreateLoop([data[0]])
                return
            # otherwise, we loop over the datanames
            keyvals = zip(data[0][0],[list(a) for a in data[1][0]])
            [self.AddSingleCifItem(a,b) for a,b in keyvals]
            # and create the loop
            self.CreateLoop(data[0][0])

        def AddSingleCifItem(self,key,value):
            """*Deprecated*. Use `AddItem` instead"""
            """Add a single data item. If it is part of a loop, a separate call should be made"""
            self.AddItem(key,value)

        def loopnames(self):
            return [self.loops[a] for a in self.loops]

### Ancestors (in MRO)

- CifBlock
- CifFile.StarFile.StarBlock
- __builtin__.object

### Methods

def AddCifItem(

self, data)

DEPRECATED. Use `AddItem` instead.

Show source ≡

    def AddCifItem(self,data):
        """ *DEPRECATED*. Use `AddItem` instead."""
        # we accept only tuples, strings and lists!!
        if not (isinstance(data[0],(unicode,tuple,list,str))):
                  raise TypeError('Cif datanames are either a string, tuple or list')
        # we catch single item loops as well...
        if isinstance(data[0],(unicode,str)):
            self.AddSingleCifItem(data[0],list(data[1]))
            if isinstance(data[1],(tuple,list)) and not isinstance(data[1],StarFile.StarList):  # a single element loop
                self.CreateLoop([data[0]])
            return
        # otherwise, we loop over the datanames
        keyvals = zip(data[0][0],[list(a) for a in data[1][0]])
        [self.AddSingleCifItem(a,b) for a,b in keyvals]
        # and create the loop
        self.CreateLoop(data[0][0])

def AddItem(

self, key, value, precheck=False)

Add dataname `key` to block with value `value`. `value` may be a single value, a list or a tuple. If `precheck` is False (the default), all values will be checked and converted to unicode strings as necessary. If `precheck` is True, this checking is bypassed. No checking is necessary when values are read from a CIF file as they are already in correct form.

Show source ≡

    def AddItem(self,key,value,precheck=False):
        """Add dataname `key` to block with value `value`.  `value` may be
        a single value, a list or a tuple. If `precheck` is False (the default),
        all values will be checked and converted to unicode strings as necessary. If
        `precheck` is True, this checking is bypassed.  No checking is necessary
        when values are read from a CIF file as they are already in correct form."""
        if not isinstance(key,(unicode,str)):
             raise TypeError('Star datanames are strings only (got %s)' % repr( key ))
        key = unicode(key)    #everything is unicode internally
        if not precheck:
             self.check_data_name(key,self.maxnamelength)    # make sure no nasty characters
        # check for overwriting
        if key in self:
             if not self.overwrite:
                 raise StarError( 'Attempt to insert duplicate item name %s' % key)
        if not precheck:   #need to sanitise
            regval,empty_val = self.regularise_data(value)
            pure_string = check_stringiness(regval)
            self.check_item_value(regval)
        else:
            regval,empty_val = value,None
            pure_string = True
        # update ancillary information first
        lower_key = key.lower()
        if not lower_key in self and self.FindLoop(lower_key)<0:      #need to add to order
            self.item_order.append(lower_key)
        # always remove from our case table in case the case is different
        try:
            del self.true_case[lower_key]
        except KeyError:
            pass
        self.true_case[lower_key] = key
        if pure_string:
            self.block.update({lower_key:[regval,empty_val]})
        else:
            self.block.update({lower_key:[empty_val,regval]})

def AddLoopItem(

self, incomingdata, precheck=False, maxlength=-1)

Deprecated. Use `AddItem` followed by `CreateLoop` if necessary.

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    def AddLoopItem(self,incomingdata,precheck=False,maxlength=-1):
        """*Deprecated*. Use `AddItem` followed by `CreateLoop` if
        necessary."""
        # print "Received data %s" % `incomingdata`
        # we accept tuples, strings, lists and dicts!!
        # Direct insertion: we have a string-valued key, with an array
        # of values -> single-item into our loop
        if isinstance(incomingdata[0],(tuple,list)):
           # a whole loop
           keyvallist = zip(incomingdata[0],incomingdata[1])
           for key,value in keyvallist:
               self.AddItem(key,value)
           self.CreateLoop(incomingdata[0])
        elif not isinstance(incomingdata[0],(unicode,str)):
             raise TypeError('Star datanames are strings only (got %s)' % repr( incomingdata[0] ))
        else:
            self.AddItem(incomingdata[0],incomingdata[1])

def AddLoopName(

self, oldname, newname)

Add `newname` to the loop containing `oldname`. If it is already in the new loop, no error is raised. If `newname` is in a different loop, it is removed from that loop. The number of values associated with `newname` must match the number of values associated with all other columns of the new loop or a `ValueError` will be raised.

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    def AddLoopName(self,oldname, newname):
        """Add `newname` to the loop containing `oldname`. If it is already in the new loop, no
        error is raised.  If `newname` is in a different loop, it is removed from that loop.
        The number of values associated with `newname` must match the number of values associated
        with all other columns of the new loop or a `ValueError` will be raised."""
        lower_newname = newname.lower()
        loop_no = self.FindLoop(oldname)
        if loop_no < 0:
            raise KeyError('%s not in loop' % oldname)
        if lower_newname in self.loops[loop_no]:
            return
        # check length
        old_provides = self.provide_value
        self.provide_value = False
        loop_len = len(self[oldname])
        self.provide_value = old_provides
        if len(self[newname]) != loop_len:
            raise ValueError('Mismatch of loop column lengths for %s: should be %d' % (newname,loop_len))
        # remove from any other loops
        [self.loops[a].remove(lower_newname) for a in self.loops if lower_newname in self.loops[a]]
        # and add to this loop
        self.loops[loop_no].append(lower_newname)
        # remove from item_order if present
        try:
            self.item_order.remove(lower_newname)
        except ValueError:
            pass

def AddSingleCifItem(

self, key, value)

Deprecated. Use `AddItem` instead

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    def AddSingleCifItem(self,key,value):
        """*Deprecated*. Use `AddItem` instead"""
        """Add a single data item. If it is part of a loop, a separate call should be made"""
        self.AddItem(key,value)

def AddToLoop(

self, dataname, loopdata)

Deprecated. Use `AddItem` followed by calls to `AddLoopName`.

Add multiple columns to the loop containing `dataname`. `loopdata` is a collection of (key,value) pairs, where `key` is the new dataname and `value` is a list of values for that dataname

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    def AddToLoop(self,dataname,loopdata):
        """*Deprecated*. Use `AddItem` followed by calls to `AddLoopName`.
        Add multiple columns to the loop containing `dataname`. `loopdata` is a
        collection of (key,value) pairs, where `key` is the new dataname and `value`
        is a list of values for that dataname"""
        # check lengths
        thisloop = self.FindLoop(dataname)
        loop_len = len(self[dataname])
        bad_vals = [a for a in loopdata.items() if len(a[1])!=loop_len]
        if len(bad_vals)>0:
           raise StarLengthError("Number of values for looped datanames %s not equal to %d" \
               % (repr( bad_vals ),loop_len))
        self.update(loopdata)
        self.loops[thisloop]+=loopdata.keys()

def ChangeItemOrder(

self, itemname, newpos)

Move the printout order of `itemname` to `newpos`. If `itemname` is in a loop, `newpos` refers to the order within the loop.

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    def ChangeItemOrder(self,itemname,newpos):
        """Move the printout order of `itemname` to `newpos`. If `itemname` is
        in a loop, `newpos` refers to the order within the loop."""
        if isinstance(itemname,(unicode,str)):
            true_name = itemname.lower()
        else:
            true_name = itemname
        loopno = self.FindLoop(true_name)
        if loopno < 0:  #top level
            self.item_order.remove(true_name)
            self.item_order.insert(newpos,true_name)
        else:
            self.loops[loopno].remove(true_name)
            self.loops[loopno].insert(newpos,true_name)

def CreateLoop(

self, datanames, order=-1, length_check=True)

Create a loop in the datablock. `datanames` is a list of datanames that together form a loop. If length_check is True, they should have been initialised in the block to have the same number of elements (possibly 0). If `order` is given, the loop will appear at this position in the block when printing out. A loop counts as a single position.

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    def CreateLoop(self,datanames,order=-1,length_check=True):
           """Create a loop in the datablock. `datanames` is a list of datanames that
           together form a loop.  If length_check is True, they should have been initialised in the block
           to have the same number of elements (possibly 0). If `order` is given,
           the loop will appear at this position in the block when printing
           out. A loop counts as a single position."""
           if length_check:
               # check lengths: these datanames should exist
               listed_values = [a for a in datanames if isinstance(self[a],list) and not isinstance(self[a],StarList)]
               if len(listed_values) == len(datanames):
                   len_set = set([len(self[a]) for a in datanames])
                   if len(len_set)>1:
                       raise ValueError('Request to loop datanames %s with different lengths: %s' % (repr( datanames ),repr( len_set )))
               elif len(listed_values) != 0:
                   raise ValueError('Request to loop datanames where some are single values and some are not')
           # store as lower case
           lc_datanames = [d.lower() for d in datanames]
           # remove these datanames from all other loops
           [self.loops[a].remove(b) for a in self.loops for b in lc_datanames if b in self.loops[a]]
           # remove empty loops
           empty_loops = [a for a in self.loops.keys() if len(self.loops[a])==0]
           for a in empty_loops:
               self.item_order.remove(a)
               del self.loops[a]
           if len(self.loops)>0:
               loopno = max(self.loops.keys()) + 1
           else:
               loopno = 1
           self.loops[loopno] = list(lc_datanames)
           if order >= 0:
               self.item_order.insert(order,loopno)
           else:
               self.item_order.append(loopno)
           # remove these datanames from item ordering
           self.item_order = [a for a in self.item_order if a not in lc_datanames]

def FindLoop(

self, keyname)

Find the loop that contains `keyname` and return its numerical index or -1 if not present. The numerical index can be used to refer to the loop in other routines.

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    def FindLoop(self,keyname):
        """Find the loop that contains `keyname` and return its numerical index or
        -1 if not present. The numerical index can be used to refer to the loop in
        other routines."""
        loop_no = [a for a in self.loops.keys() if keyname.lower() in self.loops[a]]
        if len(loop_no)>0:
            return loop_no[0]
        else:
            return -1

def GetCompoundKeyedPacket(

self, keydict)

Return the loop packet (a `StarPacket` object) where the `{key:(value,caseless)}` pairs in `keydict` take the appropriate values. Ignore case for a given `key` if `caseless` is True. `ValueError` is raised if no packet is found or more than one packet is found.

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    def GetCompoundKeyedPacket(self,keydict):
        """Return the loop packet (a `StarPacket` object) where the `{key:(value,caseless)}` pairs
        in `keydict` take the appropriate values. Ignore case for a given `key` if `caseless` is
        True.  `ValueError` is raised if no packet is found or more than one packet is found."""
        #print "Looking for %s in %s" % (keyvalue, self.parent_block[keyname])
        keynames = list(keydict.keys())
        my_loop = self.GetLoop(keynames[0])
        for one_key in keynames:
            keyval,no_case = keydict[one_key]
            if no_case:
               my_loop = list([a for a in my_loop if str(getattr(a,one_key)).lower()==str(keyval).lower()])
            else:
               my_loop = list([a for a in my_loop if getattr(a,one_key)==keyval])
        if len(my_loop)!=1:
            raise ValueError("Bad packet keys %s: returned %d packets" % (repr(keydict),len(my_loop)))
        print("Compound keyed packet: %s" % my_loop[0])
        return my_loop[0]

def GetFullItemValue(

self, itemname)

Return the value associated with `itemname`, and a boolean flagging whether (True) or not (False) it is in a form suitable for calculation. False is always returned for strings and `StarList` objects.

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    def GetFullItemValue(self,itemname):
        """Return the value associated with `itemname`, and a boolean flagging whether
        (True) or not (False) it is in a form suitable for calculation.  False is
        always returned for strings and `StarList` objects."""
        try:
            s,v = self.block[itemname.lower()]
        except KeyError:
            raise KeyError('Itemname %s not in datablock' % itemname)
        # prefer string value unless all are None
        # are we a looped value?
        if not isinstance(s,(tuple,list)) or isinstance(s,StarList):
            if not_none(s):
                return s,False    #a string value
            else:
                return v,not isinstance(v,StarList)  #a StarList is not calculation-ready
        elif not_none(s):
            return s,False         #a list of string values
        else:
            if len(v)>0:
                return v,not isinstance(v[0],StarList)
            return v,True

def GetItemOrder(

self)

Return a list of datanames in the order in which they will be printed. Loops are referred to by numerical index

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    def GetItemOrder(self):
        """Return a list of datanames in the order in which they will be printed.  Loops are
        referred to by numerical index"""
        return self.item_order[:]

def GetItemPosition(

self, itemname)

A utility function to get the numerical order in the printout of `itemname`. An item has coordinate `(loop_no,pos)` with the top level having a `loop_no` of -1. If an integer is passed to the routine then it will return the position of the loop referenced by that number.

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    def GetItemPosition(self,itemname):
        """A utility function to get the numerical order in the printout
        of `itemname`.  An item has coordinate `(loop_no,pos)` with
        the top level having a `loop_no` of -1.  If an integer is passed to
        the routine then it will return the position of the loop
        referenced by that number."""
        if isinstance(itemname,int):
            # return loop position
            return (-1, self.item_order.index(itemname))
        if not itemname in self:
            raise ValueError('No such dataname %s' % itemname)
        testname = itemname.lower()
        if testname in self.item_order:
            return (-1,self.item_order.index(testname))
        loop_no = self.FindLoop(testname)
        loop_pos = self.loops[loop_no].index(testname)
        return loop_no,loop_pos

def GetItemValue(

self, itemname)

Return value of `itemname`. If `itemname` is looped, a list of all values will be returned.

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    def GetItemValue(self,itemname):
        """Return value of `itemname`.  If `itemname` is looped, a list
        of all values will be returned."""
        return self.GetFullItemValue(itemname)[0]

def GetKeyedPacket(

self, keyname, keyvalue, no_case=False)

Return the loop packet (a `StarPacket` object) where `keyname` has value `keyvalue`. Ignore case in `keyvalue` if `no_case` is True. `ValueError` is raised if no packet is found or more than one packet is found.

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    def GetKeyedPacket(self,keyname,keyvalue,no_case=False):
        """Return the loop packet (a `StarPacket` object) where `keyname` has value
        `keyvalue`. Ignore case in `keyvalue` if `no_case` is True.  `ValueError`
        is raised if no packet is found or more than one packet is found."""
        my_loop = self.GetLoop(keyname)
        #print("Looking for %s in %s" % (keyvalue, my_loop.parent_block))
        #print('Packet check on:' + keyname)
        #[print(repr(getattr(a,keyname))) for a in my_loop]
        if no_case:
           one_pack= [a for a in my_loop if getattr(a,keyname).lower()==keyvalue.lower()]
        else:
           one_pack= [a for a in my_loop if getattr(a,keyname)==keyvalue]
        if len(one_pack)!=1:
            raise ValueError("Bad packet key %s = %s: returned %d packets" % (keyname,keyvalue,len(one_pack)))
        print("Keyed packet: %s" % one_pack[0])
        return one_pack[0]

def GetKeyedSemanticPacket(

self, keyvalue, cat_id)

Return a complete packet for category `cat_id` where the category key for the category equals `keyvalue`. This routine will understand any joined loops, so if separate loops in the datafile belong to the same category hierarchy (e.g. `_atom_site` and `_atom_site_aniso`), the returned `StarPacket` object will contain datanames from both categories.

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    def GetKeyedSemanticPacket(self,keyvalue,cat_id):
        """Return a complete packet for category `cat_id` where the
        category key for the category equals `keyvalue`.  This routine
        will understand any joined loops, so if separate loops in the
        datafile belong to the
        same category hierarchy (e.g. `_atom_site` and `_atom_site_aniso`),
        the returned `StarPacket` object will contain datanames from
        both categories."""
        target_keys = self.dictionary.cat_key_table[cat_id]
        target_keys = [k[0] for k in target_keys] #one only in each list
        p = StarPacket()
        # set case-sensitivity flag
        lcase = False
        if self.dictionary[target_keys[0]]['_type.contents'] in ['Code','Tag','Name']:
            lcase = True
        for cat_key in target_keys:
            try:
                extra_packet = self.GetKeyedPacket(cat_key,keyvalue,no_case=lcase)
            except KeyError:        #missing key
                try:
                    test_key = self[cat_key]  #generate key if possible
                    print('Test key is %s' % repr( test_key ))
                    if test_key is not None and\
                    not (isinstance(test_key,list) and (None in test_key or len(test_key)==0)):
                        print('Getting packet for key %s' % repr( keyvalue ))
                        extra_packet = self.GetKeyedPacket(cat_key,keyvalue,no_case=lcase)
                except:             #cannot be generated
                    continue
            except ValueError:      #none/more than one, assume none
                continue
                #extra_packet = self.dictionary.generate_default_packet(cat_id,cat_key,keyvalue)
            p.merge_packet(extra_packet)
        # the following attributes used to calculate missing values
        for keyname in target_keys:
            if hasattr(p,keyname):
                p.key = [keyname]
                break
        if not hasattr(p,"key"):
            raise ValueError("No key found for %s, packet is %s" % (cat_id,str(p)))
        p.cif_dictionary = self.dictionary
        p.fulldata = self
        return p

def GetLoop(

self, keyname)

Return a `StarFile.LoopBlock` object constructed from the loop containing `keyname`. `keyname` is only significant as a way to specify the loop.

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    def GetLoop(self,keyname):
        """Return a `StarFile.LoopBlock` object constructed from the loop containing `keyname`.
        `keyname` is only significant as a way to specify the loop."""
        return LoopBlock(self,keyname)

def GetLoopNames(

self, keyname)

Return all datanames appearing together with `keyname`

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    def GetLoopNames(self,keyname):
        """Return all datanames appearing together with `keyname`"""
        loop_no = self.FindLoop(keyname)
        if loop_no >= 0:
            return self.loops[loop_no]
        else:
            raise KeyError('%s is not in any loop' % keyname)

def GetMultiKeyedSemanticPacket(

self, keydict, cat_id)

Return a complete packet for category `cat_id` where the keyvalues are provided as a dictionary of key:(value,caseless) pairs This routine will understand any joined loops, so if separate loops in the datafile belong to the same category hierarchy (e.g. `_atom_site` and `_atom_site_aniso`), the returned `StarPacket` object will contain datanames from the requested category and any children.

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    def GetMultiKeyedSemanticPacket(self,keydict,cat_id):
        """Return a complete packet for category `cat_id` where the keyvalues are
        provided as a dictionary of key:(value,caseless) pairs
        This routine
        will understand any joined loops, so if separate loops in the
        datafile belong to the
        same category hierarchy (e.g. `_atom_site` and `_atom_site_aniso`),
        the returned `StarPacket` object will contain datanames from
        the requested category and any children."""
        #if len(keyvalues)==1:   #simplification
        #    return self.GetKeyedSemanticPacket(keydict[1][0],cat_id)
        target_keys = self.dictionary.cat_key_table[cat_id]
        # update the dictionary passed to us with all equivalents, for
        # simplicity.
        parallel_keys = list(zip(*target_keys))  #transpose
        print('Parallel keys:' + repr(parallel_keys))
        print('Keydict:' + repr(keydict))
        start_keys = list(keydict.keys())
        for one_name in start_keys:
            key_set = [a for a in parallel_keys if one_name in a]
            for one_key in key_set:
                keydict[one_key] = keydict[one_name]
        # target_keys is a list of lists, each of which is a compound key
        p = StarPacket()
        # a little function to return the dataname for a key
        def find_key(key):
            for one_key in self.dictionary.key_equivs.get(key,[])+[key]:
                if self.has_key(one_key):
                    return one_key
            return None
        for one_set in target_keys: #loop down the categories
            true_keys = [find_key(k) for k in one_set]
            true_keys = [k for k in true_keys if k is not None]
            if len(true_keys)==len(one_set):
                truekeydict = dict([(t,keydict[k]) for t,k in zip(true_keys,one_set)])
                try:
                    extra_packet = self.GetCompoundKeyedPacket(truekeydict)
                except KeyError:     #one or more are missing
                    continue         #should try harder?
                except ValueError:
                    continue
            else:
                continue
            print('Merging packet for keys ' + repr(one_set))
            p.merge_packet(extra_packet)
        # the following attributes used to calculate missing values
        p.key = true_keys
        p.cif_dictionary = self.dictionary
        p.fulldata = self
        return p

def RemoveCifItem(

self, itemname)

Remove `itemname` from the CifBlock

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    def RemoveCifItem(self,itemname):
        """Remove `itemname` from the CifBlock"""
        self.RemoveItem(itemname)

def RemoveItem(

self, itemname)

Remove `itemname` from the block.

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    def RemoveItem(self,itemname):
        """Remove `itemname` from the block."""
        # first check any loops
        loop_no = self.FindLoop(itemname)
        testkey = itemname.lower()
        if testkey in self:
            del self.block[testkey]
            del self.true_case[testkey]
            # now remove from loop
            if loop_no >= 0:
                self.loops[loop_no].remove(testkey)
                if len(self.loops[loop_no])==0:
                    del self.loops[loop_no]
                    self.item_order.remove(loop_no)
            else:  #will appear in order list
                self.item_order.remove(testkey)

def RemoveKeyedPacket(

self, keyname, keyvalue)

Remove the packet for which dataname `keyname` takes value `keyvalue`. Only the first such occurrence is removed.

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    def RemoveKeyedPacket(self,keyname,keyvalue):
        """Remove the packet for which dataname `keyname` takes
        value `keyvalue`.  Only the first such occurrence is
        removed."""
        packet_coord = list(self[keyname]).index(keyvalue)
        loopnames = self.GetLoopNames(keyname)
        for dataname in loopnames:
            self.block[dataname][0] = list(self.block[dataname][0])
            del self.block[dataname][0][packet_coord]
            self.block[dataname][1] = list(self.block[dataname][1])
            del self.block[dataname][1][packet_coord]

def RemoveLoopItem(

self, itemname)

Deprecated. Use `RemoveItem` instead

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    def RemoveLoopItem(self,itemname):
        """*Deprecated*. Use `RemoveItem` instead"""
        self.RemoveItem(itemname)

def SetOutputLength(

self, wraplength=80, maxoutlength=2048)

Set the maximum output line length (`maxoutlength`) and the line length to wrap at (`wraplength`). The wrap length is a target only and may not always be possible.

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    def SetOutputLength(self,wraplength=80,maxoutlength=2048):
        """Set the maximum output line length (`maxoutlength`) and the line length to
        wrap at (`wraplength`).  The wrap length is a target only and may not always be
        possible."""
        if wraplength > maxoutlength:
            raise StarError("Wrap length (requested %d) must be <= Maximum line length (requested %d)" % (wraplength,maxoutlength))
        self.wraplength = wraplength
        self.maxoutlength = maxoutlength

class CifDic

Create a Cif Dictionary object from the provided source, which can be a filename/URL or a CifFile. Optional arguments (relevant to DDLm only):

- do_minimum (Boolean): Do not set up the dREL system for auto-calculation or perform imports. This implies do_imports=False and do_dREL=False

- do_imports = No/Full/Contents/All: If not 'No', replace _import.get statements with the imported contents for Full mode/Contents mode/Both respectively.

- do_dREL = True/False: Parse and convert all dREL methods to Python. Implies do_imports=All

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    class CifDic(StarFile.StarFile):
        """Create a Cif Dictionary object from the provided source, which can
        be a filename/URL or a CifFile.  Optional arguments (relevant to DDLm
        only):

        * do_minimum (Boolean):
             Do not set up the dREL system for auto-calculation or perform
             imports.  This implies do_imports=False and do_dREL=False

        * do_imports = No/Full/Contents/All:
             If not 'No', replace _import.get statements with the imported contents for
             Full mode/Contents mode/Both respectively.

        * do_dREL = True/False:
             Parse and convert all dREL methods to Python. Implies do_imports=All

        """
        def __init__(self,dic,do_minimum=False,do_imports='All', do_dREL=True,
                                                                 grammar='auto',**kwargs):
            self.do_minimum = do_minimum
            if do_minimum:
                do_imports = 'No'
                do_dREL = False
            if do_dREL: do_imports = 'All'
            self.template_cache = {}    #for DDLm imports
            self.ddlm_functions = {}    #for DDLm functions
            self.switch_numpy(False)    #no Numpy arrays returned
            super(CifDic,self).__init__(datasource=dic,grammar=grammar,**kwargs)
            self.standard = 'Dic'    #for correct output order
            self.scoping = 'dictionary'
            (self.dicname,self.diclang) = self.dic_determine()
            print('%s is a %s dictionary' % (self.dicname,self.diclang))
            self.scopes_mandatory = {}
            self.scopes_naughty = {}
            # rename and expand out definitions using "_name" in DDL dictionaries
            if self.diclang == "DDL1":
                self.DDL1_normalise()   #this removes any non-definition entries
            self.create_def_block_table() #From now on, [] uses definition_id
            if self.diclang == "DDL1":
                self.ddl1_cat_load()
            elif self.diclang == "DDL2":
                self.DDL2_normalise()   #iron out some DDL2 tricky bits
            elif self.diclang == "DDLm":
                self.scoping = 'dictionary'   #expose all save frames
                if do_imports is not 'No':
                   self.ddlm_import(import_mode=do_imports)#recursively calls this routine
                self.create_alias_table()
                self.create_cat_obj_table()
                self.create_cat_key_table()
                if do_dREL:
                    print('Doing full dictionary initialisation')
                    self.initialise_drel()
            self.add_category_info(full=do_dREL)
            # initialise type information
            self.typedic={}
            self.primdic = {}   #typecode<->primitive type translation
            self.add_type_info()
            self.install_validation_functions()

        def dic_determine(self):
            if "on_this_dictionary" in self:
                self.master_block = super(CifDic,self).__getitem__("on_this_dictionary")
                self.def_id_spec = "_name"
                self.cat_id_spec = "_category.id"   #we add this ourselves
                self.type_spec = "_type"
                self.enum_spec = "_enumeration"
                self.cat_spec = "_category"
                self.esd_spec = "_type_conditions"
                self.must_loop_spec = "_list"
                self.must_exist_spec = "_list_mandatory"
                self.list_ref_spec = "_list_reference"
                self.key_spec = "_list_mandatory"
                self.unique_spec = "_list_uniqueness"
                self.child_spec = "_list_link_child"
                self.parent_spec = "_list_link_parent"
                self.related_func = "_related_function"
                self.related_item = "_related_item"
                self.primitive_type = "_type"
                self.dep_spec = "xxx"
                self.cat_list = []   #to save searching all the time
                name = super(CifDic,self).__getitem__("on_this_dictionary")["_dictionary_name"]
                version = super(CifDic,self).__getitem__("on_this_dictionary")["_dictionary_version"]
                return (name+version,"DDL1")
            elif len(self.get_roots()) == 1:              # DDL2/DDLm
                self.master_block = super(CifDic,self).__getitem__(self.get_roots()[0][0])
                # now change to dictionary scoping
                self.scoping = 'dictionary'
                name = self.master_block["_dictionary.title"]
                version = self.master_block["_dictionary.version"]
                if self.master_block.has_key("_dictionary.class"):   #DDLm
                    self.enum_spec = '_enumeration_set.state'
                    self.key_spec = '_category.key_id'
                    self.must_exist_spec = None
                    self.cat_spec = '_name.category_id'
                    self.primitive_type = '_type.contents'
                    self.cat_id_spec = "_definition.id"
                    self.def_id_spec = "_definition.id"
                    return(name+version,"DDLm")
                else:   #DDL2
                    self.cat_id_spec = "_category.id"
                    self.def_id_spec = "_item.name"
                    self.key_spec = "_category_mandatory.name"
                    self.type_spec = "_item_type.code"
                    self.enum_spec = "_item_enumeration.value"
                    self.esd_spec = "_item_type_conditions.code"
                    self.cat_spec = "_item.category_id"
                    self.loop_spec = "there_is_no_loop_spec!"
                    self.must_loop_spec = "xxx"
                    self.must_exist_spec = "_item.mandatory_code"
                    self.child_spec = "_item_linked.child_name"
                    self.parent_spec = "_item_linked.parent_name"
                    self.related_func = "_item_related.function_code"
                    self.related_item = "_item_related.related_name"
                    self.unique_spec = "_category_key.name"
                    self.list_ref_spec = "xxx"
                    self.primitive_type = "_type"
                    self.dep_spec = "_item_dependent.dependent_name"
                    return (name+version,"DDL2")
            else:
                raise CifError("Unable to determine dictionary DDL version")

        def DDL1_normalise(self):
            # switch off block name collision checks
            self.standard = None
            # add default type information in DDL2 style
            # initial types and constructs
            base_types = ["char","numb","null"]
            prim_types = base_types[:]
            base_constructs = [".*",
                '(-?(([0-9]*[.][0-9]+)|([0-9]+)[.]?)([(][0-9]+[)])?([eEdD][+-]?[0-9]+)?)|\?|\.',
                "\"\" "]
            for key,value in self.items():
               newnames = [key]  #keep by default
               if "_name" in value:
                   real_name = value["_name"]
                   if isinstance(real_name,list):        #looped values
                       for looped_name in real_name:
                          new_value = value.copy()
                          new_value["_name"] = looped_name  #only looped name
                          self[looped_name] = new_value
                       newnames = real_name
                   else:
                          self[real_name] = value
                          newnames = [real_name]
               # delete the old one
               if key not in newnames:
                  del self[key]
            # loop again to normalise the contents of each definition
            for key,value in self.items():
               #unlock the block
               save_overwrite = value.overwrite
               value.overwrite = True
               # deal with a missing _list, _type_conditions
               if "_list" not in value: value["_list"] = 'no'
               if "_type_conditions" not in value: value["_type_conditions"] = 'none'
               # deal with enumeration ranges
               if "_enumeration_range" in value:
                   max,min = self.getmaxmin(value["_enumeration_range"])
                   if min == ".":
                       self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,max),(max,min))))
                   elif max == ".":
                       self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,min),(min,min))))
                   else:
                       self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,max,min),(max,min,min))))
               #add any type construct information
               if "_type_construct" in value:
                   base_types.append(value["_name"]+"_type")   #ie dataname_type
                   base_constructs.append(value["_type_construct"]+"$")
                   prim_types.append(value["_type"])     #keep a record
                   value["_type"] = base_types[-1]   #the new type name

            #make categories conform with ddl2
            #note that we must remove everything from the last underscore
               if value.get("_category",None) == "category_overview":
                    last_under = value["_name"].rindex("_")
                    catid = value["_name"][1:last_under]
                    value["_category.id"] = catid  #remove square bracks
                    if catid not in self.cat_list: self.cat_list.append(catid)
               value.overwrite = save_overwrite
            # we now add any missing categories before filling in the rest of the
            # information
            for key,value in self.items():
                #print('processing ddl1 definition %s' % key)
                if "_category" in self[key]:
                    if self[key]["_category"] not in self.cat_list:
                        # rogue category, add it in
                        newcat = self[key]["_category"]
                        fake_name = "_" + newcat + "_[]"
                        newcatdata = CifBlock()
                        newcatdata["_category"] = "category_overview"
                        newcatdata["_category.id"] = newcat
                        newcatdata["_type"] = "null"
                        self[fake_name] = newcatdata
                        self.cat_list.append(newcat)
            # write out the type information in DDL2 style
            self.master_block.AddLoopItem((
                ("_item_type_list.code","_item_type_list.construct",
                  "_item_type_list.primitive_code"),
                (base_types,base_constructs,prim_types)
                ))

        def ddl1_cat_load(self):
            deflist = self.keys()       #slight optimization
            cat_mand_dic = {}
            cat_unique_dic = {}
            # a function to extract any necessary information from each definition
            def get_cat_info(single_def):
                if self[single_def].get(self.must_exist_spec)=='yes':
                    thiscat = self[single_def]["_category"]
                    curval = cat_mand_dic.get(thiscat,[])
                    curval.append(single_def)
                    cat_mand_dic[thiscat] = curval
                # now the unique items...
                # cif_core.dic throws us a curly one: the value of list_uniqueness is
                # not the same as the defined item for publ_body_label, so we have
                # to collect both together.  We assume a non-listed entry, which
                # is true for all current (May 2005) ddl1 dictionaries.
                if self[single_def].get(self.unique_spec,None)!=None:
                    thiscat = self[single_def]["_category"]
                    new_unique = self[single_def][self.unique_spec]
                    uis = cat_unique_dic.get(thiscat,[])
                    if single_def not in uis: uis.append(single_def)
                    if new_unique not in uis: uis.append(new_unique)
                    cat_unique_dic[thiscat] = uis

            [get_cat_info(a) for a in deflist] # apply the above function
            for cat in cat_mand_dic.keys():
                self[cat]["_category_mandatory.name"] = cat_mand_dic[cat]
            for cat in cat_unique_dic.keys():
                self[cat]["_category_key.name"] = cat_unique_dic[cat]

        def create_pcloop(self,definition):
            old_children = self[definition].get('_item_linked.child_name',[])
            old_parents = self[definition].get('_item_linked.parent_name',[])
            if isinstance(old_children,unicode):
                 old_children = [old_children]
            if isinstance(old_parents,unicode):
                 old_parents = [old_parents]
            if (len(old_children)==0 and len(old_parents)==0) or \
               (len(old_children) > 1 and len(old_parents)>1):
                 return
            if len(old_children)==0:
                 old_children = [definition]*len(old_parents)
            if len(old_parents)==0:
                 old_parents = [definition]*len(old_children)
            newloop = CifLoopBlock(dimension=1)
            newloop.AddLoopItem(('_item_linked.parent_name',old_parents))
            newloop.AddLoopItem(('_item_linked.child_name',old_children))
            try:
                del self[definition]['_item_linked.parent_name']
                del self[definition]['_item_linked.child_name']
            except KeyError:
                pass
            self[definition].insert_loop(newloop)

        def DDL2_normalise(self):
           listed_defs = filter(lambda a:isinstance(self[a].get('_item.name'),list),self.keys())
           # now filter out all the single element lists!
           dodgy_defs = filter(lambda a:len(self[a]['_item.name']) > 1, listed_defs)
           for item_def in dodgy_defs:
                    # print("DDL2 norm: processing %s" % item_def)
                    thisdef = self[item_def]
                    packet_no = thisdef['_item.name'].index(item_def)
                    realcat = thisdef['_item.category_id'][packet_no]
                    realmand = thisdef['_item.mandatory_code'][packet_no]
                    # first add in all the missing categories
                    # we don't replace the entry in the list corresponding to the
                    # current item, as that would wipe out the information we want
                    for child_no in range(len(thisdef['_item.name'])):
                        if child_no == packet_no: continue
                        child_name = thisdef['_item.name'][child_no]
                        child_cat = thisdef['_item.category_id'][child_no]
                        child_mand = thisdef['_item.mandatory_code'][child_no]
                        if child_name not in self:
                            self[child_name] = CifBlock()
                            self[child_name]['_item.name'] = child_name
                        self[child_name]['_item.category_id'] = child_cat
                        self[child_name]['_item.mandatory_code'] = child_mand
                    self[item_def]['_item.name'] = item_def
                    self[item_def]['_item.category_id'] = realcat
                    self[item_def]['_item.mandatory_code'] = realmand

           target_defs = [a for a in self.keys() if '_item_linked.child_name' in self[a] or \
                                         '_item_linked.parent_name' in self[a]]
           # now dodgy_defs contains all definition blocks with more than one child/parent link
           for item_def in dodgy_defs: self.create_pcloop(item_def)           #regularise appearance
           for item_def in dodgy_defs:
                 print('Processing %s' % item_def)
                 thisdef = self[item_def]
                 child_list = thisdef['_item_linked.child_name']
                 parents = thisdef['_item_linked.parent_name']
                 # for each parent, find the list of children.
                 family = list(zip(parents,child_list))
                 notmychildren = family         #We aim to remove non-children
                 # Loop over the parents, relocating as necessary
                 while len(notmychildren):
                    # get all children of first entry
                    mychildren = [a for a in family if a[0]==notmychildren[0][0]]
                    print("Parent %s: %d children" % (notmychildren[0][0],len(mychildren)))
                    for parent,child in mychildren:   #parent is the same for all
                             # Make sure that we simply add in the new entry for the child, not replace it,
                             # otherwise we might spoil the child entry loop structure
                             try:
                                 childloop = self[child].GetLoop('_item_linked.parent_name')
                             except KeyError:
                                 print('Creating new parent entry %s for definition %s' % (parent,child))
                                 self[child]['_item_linked.parent_name'] = [parent]
                                 childloop = self[child].GetLoop('_item_linked.parent_name')
                                 childloop.AddLoopItem(('_item_linked.child_name',[child]))
                                 continue
                             else:
                                 # A parent loop already exists and so will a child loop due to the
                                 # call to create_pcloop above
                                 pars = [a for a in childloop if getattr(a,'_item_linked.child_name','')==child]
                                 goodpars = [a for a in pars if getattr(a,'_item_linked.parent_name','')==parent]
                                 if len(goodpars)>0:   #no need to add it
                                     print('Skipping duplicated parent - child entry in %s: %s - %s' % (child,parent,child))
                                     continue
                                 print('Adding %s to %s entry' % (parent,child))
                                 newpacket = childloop.GetPacket(0)   #essentially a copy, I hope
                                 setattr(newpacket,'_item_linked.child_name',child)
                                 setattr(newpacket,'_item_linked.parent_name',parent)
                                 childloop.AddPacket(newpacket)
                    #
                    # Make sure the parent also points to the children.  We get
                    # the current entry, then add our
                    # new values if they are not there already
                    #
                    parent_name = mychildren[0][0]
                    old_children = self[parent_name].get('_item_linked.child_name',[])
                    old_parents = self[parent_name].get('_item_linked.parent_name',[])
                    oldfamily = zip(old_parents,old_children)
                    newfamily = []
                    print('Old parents -> %s' % repr(old_parents))
                    for jj, childname in mychildren:
                        alreadythere = [a for a in oldfamily if a[0]==parent_name and a[1] ==childname]
                        if len(alreadythere)>0: continue
                        'Adding new child %s to parent definition at %s' % (childname,parent_name)
                        old_children.append(childname)
                        old_parents.append(parent_name)
                    # Now output the loop, blowing away previous definitions.  If there is something
                    # else in this category, we are destroying it.
                    newloop = CifLoopBlock(dimension=1)
                    newloop.AddLoopItem(('_item_linked.parent_name',old_parents))
                    newloop.AddLoopItem(('_item_linked.child_name',old_children))
                    del self[parent_name]['_item_linked.parent_name']
                    del self[parent_name]['_item_linked.child_name']
                    self[parent_name].insert_loop(newloop)
                    print('New parents -> %s' % repr(self[parent_name]['_item_linked.parent_name']))
                    # now make a new,smaller list
                    notmychildren = [a for a in notmychildren if a[0]!=mychildren[0][0]]

           # now flatten any single element lists
           single_defs = filter(lambda a:len(self[a]['_item.name'])==1,listed_defs)
           for flat_def in single_defs:
               flat_keys = self[flat_def].GetLoop('_item.name').keys()
               for flat_key in flat_keys: self[flat_def][flat_key] = self[flat_def][flat_key][0]
           # now deal with the multiple lists
           # next we do aliases
           all_aliases = [a for a in self.keys() if self[a].has_key('_item_aliases.alias_name')]
           for aliased in all_aliases:
              my_aliases = listify(self[aliased]['_item_aliases.alias_name'])
              for alias in my_aliases:
                  self[alias] = self[aliased].copy()   #we are going to delete stuff...
                  del self[alias]["_item_aliases.alias_name"]

        def ddlm_parse_valid(self):
            if "_dictionary_valid.application" not in self.master_block:
                return
            for scope_pack in self.master_block.GetLoop("_dictionary_valid.application"):
                scope = getattr(scope_pack,"_dictionary_valid.application")
                valid_info = getattr(scope_pack,"_dictionary_valid.attributes")
                if scope[1] == "Mandatory":
                    self.scopes_mandatory[scope[0]] = self.expand_category_opt(valid_info)
                elif scope[1] == "Prohibited":
                    self.scopes_naughty[scope[0]] = self.expand_category_opt(valid_info)

        def ddlm_import(self,import_mode='All'):
            import_frames = list([(a,self[a]['_import.get']) for a in self.keys() if '_import.get' in self[a]])
            print ('Import mode %s applied to following frames' % import_mode)
            print (str([a[0] for a in import_frames]))
            if import_mode != 'All':
               for i in range(len(import_frames)):
                    import_frames[i] = (import_frames[i][0],[a for a in import_frames[i][1] if a.get('mode','Contents') == import_mode])
               print('Importing following frames in mode %s' % import_mode)
               print(str(import_frames))
            #resolve all references
            for parent_block,import_list in import_frames:
              for import_ref in import_list:
                file_loc = import_ref["file"]
                full_uri = self.resolve_path(file_loc)
                if full_uri not in self.template_cache:
                    dic_as_cif = CifFile(urlopen(full_uri),grammar=self.grammar)
                    self.template_cache[full_uri] = CifDic(dic_as_cif,do_imports=import_mode,do_dREL=False)  #this will recurse internal imports
                    print('Added %s to cached dictionaries' % full_uri)
                import_from = self.template_cache[full_uri]
                dupl = import_ref.get('dupl','Exit')
                miss = import_ref.get('miss','Exit')
                target_key = import_ref["save"]
                try:
                    import_target = import_from[target_key]
                except KeyError:
                    if miss == 'Exit':
                       raise CifError('Import frame %s not found in %s' % (target_key,full_uri))
                    else: continue
                # now import appropriately
                mode = import_ref.get("mode",'Contents').lower()
                if target_key in self and mode=='full':  #so blockname will be duplicated
                    if dupl == 'Exit':
                        raise CifError('Import frame %s already in dictionary' % target_key)
                    elif dupl == 'Ignore':
                        continue
                if mode == 'contents':   #merge attributes only
                    self[parent_block].merge(import_target)
                elif mode =="full":
                    # Do the syntactic merge
                    syntactic_head = self[self.get_parent(parent_block)] #root frame if no nesting
                    from_cat_head = import_target['_name.object_id']
                    child_frames = import_from.ddlm_all_children(from_cat_head)
                     # Check for Head merging Head
                    if self[parent_block].get('_definition.class','Datum')=='Head' and \
                       import_target.get('_definition.class','Datum')=='Head':
                          head_to_head = True
                    else:
                          head_to_head = False
                          child_frames.remove(from_cat_head)
                    # As we are in syntax land, we call the CifFile methods
                    child_blocks = list([import_from.block_id_table[a.lower()] for a in child_frames])
                    child_blocks = super(CifDic,import_from).makebc(child_blocks)
                    # Prune out any datablocks that have identical definitions
                    from_defs = dict([(a,child_blocks[a].get('_definition.id','').lower()) for a in child_blocks.keys()])
                    double_defs = list([b for b in from_defs.items() if self.has_key(b[1])])
                    print ('Definitions for %s superseded' % repr(double_defs))
                    for b in double_defs:
                        del child_blocks[b[0]]
                    super(CifDic,self).merge_fast(child_blocks,parent=syntactic_head)      #
                    print('Syntactic merge of %s (%d defs) in %s mode, now have %d defs' % (target_key,len(child_frames),
                       mode,len(self)))
                    # Now the semantic merge
                    # First expand our definition <-> blockname tree
                    self.create_def_block_table()
                    merging_cat = self[parent_block]['_name.object_id']      #new parent
                    if head_to_head:
                        child_frames = self.ddlm_immediate_children(from_cat_head)    #old children
                        #the new parent is the importing category for all old children
                        for f in child_frames:
                            self[f].overwrite = True
                            self[f]['_name.category_id'] = merging_cat
                            self[f].overwrite = False
                        # remove the old head
                        del self[from_cat_head]
                        print('Semantic merge: %d defs reparented from %s to %s' % (len(child_frames),from_cat_head,merging_cat))
                    else:  #imported category is only child
                        from_frame = import_from[target_key]['_definition.id'] #so we can find it
                        child_frame = [d for d in self.keys() if self[d]['_definition.id']==from_frame][0]
                        self[child_frame]['_name.category_id'] = merging_cat
                        print('Semantic merge: category for %s : now %s' % (from_frame,merging_cat))
                # it will never happen again...
                del self[parent_block]["_import.get"]

        def resolve_path(self,file_loc):
            url_comps = urlparse(file_loc)
            if url_comps[0]: return file_loc    #already full URI
            new_url = urljoin(self.my_uri,file_loc)
            #print("Transformed %s to %s for import " % (file_loc,new_url))
            return new_url

        def create_def_block_table(self):
            """ Create an internal table matching definition to block id """
            proto_table = [(super(CifDic,self).__getitem__(a),a) for a in super(CifDic,self).keys()]
            # now get the actual ids instead of blocks
            proto_table = list([(a[0].get(self.cat_id_spec,a[0].get(self.def_id_spec,a[1])),a[1]) for a in proto_table])
            # remove non-definitions
            if self.diclang != "DDL1":
                top_blocks = list([a[0].lower() for a in self.get_roots()])
            else:
                top_blocks = ["on_this_dictionary"]
            # catch dodgy duplicates
            uniques = set([a[0] for a in proto_table])
            if len(uniques)<len(proto_table):
                def_names = list([a[0] for a in proto_table])
                dodgy = [a for a in def_names if def_names.count(a)>1]
                raise CifError('Duplicate definitions in dictionary:' + repr(dodgy))
            self.block_id_table = dict([(a[0].lower(),a[1].lower()) for a in proto_table if a[1].lower() not in top_blocks])

        def __getitem__(self,key):
            """Access a datablock by definition id, after the lookup has been created"""
            try:
                return super(CifDic,self).__getitem__(self.block_id_table[key.lower()])
            except AttributeError:   #block_id_table not present yet
                return super(CifDic,self).__getitem__(key)
            except KeyError: # key is missing
                # print(Definition for %s not found, reverting to CifFile' % key)
                return super(CifDic,self).__getitem__(key)

        def __setitem__(self,key,value):
            """Add a new definition block"""
            super(CifDic,self).__setitem__(key,value)
            try:
                self.block_id_table[value['_definition.id']]=key
            except AttributeError:   #does not exist yet
                pass

        def __delitem__(self,key):
            """Remove a definition"""
            try:
                super(CifDic,self).__delitem__(self.block_id_table[key.lower()])
                del self.block_id_table[key.lower()]
            except (AttributeError,KeyError):   #block_id_table not present yet
                super(CifDic,self).__delitem__(key)
                return
            # fix other datastructures
            # cat_obj table

        def keys(self):
            """Return all definitions"""
            try:
                return self.block_id_table.keys()
            except AttributeError:
                return super(CifDic,self).keys()

        def has_key(self,key):
            return key in self

        def __contains__(self,key):
            try:
                return key.lower() in self.block_id_table
            except AttributeError:
                return super(CifDic,self).__contains__(key)

        def items(self):
            """Return (key,value) pairs"""
            return list([(a,self[a]) for a in self.keys()])

        def unlock(self):
            """Allow overwriting of all definitions in this collection"""
            for a in self.keys():
                self[a].overwrite=True

        def lock(self):
            """Disallow changes in definitions"""
            for a in self.keys():
                self[a].overwrite=False

        def rename(self,oldname,newname,blockname_as_well=True):
            """Change a _definition.id from oldname to newname, and if `blockname_as_well` is True,
            change the underlying blockname too."""
            if blockname_as_well:
                super(CifDic,self).rename(self.block_id_table[oldname.lower()],newname)
                self.block_id_table[newname.lower()]=newname
                if oldname.lower() in self.block_id_table: #not removed
                   del self.block_id_table[oldname.lower()]
            else:
                self.block_id_table[newname.lower()]=self.block_id_table[oldname.lower()]
                del self.block_id_table[oldname.lower()]
                return

        def get_root_category(self):
            """Get the single 'Head' category of this dictionary"""
            root_cats = [r for r in self.keys() if self[r].get('_definition.class','Datum')=='Head']
            if len(root_cats)>1 or len(root_cats)==0:
                raise CifError("Cannot determine a unique Head category, got" % repr(root_cats))
            return root_cats[0]

        def ddlm_immediate_children(self,catname):
            """Return a list of datanames for the immediate children of catname.  These are
            semantic children (i.e. based on _name.category_id), not structural children as
            in the case of StarFile.get_immediate_children"""

            straight_children = [a for a in self.keys() if self[a].get('_name.category_id','').lower() == catname.lower()]
            return list(straight_children)

        def ddlm_all_children(self,catname):
            """Return a list of all children, including the `catname`"""
            all_children = self.ddlm_immediate_children(catname)
            cat_children = [a for a in all_children if self[a].get('_definition.scope','Item') == 'Category']
            for c in cat_children:
                all_children.remove(c)
                all_children += self.ddlm_all_children(c)
            return all_children + [catname]

        def is_semantic_child(self,parent,maybe_child):
            """Return true if `maybe_child` is a child of `parent`"""
            all_children = self.ddlm_all_children(parent)
            return maybe_child in all_children

        def ddlm_danglers(self):
            """Return a list of definitions that do not have a category defined
            for them, or are children of an unattached category"""
            top_block = self.get_root_category()
            connected = set(self.ddlm_all_children(top_block))
            all_keys = set(self.keys())
            unconnected = all_keys - connected
            return list(unconnected)

        def get_ddlm_parent(self,itemname):
            """Get the parent category of itemname"""
            parent = self[itemname].get('_name.category_id','')
            if parent == '':  # use the top block by default
                raise CifError("%s has no parent" % itemname)
            return parent

        def expand_category_opt(self,name_list):
            """Return a list of all non-category items in a category or return the name
               if the name is not a category"""
            new_list = []
            for name in name_list:
              if self.get(name,{}).get('_definition.scope','Item') == 'Category':
                new_list += self.expand_category_opt([a for a in self.keys() if \
                         self[a].get('_name.category_id','').lower() == name.lower()])
              else:
                new_list.append(name)
            return new_list

        def get_categories(self):
            """Return a list of category names"""
            return list([c for c in self.keys() if self[c].get("_definition.scope")=='Category'])

        def names_in_cat(self,cat,names_only=False):
            names = [a for a in self.keys() if self[a].get('_name.category_id','').lower()==cat.lower()]
            if not names_only:
                return list([a for a in names if self[a].get('_definition.scope','Item')=='Item'])
            else:
                return list([self[a]["_name.object_id"] for a in names])

        def create_alias_table(self):
            """Populate an alias table that we can look up when searching for a dataname"""
            all_aliases = [a for a in self.keys() if '_alias.definition_id' in self[a]]
            self.alias_table = dict([[a,self[a]['_alias.definition_id']] for a in all_aliases])

        def create_cat_obj_table(self):
            """Populate a table indexed by (cat,obj) and returning the correct dataname"""
            base_table = dict([((self[a].get('_name.category_id','').lower(),self[a].get('_name.object_id','').lower()),[self[a].get('_definition.id','')]) \
                               for a in self.keys() if self[a].get('_definition.scope','Item')=='Item'])
            loopable = self.get_loopable_cats()
            loopers = [self.ddlm_immediate_children(a) for a in loopable]
            print('Loopable cats:' + repr(loopable))
            loop_children = [[b for b in a if b.lower() in loopable ] for a in loopers]
            expand_list = dict([(a,b) for a,b in zip(loopable,loop_children) if len(b)>0])
            print("Expansion list:" + repr(expand_list))
            extra_table = {}   #for debugging we keep it separate from base_table until the end
            def expand_base_table(parent_cat,child_cats):
                extra_names = []
                # first deal with all the child categories
                for child_cat in child_cats:
                  nn = []
                  if child_cat in expand_list:  # a nested category: grab its names
                    nn = expand_base_table(child_cat,expand_list[child_cat])
                    # store child names
                    extra_names += nn
                  # add all child names to the table
                  child_names = [(self[n]['_name.object_id'].lower(),self[n]['_definition.id']) \
                                 for n in self.names_in_cat(child_cat) if self[n].get('_type.purpose','') != 'Key']
                  child_names += extra_names
                  extra_table.update(dict([((parent_cat,obj),[name]) for obj,name in child_names if (parent_cat,name) not in extra_table]))
                # and the repeated ones get appended instead
                repeats = [a for a in child_names if a in extra_table]
                for obj,name in repeats:
                    extra_table[(parent_cat,obj)] += [name]
                # and finally, add our own names to the return list
                child_names += [(self[n]['_name.object_id'].lower(),self[n]['_definition.id']) \
                                for n in self.names_in_cat(parent_cat) if self[n].get('_type.purpose','')!='Key']
                return child_names
            [expand_base_table(parent,child) for parent,child in expand_list.items()]
            print('Expansion cat/obj values: ' + repr(extra_table))
            # append repeated ones
            non_repeats = dict([a for a in extra_table.items() if a[0] not in base_table])
            repeats = [a for a in extra_table.keys() if a in base_table]
            base_table.update(non_repeats)
            for k in repeats:
                base_table[k] += extra_table[k]
            self.cat_obj_lookup_table = base_table
            self.loop_expand_list = expand_list

        def get_loopable_cats(self):
            """A short utility function which returns a list of looped categories. This
            is preferred to a fixed attribute as that fixed attribute would need to be
            updated after any edits"""
            return [a.lower() for a in self.keys() if self[a].get('_definition.class','')=='Loop']

        def create_cat_key_table(self):
            """Create a utility table with a list of keys applicable to each category. A key is
            a compound key, that is, it is a list"""
            self.cat_key_table = dict([(c,[listify(self[c].get("_category_key.name",
                [self[c].get("_category.key_id")]))]) for c in self.get_loopable_cats()])
            def collect_keys(parent_cat,child_cats):
                    kk = []
                    for child_cat in child_cats:
                        if child_cat in self.loop_expand_list:
                            kk += collect_keys(child_cat)
                        # add these keys to our list
                        kk += [listify(self[child_cat].get('_category_key.name',[self[child_cat].get('_category.key_id')]))]
                    self.cat_key_table[parent_cat] = self.cat_key_table[parent_cat] + kk
                    return kk
            for k,v in self.loop_expand_list.items():
                collect_keys(k,v)
            print('Keys for categories' + repr(self.cat_key_table))

        def add_type_info(self):
            if "_item_type_list.construct" in self.master_block:
                types = self.master_block["_item_type_list.code"]
                prim_types = self.master_block["_item_type_list.primitive_code"]
                constructs = list([a + "$" for a in self.master_block["_item_type_list.construct"]])
                # add in \r wherever we see \n, and change \{ to \\{
                def regex_fiddle(mm_regex):
                    brack_match = r"((.*\[.+)(\\{)(.*\].*))"
                    ret_match = r"((.*\[.+)(\\n)(.*\].*))"
                    fixed_regexp = mm_regex[:]  #copy
                    # fix the brackets
                    bm = re.match(brack_match,mm_regex)
                    if bm != None:
                        fixed_regexp = bm.expand(r"\2\\\\{\4")
                    # fix missing \r
                    rm = re.match(ret_match,fixed_regexp)
                    if rm != None:
                        fixed_regexp = rm.expand(r"\2\3\\r\4")
                    #print("Regexp %s becomes %s" % (mm_regex,fixed_regexp))
                    return fixed_regexp
                constructs = map(regex_fiddle,constructs)
                for typecode,construct in zip(types,constructs):
                    self.typedic[typecode] = re.compile(construct,re.MULTILINE|re.DOTALL)
                # now make a primitive <-> type construct mapping
                for typecode,primtype in zip(types,prim_types):
                    self.primdic[typecode] = primtype

        def add_category_info(self,full=True):
            if self.diclang == "DDLm":
                catblocks = [c for c in self.keys() if self[c].get('_definition.scope')=='Category']
                looped_cats = [a for a in catblocks if self[a].get('_definition.class','Set') == 'Loop']
                self.parent_lookup = {}
                for one_cat in looped_cats:
                    parent_cat = one_cat
                    parent_def = self[parent_cat]
                    next_up = parent_def['_name.category_id'].lower()
                    while next_up in self and self[next_up].get('_definition.class','Set') == 'Loop':
                        parent_def = self[next_up]
                        parent_cat = next_up
                        next_up = parent_def['_name.category_id'].lower()
                    self.parent_lookup[one_cat] = parent_cat

                if full:
                    self.key_equivs = {}
                    for one_cat in looped_cats:   #follow them up
                        lower_keys = listify(self[one_cat]['_category_key.name'])
                        start_keys = lower_keys[:]
                        while len(lower_keys)>0:
                            this_cat = self[lower_keys[0]]['_name.category_id']
                            parent = [a for a in looped_cats if self[this_cat]['_name.category_id'].lower()==a]
                            #print(Processing %s, keys %s, parent %s" % (this_cat,repr(lower_keys),repr(parent)))
                            if len(parent)>1:
                                raise CifError("Category %s has more than one parent: %s" % (one_cat,repr(parent)))
                            if len(parent)==0: break
                            parent = parent[0]
                            parent_keys = listify(self[parent]['_category_key.name'])
                            linked_keys = [self[l]["_name.linked_item_id"] for l in lower_keys]
                            # sanity check
                            if set(parent_keys) != set(linked_keys):
                                raise CifError("Parent keys and linked keys are different! %s/%s" % (parent_keys,linked_keys))
                                # now add in our information
                            for parent,child in zip(linked_keys,start_keys):
                                self.key_equivs[child] = self.key_equivs.get(child,[])+[parent]
                            lower_keys = linked_keys  #preserves order of start keys

            else:
                self.parent_lookup = {}
                self.key_equivs = {}

        def change_category_name(self,oldname,newname):
            self.unlock()
            """Change the category name from [[oldname]] to [[newname]]"""
            if oldname not in self:
                raise KeyError('Cannot rename non-existent category %s to %s' % (oldname,newname))
            if newname in self:
                raise KeyError('Cannot rename %s to %s as %s already exists' % (oldname,newname,oldname))
            child_defs = self.ddlm_immediate_children(oldname)
            self.rename(oldname,newname)   #NB no name integrity checks
            self[newname]['_name.object_id']=newname
            self[newname]['_definition.id']=newname
            for child_def in child_defs:
                self[child_def]['_name.category_id'] = newname
                if self[child_def].get('_definition.scope','Item')=='Item':
                    newid = self.create_catobj_name(newname,self[child_def]['_name.object_id'])
                    self[child_def]['_definition.id']=newid
                    self.rename(child_def,newid[1:])  #no underscore at the beginning
            self.lock()

        def create_catobj_name(self,cat,obj):
            """Combine category and object in approved fashion to create id"""
            return ('_'+cat+'.'+obj)

        def change_category(self,itemname,catname):
            """Move itemname into catname, return new handle"""
            defid = self[itemname]
            if defid['_name.category_id'].lower()==catname.lower():
                print('Already in category, no change')
                return itemname
            if catname not in self:    #don't have it
                print('No such category %s' % catname)
                return itemname
            self.unlock()
            objid = defid['_name.object_id']
            defid['_name.category_id'] = catname
            newid = itemname # stays the same for categories
            if defid.get('_definition.scope','Item') == 'Item':
                newid = self.create_catobj_name(catname,objid)
                defid['_definition.id']= newid
                self.rename(itemname,newid)
            self.set_parent(catname,newid)
            self.lock()
            return newid

        def change_name(self,one_def,newobj):
            """Change the object_id of one_def to newobj. This is not used for
            categories, but can be used for dictionaries"""
            if '_dictionary.title' not in self[one_def]:  #a dictionary block
                newid = self.create_catobj_name(self[one_def]['_name.category_id'],newobj)
                self.unlock()
                self.rename(one_def,newid)
                self[newid]['_definition.id']=newid
                self[newid]['_name.object_id']=newobj
            else:
                self.unlock()
                newid = newobj
                self.rename(one_def,newobj)
                self[newid]['_dictionary.title'] = newid
            self.lock()
            return newid

        # Note that our semantic parent is given by catparent, but our syntactic parent is
        # always just the root block
        def add_category(self,catname,catparent=None,is_loop=True,allow_dangler=False):
            """Add a new category to the dictionary with name [[catname]].
               If [[catparent]] is None, the category will be a child of
               the topmost 'Head' category or else the top data block. If
               [[is_loop]] is false, a Set category is created. If [[allow_dangler]]
               is true, the parent category does not have to exist."""
            if catname in self:
                raise CifError('Attempt to add existing category %s' % catname)
            self.unlock()
            syntactic_root = self.get_roots()[0][0]
            if catparent is None:
                semantic_root = [a for a in self.keys() if self[a].get('_definition.class',None)=='Head']
                if len(semantic_root)>0:
                    semantic_root = semantic_root[0]
                else:
                    semantic_root = syntactic_root
            else:
                semantic_root = catparent
            realname = super(CifDic,self).NewBlock(catname,parent=syntactic_root)
            self.block_id_table[catname.lower()]=realname
            self[catname]['_name.object_id'] = catname
            if not allow_dangler or catparent is None:
                self[catname]['_name.category_id'] = self[semantic_root]['_name.object_id']
            else:
                self[catname]['_name.category_id'] = catparent
            self[catname]['_definition.id'] = catname
            self[catname]['_definition.scope'] = 'Category'
            if is_loop:
                self[catname]['_definition.class'] = 'Loop'
            else:
                self[catname]['_definition.class'] = 'Set'
            self[catname]['_description.text'] = 'No definition provided'
            self.lock()
            return catname

        def add_definition(self,itemname,catparent,def_text='PLEASE DEFINE ME',allow_dangler=False):
            """Add itemname to category [[catparent]]. If itemname contains periods,
            all text before the final period is ignored. If [[allow_dangler]] is True,
            no check for a parent category is made."""
            self.unlock()
            if '.' in itemname:
                objname = itemname.split('.')[-1]
            else:
                objname = itemname
            objname = objname.strip('_')
            if not allow_dangler and (catparent not in self or self[catparent]['_definition.scope']!='Category'):
                raise CifError('No category %s in dictionary' % catparent)
            fullname = '_'+catparent.lower()+'.'+objname
            print('New name: %s' % fullname)
            syntactic_root = self.get_roots()[0][0]
            realname = super(CifDic,self).NewBlock(fullname, fix=False, parent=syntactic_root) #low-level change
            # update our dictionary structures
            self.block_id_table[fullname]=realname
            self[fullname]['_definition.id']=fullname
            self[fullname]['_name.object_id']=objname
            self[fullname]['_name.category_id']=catparent
            self[fullname]['_definition.class']='Datum'
            self[fullname]['_description.text']=def_text

        def remove_definition(self,defname):
            """Remove a definition from the dictionary."""
            if defname not in self:
                return
            if self[defname].get('_definition.scope')=='Category':
                children = self.ddlm_immediate_children(defname)
                [self.remove_definition(a) for a in children]
                cat_id = self[defname]['_definition.id'].lower()
            del self[defname]

        def get_cat_obj(self,name):
            """Return (cat,obj) tuple. [[name]] must contain only a single period"""
            cat,obj = name.split('.')
            return (cat.strip('_'),obj)

        def get_name_by_cat_obj(self,category,object,give_default=False):
            """Return the dataname corresponding to the given category and object"""
            if category[0] == '_':    #accidentally left in
               true_cat = category[1:].lower()
            else:
               true_cat = category.lower()
            try:
                return self.cat_obj_lookup_table[(true_cat,object.lower())][0]
            except KeyError:
                if give_default:
                   return '_'+true_cat+'.'+object
            raise KeyError('No such category,object in the dictionary: %s %s' % (true_cat,object))

        def WriteOut(self,**kwargs):
            myblockorder = self.get_full_child_list()
            self.set_grammar(self.grammar)
            self.standard = 'Dic'
            return super(CifDic,self).WriteOut(blockorder = myblockorder,**kwargs)

        def get_full_child_list(self):
            """Return a list of definition blocks in order parent-child-child-child-parent-child..."""
            top_block = self.get_roots()[0][0]
            root_cat = [a for a in self.keys() if self[a].get('_definition.class','Datum')=='Head']
            if len(root_cat) == 1:
                all_names = [top_block] + self.recurse_child_list(root_cat[0])
                unrooted = self.ddlm_danglers()
                double_names =  set(unrooted).intersection(set(all_names))
                if len(double_names)>0:
                    raise CifError('Names are children of internal and external categories:%s' % repr(double_names))
                remaining = unrooted[:]
                for no_root in unrooted:
                    if self[no_root].get('_definition.scope','Item')=='Category':
                        all_names += [no_root]
                        remaining.remove(no_root)
                        these_children = [n for n in unrooted if self[n]['_name.category_id'].lower()==no_root.lower()]
                        all_names += these_children
                        [remaining.remove(n) for n in these_children]
                # now sort by category
                ext_cats = set([self[r].get('_name.category_id',self.cat_from_name(r)).lower() for r in remaining])
                for e in ext_cats:
                    cat_items = [r for r in remaining if self[r].get('_name.category_id',self.cat_from_name(r)).lower() == e]
                    [remaining.remove(n) for n in cat_items]
                    all_names += cat_items
                if len(remaining)>0:
                    print('WARNING: following items do not seem to belong to a category??')
                    print(repr(remaining))
                    all_names += remaining
                print('Final block order: ' + repr(all_names))
                return all_names
            raise ValueError('Dictionary contains no/multiple Head categories, please print as plain CIF instead')

        def cat_from_name(self,one_name):
            """Guess the category from the name. This should be used only when this is not important semantic information,
            for example, when printing out"""
            (cat,obj) = one_name.split(".")
            if cat[0] == "_": cat = cat[1:]
            return cat

        def recurse_child_list(self,parentname):
            """Recursively expand the logical child list of [[parentname]]"""
            final_list = [parentname]
            child_blocks = [a for a in self.child_table.keys() if self[a].get('_name.category_id','').lower() == parentname.lower()]
            child_blocks.sort()    #we love alphabetical order
            child_items = [a for a in child_blocks if self[a].get('_definition.scope','Item') == 'Item']
            final_list += child_items
            child_cats = [a for a in child_blocks if self[a].get('_definition.scope','Item') == 'Category']
            for child_cat in child_cats:
                final_list += self.recurse_child_list(child_cat)
            return final_list

        def get_key_pack(self,category,value,data):
            keyname = self[category][self.unique_spec]
            onepack = data.GetPackKey(keyname,value)
            return onepack

        def get_number_with_esd(numstring):
            import string
            numb_re = '((-?(([0-9]*[.]([0-9]+))|([0-9]+)[.]?))([(][0-9]+[)])?([eEdD][+-]?[0-9]+)?)|(\?)|(\.)'
            our_match = re.match(numb_re,numstring)
            if our_match:
                a,base_num,b,c,dad,dbd,esd,exp,q,dot = our_match.groups()
                # print("Debug: {} -> {!r}".format(numstring, our_match.groups()))
            else:
                return None,None
            if dot or q: return None,None     #a dot or question mark
            if exp:          #has exponent
               exp = exp.replace("d","e")     # mop up old fashioned numbers
               exp = exp.replace("D","e")
               base_num = base_num + exp
            # print("Debug: have %s for base_num from %s" % (base_num,numstring))
            base_num = float(base_num)
            # work out esd, if present.
            if esd:
                esd = float(esd[1:-1])    # no brackets
                if dad:                   # decimal point + digits
                    esd = esd * (10 ** (-1* len(dad)))
                if exp:
                    esd = esd * (10 ** (float(exp[1:])))
            return base_num,esd

        def getmaxmin(self,rangeexp):
            regexp = '(-?(([0-9]*[.]([0-9]+))|([0-9]+)[.]?)([eEdD][+-]?[0-9]+)?)*'
            regexp = regexp + ":" + regexp
            regexp = re.match(regexp,rangeexp)
            try:
                minimum = regexp.group(1)
                maximum = regexp.group(7)
            except AttributeError:
                print("Can't match %s" % rangeexp)
            if minimum == None: minimum = "."
            else: minimum = float(minimum)
            if maximum == None: maximum = "."
            else: maximum = float(maximum)
            return maximum,minimum

        def initialise_drel(self):
            """Parse drel functions and prepare data structures in dictionary"""
            self.ddlm_parse_valid() #extract validity information from data block
            self.transform_drel()   #parse the drel functions
            self.add_drel_funcs()   #put the drel functions into the namespace

        def transform_drel(self):
            from .drel import drel_ast_yacc
            from .drel import py_from_ast
            import traceback
            parser = drel_ast_yacc.parser
            lexer = drel_ast_yacc.lexer
            my_namespace = self.keys()
            my_namespace = dict(zip(my_namespace,my_namespace))
            # we provide a table of loopable categories {cat_name:((key1,key2..),[item_name,...]),...})
            loopable_cats = self.get_loopable_cats()
            loop_keys = [listify(self[a]["_category_key.name"]) for a in loopable_cats]
            loop_keys = [[self[a]['_name.object_id'] for a in b] for b in loop_keys]
            cat_names = [self.names_in_cat(a,names_only=True) for a in loopable_cats]
            loop_info = dict(zip(loopable_cats,zip(loop_keys,cat_names)))
            # parser.listable_items = [a for a in self.keys() if "*" in self[a].get("_type.dimension","")]
            derivable_list = [a for a in self.keys() if "_method.expression" in self[a] \
                                  and self[a].get("_name.category_id","")!= "function"]
            for derivable in derivable_list:
                target_id = derivable
                # reset the list of visible names for parser
                special_ids = [dict(zip(self.keys(),self.keys()))]
                print("Target id: %s" % derivable)
                drel_exprs = self[derivable]["_method.expression"]
                drel_purposes = self[derivable]["_method.purpose"]
                all_methods = []
                if not isinstance(drel_exprs,list):
                    drel_exprs = [drel_exprs]
                    drel_purposes = [drel_purposes]
                for drel_purpose,drel_expr in zip(drel_purposes,drel_exprs):
                    if drel_purpose != 'Evaluation':
                        continue
                    drel_expr = "\n".join(drel_expr.splitlines())
                    # print("Transforming %s" % drel_expr)
                    # List categories are treated differently...
                    try:
                        meth_ast = parser.parse(drel_expr+"\n",lexer=lexer)
                    except:
                        print('Syntax error in method for %s; leaving as is' % derivable)
                        a,b = sys.exc_info()[:2]
                        print((repr(a),repr(b)))
                        print(traceback.print_tb(sys.exc_info()[-1],None,sys.stdout))
                        # reset the lexer
                        lexer.begin('INITIAL')
                        continue
                    # Construct the python method
                    cat_meth = False
                    if self[derivable].get('_definition.scope','Item') == 'Category':
                        cat_meth = True
                    pyth_meth = py_from_ast.make_python_function(meth_ast,"pyfunc",target_id,
                                                                               loopable=loop_info,
                                                                 cif_dic = self,cat_meth=cat_meth)
                    all_methods.append(pyth_meth)
                if len(all_methods)>0:
                    save_overwrite = self[derivable].overwrite
                    self[derivable].overwrite = True
                    self[derivable]["_method.py_expression"] = all_methods
                    self[derivable].overwrite = save_overwrite
                #print("Final result:\n " + repr(self[derivable]["_method.py_expression"]))

        def add_drel_funcs(self):
            from .drel import drel_ast_yacc
            from .drel import py_from_ast
            funclist = [a for a in self.keys() if self[a].get("_name.category_id","")=='function']
            funcnames = [(self[a]["_name.object_id"],
                          getattr(self[a].GetKeyedPacket("_method.purpose","Evaluation"),"_method.expression")) for a in funclist]
            # create executable python code...
            parser = drel_ast_yacc.parser
            # we provide a table of loopable categories {cat_name:(key,[item_name,...]),...})
            loopable_cats = self.get_loopable_cats()
            loop_keys = [listify(self[a]["_category_key.name"]) for a in loopable_cats]
            loop_keys = [[self[a]['_name.object_id'] for a in b] for b in loop_keys]
            cat_names = [self.names_in_cat(a,names_only=True) for a in loopable_cats]
            loop_info = dict(zip(loopable_cats,zip(loop_keys,cat_names)))
            for funcname,funcbody in funcnames:
                newline_body = "\n".join(funcbody.splitlines())
                parser.target_id = funcname
                res_ast = parser.parse(newline_body)
                py_function = py_from_ast.make_python_function(res_ast,None,targetname=funcname,func_def=True,loopable=loop_info,cif_dic = self)
                #print('dREL library function ->\n' + py_function)
                global_table = globals()
                exec(py_function, global_table)    #add to namespace
            #print('Globals after dREL functions added:' + repr(globals()))
            self.ddlm_functions = globals()  #for outside access

        @track_recursion
        def derive_item(self,start_key,cifdata,store_value = False,allow_defaults=True):
            key = start_key   #starting value
            result = None     #success is a non-None value
            default_result = False #we have not used a default value
            # check for aliases
            # check for an older form of a new value
            found_it = [k for k in self.alias_table.get(key,[]) if k in cifdata]
            if len(found_it)>0:
                corrected_type = self.change_type(key,cifdata[found_it[0]])
                return corrected_type
            # now do the reverse check - any alternative form
            alias_name = [a for a in self.alias_table.items() if key in a[1]]
            print('Aliases for %s: %s' % (key,repr(alias_name)))
            if len(alias_name)==1:
                key = alias_name[0][0]   #actual definition name
                if key in cifdata: return self.change_type(key,cifdata[key])
                found_it = [k for k in alias_name[0][1] if k in cifdata]
                if len(found_it)>0:
                    return self.change_type(key,cifdata[found_it[0]])
            elif len(alias_name)>1:
                raise CifError('Dictionary error: dataname alias appears in different definitions: ' + repr(alias_name))

            the_category = self[key]["_name.category_id"]
            cat_names = [a for a in self.keys() if self[a].get("_name.category_id",None)==the_category]
            has_cat_names = [a for a in cat_names if cifdata.has_key_or_alias(a)]
            # store any default value in case we have a problem
            def_val = self[key].get("_enumeration.default","")
            def_index_val = self[key].get("_enumeration.def_index_id","")
            if len(has_cat_names)==0: # try category method
                cat_result = {}
                pulled_from_cats = [k for k in self.keys() if '_category_construct_local.components' in self[k]]
                pulled_from_cats = [(k,[
                                      self[n]['_name.category_id'] for n in self[k]['_category_construct_local.components']]
                                   ) for k in pulled_from_cats]
                pulled_to_cats = [k[0] for k in pulled_from_cats if the_category in k[1]]
                if '_category_construct_local.type' in self[the_category]:
                    print("**Now constructing category %s using DDLm attributes**" % the_category)
                    try:
                        cat_result = self.construct_category(the_category,cifdata,store_value=True)
                    except (CifRecursionError,StarFile.StarDerivationError):
                        print('** Failed to construct category %s (error)' % the_category)
                # Trying a pull-back when the category is partially populated
                # will not work, hence we test that cat_result has no keys
                if len(pulled_to_cats)>0 and len(cat_result)==0:
                    print("**Now populating category %s from pulled-back category %s" % (the_category,repr(pulled_to_cats)))
                    try:
                        cat_result = self.push_from_pullback(the_category,pulled_to_cats,cifdata,store_value=True)
                    except (CifRecursionError,StarFile.StarDerivationError):
                        print('** Failed to construct category %s from pullback information (error)' % the_category)
                if '_method.py_expression' in self[the_category] and key not in cat_result:
                    print("**Now applying category method for %s in search of %s**" % (the_category,key))
                    cat_result = self.derive_item(the_category,cifdata,store_value=True)
                print("**Tried pullbacks, obtained for %s " % the_category + repr(cat_result))
                # do we now have our value?
                if key in cat_result:
                    return cat_result[key]

            # Recalculate in case it actually worked
            has_cat_names = [a for a in cat_names if cifdata.has_key_or_alias(a)]
            the_funcs = self[key].get('_method.py_expression',"")
            if the_funcs:   #attempt to calculate it
                #global_table = globals()
                #global_table.update(self.ddlm_functions)
                for one_func in the_funcs:
                    print('Executing function for %s:' % key)
                    #print(one_func)
                    exec(one_func, globals())  #will access dREL functions, puts "pyfunc" in scope
                    # print('in following global environment: ' + repr(global_table))
                    stored_setting = cifdata.provide_value
                    cifdata.provide_value = True
                    try:
                        result = pyfunc(cifdata)
                    except CifRecursionError as s:
                        print(s)
                        result = None
                    except StarFile.StarDerivationError as s:
                        print(s)
                        result = None
                    finally:
                        cifdata.provide_value = stored_setting
                    if result is not None:
                        break
                    #print("Function returned {!r}".format(result))

            if result is None and allow_defaults:   # try defaults
                if def_val:
                    result = self.change_type(key,def_val)
                    default_result = True
                elif def_index_val:            #derive a default value
                    index_vals = self[key]["_enumeration_default.index"]
                    val_to_index = cifdata[def_index_val]     #what we are keying on
                    if self[def_index_val]['_type.contents'] in ['Code','Name','Tag']:
                        lcase_comp = True
                        index_vals = [a.lower() for a in index_vals]
                    # Handle loops
                    if isinstance(val_to_index,list):
                        if lcase_comp:
                            val_to_index = [a.lower() for a in val_to_index]
                        keypos = [index_vals.index(a) for a in val_to_index]
                        result = [self[key]["_enumeration_default.value"][a]  for a in keypos]
                    else:
                        if lcase_comp:
                            val_to_index = val_to_index.lower()
                        keypos = index_vals.index(val_to_index)   #value error if no such value available
                        result = self[key]["_enumeration_default.value"][keypos]
                        default_result = True   #flag that it must be extended
                    result = self.change_type(key,result)
                    print("Indexed on %s to get %s for %s" % (def_index_val,repr(result),repr(val_to_index)))

            # read it in
            if result is None:   #can't do anything else
                print('Warning: no way of deriving item %s, allow_defaults is %s' % (key,repr(allow_defaults)))
                raise StarFile.StarDerivationError(start_key)
            is_looped = False
            if self[the_category].get('_definition.class','Set')=='Loop':
                is_looped = True
                if len(has_cat_names)>0:   #this category already exists
                    if result is None or default_result: #need to create a list of values
                        loop_len = len(cifdata[has_cat_names[0]])
                        out_result = [result]*loop_len
                        result = out_result
                else:   #nothing exists in this category, we can't store this at all
                    print('Resetting result %s for %s to null list as category is empty' % (key,result))
                    result = []

            # now try to insert the new information into the right place
            # find if items of this category already appear...
            # Never cache empty values
            if not (isinstance(result,list) and len(result)==0) and\
              store_value:
                if self[key].get("_definition.scope","Item")=='Item':
                    if is_looped:
                        result = self.store_new_looped_value(key,cifdata,result,default_result)
                    else:
                        result = self.store_new_unlooped_value(key,cifdata,result)
                else:
                    self.store_new_cat_values(cifdata,result,the_category)
            return result

        def store_new_looped_value(self,key,cifdata,result,default_result):
              """Store a looped value from the dREL system into a CifFile"""
              # try to change any matrices etc. to lists
              the_category = self[key]["_name.category_id"]
              out_result = result
              if result is not None and not default_result:
                      # find any numpy arrays
                      def conv_from_numpy(one_elem):
                          if not hasattr(one_elem,'dtype'):
                             if isinstance(one_elem,(list,tuple)):
                                return StarFile.StarList([conv_from_numpy(a) for a in one_elem])
                             return one_elem
                          if one_elem.size > 1:   #so is not a float
                             return StarFile.StarList([conv_from_numpy(a) for a in one_elem.tolist()])
                          else:
                              try:
                                return one_elem.item(0)
                              except:
                                return one_elem
                      out_result = [conv_from_numpy(a) for a in result]
              # so out_result now contains a value suitable for storage
              cat_names = [a for a in self.keys() if self[a].get("_name.category_id",None)==the_category]
              has_cat_names = [a for a in cat_names if a in cifdata]
              print('Adding {}, found pre-existing names: '.format(key) + repr(has_cat_names))
              if len(has_cat_names)>0:   #this category already exists
                  cifdata[key] = out_result      #lengths must match or else!!
                  cifdata.AddLoopName(has_cat_names[0],key)
              else:
                  cifdata[key] = out_result
                  cifdata.CreateLoop([key])
              print('Loop info:' + repr(cifdata.loops))
              return out_result

        def store_new_unlooped_value(self,key,cifdata,result):
              """Store a single value from the dREL system"""
              if result is not None and hasattr(result,'dtype'):
                  if result.size > 1:
                      out_result = StarFile.StarList(result.tolist())
                      cifdata[key] = out_result
                  else:
                      cifdata[key] = result.item(0)
              else:
                  cifdata[key] = result
              return result

        def construct_category(self,category,cifdata,store_value=True):
            """Construct a category using DDLm attributes"""
            con_type = self[category].get('_category_construct_local.type',None)
            if con_type == None:
                return {}
            if con_type == 'Pullback' or con_type == 'Filter':
                morphisms  = self[category]['_category_construct_local.components']
                morph_values = [cifdata[a] for a in morphisms] # the mapped values for each cat
                cats = [self[a]['_name.category_id'] for a in morphisms]
                cat_keys = [self[a]['_category.key_id'] for a in cats]
                cat_values = [list(cifdata[a]) for a in cat_keys] #the category key values for each cat
                if con_type == 'Filter':
                    int_filter = self[category].get('_category_construct_local.integer_filter',None)
                    text_filter = self[category].get('_category_construct_local.text_filter',None)
                    if int_filter is not None:
                        morph_values.append([int(a) for a in int_filter])
                    if text_filter is not None:
                        morph_values.append(text_filter)
                    cat_values.append(range(len(morph_values[-1])))
                # create the mathematical product filtered by equality of dataname values
                pullback_ids = [(x,y) for x in cat_values[0] for y in cat_values[1] \
                                if morph_values[0][cat_values[0].index(x)]==morph_values[1][cat_values[1].index(y)]]
                # now prepare for return
                if len(pullback_ids)==0:
                    return {}
                newids = self[category]['_category_construct_local.new_ids']
                fullnewids = [self.cat_obj_lookup_table[(category,n)][0] for n in newids]
                if con_type == 'Pullback':
                    final_results = {fullnewids[0]:[x[0] for x in pullback_ids],fullnewids[1]:[x[1] for x in pullback_ids]}
                    final_results.update(self.duplicate_datanames(cifdata,cats[0],category,key_vals = final_results[fullnewids[0]],skip_names=newids))
                    final_results.update(self.duplicate_datanames(cifdata,cats[1],category,key_vals = final_results[fullnewids[1]],skip_names=newids))
                elif con_type == 'Filter':   #simple filter
                    final_results = {fullnewids[0]:[x[0] for x in pullback_ids]}
                    final_results.update(self.duplicate_datanames(cifdata,cats[0],category,key_vals = final_results[fullnewids[0]],skip_names=newids))
                if store_value:
                    self.store_new_cat_values(cifdata,final_results,category)
                return final_results

        def push_from_pullback(self,target_category,source_categories,cifdata,store_value=True):
            """Each of the categories in source_categories are pullbacks that include
            the target_category"""
            target_key = self[target_category]['_category.key_id']
            result = {target_key:[]}
            first_time = True
            # for each source category, determine which element goes to the target
            for sc in source_categories:
                components = self[sc]['_category_construct_local.components']
                comp_cats = [self[c]['_name.category_id'] for c in components]
                new_ids = self[sc]['_category_construct_local.new_ids']
                source_ids = [self.cat_obj_lookup_table[(sc,n)][0] for n in new_ids]
                if len(components) == 2:  # not a filter
                    element_pos = comp_cats.index(target_category)
                    old_id = source_ids[element_pos]
                    print('Using %s to populate %s' % (old_id,target_key))
                    result[target_key].extend(cifdata[old_id])
                    # project through all identical names
                    extra_result = self.duplicate_datanames(cifdata,sc,target_category,skip_names=new_ids+[target_key])
                    # we only include keys that are common to all categories
                    if first_time:
                        result.update(extra_result)
                    else:
                        for k in extra_result.keys():
                            if k in result:
                                print('Updating %s: was %s' % (k,repr(result[k])))
                                result[k].extend(extra_result[k])
                else:
                    extra_result = self.duplicate_datanames(cifdata,sc,target_category,skip_names=new_ids)
                    if len(extra_result)>0 or source_ids[0] in cifdata:  #something is present
                        result[target_key].extend(cifdata[source_ids[0]])
                        for k in extra_result.keys():
                            if k in result:
                                print('Reverse filter: Updating %s: was %s' % (k,repr(result[k])))
                                result[k].extend(extra_result[k])
                            else:
                                result[k]=extra_result[k]
        # Bonus derivation if there is a singleton filter
                        if self[sc]['_category_construct_local.type'] == 'Filter':
                            int_filter = self[sc].get('_category_construct_local.integer_filter',None)
                            text_filter = self[sc].get('_category_construct_local.text_filter',None)
                            if int_filter is not None:
                                filter_values = int_filter
                            else:
                                filter_values = text_filter
                            if len(filter_values)==1:    #a singleton
                                extra_dataname = self[sc]['_category_construct_local.components'][0]
                                if int_filter is not None:
                                    new_value = [int(filter_values[0])] * len(cifdata[source_ids[0]])
                                else:
                                    new_value = filter_values * len(cifdata[source_ids[0]])
                                if extra_dataname not in result:
                                    result[extra_dataname] = new_value
                                else:
                                    result[extra_dataname].extend(new_value)
                        else:
                            raise ValueError('Unexpected category construct type' + self[sc]['_category_construct_local.type'])
                first_time = False
            # check for sanity - all dataname lengths must be identical
            datalen = len(set([len(a) for a in result.values()]))
            if datalen != 1:
                raise AssertionError('Failed to construct equal-length category items,'+ repr(result))
            if store_value:
                print('Now storing ' + repr(result))
                self.store_new_cat_values(cifdata,result,target_category)
            return result

        def duplicate_datanames(self,cifdata,from_category,to_category,key_vals=None,skip_names=[]):
            """Copy across datanames for which the from_category key equals [[key_vals]]"""
            result = {}
            s_names_in_cat = set(self.names_in_cat(from_category,names_only=True))
            t_names_in_cat = set(self.names_in_cat(to_category,names_only=True))
            can_project = s_names_in_cat & t_names_in_cat
            can_project -= set(skip_names)  #already dealt with
            source_key = self[from_category]['_category.key_id']
            print('Source dataname set: ' + repr(s_names_in_cat))
            print('Target dataname set: ' + repr(t_names_in_cat))
            print('Projecting through following datanames from %s to %s' % (from_category,to_category) + repr(can_project))
            for project_name in can_project:
                full_from_name = self.cat_obj_lookup_table[(from_category.lower(),project_name.lower())][0]
                full_to_name = self.cat_obj_lookup_table[(to_category.lower(),project_name.lower())][0]
                if key_vals is None:
                    try:
                        result[full_to_name] = cifdata[full_from_name]
                    except StarFile.StarDerivationError:
                        pass
                else:
                    all_key_vals = cifdata[source_key]
                    filter_pos = [all_key_vals.index(a) for a in key_vals]
                    try:
                        all_data_vals = cifdata[full_from_name]
                    except StarFile.StarDerivationError:
                        pass
                    result[full_to_name] = [all_data_vals[i] for i in filter_pos]
            return result

        def store_new_cat_values(self,cifdata,result,the_category):
            """Store the values in [[result]] into [[cifdata]]"""
            the_key = [a for a in result.keys() if self[a].get('_type.purpose','')=='Key']
            double_names = [a for a in result.keys() if a in cifdata]
            if len(double_names)>0:
                already_present = [a for a in self.names_in_cat(the_category) if a in cifdata]
                if set(already_present) != set(result.keys()):
                    print("Category %s not updated, mismatched datanames: %s" % (the_category, repr(set(already_present)^set(result.keys()))))
                    return
                #check key values
                old_keys = set(cifdata[the_key])
                common_keys = old_keys & set(result[the_key])
                if len(common_keys)>0:
                    print("Category %s not updated, key values in common:" % (common_keys))
                    return
                #extend result values with old values
                for one_name,one_value in result.items():
                    result[one_name].extend(cifdata[one_name])
            for one_name, one_value in result.items():
                try:
                    self.store_new_looped_value(one_name,cifdata,one_value,False)
                except StarFile.StarError:
                    print('%s: Not replacing %s with calculated %s' % (one_name,repr(cifdata[one_name]),repr(one_value)))
            #put the key as the first item
            print('Fixing item order for {}'.format(repr(the_key)))
            for one_key in the_key:  #should only be one
                cifdata.ChangeItemOrder(one_key,0)

        def generate_default_packet(self,catname,catkey,keyvalue):
            """Return a StarPacket with items from ``catname`` and a key value
            of ``keyvalue``"""
            newpack = StarPacket()
            for na in self.names_in_cat(catname):
                def_val = self[na].get("_enumeration.default","")
                if def_val:
                    final_val = self.change_type(na,def_val)
                    newpack.extend(final_val)
                    setattr(newpack,na,final_val)
            if len(newpack)>0:
                newpack.extend(keyvalue)
                setattr(newpack,catkey,keyvalue)
            return newpack

        def switch_numpy(self,to_val):
            pass

        def change_type(self,itemname,inval):
            import numpy
            if inval == "?": return inval
            change_function = convert_type(self[itemname])
            if isinstance(inval,list) and not isinstance(inval,StarFile.StarList):   #from a loop
                newval = list([change_function(a) for a in inval])
            else:
                newval = change_function(inval)
            return newval

        def install_validation_functions(self):
            """Install the DDL-appropriate validation checks"""
            if self.diclang != 'DDLm':
              self.item_validation_funs = [
                self.validate_item_type,
                self.validate_item_esd,
                self.validate_item_enum,   # functions which check conformance
                self.validate_enum_range,
                self.validate_looping]
              self.loop_validation_funs = [
                self.validate_loop_membership,
                self.validate_loop_key,
                self.validate_loop_references]    # functions checking loop values
              self.global_validation_funs = [
                self.validate_exclusion,
                self.validate_parent,
                self.validate_child,
                self.validate_dependents,
                self.validate_uniqueness] # where we need to look at other values
              self.block_validation_funs = [  # where only a full block will do
                self.validate_mandatory_category]
              self.global_remove_validation_funs = [
                self.validate_remove_parent_child] # removal is quicker with special checks
            elif self.diclang == 'DDLm':
                self.item_validation_funs = [
                    self.validate_item_enum,
                    self.validate_item_esd_ddlm,
                    ]
                self.loop_validation_funs = [
                    self.validate_looping_ddlm,
                    self.validate_loop_key_ddlm,
                    self.validate_loop_membership
                    ]
                self.global_validation_funs = []
                self.block_validation_funs = [
                    self.check_mandatory_items,
                    self.check_prohibited_items
                    ]
                self.global_remove_validation_funs = []
            self.optimize = False        # default value
            self.done_parents = []
            self.done_children = []
            self.done_keys = []

        def validate_item_type(self,item_name,item_value):
            def mymatch(m,a):
                res = m.match(a)
                if res != None: return res.group()
                else: return ""
            target_type = self[item_name].get(self.type_spec)
            if target_type == None:          # e.g. a category definition
                return {"result":True}                  # not restricted in any way
            matchexpr = self.typedic[target_type]
            item_values = listify(item_value)
            #for item in item_values:
                #print("Type match " + item_name + " " + item + ":",)
            #skip dots and question marks
            check_all = [a for a in item_values if a !="." and a != "?"]
            check_all = [a for a in check_all if mymatch(matchexpr,a) != a]
            if len(check_all)>0: return {"result":False,"bad_values":check_all}
            else: return {"result":True}

        def decide(self,result_list):
            """Construct the return list"""
            if len(result_list)==0:
                   return {"result":True}
            else:
                   return {"result":False,"bad_values":result_list}

        def validate_item_container(self, item_name,item_value):
            container_type = self[item_name]['_type.container']
            item_values = listify(item_value)
            if container_type == 'Single':
               okcheck = [a for a in item_values if not isinstance(a,(int,float,long,unicode))]
               return decide(okcheck)
            if container_type in ('Multiple','List'):
               okcheck = [a for a in item_values if not isinstance(a,StarList)]
               return decide(okcheck)
            if container_type == 'Array':    #A list with numerical values
               okcheck = [a for a in item_values if not isinstance(a,StarList)]
               first_check = decide(okcheck)
               if not first_check['result']: return first_check
               #num_check = [a for a in item_values if len([b for b in a if not isinstance

        def validate_item_esd(self,item_name,item_value):
            if self[item_name].get(self.primitive_type) != 'numb':
                return {"result":None}
            can_esd = self[item_name].get(self.esd_spec,"none") == "esd"
            if can_esd: return {"result":True}         #must be OK!
            item_values = listify(item_value)
            check_all = list([a for a in item_values if get_number_with_esd(a)[1] != None])
            if len(check_all)>0: return {"result":False,"bad_values":check_all}
            return {"result":True}

        def validate_item_esd_ddlm(self,item_name,item_value):
            if self[item_name].get('self.primitive_type') not in \
            ['Count','Index','Integer','Real','Imag','Complex','Binary','Hexadecimal','Octal']:
                return {"result":None}
            can_esd = True
            if self[item_name].get('_type.purpose') != 'Measurand':
                can_esd = False
            item_values = listify(item_value)
            check_all = [get_number_with_esd(a)[1] for a in item_values]
            check_all = [v for v in check_all if (can_esd and v == None) or \
                     (not can_esd and v != None)]
            if len(check_all)>0: return {"result":False,"bad_values":check_all}
            return {"result":True}

        def validate_enum_range(self,item_name,item_value):
            if "_item_range.minimum" not in self[item_name] and \
               "_item_range.maximum" not in self[item_name]:
                return {"result":None}
            minvals = self[item_name].get("_item_range.minimum",default = ["."])
            maxvals = self[item_name].get("_item_range.maximum",default = ["."])
            def makefloat(a):
                if a == ".": return a
                else: return float(a)
            maxvals = map(makefloat, maxvals)
            minvals = map(makefloat, minvals)
            rangelist = list(zip(minvals,maxvals))
            item_values = listify(item_value)
            def map_check(rangelist,item_value):
                if item_value == "?" or item_value == ".": return True
                iv,esd = get_number_with_esd(item_value)
                if iv==None: return None  #shouldn't happen as is numb type
                for lower,upper in rangelist:
                    #check the minima
                    if lower == ".": lower = iv - 1
                    if upper == ".": upper = iv + 1
                    if iv > lower and iv < upper: return True
                    if upper == lower and iv == upper: return True
                # debug
                # print("Value %s fails range check %d < x < %d" % (item_value,lower,upper))
                return False
            check_all = [a for a in item_values if map_check(rangelist,a) != True]
            if len(check_all)>0: return {"result":False,"bad_values":check_all}
            else: return {"result":True}

        def validate_item_enum(self,item_name,item_value):
            try:
                enum_list = self[item_name][self.enum_spec][:]
            except KeyError:
                return {"result":None}
            enum_list.append(".")   #default value
            enum_list.append("?")   #unknown
            item_values = listify(item_value)
            #print("Enum check: {!r} in {!r}".format(item_values, enum_list))
            check_all = [a for a in item_values if a not in enum_list]
            if len(check_all)>0: return {"result":False,"bad_values":check_all}
            else: return {"result":True}

        def validate_looping(self,item_name,item_value):
            try:
                must_loop = self[item_name][self.must_loop_spec]
            except KeyError:
                return {"result":None}
            if must_loop == 'yes' and isinstance(item_value,(unicode,str)): # not looped
                return {"result":False}      #this could be triggered
            if must_loop == 'no' and not isinstance(item_value,(unicode,str)):
                return {"result":False}
            return {"result":True}

        def validate_looping_ddlm(self,loop_names):
            """Check that all names are loopable"""
            truly_loopy = self.get_final_cats(loop_names)
            if len(truly_loopy)<len(loop_names):  #some are bad
                categories = [(a,self[a][self.cat_spec].lower()) for a in loop_names]
                not_looped = [a[0] for a in categories if a[1] not in self.parent_lookup.keys()]
                return {"result":False,"bad_items":not_looped}
            return {"result":True}

        def validate_loop_membership(self,loop_names):
            final_cat = self.get_final_cats(loop_names)
            bad_items =  [a for a in final_cat if a != final_cat[0]]
            if len(bad_items)>0:
                return {"result":False,"bad_items":bad_items}
            else: return {"result":True}

        def get_final_cats(self,loop_names):
            """Return a list of the uppermost parent categories for the loop_names. Names
            that are not from loopable categories are ignored."""
            try:
                categories = [self[a][self.cat_spec].lower() for a in loop_names]
            except KeyError:       #category is mandatory
                raise ValidCifError( "%s missing from dictionary %s for item in loop containing %s" % (self.cat_spec,self.dicname,loop_names[0]))
            truly_looped = [a for a in categories if a in self.parent_lookup.keys()]
            return [self.parent_lookup[a] for a in truly_looped]

        def validate_loop_key(self,loop_names):
            category = self[loop_names[0]][self.cat_spec]
            # find any unique values which must be present
            key_spec = self[category].get(self.key_spec,[])
            for names_to_check in key_spec:
                if isinstance(names_to_check,unicode):   #only one
                    names_to_check = [names_to_check]
                for loop_key in names_to_check:
                    if loop_key not in loop_names:
                        #is this one of those dang implicit items?
                        if self[loop_key].get(self.must_exist_spec,None) == "implicit":
                            continue          #it is virtually there...
                        alternates = self.get_alternates(loop_key)
                        if alternates == []:
                            return {"result":False,"bad_items":loop_key}
                        for alt_names in alternates:
                            alt = [a for a in alt_names if a in loop_names]
                            if len(alt) == 0:
                                return {"result":False,"bad_items":loop_key}  # no alternates
            return {"result":True}

        def validate_loop_key_ddlm(self,loop_names):
            """Make sure at least one of the necessary keys are available"""
            final_cats = self.get_final_cats(loop_names)
            if len(final_cats)>0:
                poss_keys = self.cat_key_table[final_cats[0]]
                found_keys = [a for a in poss_keys if a in loop_names]
                if len(found_keys)>0:
                    return {"result":True}
                else:
                    return {"result":False,"bad_items":poss_keys}
            else:
                return {"result":True}

        def validate_loop_references(self,loop_names):
            must_haves = [self[a].get(self.list_ref_spec,None) for a in loop_names]
            must_haves = [a for a in must_haves if a != None]
            # build a flat list.  For efficiency we don't remove duplicates,as
            # we expect no more than the order of 10 or 20 looped names.
            def flat_func(a,b):
                if isinstance(b,unicode):
                   a.append(b)       #single name
                else:
                   a.extend(b)       #list of names
                return a
            flat_mh = []
            [flat_func(flat_mh,a) for a in must_haves]
            group_mh = filter(lambda a:a[-1]=="_",flat_mh)
            single_mh = filter(lambda a:a[-1]!="_",flat_mh)
            res = [a for a in single_mh if a not in loop_names]
            def check_gr(s_item, name_list):
                nl = map(lambda a:a[:len(s_item)],name_list)
                if s_item in nl: return True
                return False
            res_g = [a for a in group_mh if check_gr(a,loop_names)]
            if len(res) == 0 and len(res_g) == 0: return {"result":True}
            # construct alternate list
            alternates = map(lambda a: (a,self.get_alternates(a)),res)
            alternates = [a for a in alternates if a[1] != []]
            # next line purely for error reporting
            missing_alts = [a[0] for a in alternates if a[1] == []]
            if len(alternates) != len(res):
               return {"result":False,"bad_items":missing_alts}   #short cut; at least one
                                                           #doesn't have an altern
            #loop over alternates
            for orig_name,alt_names in alternates:
                 alt = [a for a in alt_names if a in loop_names]
                 if len(alt) == 0: return {"result":False,"bad_items":orig_name}# no alternates
            return {"result":True}        #found alternates

        def get_alternates(self,main_name,exclusive_only=False):
            alternates = self[main_name].get(self.related_func,None)
            alt_names = []
            if alternates != None:
                alt_names =  self[main_name].get(self.related_item,None)
                if isinstance(alt_names,unicode):
                    alt_names = [alt_names]
                    alternates = [alternates]
                together = zip(alt_names,alternates)
                if exclusive_only:
                    alt_names = [a for a in together if a[1]=="alternate_exclusive" \
                                                 or a[1]=="replace"]
                else:
                    alt_names = [a for a in together if a[1]=="alternate" or a[1]=="replace"]
                alt_names = list([a[0] for a in alt_names])
            # now do the alias thing
            alias_names = listify(self[main_name].get("_item_aliases.alias_name",[]))
            alt_names.extend(alias_names)
            # print("Alternates for {}: {!r}".format(main_name, alt_names))
            return alt_names

        def validate_exclusion(self,item_name,item_value,whole_block,provisional_items={},globals={}):
           alternates = [a.lower() for a in self.get_alternates(item_name,exclusive_only=True)]
           item_name_list = [a.lower() for a in whole_block.keys()]
           item_name_list.extend([a.lower() for a in provisional_items.keys()])
           bad = [a for a in alternates if a in item_name_list]
           if len(bad)>0:
               print("Bad: %s, alternates %s" % (repr(bad),repr(alternates)))
               return {"result":False,"bad_items":bad}
           else: return {"result":True}

        # validate that parent exists and contains matching values
        def validate_parent(self,item_name,item_value,whole_block,provisional_items={},globals={}):
            parent_item = self[item_name].get(self.parent_spec)
            if not parent_item: return {"result":None}   #no parent specified
            if isinstance(parent_item,list):
                parent_item = parent_item[0]
            if self.optimize:
                if parent_item in self.done_parents:
                    return {"result":None}
                else:
                    self.done_parents.append(parent_item)
                    print("Done parents %s" % repr(self.done_parents))
            # initialise parent/child values
            if isinstance(item_value,unicode):
                child_values = [item_value]
            else: child_values = item_value[:]    #copy for safety
            # track down the parent
            # print("Looking for {} parent item {} in {!r}".format(item_name, parent_item, whole_block))
            # if globals contains the parent values, we are doing a DDL2 dictionary, and so
            # we have collected all parent values into the global block - so no need to search
            # for them elsewhere.
            # print("Looking for {!r}".format(parent_item))
            parent_values = globals.get(parent_item)
            if not parent_values:
                parent_values = provisional_items.get(parent_item,whole_block.get(parent_item))
            if not parent_values:
                # go for alternates
                namespace = whole_block.keys()
                namespace.extend(provisional_items.keys())
                namespace.extend(globals.keys())
                alt_names = filter_present(self.get_alternates(parent_item),namespace)
                if len(alt_names) == 0:
                    if len([a for a in child_values if a != "." and a != "?"])>0:
                        return {"result":False,"parent":parent_item}#no parent available -> error
                    else:
                        return {"result":None}       #maybe True is more appropriate??
                parent_item = alt_names[0]           #should never be more than one??
                parent_values = provisional_items.get(parent_item,whole_block.get(parent_item))
                if not parent_values:   # check global block
                    parent_values = globals.get(parent_item)
            if isinstance(parent_values,unicode):
                parent_values = [parent_values]
            #print("Checking parent %s against %s, values %r/%r" % (parent_item,
            #                                          item_name, parent_values, child_values))
            missing = self.check_parent_child(parent_values,child_values)
            if len(missing) > 0:
                return {"result":False,"bad_values":missing,"parent":parent_item}
            return {"result":True}

        def validate_child(self,item_name,item_value,whole_block,provisional_items={},globals={}):
            try:
                child_items = self[item_name][self.child_spec][:]  #copy
            except KeyError:
                return {"result":None}    #not relevant
            # special case for dictionaries  -> we check parents of children only
            if item_name in globals:  #dictionary so skip
                return {"result":None}
            if isinstance(child_items,unicode): # only one child
                child_items = [child_items]
            if isinstance(item_value,unicode): # single value
                parent_values = [item_value]
            else: parent_values = item_value[:]
            # expand child list with list of alternates
            for child_item in child_items[:]:
                child_items.extend(self.get_alternates(child_item))
            # now loop over the children
            for child_item in child_items:
                if self.optimize:
                    if child_item in self.done_children:
                        return {"result":None}
                    else:
                        self.done_children.append(child_item)
                        print("Done children %s" % repr(self.done_children))
                if child_item in provisional_items:
                    child_values = provisional_items[child_item][:]
                elif child_item in whole_block:
                    child_values = whole_block[child_item][:]
                else:  continue
                if isinstance(child_values,unicode):
                    child_values = [child_values]
                    # print("Checking child %s against %s, values %r/%r" % (child_item,
                    #       item_name, child_values, parent_values))
                missing = self.check_parent_child(parent_values,child_values)
                if len(missing)>0:
                    return {"result":False,"bad_values":missing,"child":child_item}
            return {"result":True}       #could mean that no child items present

        #a generic checker: all child vals should appear in parent_vals
        def check_parent_child(self,parent_vals,child_vals):
            # shield ourselves from dots and question marks
            pv = parent_vals[:]
            pv.extend([".","?"])
            res =  [a for a in child_vals if a not in pv]
            #print("Missing: %s" % res)
            return res

        def validate_remove_parent_child(self,item_name,whole_block):
            try:
                child_items = self[item_name][self.child_spec]
            except KeyError:
                return {"result":None}
            if isinstance(child_items,unicode): # only one child
                child_items = [child_items]
            for child_item in child_items:
                if child_item in whole_block:
                    return {"result":False,"child":child_item}
            return {"result":True}

        def validate_dependents(self,item_name,item_value,whole_block,prov={},globals={}):
            try:
                dep_items = self[item_name][self.dep_spec][:]
            except KeyError:
                return {"result":None}    #not relevant
            if isinstance(dep_items,unicode):
                dep_items = [dep_items]
            actual_names = whole_block.keys()
            actual_names.extend(prov.keys())
            actual_names.extend(globals.keys())
            missing = [a for a in dep_items if a not in actual_names]
            if len(missing) > 0:
                alternates = map(lambda a:[self.get_alternates(a),a],missing)
                # compact way to get a list of alternative items which are
                # present
                have_check = [(filter_present(b[0],actual_names),
                                           b[1]) for b in alternates]
                have_check = list([a for a in have_check if len(a[0])==0])
                if len(have_check) > 0:
                    have_check = [a[1] for a in have_check]
                    return {"result":False,"bad_items":have_check}
            return {"result":True}

        def validate_uniqueness(self,item_name,item_value,whole_block,provisional_items={},
                                                                      globals={}):
            category = self[item_name].get(self.cat_spec)
            if category == None:
                print("No category found for %s" % item_name)
                return {"result":None}
            # print("Category {!r} for item {}".format(category, item_name))
            # we make a copy in the following as we will be removing stuff later!
            unique_i = self[category].get("_category_key.name",[])[:]
            if isinstance(unique_i,unicode):
                unique_i = [unique_i]
            if item_name not in unique_i:       #no need to verify
                return {"result":None}
            if isinstance(item_value,unicode):  #not looped
                return {"result":None}
            # print("Checking %s -> %s -> %s ->Unique: %r" % (item_name,category,catentry, unique_i))
            # check that we can't optimize by not doing this check
            if self.optimize:
                if unique_i in self.done_keys:
                    return {"result":None}
                else:
                    self.done_keys.append(unique_i)
            val_list = []
            # get the matching data from any other data items
            unique_i.remove(item_name)
            other_data = []
            if len(unique_i) > 0:            # i.e. do have others to think about
               for other_name in unique_i:
               # we look for the value first in the provisional dict, then the main block
               # the logic being that anything in the provisional dict overrides the
               # main block
                   if other_name in provisional_items:
                       other_data.append(provisional_items[other_name])
                   elif other_name in whole_block:
                       other_data.append(whole_block[other_name])
                   elif self[other_name].get(self.must_exist_spec)=="implicit":
                       other_data.append([item_name]*len(item_value))  #placeholder
                   else:
                       return {"result":False,"bad_items":other_name}#missing data name
            # ok, so we go through all of our values
            # this works by comparing lists of strings to one other, and
            # so could be fooled if you think that '1.' and '1' are
            # identical
            for i in range(len(item_value)):
                #print("Value no. %d" % i, end=" ")
                this_entry = item_value[i]
                for j in range(len(other_data)):
                    this_entry = " ".join([this_entry,other_data[j][i]])
                #print("Looking for {!r} in {!r}: ".format(this_entry, val_list))
                if this_entry in val_list:
                    return {"result":False,"bad_values":this_entry}
                val_list.append(this_entry)
            return {"result":True}

        def validate_mandatory_category(self,whole_block):
            mand_cats = [self[a]['_category.id'] for a in self.keys() if self[a].get("_category.mandatory_code","no")=="yes"]
            if len(mand_cats) == 0:
                return {"result":True}
            # print("Mandatory categories - {!r}".format(mand_cats)
            # find which categories each of our datanames belongs to
            all_cats = [self[a].get(self.cat_spec) for a in whole_block.keys()]
            missing = set(mand_cats) - set(all_cats)
            if len(missing) > 0:
                return {"result":False,"bad_items":repr(missing)}
            return {"result":True}

        def check_mandatory_items(self,whole_block,default_scope='Item'):
            """Return an error if any mandatory items are missing"""
            if len(self.scopes_mandatory)== 0: return {"result":True}
            if default_scope == 'Datablock':
                return {"result":True}     #is a data file
            scope = whole_block.get('_definition.scope',default_scope)
            if '_dictionary.title' in whole_block:
               scope = 'Dictionary'
            missing = list([a for a in self.scopes_mandatory[scope] if a not in whole_block])
            if len(missing)==0:
                return {"result":True}
            else:
                return {"result":False,"bad_items":missing}

        def check_prohibited_items(self,whole_block,default_scope='Item'):
            """Return an error if any prohibited items are present"""
            if len(self.scopes_naughty)== 0: return {"result":True}
            if default_scope == 'Datablock':
                return {"result":True}     #is a data file
            scope = whole_block.get('_definition.scope',default_scope)
            if '_dictionary.title' in whole_block:
               scope = 'Dictionary'
            present = list([a for a in self.scopes_naughty[scope] if a in whole_block])
            if len(present)==0:
                return {"result":True}
            else:
                return {"result":False,"bad_items":present}

        def run_item_validation(self,item_name,item_value):
            return {item_name:list([(f.__name__,f(item_name,item_value)) for f in self.item_validation_funs])}

        def run_loop_validation(self,loop_names):
            return {loop_names[0]:list([(f.__name__,f(loop_names)) for f in self.loop_validation_funs])}

        def run_global_validation(self,item_name,item_value,data_block,provisional_items={},globals={}):
            results = list([(f.__name__,f(item_name,item_value,data_block,provisional_items,globals)) for f in self.global_validation_funs])
            return {item_name:results}

        def run_block_validation(self,whole_block,block_scope='Item'):
            results = list([(f.__name__,f(whole_block)) for f in self.block_validation_funs])
            # fix up the return values
            return {"whole_block":results}

        def optimize_on(self):
            self.optimize = True
            self.done_keys = []
            self.done_children = []
            self.done_parents = []

        def optimize_off(self):
            self.optimize = False
            self.done_keys = []
            self.done_children = []
            self.done_parents = []

### Ancestors (in MRO)

- CifDic
- CifFile.StarFile.StarFile
- CifFile.StarFile.BlockCollection
- __builtin__.object

### Methods

def DDL1_normalise(

self)

Show source ≡

    def DDL1_normalise(self):
        # switch off block name collision checks
        self.standard = None
        # add default type information in DDL2 style
        # initial types and constructs
        base_types = ["char","numb","null"]
        prim_types = base_types[:]
        base_constructs = [".*",
            '(-?(([0-9]*[.][0-9]+)|([0-9]+)[.]?)([(][0-9]+[)])?([eEdD][+-]?[0-9]+)?)|\?|\.',
            "\"\" "]
        for key,value in self.items():
           newnames = [key]  #keep by default
           if "_name" in value:
               real_name = value["_name"]
               if isinstance(real_name,list):        #looped values
                   for looped_name in real_name:
                      new_value = value.copy()
                      new_value["_name"] = looped_name  #only looped name
                      self[looped_name] = new_value
                   newnames = real_name
               else:
                      self[real_name] = value
                      newnames = [real_name]
           # delete the old one
           if key not in newnames:
              del self[key]
        # loop again to normalise the contents of each definition
        for key,value in self.items():
           #unlock the block
           save_overwrite = value.overwrite
           value.overwrite = True
           # deal with a missing _list, _type_conditions
           if "_list" not in value: value["_list"] = 'no'
           if "_type_conditions" not in value: value["_type_conditions"] = 'none'
           # deal with enumeration ranges
           if "_enumeration_range" in value:
               max,min = self.getmaxmin(value["_enumeration_range"])
               if min == ".":
                   self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,max),(max,min))))
               elif max == ".":
                   self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,min),(min,min))))
               else:
                   self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,max,min),(max,min,min))))
           #add any type construct information
           if "_type_construct" in value:
               base_types.append(value["_name"]+"_type")   #ie dataname_type
               base_constructs.append(value["_type_construct"]+"$")
               prim_types.append(value["_type"])     #keep a record
               value["_type"] = base_types[-1]   #the new type name
        #make categories conform with ddl2
        #note that we must remove everything from the last underscore
           if value.get("_category",None) == "category_overview":
                last_under = value["_name"].rindex("_")
                catid = value["_name"][1:last_under]
                value["_category.id"] = catid  #remove square bracks
                if catid not in self.cat_list: self.cat_list.append(catid)
           value.overwrite = save_overwrite
        # we now add any missing categories before filling in the rest of the
        # information
        for key,value in self.items():
            #print('processing ddl1 definition %s' % key)
            if "_category" in self[key]:
                if self[key]["_category"] not in self.cat_list:
                    # rogue category, add it in
                    newcat = self[key]["_category"]
                    fake_name = "_" + newcat + "_[]"
                    newcatdata = CifBlock()
                    newcatdata["_category"] = "category_overview"
                    newcatdata["_category.id"] = newcat
                    newcatdata["_type"] = "null"
                    self[fake_name] = newcatdata
                    self.cat_list.append(newcat)
        # write out the type information in DDL2 style
        self.master_block.AddLoopItem((
            ("_item_type_list.code","_item_type_list.construct",
              "_item_type_list.primitive_code"),
            (base_types,base_constructs,prim_types)
            ))

def DDL2_normalise(

self)

Show source ≡

    def DDL2_normalise(self):
       listed_defs = filter(lambda a:isinstance(self[a].get('_item.name'),list),self.keys())
       # now filter out all the single element lists!
       dodgy_defs = filter(lambda a:len(self[a]['_item.name']) > 1, listed_defs)
       for item_def in dodgy_defs:
                # print("DDL2 norm: processing %s" % item_def)
                thisdef = self[item_def]
                packet_no = thisdef['_item.name'].index(item_def)
                realcat = thisdef['_item.category_id'][packet_no]
                realmand = thisdef['_item.mandatory_code'][packet_no]
                # first add in all the missing categories
                # we don't replace the entry in the list corresponding to the
                # current item, as that would wipe out the information we want
                for child_no in range(len(thisdef['_item.name'])):
                    if child_no == packet_no: continue
                    child_name = thisdef['_item.name'][child_no]
                    child_cat = thisdef['_item.category_id'][child_no]
                    child_mand = thisdef['_item.mandatory_code'][child_no]
                    if child_name not in self:
                        self[child_name] = CifBlock()
                        self[child_name]['_item.name'] = child_name
                    self[child_name]['_item.category_id'] = child_cat
                    self[child_name]['_item.mandatory_code'] = child_mand
                self[item_def]['_item.name'] = item_def
                self[item_def]['_item.category_id'] = realcat
                self[item_def]['_item.mandatory_code'] = realmand
       target_defs = [a for a in self.keys() if '_item_linked.child_name' in self[a] or \
                                     '_item_linked.parent_name' in self[a]]
       # now dodgy_defs contains all definition blocks with more than one child/parent link
       for item_def in dodgy_defs: self.create_pcloop(item_def)           #regularise appearance
       for item_def in dodgy_defs:
             print('Processing %s' % item_def)
             thisdef = self[item_def]
             child_list = thisdef['_item_linked.child_name']
             parents = thisdef['_item_linked.parent_name']
             # for each parent, find the list of children.
             family = list(zip(parents,child_list))
             notmychildren = family         #We aim to remove non-children
             # Loop over the parents, relocating as necessary
             while len(notmychildren):
                # get all children of first entry
                mychildren = [a for a in family if a[0]==notmychildren[0][0]]
                print("Parent %s: %d children" % (notmychildren[0][0],len(mychildren)))
                for parent,child in mychildren:   #parent is the same for all
                         # Make sure that we simply add in the new entry for the child, not replace it,
                         # otherwise we might spoil the child entry loop structure
                         try:
                             childloop = self[child].GetLoop('_item_linked.parent_name')
                         except KeyError:
                             print('Creating new parent entry %s for definition %s' % (parent,child))
                             self[child]['_item_linked.parent_name'] = [parent]
                             childloop = self[child].GetLoop('_item_linked.parent_name')
                             childloop.AddLoopItem(('_item_linked.child_name',[child]))
                             continue
                         else:
                             # A parent loop already exists and so will a child loop due to the
                             # call to create_pcloop above
                             pars = [a for a in childloop if getattr(a,'_item_linked.child_name','')==child]
                             goodpars = [a for a in pars if getattr(a,'_item_linked.parent_name','')==parent]
                             if len(goodpars)>0:   #no need to add it
                                 print('Skipping duplicated parent - child entry in %s: %s - %s' % (child,parent,child))
                                 continue
                             print('Adding %s to %s entry' % (parent,child))
                             newpacket = childloop.GetPacket(0)   #essentially a copy, I hope
                             setattr(newpacket,'_item_linked.child_name',child)
                             setattr(newpacket,'_item_linked.parent_name',parent)
                             childloop.AddPacket(newpacket)
                #
                # Make sure the parent also points to the children.  We get
                # the current entry, then add our
                # new values if they are not there already
                #
                parent_name = mychildren[0][0]
                old_children = self[parent_name].get('_item_linked.child_name',[])
                old_parents = self[parent_name].get('_item_linked.parent_name',[])
                oldfamily = zip(old_parents,old_children)
                newfamily = []
                print('Old parents -> %s' % repr(old_parents))
                for jj, childname in mychildren:
                    alreadythere = [a for a in oldfamily if a[0]==parent_name and a[1] ==childname]
                    if len(alreadythere)>0: continue
                    'Adding new child %s to parent definition at %s' % (childname,parent_name)
                    old_children.append(childname)
                    old_parents.append(parent_name)
                # Now output the loop, blowing away previous definitions.  If there is something
                # else in this category, we are destroying it.
                newloop = CifLoopBlock(dimension=1)
                newloop.AddLoopItem(('_item_linked.parent_name',old_parents))
                newloop.AddLoopItem(('_item_linked.child_name',old_children))
                del self[parent_name]['_item_linked.parent_name']
                del self[parent_name]['_item_linked.child_name']
                self[parent_name].insert_loop(newloop)
                print('New parents -> %s' % repr(self[parent_name]['_item_linked.parent_name']))
                # now make a new,smaller list
                notmychildren = [a for a in notmychildren if a[0]!=mychildren[0][0]]
       # now flatten any single element lists
       single_defs = filter(lambda a:len(self[a]['_item.name'])==1,listed_defs)
       for flat_def in single_defs:
           flat_keys = self[flat_def].GetLoop('_item.name').keys()
           for flat_key in flat_keys: self[flat_def][flat_key] = self[flat_def][flat_key][0]
       # now deal with the multiple lists
       # next we do aliases
       all_aliases = [a for a in self.keys() if self[a].has_key('_item_aliases.alias_name')]
       for aliased in all_aliases:
          my_aliases = listify(self[aliased]['_item_aliases.alias_name'])
          for alias in my_aliases:
              self[alias] = self[aliased].copy()   #we are going to delete stuff...
              del self[alias]["_item_aliases.alias_name"]

def NewBlock(

self, blockname, blockcontents=None, fix=True, parent=None)

Add a new block named `blockname` with contents `blockcontents`. If `fix` is True, `blockname` will have spaces and tabs replaced by underscores. `parent` allows a parent block to be set so that block hierarchies can be created. Depending on the output standard, these blocks will be printed out as nested save frames or ignored.

Show source ≡

    def NewBlock(self,blockname,blockcontents=None,fix=True,parent=None):
        """Add a new block named `blockname` with contents `blockcontents`. If `fix`
        is True, `blockname` will have spaces and tabs replaced by underscores. `parent`
        allows a parent block to be set so that block hierarchies can be created.  Depending on
        the output standard, these blocks will be printed out as nested save frames or
        ignored."""
        if blockcontents is None:
            blockcontents = self.blocktype()
        if self.standard == "CIF":
            blockcontents.setmaxnamelength(75)
        if len(blockname)>75:
                 raise StarError('Blockname %s is longer than 75 characters' % blockname)
        if fix:
            newblockname = re.sub('[  \t]','_',blockname)
        else: newblockname = blockname
        new_lowerbn = newblockname.lower()
        if new_lowerbn in self.lower_keys:   #already there
            if self.standard is not None:
               toplevelnames = [a[0] for a in self.child_table.items() if a[1].parent==None]
               if parent is None and new_lowerbn not in toplevelnames:  #can give a new key to this one
                  while new_lowerbn in self.lower_keys: new_lowerbn = new_lowerbn + '+'
               elif parent is not None and new_lowerbn in toplevelnames: #can fix a different one
                  replace_name = new_lowerbn
                  while replace_name in self.lower_keys: replace_name = replace_name + '+'
                  self._rekey(new_lowerbn,replace_name)
                  # now continue on to add in the new block
                  if parent.lower() == new_lowerbn:        #the new block's requested parent just got renamed!!
                      parent = replace_name
               else:
                  raise StarError( "Attempt to replace existing block " + blockname)
            else:
               del self[new_lowerbn]
        self.dictionary.update({new_lowerbn:blockcontents})
        self.lower_keys.add(new_lowerbn)
        self.block_input_order.append(new_lowerbn)
        if parent is None:
           self.child_table[new_lowerbn]=self.PC(newblockname,None)
           self.visible_keys.append(new_lowerbn)
        else:
           if parent.lower() in self.lower_keys:
              if self.scoping == 'instance':
                 self.child_table[new_lowerbn]=self.PC(newblockname,parent.lower())
              else:
                 self.child_table[new_lowerbn]=self.PC(newblockname,parent.lower())
                 self.visible_keys.append(new_lowerbn)
           else:
               print('Warning:Parent block %s does not exist for child %s' % (parent,newblockname))
        self[new_lowerbn].set_grammar(self.grammar)
        self[new_lowerbn].set_characterset(self.characterset)
        self[new_lowerbn].formatting_hints = self.master_template
        return new_lowerbn  #in case calling routine wants to know

def SetTemplate(

self, template_file)

Use `template_file` as a template for all block output

Show source ≡

    def SetTemplate(self,template_file):
            """Use `template_file` as a template for all block output"""
            self.master_template = process_template(template_file)
            for b in self.dictionary.values():
                b.formatting_hints = self.master_template

def WriteOut(

self, **kwargs)

Show source ≡

    def WriteOut(self,**kwargs):
        myblockorder = self.get_full_child_list()
        self.set_grammar(self.grammar)
        self.standard = 'Dic'
        return super(CifDic,self).WriteOut(blockorder = myblockorder,**kwargs)

class CifError

Show source ≡

    class CifError(Exception):
        def __init__(self,value):
            self.value = value
        def __str__(self):
            return '\nCif Format error: '+ self.value

### Ancestors (in MRO)

- CifError
- exceptions.Exception
- exceptions.BaseException
- __builtin__.object

class CifFile

Show source ≡

    class CifFile(StarFile.StarFile):
        def __init__(self,datasource=None,strict=1,standard='CIF',**kwargs):
            super(CifFile,self).__init__(datasource=datasource,standard=standard, **kwargs)
            self.strict = strict
            self.header_comment = \
    """
    ##########################################################################
    #               Crystallographic Information Format file
    #               Produced by PyCifRW module
    #
    #  This is a CIF file.  CIF has been adopted by the International
    #  Union of Crystallography as the standard for data archiving and
    #  transmission.
    #
    #  For information on this file format, follow the CIF links at
    #  http://www.iucr.org
    ##########################################################################
    """

### Ancestors (in MRO)

- CifFile
- CifFile.StarFile.StarFile
- CifFile.StarFile.BlockCollection
- __builtin__.object

### Methods

def NewBlock(

self, blockname, blockcontents=None, fix=True, parent=None)

Add a new block named `blockname` with contents `blockcontents`. If `fix` is True, `blockname` will have spaces and tabs replaced by underscores. `parent` allows a parent block to be set so that block hierarchies can be created. Depending on the output standard, these blocks will be printed out as nested save frames or ignored.

Show source ≡

    def NewBlock(self,blockname,blockcontents=None,fix=True,parent=None):
        """Add a new block named `blockname` with contents `blockcontents`. If `fix`
        is True, `blockname` will have spaces and tabs replaced by underscores. `parent`
        allows a parent block to be set so that block hierarchies can be created.  Depending on
        the output standard, these blocks will be printed out as nested save frames or
        ignored."""
        if blockcontents is None:
            blockcontents = self.blocktype()
        if self.standard == "CIF":
            blockcontents.setmaxnamelength(75)
        if len(blockname)>75:
                 raise StarError('Blockname %s is longer than 75 characters' % blockname)
        if fix:
            newblockname = re.sub('[  \t]','_',blockname)
        else: newblockname = blockname
        new_lowerbn = newblockname.lower()
        if new_lowerbn in self.lower_keys:   #already there
            if self.standard is not None:
               toplevelnames = [a[0] for a in self.child_table.items() if a[1].parent==None]
               if parent is None and new_lowerbn not in toplevelnames:  #can give a new key to this one
                  while new_lowerbn in self.lower_keys: new_lowerbn = new_lowerbn + '+'
               elif parent is not None and new_lowerbn in toplevelnames: #can fix a different one
                  replace_name = new_lowerbn
                  while replace_name in self.lower_keys: replace_name = replace_name + '+'
                  self._rekey(new_lowerbn,replace_name)
                  # now continue on to add in the new block
                  if parent.lower() == new_lowerbn:        #the new block's requested parent just got renamed!!
                      parent = replace_name
               else:
                  raise StarError( "Attempt to replace existing block " + blockname)
            else:
               del self[new_lowerbn]
        self.dictionary.update({new_lowerbn:blockcontents})
        self.lower_keys.add(new_lowerbn)
        self.block_input_order.append(new_lowerbn)
        if parent is None:
           self.child_table[new_lowerbn]=self.PC(newblockname,None)
           self.visible_keys.append(new_lowerbn)
        else:
           if parent.lower() in self.lower_keys:
              if self.scoping == 'instance':
                 self.child_table[new_lowerbn]=self.PC(newblockname,parent.lower())
              else:
                 self.child_table[new_lowerbn]=self.PC(newblockname,parent.lower())
                 self.visible_keys.append(new_lowerbn)
           else:
               print('Warning:Parent block %s does not exist for child %s' % (parent,newblockname))
        self[new_lowerbn].set_grammar(self.grammar)
        self[new_lowerbn].set_characterset(self.characterset)
        self[new_lowerbn].formatting_hints = self.master_template
        return new_lowerbn  #in case calling routine wants to know

def SetTemplate(

self, template_file)

Use `template_file` as a template for all block output

Show source ≡

    def SetTemplate(self,template_file):
            """Use `template_file` as a template for all block output"""
            self.master_template = process_template(template_file)
            for b in self.dictionary.values():
                b.formatting_hints = self.master_template

def WriteOut(

self, comment=u'', wraplength=80, maxoutlength=0, blockorder=None, saves_after=None)

Return the contents of this file as a string, wrapping if possible at `wraplength` characters and restricting maximum line length to `maxoutlength`. Delimiters and save frame nesting are controlled by `self.grammar`. If `blockorder` is provided, blocks are output in this order unless nested save frames have been requested (STAR2). The default block order is the order in which blocks were input. `saves_after` inserts all save frames after the given dataname, which allows less important items to appear later. Useful in conjunction with a template for dictionary files.

Show source ≡

    def WriteOut(self,comment='',wraplength=80,maxoutlength=0,blockorder=None,saves_after=None):
        """Return the contents of this file as a string, wrapping if possible at `wraplength`
        characters and restricting maximum line length to `maxoutlength`.  Delimiters and
        save frame nesting are controlled by `self.grammar`. If `blockorder` is
        provided, blocks are output in this order unless nested save frames have been
        requested (STAR2). The default block order is the order in which blocks were input.
        `saves_after` inserts all save frames after the given dataname,
        which allows less important items to appear later.  Useful in conjunction with a
        template for dictionary files."""
        if maxoutlength != 0:
            self.SetOutputLength(maxoutlength)
        if not comment:
            comment = self.header_comment
        outstring = StringIO()
        if self.grammar == "2.0" and comment[0:10] != r"#\#CIF_2.0":
            outstring.write(r"#\#CIF_2.0" + "\n")
        outstring.write(comment)
        # prepare all blocks
        for b in self.dictionary.values():
            b.set_grammar(self.grammar)
            b.formatting_hints = self.master_template
            b.SetOutputLength(wraplength,self.maxoutlength)
        # loop over top-level
        # monitor output
        all_names = list(self.child_table.keys())   #i.e. lower case
        if blockorder is None:
            blockorder = self.block_input_order
        top_block_names = [(a,self.child_table[a].block_id) for a in blockorder if self.child_table[a].parent is None]
        for blockref,blockname in top_block_names:
            print('Writing %s, ' % blockname + repr(self[blockref]))
            outstring.write('\n' + 'data_' +blockname+'\n')
            all_names.remove(blockref)
            if self.standard == 'Dic':              #put contents before save frames
                outstring.write(self[blockref].printsection(finish_at='_dictionary_valid.application'))
            if self.grammar == 'STAR2':  #nested save frames
                child_refs = self.get_immediate_children(blockref)
                for child_ref,child_info in child_refs:
                    child_name = child_info.block_id
                    outstring.write('\n\n' + 'save_' + child_name + '\n')
                    self.block_to_string_nested(child_ref,child_name,outstring,4)
                    outstring.write('\n' + 'save_'+ '\n')
            elif self.grammar in ('1.0','1.1','2.0'):                   #non-nested save frames
                child_refs = [a for a in blockorder if self.is_child_of_parent(blockref,a)]
                for child_ref in child_refs:
                    child_name = self.child_table[child_ref].block_id
                    outstring.write('\n\n' + 'save_' + child_name + '\n')
                    outstring.write(str(self[child_ref]))
                    outstring.write('\n\n' + 'save_' + '\n')
                    all_names.remove(child_ref.lower())
            else:
                raise StarError('Grammar %s is not recognised for output' % self.grammar)
            if self.standard != 'Dic':              #put contents after save frames
                outstring.write(str(self[blockref]))
            else:
                outstring.write(self[blockref].printsection(start_from='_dictionary_valid.application'))
        returnstring =  outstring.getvalue()
        outstring.close()
        if len(all_names)>0:
            print('WARNING: following blocks not output: %s' % repr(all_names))
        else:
            print('All blocks output.')
        return returnstring

class CifLoopBlock

Show source ≡

    class CifLoopBlock(StarFile.LoopBlock):
        def __init__(self,data=(),**kwargs):
            super(CifLoopBlock,self).__init__(data,**kwargs)

### Ancestors (in MRO)

- CifLoopBlock
- CifFile.StarFile.LoopBlock
- __builtin__.object

### Methods

def AddPacket(

self, packet)

Show source ≡

    def AddPacket(self,packet):
        for myitem in self.parent_block.loops[self.loop_no]:
            old_values = self.parent_block[myitem]
            old_values.append(packet.__getattribute__(myitem))
            self.parent_block[myitem] = old_values

def AddToLoop(

self, dataname, loopdata)

Deprecated. Use `AddItem` followed by calls to `AddLoopName`.

Add multiple columns to the loop containing `dataname`. `loopdata` is a collection of (key,value) pairs, where `key` is the new dataname and `value` is a list of values for that dataname

Show source ≡

    def AddToLoop(self,dataname,loopdata):
        """*Deprecated*. Use `AddItem` followed by calls to `AddLoopName`.
        Add multiple columns to the loop containing `dataname`. `loopdata` is a
        collection of (key,value) pairs, where `key` is the new dataname and `value`
        is a list of values for that dataname"""
        # check lengths
        thisloop = self.FindLoop(dataname)
        loop_len = len(self[dataname])
        bad_vals = [a for a in loopdata.items() if len(a[1])!=loop_len]
        if len(bad_vals)>0:
           raise StarLengthError("Number of values for looped datanames %s not equal to %d" \
               % (repr( bad_vals ),loop_len))
        self.update(loopdata)
        self.loops[thisloop]+=loopdata.keys()

def ChangeItemOrder(

self, itemname, newpos)

Change the position at which `itemname` appears when printing out to `newpos`.

Show source ≡

    def ChangeItemOrder(self,itemname,newpos):
        """Change the position at which `itemname` appears when printing out to `newpos`."""
        self.parent_block.loops[self.loop_no].remove(itemname.lower())
        self.parent_block.loops[self.loop_no].insert(newpos,itemname.lower())

def GetItemOrder(

self)

Return a list of datanames in this `LoopBlock` in the order that they will be printed

Show source ≡

    def GetItemOrder(self):
        """Return a list of datanames in this `LoopBlock` in the order that they will be
        printed"""
        return self.parent_block.loops[self.loop_no][:]

def GetItemPosition(

self, itemname)

A utility function to get the numerical order in the printout of `itemname`. An item has coordinate `(loop_no,pos)` with the top level having a `loop_no` of -1. If an integer is passed to the routine then it will return the position of the loop referenced by that number.

Show source ≡

    def GetItemPosition(self,itemname):
        """A utility function to get the numerical order in the printout
        of `itemname`.  An item has coordinate `(loop_no,pos)` with
        the top level having a `loop_no` of -1.  If an integer is passed to
        the routine then it will return the position of the loop
        referenced by that number."""
        if isinstance(itemname,int):
            # return loop position
            return (-1, self.item_order.index(itemname))
        if not itemname in self:
            raise ValueError('No such dataname %s' % itemname)
        testname = itemname.lower()
        if testname in self.item_order:
            return (-1,self.item_order.index(testname))
        loop_no = self.FindLoop(testname)
        loop_pos = self.loops[loop_no].index(testname)
        return loop_no,loop_pos

def GetLoop(

self, keyname)

Return a `StarFile.LoopBlock` object constructed from the loop containing `keyname`. `keyname` is only significant as a way to specify the loop.

Show source ≡

    def GetLoop(self,keyname):
        """Return a `StarFile.LoopBlock` object constructed from the loop containing `keyname`.
        `keyname` is only significant as a way to specify the loop."""
        return LoopBlock(self,keyname)

def GetLoopNames(

self, keyname)

Return all datanames appearing together with `keyname`

Show source ≡

    def GetLoopNames(self,keyname):
        """Return all datanames appearing together with `keyname`"""
        loop_no = self.FindLoop(keyname)
        if loop_no >= 0:
            return self.loops[loop_no]
        else:
            raise KeyError('%s is not in any loop' % keyname)

def GetPacket(

self, index)

Show source ≡

    def GetPacket(self,index):
        thispack = StarPacket([])
        for myitem in self.parent_block.loops[self.loop_no]:
            thispack.append(self[myitem][index])
            setattr(thispack,myitem,thispack[-1])
        return thispack

def RemoveItem(

self, itemname)

Remove `itemname` from the block.

Show source ≡

    def RemoveItem(self,itemname):
        """Remove `itemname` from the block."""
        # first check any loops
        loop_no = self.FindLoop(itemname)
        testkey = itemname.lower()
        if testkey in self:
            del self.block[testkey]
            del self.true_case[testkey]
            # now remove from loop
            if loop_no >= 0:
                self.loops[loop_no].remove(testkey)
                if len(self.loops[loop_no])==0:
                    del self.loops[loop_no]
                    self.item_order.remove(loop_no)
            else:  #will appear in order list
                self.item_order.remove(testkey)

def RemoveLoopItem(

self, itemname)

Deprecated. Use `RemoveItem` instead

Show source ≡

    def RemoveLoopItem(self,itemname):
        """*Deprecated*. Use `RemoveItem` instead"""
        self.RemoveItem(itemname)

class CifRecursionError

Show source ≡

    class CifRecursionError(Exception):
        def __init__(self,key_value,call_stack):
            self.key_value = key_value
            self.call_stack = call_stack
        def __str__(self):
            return "Derivation has recursed, %s seen twice (call stack %s)" % (self.key_value,repr(self.call_stack))

### Ancestors (in MRO)

- CifRecursionError
- exceptions.Exception
- exceptions.BaseException
- __builtin__.object

class ValidCifBlock

A `CifBlock` that is valid with respect to a given CIF dictionary. Methods of `CifBlock` are overridden where necessary to disallow addition of invalid items to the `CifBlock`.

## Initialisation

- `dic` is a `CifDic` object to be used for validation.

Show source ≡

    class ValidCifBlock(CifBlock):
        """A `CifBlock` that is valid with respect to a given CIF dictionary.  Methods
        of `CifBlock` are overridden where necessary to disallow addition of invalid items to the
        `CifBlock`.

        ## Initialisation

        * `dic` is a `CifDic` object to be used for validation.

        """
        def __init__(self,dic = None, diclist=[], mergemode = "replace",*args,**kwords):
            CifBlock.__init__(self,*args,**kwords)
            if dic and diclist:
                print("Warning: diclist argument ignored when initialising ValidCifBlock")
            if isinstance(dic,CifDic):
                self.fulldic = dic
            else:
                raise TypeError( "ValidCifBlock passed non-CifDic type in dic argument")
            if len(diclist)==0 and not dic:
                raise ValidCifError( "At least one dictionary must be specified")
            if diclist and not dic:
                self.fulldic = merge_dic(diclist,mergemode)
            if not self.run_data_checks()[0]:
                raise ValidCifError( self.report())

        def run_data_checks(self,verbose=False):
            self.v_result = {}
            self.fulldic.optimize_on()
            for dataname in self.keys():
                update_value(self.v_result,self.fulldic.run_item_validation(dataname,self[dataname]))
                update_value(self.v_result,self.fulldic.run_global_validation(dataname,self[dataname],self))
            for loop_names in self.loops.values():
                update_value(self.v_result,self.fulldic.run_loop_validation(loop_names))
            # now run block-level checks
            update_value(self.v_result,self.fulldic.run_block_validation(self))
            # return false and list of baddies if anything didn't match
            self.fulldic.optimize_off()
            all_keys = list(self.v_result.keys()) #dictionary will change
            for test_key in all_keys:
                #print("%s: %r" % (test_key, self.v_result[test_key]))
                self.v_result[test_key] = [a for a in self.v_result[test_key] if a[1]["result"]==False]
                if len(self.v_result[test_key]) == 0:
                    del self.v_result[test_key]
            isvalid = len(self.v_result)==0
            #if not isvalid:
            #    print("Baddies: {!r}".format(self.v_result))
            return isvalid,self.v_result

        def single_item_check(self,item_name,item_value):
            #self.match_single_item(item_name)
            if item_name not in self.fulldic:
                result = {item_name:[]}
            else:
                result = self.fulldic.run_item_validation(item_name,item_value)
            baddies = list([a for a in result[item_name] if a[1]["result"]==False])
            # if even one false one is found, this should trigger
            isvalid = (len(baddies) == 0)
            # if not isvalid: print("Failures for {}: {!r}".format(item_name, baddies))
            return isvalid,baddies

        def loop_item_check(self,loop_names):
            in_dic_names = list([a for a in loop_names if a in self.fulldic])
            if len(in_dic_names)==0:
                result = {loop_names[0]:[]}
            else:
                result = self.fulldic.run_loop_validation(in_dic_names)
            baddies = list([a for a in result[in_dic_names[0]] if a[1]["result"]==False])
            # if even one false one is found, this should trigger
            isvalid = (len(baddies) == 0)
            # if not isvalid: print("Failures for {}: {!r}".format(loop_names, baddies))
            return isvalid,baddies

        def global_item_check(self,item_name,item_value,provisional_items={}):
            if item_name not in self.fulldic:
                result = {item_name:[]}
            else:
                result = self.fulldic.run_global_validation(item_name,
                   item_value,self,provisional_items = provisional_items)
            baddies = list([a for a in result[item_name] if a[1]["result"] is False])
            # if even one false one is found, this should trigger
            isvalid = (len(baddies) == 0)
            # if not isvalid: print("Failures for {}: {!r}".format(item_name, baddies))
            return isvalid,baddies

        def remove_global_item_check(self,item_name):
            if item_name not in self.fulldic:
                result = {item_name:[]}
            else:
                result = self.fulldic.run_remove_global_validation(item_name,self,False)
            baddies = list([a for a in result[item_name] if a[1]["result"]==False])
            # if even one false one is found, this should trigger
            isvalid = (len(baddies) == 0)
            # if not isvalid: print("Failures for {}: {!r}".format(item_name, baddies))
            return isvalid,baddies

        def AddToLoop(self,dataname,loopdata):
            # single item checks
            paired_data = loopdata.items()
            for name,value in paired_data:
                valid,problems = self.single_item_check(name,value)
                self.report_if_invalid(valid,problems)
            # loop item checks; merge with current loop
            found = 0
            for aloop in self.block["loops"]:
                if dataname in aloop:
                    loopnames = aloop.keys()
                    for new_name in loopdata.keys():
                        if new_name not in loopnames: loopnames.append(new_name)
                    valid,problems = self.looped_item_check(loopnames)
                    self.report_if_invalid(valid,problems)
            prov_dict = loopdata.copy()
            for name,value in paired_data:
                del prov_dict[name]   # remove temporarily
                valid,problems = self.global_item_check(name,value,prov_dict)
                prov_dict[name] = value  # add back in
                self.report_if_invalid(valid,problems)
            CifBlock.AddToLoop(self,dataname,loopdata)

        def AddCifItem(self,data):
            if isinstance(data[0],(unicode,str)):   # single item
                valid,problems = self.single_item_check(data[0],data[1])
                self.report_if_invalid(valid,problems,data[0])
                valid,problems = self.global_item_check(data[0],data[1])
                self.report_if_invalid(valid,problems,data[0])
            elif isinstance(data[0],tuple) or isinstance(data[0],list):
                paired_data = list(zip(data[0],data[1]))
                for name,value in paired_data:
                    valid,problems = self.single_item_check(name,value)
                    self.report_if_invalid(valid,problems,name)
                valid,problems = self.loop_item_check(data[0])
                self.report_if_invalid(valid,problems,data[0])
                prov_dict = {}            # for storing temporary items
                for name,value in paired_data: prov_dict[name]=value
                for name,value in paired_data:
                    del prov_dict[name]   # remove temporarily
                    valid,problems = self.global_item_check(name,value,prov_dict)
                    prov_dict[name] = value  # add back in
                    self.report_if_invalid(valid,problems,name)
            else:
                raise ValueError("Programming error: AddCifItem passed non-tuple,non-string item")
            super(ValidCifBlock,self).AddCifItem(data)

        def AddItem(self,key,value,**kwargs):
            """Set value of dataname `key` to `value` after checking for conformance with CIF dictionary"""
            valid,problems = self.single_item_check(key,value)
            self.report_if_invalid(valid,problems,key)
            valid,problems = self.global_item_check(key,value)
            self.report_if_invalid(valid,problems,key)
            super(ValidCifBlock,self).AddItem(key,value,**kwargs)

        # utility function
        def report_if_invalid(self,valid,bad_list,data_name):
            if not valid:
                bad_tests = [a[0] for a in bad_list]
                error_string = ",".join(bad_tests)
                error_string = repr(data_name) + " fails following validity checks: "  + error_string
                raise ValidCifError( error_string)

        def __delitem__(self,key):
            # we don't need to run single item checks; we do need to run loop and
            # global checks.
            if key in self:
                try:
                    loop_items = self.GetLoop(key)
                except TypeError:
                    loop_items = []
                if loop_items:             #need to check loop conformance
                    loop_names = [a[0] for a in loop_items if a[0] != key]
                    valid,problems = self.loop_item_check(loop_names)
                    self.report_if_invalid(valid,problems)
                valid,problems = self.remove_global_item_check(key)
                self.report_if_invalid(valid,problems)
            self.RemoveCifItem(key)

        def report(self):
           outstr = StringIO()
           outstr.write( "Validation results\n")
           outstr.write( "------------------\n")
           print("%d invalid items found\n" % len(self.v_result))
           for item_name,val_func_list in self.v_result.items():
               outstr.write("%s fails following tests:\n" % item_name)
               for val_func in val_func_list:
                   outstr.write("\t%s\n")
           return outstr.getvalue()

### Ancestors (in MRO)

- ValidCifBlock
- CifBlock
- CifFile.StarFile.StarBlock
- __builtin__.object

### Methods

def AddCifItem(

self, data)

Inheritance: `CifBlock`.`AddCifItem`

DEPRECATED. Use `AddItem` instead.

Show source ≡

    def AddCifItem(self,data):
        if isinstance(data[0],(unicode,str)):   # single item
            valid,problems = self.single_item_check(data[0],data[1])
            self.report_if_invalid(valid,problems,data[0])
            valid,problems = self.global_item_check(data[0],data[1])
            self.report_if_invalid(valid,problems,data[0])
        elif isinstance(data[0],tuple) or isinstance(data[0],list):
            paired_data = list(zip(data[0],data[1]))
            for name,value in paired_data:
                valid,problems = self.single_item_check(name,value)
                self.report_if_invalid(valid,problems,name)
            valid,problems = self.loop_item_check(data[0])
            self.report_if_invalid(valid,problems,data[0])
            prov_dict = {}            # for storing temporary items
            for name,value in paired_data: prov_dict[name]=value
            for name,value in paired_data:
                del prov_dict[name]   # remove temporarily
                valid,problems = self.global_item_check(name,value,prov_dict)
                prov_dict[name] = value  # add back in
                self.report_if_invalid(valid,problems,name)
        else:
            raise ValueError("Programming error: AddCifItem passed non-tuple,non-string item")
        super(ValidCifBlock,self).AddCifItem(data)

def AddItem(

self, key, value, **kwargs)

Inheritance: `CifBlock`.`AddItem`

Set value of dataname `key` to `value` after checking for conformance with CIF dictionary

Show source ≡

    def AddItem(self,key,value,**kwargs):
        """Set value of dataname `key` to `value` after checking for conformance with CIF dictionary"""
        valid,problems = self.single_item_check(key,value)
        self.report_if_invalid(valid,problems,key)
        valid,problems = self.global_item_check(key,value)
        self.report_if_invalid(valid,problems,key)
        super(ValidCifBlock,self).AddItem(key,value,**kwargs)

def AddLoopItem(

self, incomingdata, precheck=False, maxlength=-1)

Inheritance: `CifBlock`.`AddLoopItem`

Deprecated. Use `AddItem` followed by `CreateLoop` if necessary.

Show source ≡

    def AddLoopItem(self,incomingdata,precheck=False,maxlength=-1):
        """*Deprecated*. Use `AddItem` followed by `CreateLoop` if
        necessary."""
        # print "Received data %s" % `incomingdata`
        # we accept tuples, strings, lists and dicts!!
        # Direct insertion: we have a string-valued key, with an array
        # of values -> single-item into our loop
        if isinstance(incomingdata[0],(tuple,list)):
           # a whole loop
           keyvallist = zip(incomingdata[0],incomingdata[1])
           for key,value in keyvallist:
               self.AddItem(key,value)
           self.CreateLoop(incomingdata[0])
        elif not isinstance(incomingdata[0],(unicode,str)):
             raise TypeError('Star datanames are strings only (got %s)' % repr( incomingdata[0] ))
        else:
            self.AddItem(incomingdata[0],incomingdata[1])

def AddLoopName(

self, oldname, newname)

Inheritance: `CifBlock`.`AddLoopName`

Add `newname` to the loop containing `oldname`. If it is already in the new loop, no error is raised. If `newname` is in a different loop, it is removed from that loop. The number of values associated with `newname` must match the number of values associated with all other columns of the new loop or a `ValueError` will be raised.

Show source ≡

    def AddLoopName(self,oldname, newname):
        """Add `newname` to the loop containing `oldname`. If it is already in the new loop, no
        error is raised.  If `newname` is in a different loop, it is removed from that loop.
        The number of values associated with `newname` must match the number of values associated
        with all other columns of the new loop or a `ValueError` will be raised."""
        lower_newname = newname.lower()
        loop_no = self.FindLoop(oldname)
        if loop_no < 0:
            raise KeyError('%s not in loop' % oldname)
        if lower_newname in self.loops[loop_no]:
            return
        # check length
        old_provides = self.provide_value
        self.provide_value = False
        loop_len = len(self[oldname])
        self.provide_value = old_provides
        if len(self[newname]) != loop_len:
            raise ValueError('Mismatch of loop column lengths for %s: should be %d' % (newname,loop_len))
        # remove from any other loops
        [self.loops[a].remove(lower_newname) for a in self.loops if lower_newname in self.loops[a]]
        # and add to this loop
        self.loops[loop_no].append(lower_newname)
        # remove from item_order if present
        try:
            self.item_order.remove(lower_newname)
        except ValueError:
            pass

def AddSingleCifItem(

self, key, value)

Inheritance: `CifBlock`.`AddSingleCifItem`

Deprecated. Use `AddItem` instead

Show source ≡

    def AddSingleCifItem(self,key,value):
        """*Deprecated*. Use `AddItem` instead"""
        """Add a single data item. If it is part of a loop, a separate call should be made"""
        self.AddItem(key,value)

def AddToLoop(

self, dataname, loopdata)

Inheritance: `CifBlock`.`AddToLoop`

Deprecated. Use `AddItem` followed by calls to `AddLoopName`.

Add multiple columns to the loop containing `dataname`. `loopdata` is a collection of (key,value) pairs, where `key` is the new dataname and `value` is a list of values for that dataname

Show source ≡

    def AddToLoop(self,dataname,loopdata):
        # single item checks
        paired_data = loopdata.items()
        for name,value in paired_data:
            valid,problems = self.single_item_check(name,value)
            self.report_if_invalid(valid,problems)
        # loop item checks; merge with current loop
        found = 0
        for aloop in self.block["loops"]:
            if dataname in aloop:
                loopnames = aloop.keys()
                for new_name in loopdata.keys():
                    if new_name not in loopnames: loopnames.append(new_name)
                valid,problems = self.looped_item_check(loopnames)
                self.report_if_invalid(valid,problems)
        prov_dict = loopdata.copy()
        for name,value in paired_data:
            del prov_dict[name]   # remove temporarily
            valid,problems = self.global_item_check(name,value,prov_dict)
            prov_dict[name] = value  # add back in
            self.report_if_invalid(valid,problems)
        CifBlock.AddToLoop(self,dataname,loopdata)

def ChangeItemOrder(

self, itemname, newpos)

Inheritance: `CifBlock`.`ChangeItemOrder`

Move the printout order of `itemname` to `newpos`. If `itemname` is in a loop, `newpos` refers to the order within the loop.

Show source ≡

    def ChangeItemOrder(self,itemname,newpos):
        """Move the printout order of `itemname` to `newpos`. If `itemname` is
        in a loop, `newpos` refers to the order within the loop."""
        if isinstance(itemname,(unicode,str)):
            true_name = itemname.lower()
        else:
            true_name = itemname
        loopno = self.FindLoop(true_name)
        if loopno < 0:  #top level
            self.item_order.remove(true_name)
            self.item_order.insert(newpos,true_name)
        else:
            self.loops[loopno].remove(true_name)
            self.loops[loopno].insert(newpos,true_name)

def CreateLoop(

self, datanames, order=-1, length_check=True)

Inheritance: `CifBlock`.`CreateLoop`

Create a loop in the datablock. `datanames` is a list of datanames that together form a loop. If length_check is True, they should have been initialised in the block to have the same number of elements (possibly 0). If `order` is given, the loop will appear at this position in the block when printing out. A loop counts as a single position.

Show source ≡

    def CreateLoop(self,datanames,order=-1,length_check=True):
           """Create a loop in the datablock. `datanames` is a list of datanames that
           together form a loop.  If length_check is True, they should have been initialised in the block
           to have the same number of elements (possibly 0). If `order` is given,
           the loop will appear at this position in the block when printing
           out. A loop counts as a single position."""
           if length_check:
               # check lengths: these datanames should exist
               listed_values = [a for a in datanames if isinstance(self[a],list) and not isinstance(self[a],StarList)]
               if len(listed_values) == len(datanames):
                   len_set = set([len(self[a]) for a in datanames])
                   if len(len_set)>1:
                       raise ValueError('Request to loop datanames %s with different lengths: %s' % (repr( datanames ),repr( len_set )))
               elif len(listed_values) != 0:
                   raise ValueError('Request to loop datanames where some are single values and some are not')
           # store as lower case
           lc_datanames = [d.lower() for d in datanames]
           # remove these datanames from all other loops
           [self.loops[a].remove(b) for a in self.loops for b in lc_datanames if b in self.loops[a]]
           # remove empty loops
           empty_loops = [a for a in self.loops.keys() if len(self.loops[a])==0]
           for a in empty_loops:
               self.item_order.remove(a)
               del self.loops[a]
           if len(self.loops)>0:
               loopno = max(self.loops.keys()) + 1
           else:
               loopno = 1
           self.loops[loopno] = list(lc_datanames)
           if order >= 0:
               self.item_order.insert(order,loopno)
           else:
               self.item_order.append(loopno)
           # remove these datanames from item ordering
           self.item_order = [a for a in self.item_order if a not in lc_datanames]

def FindLoop(

self, keyname)

Inheritance: `CifBlock`.`FindLoop`

Find the loop that contains `keyname` and return its numerical index or -1 if not present. The numerical index can be used to refer to the loop in other routines.

Show source ≡

    def FindLoop(self,keyname):
        """Find the loop that contains `keyname` and return its numerical index or
        -1 if not present. The numerical index can be used to refer to the loop in
        other routines."""
        loop_no = [a for a in self.loops.keys() if keyname.lower() in self.loops[a]]
        if len(loop_no)>0:
            return loop_no[0]
        else:
            return -1

def GetCompoundKeyedPacket(

self, keydict)

Inheritance: `CifBlock`.`GetCompoundKeyedPacket`

Return the loop packet (a `StarPacket` object) where the `{key:(value,caseless)}` pairs in `keydict` take the appropriate values. Ignore case for a given `key` if `caseless` is True. `ValueError` is raised if no packet is found or more than one packet is found.

Show source ≡

    def GetCompoundKeyedPacket(self,keydict):
        """Return the loop packet (a `StarPacket` object) where the `{key:(value,caseless)}` pairs
        in `keydict` take the appropriate values. Ignore case for a given `key` if `caseless` is
        True.  `ValueError` is raised if no packet is found or more than one packet is found."""
        #print "Looking for %s in %s" % (keyvalue, self.parent_block[keyname])
        keynames = list(keydict.keys())
        my_loop = self.GetLoop(keynames[0])
        for one_key in keynames:
            keyval,no_case = keydict[one_key]
            if no_case:
               my_loop = list([a for a in my_loop if str(getattr(a,one_key)).lower()==str(keyval).lower()])
            else:
               my_loop = list([a for a in my_loop if getattr(a,one_key)==keyval])
        if len(my_loop)!=1:
            raise ValueError("Bad packet keys %s: returned %d packets" % (repr(keydict),len(my_loop)))
        print("Compound keyed packet: %s" % my_loop[0])
        return my_loop[0]

def GetFullItemValue(

self, itemname)

Inheritance: `CifBlock`.`GetFullItemValue`

Return the value associated with `itemname`, and a boolean flagging whether (True) or not (False) it is in a form suitable for calculation. False is always returned for strings and `StarList` objects.

Show source ≡

    def GetFullItemValue(self,itemname):
        """Return the value associated with `itemname`, and a boolean flagging whether
        (True) or not (False) it is in a form suitable for calculation.  False is
        always returned for strings and `StarList` objects."""
        try:
            s,v = self.block[itemname.lower()]
        except KeyError:
            raise KeyError('Itemname %s not in datablock' % itemname)
        # prefer string value unless all are None
        # are we a looped value?
        if not isinstance(s,(tuple,list)) or isinstance(s,StarList):
            if not_none(s):
                return s,False    #a string value
            else:
                return v,not isinstance(v,StarList)  #a StarList is not calculation-ready
        elif not_none(s):
            return s,False         #a list of string values
        else:
            if len(v)>0:
                return v,not isinstance(v[0],StarList)
            return v,True

def GetItemOrder(

self)

Inheritance: `CifBlock`.`GetItemOrder`

Return a list of datanames in the order in which they will be printed. Loops are referred to by numerical index

Show source ≡

    def GetItemOrder(self):
        """Return a list of datanames in the order in which they will be printed.  Loops are
        referred to by numerical index"""
        return self.item_order[:]

def GetItemPosition(

self, itemname)

Inheritance: `CifBlock`.`GetItemPosition`

A utility function to get the numerical order in the printout of `itemname`. An item has coordinate `(loop_no,pos)` with the top level having a `loop_no` of -1. If an integer is passed to the routine then it will return the position of the loop referenced by that number.

Show source ≡

    def GetItemPosition(self,itemname):
        """A utility function to get the numerical order in the printout
        of `itemname`.  An item has coordinate `(loop_no,pos)` with
        the top level having a `loop_no` of -1.  If an integer is passed to
        the routine then it will return the position of the loop
        referenced by that number."""
        if isinstance(itemname,int):
            # return loop position
            return (-1, self.item_order.index(itemname))
        if not itemname in self:
            raise ValueError('No such dataname %s' % itemname)
        testname = itemname.lower()
        if testname in self.item_order:
            return (-1,self.item_order.index(testname))
        loop_no = self.FindLoop(testname)
        loop_pos = self.loops[loop_no].index(testname)
        return loop_no,loop_pos

def GetItemValue(

self, itemname)

Inheritance: `CifBlock`.`GetItemValue`

Return value of `itemname`. If `itemname` is looped, a list of all values will be returned.

Show source ≡

    def GetItemValue(self,itemname):
        """Return value of `itemname`.  If `itemname` is looped, a list
        of all values will be returned."""
        return self.GetFullItemValue(itemname)[0]

def GetKeyedPacket(

self, keyname, keyvalue, no_case=False)

Inheritance: `CifBlock`.`GetKeyedPacket`

Return the loop packet (a `StarPacket` object) where `keyname` has value `keyvalue`. Ignore case in `keyvalue` if `no_case` is True. `ValueError` is raised if no packet is found or more than one packet is found.

Show source ≡

    def GetKeyedPacket(self,keyname,keyvalue,no_case=False):
        """Return the loop packet (a `StarPacket` object) where `keyname` has value
        `keyvalue`. Ignore case in `keyvalue` if `no_case` is True.  `ValueError`
        is raised if no packet is found or more than one packet is found."""
        my_loop = self.GetLoop(keyname)
        #print("Looking for %s in %s" % (keyvalue, my_loop.parent_block))
        #print('Packet check on:' + keyname)
        #[print(repr(getattr(a,keyname))) for a in my_loop]
        if no_case:
           one_pack= [a for a in my_loop if getattr(a,keyname).lower()==keyvalue.lower()]
        else:
           one_pack= [a for a in my_loop if getattr(a,keyname)==keyvalue]
        if len(one_pack)!=1:
            raise ValueError("Bad packet key %s = %s: returned %d packets" % (keyname,keyvalue,len(one_pack)))
        print("Keyed packet: %s" % one_pack[0])
        return one_pack[0]

def GetKeyedSemanticPacket(

self, keyvalue, cat_id)

Inheritance: `CifBlock`.`GetKeyedSemanticPacket`

Return a complete packet for category `cat_id` where the category key for the category equals `keyvalue`. This routine will understand any joined loops, so if separate loops in the datafile belong to the same category hierarchy (e.g. `_atom_site` and `_atom_site_aniso`), the returned `StarPacket` object will contain datanames from both categories.

Show source ≡

    def GetKeyedSemanticPacket(self,keyvalue,cat_id):
        """Return a complete packet for category `cat_id` where the
        category key for the category equals `keyvalue`.  This routine
        will understand any joined loops, so if separate loops in the
        datafile belong to the
        same category hierarchy (e.g. `_atom_site` and `_atom_site_aniso`),
        the returned `StarPacket` object will contain datanames from
        both categories."""
        target_keys = self.dictionary.cat_key_table[cat_id]
        target_keys = [k[0] for k in target_keys] #one only in each list
        p = StarPacket()
        # set case-sensitivity flag
        lcase = False
        if self.dictionary[target_keys[0]]['_type.contents'] in ['Code','Tag','Name']:
            lcase = True
        for cat_key in target_keys:
            try:
                extra_packet = self.GetKeyedPacket(cat_key,keyvalue,no_case=lcase)
            except KeyError:        #missing key
                try:
                    test_key = self[cat_key]  #generate key if possible
                    print('Test key is %s' % repr( test_key ))
                    if test_key is not None and\
                    not (isinstance(test_key,list) and (None in test_key or len(test_key)==0)):
                        print('Getting packet for key %s' % repr( keyvalue ))
                        extra_packet = self.GetKeyedPacket(cat_key,keyvalue,no_case=lcase)
                except:             #cannot be generated
                    continue
            except ValueError:      #none/more than one, assume none
                continue
                #extra_packet = self.dictionary.generate_default_packet(cat_id,cat_key,keyvalue)
            p.merge_packet(extra_packet)
        # the following attributes used to calculate missing values
        for keyname in target_keys:
            if hasattr(p,keyname):
                p.key = [keyname]
                break
        if not hasattr(p,"key"):
            raise ValueError("No key found for %s, packet is %s" % (cat_id,str(p)))
        p.cif_dictionary = self.dictionary
        p.fulldata = self
        return p

def GetLoop(

self, keyname)

Inheritance: `CifBlock`.`GetLoop`

Return a `StarFile.LoopBlock` object constructed from the loop containing `keyname`. `keyname` is only significant as a way to specify the loop.

Show source ≡

    def GetLoop(self,keyname):
        """Return a `StarFile.LoopBlock` object constructed from the loop containing `keyname`.
        `keyname` is only significant as a way to specify the loop."""
        return LoopBlock(self,keyname)

def GetLoopNames(

self, keyname)

Inheritance: `CifBlock`.`GetLoopNames`

Return all datanames appearing together with `keyname`

Show source ≡

    def GetLoopNames(self,keyname):
        """Return all datanames appearing together with `keyname`"""
        loop_no = self.FindLoop(keyname)
        if loop_no >= 0:
            return self.loops[loop_no]
        else:
            raise KeyError('%s is not in any loop' % keyname)

def GetMultiKeyedSemanticPacket(

self, keydict, cat_id)

Inheritance: `CifBlock`.`GetMultiKeyedSemanticPacket`

Return a complete packet for category `cat_id` where the keyvalues are provided as a dictionary of key:(value,caseless) pairs This routine will understand any joined loops, so if separate loops in the datafile belong to the same category hierarchy (e.g. `_atom_site` and `_atom_site_aniso`), the returned `StarPacket` object will contain datanames from the requested category and any children.

Show source ≡

    def GetMultiKeyedSemanticPacket(self,keydict,cat_id):
        """Return a complete packet for category `cat_id` where the keyvalues are
        provided as a dictionary of key:(value,caseless) pairs
        This routine
        will understand any joined loops, so if separate loops in the
        datafile belong to the
        same category hierarchy (e.g. `_atom_site` and `_atom_site_aniso`),
        the returned `StarPacket` object will contain datanames from
        the requested category and any children."""
        #if len(keyvalues)==1:   #simplification
        #    return self.GetKeyedSemanticPacket(keydict[1][0],cat_id)
        target_keys = self.dictionary.cat_key_table[cat_id]
        # update the dictionary passed to us with all equivalents, for
        # simplicity.
        parallel_keys = list(zip(*target_keys))  #transpose
        print('Parallel keys:' + repr(parallel_keys))
        print('Keydict:' + repr(keydict))
        start_keys = list(keydict.keys())
        for one_name in start_keys:
            key_set = [a for a in parallel_keys if one_name in a]
            for one_key in key_set:
                keydict[one_key] = keydict[one_name]
        # target_keys is a list of lists, each of which is a compound key
        p = StarPacket()
        # a little function to return the dataname for a key
        def find_key(key):
            for one_key in self.dictionary.key_equivs.get(key,[])+[key]:
                if self.has_key(one_key):
                    return one_key
            return None
        for one_set in target_keys: #loop down the categories
            true_keys = [find_key(k) for k in one_set]
            true_keys = [k for k in true_keys if k is not None]
            if len(true_keys)==len(one_set):
                truekeydict = dict([(t,keydict[k]) for t,k in zip(true_keys,one_set)])
                try:
                    extra_packet = self.GetCompoundKeyedPacket(truekeydict)
                except KeyError:     #one or more are missing
                    continue         #should try harder?
                except ValueError:
                    continue
            else:
                continue
            print('Merging packet for keys ' + repr(one_set))
            p.merge_packet(extra_packet)
        # the following attributes used to calculate missing values
        p.key = true_keys
        p.cif_dictionary = self.dictionary
        p.fulldata = self
        return p

def RemoveCifItem(

self, itemname)

Inheritance: `CifBlock`.`RemoveCifItem`

Remove `itemname` from the CifBlock

Show source ≡

    def RemoveCifItem(self,itemname):
        """Remove `itemname` from the CifBlock"""
        self.RemoveItem(itemname)

def RemoveItem(

self, itemname)

Inheritance: `CifBlock`.`RemoveItem`

Remove `itemname` from the block.

Show source ≡

    def RemoveItem(self,itemname):
        """Remove `itemname` from the block."""
        # first check any loops
        loop_no = self.FindLoop(itemname)
        testkey = itemname.lower()
        if testkey in self:
            del self.block[testkey]
            del self.true_case[testkey]
            # now remove from loop
            if loop_no >= 0:
                self.loops[loop_no].remove(testkey)
                if len(self.loops[loop_no])==0:
                    del self.loops[loop_no]
                    self.item_order.remove(loop_no)
            else:  #will appear in order list
                self.item_order.remove(testkey)

def RemoveKeyedPacket(

self, keyname, keyvalue)

Inheritance: `CifBlock`.`RemoveKeyedPacket`

Remove the packet for which dataname `keyname` takes value `keyvalue`. Only the first such occurrence is removed.

Show source ≡

    def RemoveKeyedPacket(self,keyname,keyvalue):
        """Remove the packet for which dataname `keyname` takes
        value `keyvalue`.  Only the first such occurrence is
        removed."""
        packet_coord = list(self[keyname]).index(keyvalue)
        loopnames = self.GetLoopNames(keyname)
        for dataname in loopnames:
            self.block[dataname][0] = list(self.block[dataname][0])
            del self.block[dataname][0][packet_coord]
            self.block[dataname][1] = list(self.block[dataname][1])
            del self.block[dataname][1][packet_coord]

def RemoveLoopItem(

self, itemname)

Inheritance: `CifBlock`.`RemoveLoopItem`

Deprecated. Use `RemoveItem` instead

Show source ≡

    def RemoveLoopItem(self,itemname):
        """*Deprecated*. Use `RemoveItem` instead"""
        self.RemoveItem(itemname)

def SetOutputLength(

self, wraplength=80, maxoutlength=2048)

Inheritance: `CifBlock`.`SetOutputLength`

Set the maximum output line length (`maxoutlength`) and the line length to wrap at (`wraplength`). The wrap length is a target only and may not always be possible.

Show source ≡

    def SetOutputLength(self,wraplength=80,maxoutlength=2048):
        """Set the maximum output line length (`maxoutlength`) and the line length to
        wrap at (`wraplength`).  The wrap length is a target only and may not always be
        possible."""
        if wraplength > maxoutlength:
            raise StarError("Wrap length (requested %d) must be <= Maximum line length (requested %d)" % (wraplength,maxoutlength))
        self.wraplength = wraplength
        self.maxoutlength = maxoutlength

class ValidCifError

Show source ≡

    class ValidCifError(Exception):
        def __init__(self,value):
            self.value = value
        def __str__(self):
            return '\nCif Validity error: ' + self.value

### Ancestors (in MRO)

- ValidCifError
- exceptions.Exception
- exceptions.BaseException
- __builtin__.object

class ValidCifFile

A CIF file for which all datablocks are valid. Argument `dic` to initialisation specifies a `CifDic` object to use for validation.

Show source ≡

    class ValidCifFile(CifFile):
        """A CIF file for which all datablocks are valid.  Argument `dic` to
        initialisation specifies a `CifDic` object to use for validation."""
        def __init__(self,dic=None,diclist=[],mergemode="replace",*args,**kwargs):
            if not diclist and not dic and not hasattr(self,'bigdic'):
                raise ValidCifError( "At least one dictionary is required to create a ValidCifFile object")
            if not dic and diclist:     #merge here for speed
                self.bigdic = merge_dic(diclist,mergemode)
            elif dic and not diclist:
                self.bigdic = dic
            CifFile.__init__(self,*args,**kwargs)
            for blockname in self.keys():
                self.dictionary[blockname]=ValidCifBlock(data=self.dictionary[blockname],dic=self.bigdic)

        def NewBlock(self,blockname,blockcontents,**kwargs):
            CifFile.NewBlock(self,blockname,blockcontents,**kwargs)
            # dictionary[blockname] is now a CifBlock object.  We
            # turn it into a ValidCifBlock object
            self.dictionary[blockname] = ValidCifBlock(dic=self.bigdic,
                                             data=self.dictionary[blockname])

### Ancestors (in MRO)

- ValidCifFile
- CifFile
- CifFile.StarFile.StarFile
- CifFile.StarFile.BlockCollection
- __builtin__.object

### Methods

def NewBlock(

self, blockname, blockcontents, **kwargs)

Inheritance: `CifFile`.`NewBlock`

Add a new block named `blockname` with contents `blockcontents`. If `fix` is True, `blockname` will have spaces and tabs replaced by underscores. `parent` allows a parent block to be set so that block hierarchies can be created. Depending on the output standard, these blocks will be printed out as nested save frames or ignored.

Show source ≡

    def NewBlock(self,blockname,blockcontents,**kwargs):
        CifFile.NewBlock(self,blockname,blockcontents,**kwargs)
        # dictionary[blockname] is now a CifBlock object.  We
        # turn it into a ValidCifBlock object
        self.dictionary[blockname] = ValidCifBlock(dic=self.bigdic,
                                         data=self.dictionary[blockname])

def SetTemplate(

self, template_file)

Inheritance: `CifFile`.`SetTemplate`

Use `template_file` as a template for all block output

Show source ≡

    def SetTemplate(self,template_file):
            """Use `template_file` as a template for all block output"""
            self.master_template = process_template(template_file)
            for b in self.dictionary.values():
                b.formatting_hints = self.master_template

def WriteOut(

self, comment=u'', wraplength=80, maxoutlength=0, blockorder=None, saves_after=None)

Inheritance: `CifFile`.`WriteOut`

Return the contents of this file as a string, wrapping if possible at `wraplength` characters and restricting maximum line length to `maxoutlength`. Delimiters and save frame nesting are controlled by `self.grammar`. If `blockorder` is provided, blocks are output in this order unless nested save frames have been requested (STAR2). The default block order is the order in which blocks were input. `saves_after` inserts all save frames after the given dataname, which allows less important items to appear later. Useful in conjunction with a template for dictionary files.

Show source ≡

    def WriteOut(self,comment='',wraplength=80,maxoutlength=0,blockorder=None,saves_after=None):
        """Return the contents of this file as a string, wrapping if possible at `wraplength`
        characters and restricting maximum line length to `maxoutlength`.  Delimiters and
        save frame nesting are controlled by `self.grammar`. If `blockorder` is
        provided, blocks are output in this order unless nested save frames have been
        requested (STAR2). The default block order is the order in which blocks were input.
        `saves_after` inserts all save frames after the given dataname,
        which allows less important items to appear later.  Useful in conjunction with a
        template for dictionary files."""
        if maxoutlength != 0:
            self.SetOutputLength(maxoutlength)
        if not comment:
            comment = self.header_comment
        outstring = StringIO()
        if self.grammar == "2.0" and comment[0:10] != r"#\#CIF_2.0":
            outstring.write(r"#\#CIF_2.0" + "\n")
        outstring.write(comment)
        # prepare all blocks
        for b in self.dictionary.values():
            b.set_grammar(self.grammar)
            b.formatting_hints = self.master_template
            b.SetOutputLength(wraplength,self.maxoutlength)
        # loop over top-level
        # monitor output
        all_names = list(self.child_table.keys())   #i.e. lower case
        if blockorder is None:
            blockorder = self.block_input_order
        top_block_names = [(a,self.child_table[a].block_id) for a in blockorder if self.child_table[a].parent is None]
        for blockref,blockname in top_block_names:
            print('Writing %s, ' % blockname + repr(self[blockref]))
            outstring.write('\n' + 'data_' +blockname+'\n')
            all_names.remove(blockref)
            if self.standard == 'Dic':              #put contents before save frames
                outstring.write(self[blockref].printsection(finish_at='_dictionary_valid.application'))
            if self.grammar == 'STAR2':  #nested save frames
                child_refs = self.get_immediate_children(blockref)
                for child_ref,child_info in child_refs:
                    child_name = child_info.block_id
                    outstring.write('\n\n' + 'save_' + child_name + '\n')
                    self.block_to_string_nested(child_ref,child_name,outstring,4)
                    outstring.write('\n' + 'save_'+ '\n')
            elif self.grammar in ('1.0','1.1','2.0'):                   #non-nested save frames
                child_refs = [a for a in blockorder if self.is_child_of_parent(blockref,a)]
                for child_ref in child_refs:
                    child_name = self.child_table[child_ref].block_id
                    outstring.write('\n\n' + 'save_' + child_name + '\n')
                    outstring.write(str(self[child_ref]))
                    outstring.write('\n\n' + 'save_' + '\n')
                    all_names.remove(child_ref.lower())
            else:
                raise StarError('Grammar %s is not recognised for output' % self.grammar)
            if self.standard != 'Dic':              #put contents after save frames
                outstring.write(str(self[blockref]))
            else:
                outstring.write(self[blockref].printsection(start_from='_dictionary_valid.application'))
        returnstring =  outstring.getvalue()
        outstring.close()
        if len(all_names)>0:
            print('WARNING: following blocks not output: %s' % repr(all_names))
        else:
            print('All blocks output.')
        return returnstring

class ValidationResult

Represents validation result. It is initialised with

Show source ≡

    class ValidationResult:
        """Represents validation result. It is initialised with """
        def __init__(self,results):
            """results is return value of validate function"""
            self.valid_result, self.no_matches = results

        def report(self,use_html):
            """Return string with human-readable description of validation result"""
            return validate_report((self.valid_result, self.no_matches),use_html)

        def is_valid(self,block_name=None):
            """Return True for valid CIF file, otherwise False"""
            if block_name is not None:
                block_names = [block_name]
            else:
                block_names = self.valid_result.iterkeys()
            for block_name in block_names:
                if not self.valid_result[block_name] == (True,{}):
                    valid = False
                    break
                else:
                    valid = True
            return valid

        def has_no_match_items(self,block_name=None):
            """Return true if some items are not found in dictionary"""
            if block_name is not None:
                block_names = [block_name]
            else:
                block_names = self.no_matches.iter_keys()
            for block_name in block_names:
                if self.no_matches[block_name]:
                    has_no_match_items = True
                    break
                else:
                    has_no_match_items = False
            return has_no_match_items

### Ancestors (in MRO)

- ValidationResult