Uses of Class
org.jmol.adapter.smarter.AtomSetCollectionReader
Packages that use AtomSetCollectionReader
Package
Description
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Uses of AtomSetCollectionReader in org.jmol.adapter.readers.cif
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.cifModifier and TypeClassDescriptionclassA very simple Binary CIF file reader extention of MMCifReader extends CifReader.classPreliminary Cif2 reader.classA true line-free CIF file reader for CIF files.classmmCIF files are recognized prior to class creation.classJmolData RCSB MMTF (macromolecular transmission format) file reader see https://github.com/rcsb/mmtf/blob/master/spec.md Note added 2024.01.19 Jose Duarte 2:03 PM (email) to MMTF-Users From July 2024 the PDB file archive will not be offered in the compressed MMTF format anymore.Fields in org.jmol.adapter.readers.cif declared as AtomSetCollectionReaderMethods in org.jmol.adapter.readers.cif with parameters of type AtomSetCollectionReaderModifier and TypeMethodDescriptionintMSRdr.initialize(AtomSetCollectionReader r, int modDim) MMCifValidationParser.set(AtomSetCollectionReader reader) -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.molxyz
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.molxyzModifier and TypeClassDescriptionclass3D onlyclassA reader for MDLI mol and sdf files.classMinnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) applySymmetryAndSetTrajectory() extended to read XYZI files (Bob's invention -- allows isotope numbers) extended to read XYZ files with fractional charges as, for example: http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.more
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.moreModifier and TypeClassDescriptionclassA reader for various AFLOW file types.classDCD binary trajectory file reader.classA reader for ChemDraw binary CDX files.classclassclassA preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS=acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ... classAmber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD commandclassA reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" fileclassA minimal multi-file reader for TRIPOS SYBYL mol2 files.class -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.pdb
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.pdbModifier and TypeClassDescriptionclassJmolData file reader, for a modified PDB format This class also holds pseudo-static methods for spinclassP2N file reader.classPDB file reader.classPQR file reader. -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.pymol
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.pymolModifier and TypeClassDescriptionclassPyMOL PSE (binary Python session) file reader. -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.quantum
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.quantumModifier and TypeClassDescriptionclassTODO: adf-2007.out causes failure reading basis functions A reader for ADF output.classA reader for AMS output subclassing the older AdfReader.classclassCSF file reader based on CIF idea -- fluid property fields.classA reader for Dgrid BASISFILE data.classclassclassclassReader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq dataclassReader for Gaussian 94/98/03/09 output files.classReader for Gaussian Wfn files -- not implemented yetclassNBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold upgrade to NBO 6 allows reading of resonance structures, including base structureclassJaguar reader tested for the two samples files in CVS.classA molecular structure and orbital reader for MolDen files.classReads Mopac 2007 GRAPHF output filesclassGeneral methods for reading molecular orbital data, including embedded output from the NBO program.classA reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.classReads ORCA input and output filesclassReader for Psi3 output files.classA reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.classA molecular structure and orbital reader for MolDen files.classA molecular orbital reader for WebMO files. -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.simple
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.simpleModifier and TypeClassDescriptionclassTRIPOS simple Alchemy reader.classA reader for AMPAC output.classGaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files.classFoldingAtHome json reader.classThis reader is for current.xyz files generated by Folding@Home project (see http://folding.stanford.edu) I have not found a precise description of the file format.classReads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.classSupport for .hin, HyperChem's native file format.classclassclassclassMopac Archive reader -- presumes "zMatrix" is really Cartesians use FILTER "NOCENTER" to NOT center atoms in unit cell use CENTROID for complete molecules with centroids within unit cell use PACKED CENTROID for complete molecules with any atoms within unit cellclassReads Mopac 93, 6, 7, 2002, or 2009 output filesclassReads ORCA input and output filesclasssimple Tinker format requires Tinker:: prefix: load Tinker::mydata.xyz 1/2014 hansonr@stolaf.edu -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.spartan
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.spartanModifier and TypeClassDescriptionclassclassclassclass -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.xml
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.xmlModifier and TypeClassDescriptionclassA crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.classA reader for CambridgeSoft CDXML files.classAn chem3d c3xml readerclassA CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection.classclassA Molpro 2005 readerclassAn abstract class accessing MOReader -- currently just for XmlMolproReader only.classA reader for the structure part of an nmrML fileclassAn Odyssey xodydata readerclassQuantumEspresso XML readerclassA generic XML reader template -- by itself, does nothing.classVasp vasprun.xml readerclassAn XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09 -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.xtal
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.xtalModifier and TypeClassDescriptionclassclassFHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format samples of relevant lines in geometry.in file are included as comments below modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines and to bring it into compliance with other load options (such as overriding file-based symmetry or unit cell parameters).classBilbao Crystallographic Database file reader see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of Crystal Structures with the same Symmetry Note that this reader scrapes HTML.classCASTEP (http://www.castep.org) .cell file format relevant section of .cell file are included as comments below preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many thanks to Keith Refson for his assistance with this implementation -- atom's mass is encoded as bfactor -- FILTER options include "q=n" where n is an integer "q={1/4 1/4 0}" "q=ALL" -- for non-simple fractions, you must use the exact form of the wavevector description: -- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just specify SUPERCELL {a b c} where the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example note: following was never implemented? -- following this with ".1" ".2" etc.classA reader for TOPOS systre file Crystal Graph Data format.classA reader for CrystalMaker CMDF binary/text files.classA reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/classclassclassA reader for JSON output from the FINDSPINGROUP program.classProblems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.classA reader for Jana M50+M40 file pairs.classclassA (preliminary) reader for OPTIMADE resources.classcrude PWmat atom.config reader http://pwmatus.com/manualclassA reader for SHELX output (RES) files.classBH note: this reader was never set up to read Z-matrix structures such as benzenev4.1.fdf SIESTA http://www.icmab.es/siesta/classhttp://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.classhttp://cms.mpi.univie.ac.at/vasp/classadjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/classA reader for Wein2k DFT files.class -
Uses of AtomSetCollectionReader in org.jmol.adapter.smarter
Methods in org.jmol.adapter.smarter with parameters of type AtomSetCollectionReaderModifier and TypeMethodDescriptionintMSInterface.initialize(AtomSetCollectionReader r, int modDim) protected voidXtalSymmetry.FileSymmetry.preSymmetryFinalizeMoments(AtomSetCollectionReader acr, AtomSetCollection asc, String spinFrameStr, String spinFrameExt) Scale the magnetic moments of magCIF and spinCIF files.XtalSymmetry.set(AtomSetCollectionReader reader) static ObjectSmarterJmolAdapter.staticGetAtomSetCollection(AtomSetCollectionReader a) Constructors in org.jmol.adapter.smarter with parameters of type AtomSetCollectionReaderModifierConstructorDescriptionAtomSetCollection(String fileTypeName, AtomSetCollectionReader reader, AtomSetCollection[] array, Lst<?> list)