residue.h File Reference

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residue.h File Reference
`#include <openbabel/babelconfig.h>`
`#include <vector>`
`#include <string>`
`#include <openbabel/base.h>`
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Go to the source code of this file.

## Classes
class | OBResidue
| Residue information. More...
## Namespaces
namespace | OpenBabel
namespace | OpenBabel::OBAminoAcidProperty
namespace | OpenBabel::OBResidueAtomProperty
namespace | OpenBabel::OBResidueIndex
namespace | OpenBabel::OBResidueProperty
## Defines
#define | MAXSETNO 40
#define | MAXELEM 1024
#define | MINELEM 29
#define | MAXRES 100
#define | MINRES 54
#define | AA_ALA (1<<1)
#define | AA_GLY (1<<2)
#define | AA_LEU (1<<3)
#define | AA_SER (1<<4)
#define | AA_VAL (1<<5)
#define | AA_THR (1<<6)
#define | AA_LYS (1<<7)
#define | AA_ASP (1<<8)
#define | AA_ILE (1<<9)
#define | AA_ASN (1<<10)
#define | AA_GLU (1<<11)
#define | AA_PRO (1<<12)
#define | AA_ARG (1<<13)
#define | AA_PHE (1<<14)
#define | AA_GLN (1<<15)
#define | AA_TYR (1<<16)
#define | AA_HIS (1<<17)
#define | AA_CYS (1<<18)
#define | AA_MET (1<<19)
#define | AA_TRP (1<<20)
#define | IS_ACIDIC(x) ((x) & ((AA_ASP)|(AA_GLU)))
#define | IS_ACYCLIC(x)
#define | IS_ALIPHATIC(x)
#define | IS_AROMATIC(x) ((x) & ((AA_HIS)|(AA_PHE)|(AA_TRP)|(AA_TYR)))
#define | IS_BASIC(x) ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))
#define | IS_BURIED(x)
#define | IS_CHARGED(x)
#define | IS_CYCLIC(x)
#define | IS_HYDROPHOBIC(x)
#define | IS_LARGE(x)
#define | IS_MEDIUM(x)
#define | IS_NEGATIVE(x) ((x) & ((AA_ASP)|(AA_GLU)))
#define | IS_NEUTRAL(x)
#define | IS_POLAR(x)
#define | IS_POSITIVE(x) ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))
#define | IS_SMALL(x) ((x) & ((AA_ALA)|(AA_GLY)|(AA_SER)))
#define | IS_SURFACE(x)
## Typedefs
typedef std::vector< OBResidue * > ::iterator | OBResidueIterator
## Enumerations
enum | { ACIDIC = 0, ACYCLIC = 1, ALIPHATIC = 2, AROMATIC = 3, BASIC = 4, BURIED = 5, CHARGED = 6, CYCLIC = 7, HYDROPHOBIC = 8, LARGE = 9, MEDIUM = 10, NEGATIVE = 11, NEUTRAL = 12, POLAR = 13, POSITIVE = 14, SMALL = 15, SURFACE = 16 }
enum | { ALPHA_CARBON = 0, AMINO_BACKBONE = 1, BACKBONE = 2, CYSTEINE_SULPHUR = 3, LIGAND = 4, NUCLEIC_BACKBONE = 5, SHAPELY_BACKBONE = 6, SHAPELY_SPECIAL = 7, SIDECHAIN = 8, SUGAR_PHOSPHATE = 9 }
enum | { ALA = 0, GLY = 1, LEU = 2, SER = 3, VAL = 4, THR = 5, LYS = 6, ASP = 7, ILE = 8, ASN = 9, GLU = 10, PRO = 11, ARG = 12, PHE = 13, GLN = 14, TYR = 15, HIS = 16, CYS = 17, MET = 18, TRP = 19, ASX = 20, GLX = 21, PCA = 22, HYP = 23, A = 24, C = 25, G = 26, T = 27, U = 28, UPLUS = 29, I = 30, _1MA = 32, _5MC = 32, OMC = 33, _1MG = 34, _2MG = 35, M2G = 36, _7MG = 37, OMG = 38, YG = 39, H2U = 40, _5MU = 41, PSU = 42, UNK = 43, ACE = 44, FOR = 45, HOH = 46, DOD = 47, SO4 = 48, PO4 = 49, NAD = 50, COA = 51, NAP = 52, NDP = 53 }
enum | { AMINO = 0, AMINO_NUCLEO = 1, COENZYME = 2, ION = 3, NUCLEO = 4, PROTEIN = 5, PURINE = 6, PYRIMIDINE = 7, SOLVENT = 8, WATER = 9 }
## Variables
char | Residue [MAXRES][4]
char | ElemDesc [MAXELEM][4]
unsigned int | ResNo = MINRES
unsigned int | ElemNo = MINELEM

## Detailed Description

Defines for residue properties, names, etc.

## Define Documentation

#define MAXSETNO 40

#define MAXELEM 1024

Referenced by OpenBabel::GetAtomIDNumber().

#define MINELEM 29

Referenced by OpenBabel::GetAtomIDNumber().

#define MAXRES 100

Referenced by OpenBabel::GetResidueNumber().

#define MINRES 54

Referenced by OpenBabel::GetResidueNumber().

#define AA_ALA (1<<1)

Referenced by OpenBabel::SetResidueKeys().

#define AA_GLY (1<<2)

Referenced by OpenBabel::SetResidueKeys().

#define AA_LEU (1<<3)

Referenced by OpenBabel::SetResidueKeys().

#define AA_SER (1<<4)

Referenced by OpenBabel::SetResidueKeys().

#define AA_VAL (1<<5)

Referenced by OpenBabel::SetResidueKeys().

#define AA_THR (1<<6)

Referenced by OpenBabel::SetResidueKeys().

#define AA_LYS (1<<7)

Referenced by OpenBabel::SetResidueKeys().

#define AA_ASP (1<<8)

Referenced by OpenBabel::SetResidueKeys().

#define AA_ILE (1<<9)

Referenced by OpenBabel::SetResidueKeys().

#define AA_ASN (1<<10)

Referenced by OpenBabel::SetResidueKeys().

#define AA_GLU (1<<11)

Referenced by OpenBabel::SetResidueKeys().

#define AA_PRO (1<<12)

Referenced by OpenBabel::SetResidueKeys().

#define AA_ARG (1<<13)

Referenced by OpenBabel::SetResidueKeys().

#define AA_PHE (1<<14)

Referenced by OpenBabel::SetResidueKeys().

#define AA_GLN (1<<15)

Referenced by OpenBabel::SetResidueKeys().

#define AA_TYR (1<<16)

Referenced by OpenBabel::SetResidueKeys().

#define AA_HIS (1<<17)

Referenced by OpenBabel::SetResidueKeys().

#define AA_CYS (1<<18)

Referenced by OpenBabel::SetResidueKeys().

#define AA_MET (1<<19)

Referenced by OpenBabel::SetResidueKeys().

#define AA_TRP (1<<20)

Referenced by OpenBabel::SetResidueKeys().

#define IS_ACIDIC | ( |  | x | ) | ((x) & ((AA_ASP)|(AA_GLU)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_ACYCLIC | ( |  | x | ) |

Value:

    ((x) & ((AA_ALA)|(AA_GLY)|(AA_LEU)|(AA_SER)|  \
                                      (AA_VAL)|(AA_THR)|(AA_LYS)|(AA_ASP)|  \
                                      (AA_ILE)|(AA_ASN)|(AA_GLU)|(AA_GLN)|  \
                                      (AA_CYS)|(AA_MET)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_ALIPHATIC | ( |  | x | ) |

Value:

    ((x) & ((AA_ALA)|(AA_GLY)|(AA_ILE)|(AA_LEU)|  \
                                      (AA_VAL)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_AROMATIC | ( |  | x | ) | ((x) & ((AA_HIS)|(AA_PHE)|(AA_TRP)|(AA_TYR)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_BASIC | ( |  | x | ) | ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_BURIED | ( |  | x | ) |

Value:

    ((x) & ((AA_ALA)|(AA_CYS)|(AA_ILE)|(AA_LEU)|  \
                                      (AA_MET)|(AA_PHE)|(AA_TRP)|(AA_VAL)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_CHARGED | ( |  | x | ) |

Value:

    ((x) & ((AA_ASP)|(AA_GLU)|(AA_ARG)|(AA_HIS)|  \
                                      (AA_LYS)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_CYCLIC | ( |  | x | ) |

Value:

    ((x) & ((AA_HIS)|(AA_PHE)|(AA_PRO)|(AA_TRP)|  \
                                      (AA_TYR)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_HYDROPHOBIC | ( |  | x | ) |

Value:

    ((x) & ((AA_ALA)|(AA_LEU)|(AA_VAL)|(AA_ILE)|  \
                                      (AA_PRO)|(AA_PHE)|(AA_MET)|(AA_TRP)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_LARGE | ( |  | x | ) |

Value:

    ((x) & ((AA_ARG)|(AA_PHE)|(AA_GLN)|(AA_TYR)|  \
                                      (AA_HIS)|(AA_LEU)|(AA_LYS)|(AA_ILE)|  \
                                      (AA_GLU)|(AA_MET)|(AA_TRP)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_MEDIUM | ( |  | x | ) |

Value:

    ((x) & ((AA_VAL)|(AA_THR)|(AA_ASP)|(AA_ASN)|  \
                                      (AA_PRO)|(AA_CYS)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_NEGATIVE | ( |  | x | ) | ((x) & ((AA_ASP)|(AA_GLU)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_NEUTRAL | ( |  | x | ) |

Value:

    ((x) & ((AA_ALA)|(AA_GLY)|(AA_LEU)|(AA_SER)|  \
                                      (AA_VAL)|(AA_THR)|(AA_PHE)|(AA_GLN)|  \
                                      (AA_TYR)|(AA_HIS)|(AA_CYS)|(AA_MET)|  \
                                      (AA_TRP)|(AA_ILE)|(AA_ASN)|(AA_PRO)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_POLAR | ( |  | x | ) |

Value:

    ((x) & ((AA_ASP)|(AA_ILE)|(AA_ASN)|(AA_GLU)|  \
                                      (AA_SER)|(AA_THR)|(AA_ARG)|(AA_GLN)|  \
                                      (AA_CYS)|(AA_HIS)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_POSITIVE | ( |  | x | ) | ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_SMALL | ( |  | x | ) | ((x) & ((AA_ALA)|(AA_GLY)|(AA_SER)))

Referenced by OBResidue::GetAminoAcidProperty().

#define IS_SURFACE | ( |  | x | ) |

Value:

    ((x) & ((AA_THR)|(AA_LYS)|(AA_ASP)|(AA_ILE)|  \
                                      (AA_ASN)|(AA_GLU)|(AA_PRO)|(AA_ARG)|  \
                                      (AA_GLY)|(AA_SER)|(AA_GLN)|(AA_TYR)|  \
                                      (AA_HIS)))

Referenced by OBResidue::GetAminoAcidProperty().

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