residue.h File Reference

Defines for residue properties, names, etc. More...

#include <openbabel/babelconfig.h>
#include <vector>
#include <string>
#include <openbabel/base.h>

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Namespaces

namespace OpenBabel

namespace OpenBabel::OBAminoAcidProperty

namespace OpenBabel::OBResidueAtomProperty

namespace OpenBabel::OBResidueIndex

namespace OpenBabel::OBResidueProperty

Classes

class OBResidue

Residue information. More...

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().


Namespaces
namespace	OpenBabel
namespace	OpenBabel::OBAminoAcidProperty
namespace	OpenBabel::OBResidueAtomProperty
namespace	OpenBabel::OBResidueIndex
namespace	OpenBabel::OBResidueProperty
Classes
class	OBResidue
	Residue information. More...
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