residue.h File Reference

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

Go to the source code of this file.

Classes
class	OBResidue

Namespaces
	OpenBabel
	OpenBabel::OBAminoAcidProperty
	OpenBabel::OBResidueAtomProperty
	OpenBabel::OBResidueIndex
	OpenBabel::OBResidueProperty

Macros
#define	MAXSETNO   40
#define	MAXELEM   29
#define	MAXRES   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)

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 }

Detailed Description

Defines for residue properties, names, etc.

Macro Definition Documentation

MAXSETNO

#define MAXSETNO   40

MAXELEM

#define MAXELEM   29

Referenced by OpenBabel::GetAtomIDNumber().

MAXRES

#define MAXRES   54

AA_ALA

#define AA_ALA   (1<<1)

Referenced by OpenBabel::SetResidueKeys().

AA_GLY

#define AA_GLY   (1<<2)

Referenced by OpenBabel::SetResidueKeys().

AA_LEU

#define AA_LEU   (1<<3)

Referenced by OpenBabel::SetResidueKeys().

AA_SER

#define AA_SER   (1<<4)

Referenced by OpenBabel::SetResidueKeys().

AA_VAL

#define AA_VAL   (1<<5)

Referenced by OpenBabel::SetResidueKeys().

AA_THR

#define AA_THR   (1<<6)

Referenced by OpenBabel::SetResidueKeys().

AA_LYS

#define AA_LYS   (1<<7)

Referenced by OpenBabel::SetResidueKeys().

AA_ASP

#define AA_ASP   (1<<8)

Referenced by OpenBabel::SetResidueKeys().

AA_ILE

#define AA_ILE   (1<<9)

Referenced by OpenBabel::SetResidueKeys().

AA_ASN

#define AA_ASN   (1<<10)

Referenced by OpenBabel::SetResidueKeys().

AA_GLU

#define AA_GLU   (1<<11)

Referenced by OpenBabel::SetResidueKeys().

AA_PRO

#define AA_PRO   (1<<12)

Referenced by OpenBabel::SetResidueKeys().

AA_ARG

#define AA_ARG   (1<<13)

Referenced by OpenBabel::SetResidueKeys().

AA_PHE

#define AA_PHE   (1<<14)

Referenced by OpenBabel::SetResidueKeys().

AA_GLN

#define AA_GLN   (1<<15)

Referenced by OpenBabel::SetResidueKeys().

AA_TYR

#define AA_TYR   (1<<16)

Referenced by OpenBabel::SetResidueKeys().

AA_HIS

#define AA_HIS   (1<<17)

Referenced by OpenBabel::SetResidueKeys().

AA_CYS

#define AA_CYS   (1<<18)

Referenced by OpenBabel::SetResidueKeys().

AA_MET

#define AA_MET   (1<<19)

Referenced by OpenBabel::SetResidueKeys().

AA_TRP

#define AA_TRP   (1<<20)

Referenced by OpenBabel::SetResidueKeys().

IS_ACIDIC

#define IS_ACIDIC

(

x

)

((x) & ((AA_ASP)|(AA_GLU)))

Referenced by OBResidue::GetAminoAcidProperty().

IS_ACYCLIC

#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().

IS_ALIPHATIC

#define IS_ALIPHATIC

(

x

)

Value:

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

Referenced by OBResidue::GetAminoAcidProperty().

IS_AROMATIC

#define IS_AROMATIC

(

x

)

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

Referenced by OBResidue::GetAminoAcidProperty().

IS_BASIC

#define IS_BASIC

(

x

)

((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))

Referenced by OBResidue::GetAminoAcidProperty().

IS_BURIED

#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().

IS_CHARGED

#define IS_CHARGED

(

x

)

Value:

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

Referenced by OBResidue::GetAminoAcidProperty().

IS_CYCLIC

#define IS_CYCLIC

(

x

)

Value:

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

Referenced by OBResidue::GetAminoAcidProperty().

IS_HYDROPHOBIC

#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().

IS_LARGE

#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().

IS_MEDIUM

#define IS_MEDIUM

(

x

)

Value:

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

Referenced by OBResidue::GetAminoAcidProperty().

IS_NEGATIVE

#define IS_NEGATIVE

(

x

)

((x) & ((AA_ASP)|(AA_GLU)))

Referenced by OBResidue::GetAminoAcidProperty().

IS_NEUTRAL

#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().

IS_POLAR

#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().

IS_POSITIVE

#define IS_POSITIVE

(

x

)

((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))

Referenced by OBResidue::GetAminoAcidProperty().

IS_SMALL

#define IS_SMALL

(

x

)

((x) & ((AA_ALA)|(AA_GLY)|(AA_SER)))

Referenced by OBResidue::GetAminoAcidProperty().

IS_SURFACE

#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().