#include <openbabel/babelconfig.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <ctype.h>
#include <map>
#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/bond.h>
#include <openbabel/chains.h>
#include <openbabel/oberror.h>
#include <openbabel/obiter.h>
#include <openbabel/elements.h>

Namespaces
	OpenBabel

Macros
#define	RESIDMIN 4

#define	RESIDMAX 64

#define	ATOMMINAMINO 4

#define	ATOMMINNUCLEIC 50

#define	MAXPEPTIDE 11

#define	MAXNUCLEIC 15

#define	AMINOMAX 21

#define	NUCLEOMAX 6

#define	STACKSIZE 20

#define	AI_N 0

#define	AI_CA 1

#define	AI_C 2

#define	AI_O 3

#define	AI_OXT 37

#define	AI_P 38

#define	AI_O1P 39

#define	AI_O2P 40

#define	AI_O5 41

#define	AI_C5 42

#define	AI_C4 43

#define	AI_O4 44

#define	AI_C3 45

#define	AI_O3 46

#define	AI_C2 47

#define	AI_O2 48

#define	AI_C1 49

#define	BitN 0x0001

#define	BitNTer 0x0002

#define	BitNPro 0x0004

#define	BitNPT 0x0008

#define	BitCA 0x0010

#define	BitCAGly 0x0020

#define	BitC 0x0100

#define	BitCTer 0x0200

#define	BitCOXT 0x0400

#define	BitO 0x1000

#define	BitOXT 0x2000

#define	BitNAll 0x000F

#define	BitCAAll 0x0030

#define	BitCAll 0x0700

#define	BitOAll 0x3000

#define	BitP 0x0001

#define	BitPTer 0x0002

#define	BitOP 0x0004

#define	BitO5 0x0008

#define	BitO5Ter 0x0010

#define	BitC5 0x0020

#define	BitC4 0x0040

#define	BitO4 0x0080

#define	BitC3 0x0100

#define	BitO3 0x0200

#define	BitO3Ter 0x0400

#define	BitC2RNA 0x0800

#define	BitC2DNA 0x1000

#define	BitO2 0x2000

#define	BitC1 0x4000

#define	BitPAll 0x0003

#define	Bit05All 0x0018

#define	BitO3All 0x0600

#define	BitC2All 0x1800

#define	BC_ASSIGN 0x01

#define	BC_COUNT 0x02

#define	BC_ELEM 0x03

#define	BC_EVAL 0x04

#define	BC_IDENT 0x05

#define	BC_LOCAL 0x06

#define	BF_SINGLE 0x01

#define	BF_DOUBLE 0x02

#define	BF_TRIPLE 0x04

#define	BF_AROMATIC 0x08

#define	ATOMMAX 68

Typedefs
typedef union OpenBabel::_ByteCode	ByteCode

Functions
static ByteCode *	AllocateByteCode (int type)

static void	DeleteByteCode (ByteCode *node)

static void	FatalMemoryError (void)

void	GenerateByteCodes (ByteCode **node, int resid, int curr, int prev, int bond)

Variables
static char	ChainsResName [RESIDMAX][4]

static Template	Peptide [MAXPEPTIDE]

static Template	Nucleotide [MAXNUCLEIC]

static char	ChainsAtomName [ATOMMAX][4]

static ResidType	AminoAcids [AMINOMAX]

static ResidType	Nucleotides [NUCLEOMAX]

static MonoAtomType	MonoAtom [MaxMonoAtom]

static MonoBondType	MonoBond [MaxMonoBond]

static int	MonoAtomCount

static int	MonoBondCount

static StackType	Stack [STACKSIZE]

static int	StackPtr

static int	AtomIndex

static int	BondIndex

static bool	StrictFlag = false

Detailed Description

Parse for macromolecule chains and residues.

Macro Definition Documentation

◆ RESIDMIN

#define RESIDMIN 4

The first available index for actual residues 0, 1, 2 reserved for UNK, HOH, UNL

Referenced by OBChainsParser::OBChainsParser(), and OBChainsParser::~OBChainsParser().

◆ RESIDMAX

#define RESIDMAX 64

The maximum number of residue IDs for this code.

◆ ATOMMINAMINO

#define ATOMMINAMINO 4

Referenced by OpenBabel::GenerateByteCodes().

◆ ATOMMINNUCLEIC

#define ATOMMINNUCLEIC 50

◆ MAXPEPTIDE

#define MAXPEPTIDE 11

Referenced by OBChainsParser::PerceiveChains().

◆ MAXNUCLEIC

#define MAXNUCLEIC 15

Referenced by OBChainsParser::PerceiveChains().

◆ AMINOMAX

#define AMINOMAX 21

The number of amino acids recognized by this code Currently: ILE, VAL, ALA, ASN, ASP, ARG, CYS, GLN, GLU GLY, HIS, HYP, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR

Referenced by OBChainsParser::OBChainsParser().

◆ NUCLEOMAX

#define NUCLEOMAX 6

The number of nucleic acids recognized by this code Currently A, C, T, G, U, I

Referenced by OBChainsParser::OBChainsParser().

◆ STACKSIZE

#define STACKSIZE 20

◆ AI_N

#define AI_N 0

Referenced by OBChainsParser::PerceiveChains().

◆ AI_CA

#define AI_CA 1

Referenced by OBChainsParser::PerceiveChains().

◆ AI_C

#define AI_C 2

Referenced by OBChainsParser::PerceiveChains().

◆ AI_O

#define AI_O 3

Referenced by OBChainsParser::PerceiveChains().

◆ AI_OXT

#define AI_OXT 37

Referenced by OBChainsParser::PerceiveChains().

◆ AI_P

#define AI_P 38

Referenced by OBChainsParser::PerceiveChains().

◆ AI_O1P

#define AI_O1P 39

Referenced by OBChainsParser::PerceiveChains().

◆ AI_O2P

#define AI_O2P 40

Referenced by OBChainsParser::PerceiveChains().

◆ AI_O5

#define AI_O5 41

Referenced by OBChainsParser::PerceiveChains().

◆ AI_C5

#define AI_C5 42

Referenced by OBChainsParser::PerceiveChains().

◆ AI_C4

#define AI_C4 43

Referenced by OBChainsParser::PerceiveChains().

◆ AI_O4

#define AI_O4 44

Referenced by OBChainsParser::PerceiveChains().

◆ AI_C3

#define AI_C3 45

Referenced by OBChainsParser::PerceiveChains().

◆ AI_O3

#define AI_O3 46

Referenced by OBChainsParser::PerceiveChains().

◆ AI_C2

#define AI_C2 47

Referenced by OBChainsParser::PerceiveChains().

◆ AI_O2

#define AI_O2 48

Referenced by OBChainsParser::PerceiveChains().

◆ AI_C1

#define AI_C1 49

Referenced by OBChainsParser::PerceiveChains().

◆ BitN

#define BitN 0x0001

Referenced by OBChainsParser::PerceiveChains().

◆ BitNTer

#define BitNTer 0x0002

Referenced by OBChainsParser::PerceiveChains().

◆ BitNPro

#define BitNPro 0x0004

◆ BitNPT

#define BitNPT 0x0008

Referenced by OBChainsParser::PerceiveChains().

◆ BitCA

#define BitCA 0x0010

◆ BitCAGly

#define BitCAGly 0x0020

◆ BitC

#define BitC 0x0100

Referenced by OBChainsParser::PerceiveChains().

◆ BitCTer

#define BitCTer 0x0200

◆ BitCOXT

#define BitCOXT 0x0400

◆ BitO

#define BitO 0x1000

◆ BitOXT

#define BitOXT 0x2000

◆ BitNAll

#define BitNAll 0x000F

Referenced by OBChainsParser::PerceiveChains().

◆ BitCAAll

#define BitCAAll 0x0030

Referenced by OBChainsParser::PerceiveChains().

◆ BitCAll

#define BitCAll 0x0700

Referenced by OBChainsParser::PerceiveChains().

◆ BitOAll

#define BitOAll 0x3000

Referenced by OBChainsParser::PerceiveChains().

◆ BitP

#define BitP 0x0001

Referenced by OBChainsParser::PerceiveChains().

◆ BitPTer

#define BitPTer 0x0002

Referenced by OBChainsParser::PerceiveChains().

◆ BitOP

#define BitOP 0x0004

Referenced by OBChainsParser::PerceiveChains().

◆ BitO5

#define BitO5 0x0008

Referenced by OBChainsParser::PerceiveChains().

◆ BitO5Ter

#define BitO5Ter 0x0010

Referenced by OBChainsParser::PerceiveChains().

◆ BitC5

#define BitC5 0x0020

Referenced by OBChainsParser::PerceiveChains().

◆ BitC4

#define BitC4 0x0040

Referenced by OBChainsParser::PerceiveChains().

◆ BitO4

#define BitO4 0x0080

Referenced by OBChainsParser::PerceiveChains().

◆ BitC3

#define BitC3 0x0100

Referenced by OBChainsParser::PerceiveChains().

◆ BitO3

#define BitO3 0x0200

◆ BitO3Ter

#define BitO3Ter 0x0400

◆ BitC2RNA

#define BitC2RNA 0x0800

◆ BitC2DNA

#define BitC2DNA 0x1000

◆ BitO2

#define BitO2 0x2000

Referenced by OBChainsParser::PerceiveChains().

◆ BitC1

#define BitC1 0x4000

Referenced by OBChainsParser::PerceiveChains().

◆ BitPAll

#define BitPAll 0x0003

◆ Bit05All

#define Bit05All 0x0018

◆ BitO3All

#define BitO3All 0x0600

Referenced by OBChainsParser::PerceiveChains().

◆ BitC2All

#define BitC2All 0x1800

Referenced by OBChainsParser::PerceiveChains().

◆ BC_ASSIGN

#define BC_ASSIGN 0x01

Referenced by OpenBabel::DeleteByteCode(), OpenBabel::GenerateByteCodes(), and OBChainsParser::PerceiveChains().

◆ BC_COUNT

#define BC_COUNT 0x02

Referenced by OpenBabel::DeleteByteCode(), OpenBabel::GenerateByteCodes(), and OBChainsParser::PerceiveChains().

◆ BC_ELEM

#define BC_ELEM 0x03

Referenced by OpenBabel::DeleteByteCode(), OpenBabel::GenerateByteCodes(), and OBChainsParser::PerceiveChains().

◆ BC_EVAL

#define BC_EVAL 0x04

Referenced by OpenBabel::DeleteByteCode(), OpenBabel::GenerateByteCodes(), and OBChainsParser::PerceiveChains().

◆ BC_IDENT

#define BC_IDENT 0x05

Referenced by OpenBabel::DeleteByteCode(), OpenBabel::GenerateByteCodes(), and OBChainsParser::PerceiveChains().

◆ BC_LOCAL

#define BC_LOCAL 0x06

Referenced by OpenBabel::DeleteByteCode(), OpenBabel::GenerateByteCodes(), and OBChainsParser::PerceiveChains().

◆ BF_SINGLE

#define BF_SINGLE 0x01

Referenced by OBChainsParser::PerceiveChains().

◆ BF_DOUBLE

#define BF_DOUBLE 0x02

Referenced by OBChainsParser::PerceiveChains().

◆ BF_TRIPLE

#define BF_TRIPLE 0x04

Referenced by OBChainsParser::PerceiveChains().

◆ BF_AROMATIC

#define BF_AROMATIC 0x08

Referenced by OBChainsParser::PerceiveChains().

◆ ATOMMAX

#define ATOMMAX 68

The number of PDB atom type names recognized by this code.

Variable Documentation

◆ ChainsResName

char ChainsResName[RESIDMAX][4]

static

Initial value:

= {
   "UNK",
   "HOH",
   "UNL",
   "ACE"
}

An index of the residue names perceived during a run 0, 1, and 2 reserved for UNK, HOH, LIG

Referenced by OpenBabel::GenerateByteCodes(), OBChainsParser::OBChainsParser(), and OBChainsParser::~OBChainsParser().

Namespaces

Macros

Typedefs

Functions

Variables

Detailed Description

Macro Definition Documentation

◆ RESIDMIN

◆ RESIDMAX

◆ ATOMMINAMINO

◆ ATOMMINNUCLEIC

◆ MAXPEPTIDE

◆ MAXNUCLEIC

◆ AMINOMAX

◆ NUCLEOMAX

◆ STACKSIZE

◆ AI_N

◆ AI_CA

◆ AI_C

◆ AI_O

◆ AI_OXT

◆ AI_P

◆ AI_O1P

◆ AI_O2P

◆ AI_O5

◆ AI_C5

◆ AI_C4

◆ AI_O4

◆ AI_C3

◆ AI_O3

◆ AI_C2

◆ AI_O2

◆ AI_C1

◆ BitN

◆ BitNTer

◆ BitNPro

◆ BitNPT

◆ BitCA

◆ BitCAGly

◆ BitC

◆ BitCTer

◆ BitCOXT

◆ BitO

◆ BitOXT

◆ BitNAll

◆ BitCAAll

◆ BitCAll

◆ BitOAll

◆ BitP

◆ BitPTer

◆ BitOP

◆ BitO5

◆ BitO5Ter

◆ BitC5

◆ BitC4

◆ BitO4

◆ BitC3

◆ BitO3

◆ BitO3Ter

◆ BitC2RNA

◆ BitC2DNA

◆ BitO2

◆ BitC1

◆ BitPAll

◆ Bit05All

◆ BitO3All

◆ BitC2All

◆ BC_ASSIGN

◆ BC_COUNT

◆ BC_ELEM

◆ BC_EVAL

◆ BC_IDENT

◆ BC_LOCAL

◆ BF_SINGLE

◆ BF_DOUBLE

◆ BF_TRIPLE

◆ BF_AROMATIC

◆ ATOMMAX

Variable Documentation

◆ ChainsResName