#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().