mol_fmt1.c File Reference

#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include <math.h>
#include <float.h>
#include <limits.h>
#include "mode.h"
#include "mol_fmt.h"
#include "ichierr.h"
#include "util.h"
#include "ichi_io.h"
#include "strutil.h"
#include "bcf_s.h"

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Functions
static int	MolfileReadSTextBlock (MOL_FMT_CTAB *ctab, INCHI_IOSTREAM *inp_file, int err, char *pStrErr)
static int	MolfileReadPropBlock (MOL_FMT_CTAB *ctab, MOL_FMT_HEADER_BLOCK *pHdr, INCHI_IOSTREAM *inp_file, int treat_polymers, int err, char *pStrErr, int bNoWarnings)
static int	MolfileReadSgroupOfPolymer (MOL_FMT_CTAB *ctab, MOL_FMT_HEADER_BLOCK *pHdr, INCHI_IOSTREAM *inp_file, char line[MOL_FMT_INPLINELEN], char *szType, char *p, int err, char *pStrErr)
static int	MolfileTreatPseudoElementAtoms (MOL_FMT_CTAB *ctab, int pseudos_allowed, int *err, char *pStrErr)
MOL_FMT_DATA *	ReadMolfile (INCHI_IOSTREAM *inp_file, MOL_FMT_HEADER_BLOCK *OnlyHeaderBlock, MOL_FMT_CTAB *OnlyCTab, int bGetOrigCoord, int treat_polymers, int treat_NPZz, char *pname, int lname, unsigned long *Id, const char *pSdfLabel, char *pSdfValue, int *err, char *pStrErr, int bNoWarnings)
	Reads a substance text block.
MOL_FMT_DATA *	MolfileReadDataLines (INCHI_IOSTREAM *inp_file, MOL_FMT_HEADER_BLOCK *OnlyHeaderBlock, MOL_FMT_CTAB *OnlyCTab, int bGetOrigCoord, int treat_polymers, int *err, char *pStrErr, int bNoWarnings)
	Reads header lines and connection table block from input SD or MOL file, ignore STEXT block, queries, and 3D features.
int	MolfileReadHeaderLines (MOL_FMT_HEADER_BLOCK *hdr, INCHI_IOSTREAM *inp_file, char *pStrErr)
	Reads header lines from input MOL file. A MOL file can have 3 header lines: (1) the name of the molecule, (2) details about the software used and (3) a comment line.
int	MolfileReadCountsLine (MOL_FMT_CTAB *ctab, INCHI_IOSTREAM *inp_file, char *pStrErr)
	Reads counts line from input MOL file, includes information about the number of atoms, bonds, and atom lists, the chiral flag setting, and the Ctab version.
int	MolfileReadAtomsBlock (MOL_FMT_CTAB *ctab, INCHI_IOSTREAM *inp_file, int err, char *pStrErr)
	Reads an atom block from input MOL file (V2000).
int	MolfileReadBondsBlock (MOL_FMT_CTAB *ctab, INCHI_IOSTREAM *inp_file, int err, char *pStrErr)
	Reads a bond block from input MOL file (V2000)

Function Documentation

MolfileReadAtomsBlock()

int MolfileReadAtomsBlock	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Reads an atom block from input MOL file (V2000).

Parameters

ctab	Connection table data structure
inp_file	Input file
err	Error code
pStrErr	Error string

Returns

int Error code, returns 0 - no error, 4 - error: can't interpret atom block, 5 - error: can't interpret second half of atom block?

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MolfileReadBondsBlock()

int MolfileReadBondsBlock	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Reads a bond block from input MOL file (V2000)

Parameters

ctab	Connection table data structure
inp_file	Input file
err	Error code
pStrErr	Error string

Returns

int Error code

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MolfileReadCountsLine()

int MolfileReadCountsLine	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		char *	pStrErr
	)

Reads counts line from input MOL file, includes information about the number of atoms, bonds, and atom lists, the chiral flag setting, and the Ctab version.

Parameters

ctab	Connection table data structure
inp_file	Input file
pStrErr	Error string

Returns

int Error code, returns 0 - no error, 3 - error: can't read counts line, -1 - error: out of RAM

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MolfileReadDataLines()

MOL_FMT_DATA * MolfileReadDataLines	(	INCHI_IOSTREAM *	inp_file,
		MOL_FMT_HEADER_BLOCK *	OnlyHeaderBlock,
		MOL_FMT_CTAB *	OnlyCTab,
		int	bGetOrigCoord,
		int	treat_polymers,
		int *	err,
		char *	pStrErr,
		int	bNoWarnings
	)

Reads header lines and connection table block from input SD or MOL file, ignore STEXT block, queries, and 3D features.

Parameters

inp_file	Input file
OnlyHeaderBlock	Output header data structure, return MOL_FMT_DATA will point to it
OnlyCTab	Output connection table data structure, return MOL_FMT_DATA will point to it
bGetOrigCoord	Flag to get original coordinates
treat_polymers	Flag to treat polymers
err	Error code
pStrErr	Error string
bNoWarnings	Flag to show warnings

Returns

MOL_FMT_DATA* returns mol file data structure, includes e.g. header block, connection table, ...

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MolfileReadHeaderLines()

int MolfileReadHeaderLines	(	MOL_FMT_HEADER_BLOCK *	hdr,
		INCHI_IOSTREAM *	inp_file,
		char *	pStrErr
	)

Reads header lines from input MOL file. A MOL file can have 3 header lines: (1) the name of the molecule, (2) details about the software used and (3) a comment line.

Parameters

hdr	Output header data structure
inp_file	Input file
pStrErr	Error string

Returns

* int Error code, retuns 0 - no error, 1 - error: can't read header block name, 3 - error: can't read header block 2 line, 7 - error: cant' read header block comment line

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MolfileReadPropBlock()

int MolfileReadPropBlock ( MOL_FMT_CTAB *  ctab, MOL_FMT_HEADER_BLOCK *  pHdr, INCHI_IOSTREAM *  inp_file, int  treat_polymers, int  err, char *  pStrErr, int  bNoWarnings  )

static

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MolfileReadSgroupOfPolymer()

int MolfileReadSgroupOfPolymer ( MOL_FMT_CTAB *  ctab, MOL_FMT_HEADER_BLOCK *  pHdr, INCHI_IOSTREAM *  inp_file, char  line[MOL_FMT_INPLINELEN], char *  szType, char *  p, int  err, char *  pStrErr  )

static

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MolfileReadSTextBlock()

int MolfileReadSTextBlock ( MOL_FMT_CTAB *  ctab, INCHI_IOSTREAM *  inp_file, int  err, char *  pStrErr  )

static

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MolfileTreatPseudoElementAtoms()

static int MolfileTreatPseudoElementAtoms ( MOL_FMT_CTAB *  ctab, int  pseudos_allowed, int *  err, char *  pStrErr  )

static

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ReadMolfile()

MOL_FMT_DATA * ReadMolfile	(	INCHI_IOSTREAM *	inp_file,
		MOL_FMT_HEADER_BLOCK *	OnlyHeaderBlock,
		MOL_FMT_CTAB *	OnlyCTab,
		int	bGetOrigCoord,
		int	treat_polymers,
		int	pseudos_allowed,
		char *	pname,
		int	lname,
		unsigned long *	Id,
		const char *	pSdfLabel,
		char *	pSdfValue,
		int *	err,
		char *	pStrErr,
		int	bNoWarnings
	)

Reads a substance text block.

Parameters

ctab	Connection table data structure
inp_file	Input file
err	Error code
pStrErr	Error string

Returns

int Error code

Read MOL file data in to data structures.

Parameters

inp_file	Pointer to the input file stream.
OnlyHeaderBlock	Pointer to the header block to read.
OnlyCTab	Pointer to the connection table to read.
bGetOrigCoord	Flag indicating whether to get original coordinates.
treat_polymers	Flag indicating whether to treat polymers.
pseudos_allowed	Flag indicating whether pseudo atoms are allowed.
pname	Pointer to the name buffer.
lname	Length of the name buffer.
Id	Pointer to the ID buffer.
pSdfLabel	Pointer to the SDF label buffer.
pSdfValue	Pointer to the SDF value buffer.
err	Pointer to the error code.
pStrErr	Pointer to the error string buffer.
bNoWarnings	Flag indicating whether to suppress warnings.

Returns

MOL_FMT_DATA*

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