mol_fmt2.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 "bcf_s.h"

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Macros
#define	MIN_STDATA_X_COORD   0.0
#define	MAX_STDATA_X_COORD   256.0
#define	MIN_STDATA_Y_COORD   0.0
#define	MAX_STDATA_Y_COORD   256.0
#define	MIN_STDATA_Z_COORD   0.0
#define	MAX_STDATA_Z_COORD   256.0
#define	MAX_STDATA_AVE_BOND_LENGTH   20.0
#define	MIN_STDATA_AVE_BOND_LENGTH   10.0

Functions
int	MolfileStrnread (char *dest, char *source, int len, char **first_space)
	Read a string from a source buffer into a destination buffer.
int	MolfileReadField (void *data, int field_len, int data_type, char **line_ptr)
	Extract the 'data' in the MOL file field at given text position 'line_ptr'.
long	MolfileExtractStrucNum (MOL_FMT_HEADER_BLOCK *pHdr)
	Extract the MOL file number from the header name line like "Structure #22".
int	MolfileHasNoChemStruc (MOL_FMT_DATA *mfdata)
	Check if the MOL file has no chemical structure.
int	MolfileSaveCopy (INCHI_IOSTREAM *inp_file, long fPtrStart, long fPtrEnd, FILE *outfile, long num)
	Copy MOL-formatted data of SDF record or Molfile to another file.
int	MolfileGetXYZDimAndNormFactors (MOL_FMT_DATA *mfdata, int find_norm_factors, double *x0, double *y0, double *z0, double *xmin, double *ymin, double *zmin, double *scaler, int *err, char *pStrErr)
	Get xyz dimensionality and normalization factors in the MOL file.
MOL_FMT_DATA *	FreeMolfileData (MOL_FMT_DATA *mfdata)
	Free MOL file data structure.

Macro Definition Documentation

MAX_STDATA_AVE_BOND_LENGTH

#define MAX_STDATA_AVE_BOND_LENGTH   20.0

MAX_STDATA_X_COORD

#define MAX_STDATA_X_COORD   256.0

MAX_STDATA_Y_COORD

#define MAX_STDATA_Y_COORD   256.0

MAX_STDATA_Z_COORD

#define MAX_STDATA_Z_COORD   256.0

MIN_STDATA_AVE_BOND_LENGTH

#define MIN_STDATA_AVE_BOND_LENGTH   10.0

MIN_STDATA_X_COORD

#define MIN_STDATA_X_COORD   0.0

MIN_STDATA_Y_COORD

#define MIN_STDATA_Y_COORD   0.0

MIN_STDATA_Z_COORD

#define MIN_STDATA_Z_COORD   0.0

Function Documentation

FreeMolfileData()

MOL_FMT_DATA * FreeMolfileData

(

MOL_FMT_DATA *

mfdata

)

Free MOL file data structure.

Parameters

mfdata

Pointer to the MOL file data structure to free.

Returns

NULL pointer.

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MolfileExtractStrucNum()

long MolfileExtractStrucNum

(

MOL_FMT_HEADER_BLOCK *

pHdr

)

Extract the MOL file number from the header name line like "Structure #22".

Parameters

pHdr	Pointer to the header block.

Returns

The structure number.

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MolfileGetXYZDimAndNormFactors()

int MolfileGetXYZDimAndNormFactors	(	MOL_FMT_DATA *	mfdata,
		int	find_norm_factors,
		double *	x0,
		double *	y0,
		double *	z0,
		double *	xmin,
		double *	ymin,
		double *	zmin,
		double *	scaler,
		int *	err,
		char *	pStrErr
	)

Get xyz dimensionality and normalization factors in the MOL file.

Parameters

mfdata	Pointer to the MOL file data structure.
find_norm_factors	Flag indicating whether to find normalization/scaling factors.
x0	Pointer to the minimum x-coordinate of the molecule.
y0	Pointer to the minimum y-coordinate of the molecule.
z0	Pointer to the minimum z-coordinate of the molecule.
xmin	Pointer to the x-coordinate (is set to 0).
ymin	Pointer to the y-coordinate (is set to 0).
zmin	Pointer to the z-coordinate (is set to 0).
scaler	Pointer to the scaling factor.
err	Pointer to the error code.
pStrErr	Pointer to the error string buffer.

Returns

number of dimensions: 0, 2, 3

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MolfileHasNoChemStruc()

int MolfileHasNoChemStruc

(

MOL_FMT_DATA *

mfdata

)

Check if the MOL file has no chemical structure.

Parameters

mfdata

Pointer to the MOL file data structure.

Returns

1 if no chemical structure, 0 otherwise.

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MolfileReadField()

int MolfileReadField	(	void *	data,
		int	field_len,
		int	data_type,
		char **	line_ptr
	)

Extract the 'data' in the MOL file field at given text position 'line_ptr'.

Parameters

data	Pointer to the destination buffer.
field_len	Length of the field to read. For MOL_FMT_STRING_DATA does not include trailing zero, that is actual length of the string pointed by 'data' should be at least field_len+1 bytes. For numerical data 'field_len' is length of input data field For numerical integral data field_len <= 0 means read up to first non-numeric character as strtod() does ("free format")
data_type	Type of the data to read. E.g. MOL_FMT_STRING_DATA, MOL_FMT_CHAR_INT_DATA, etc.
line_ptr	Pointer to a variable that will receive the address of the next line.

Returns

for MOL_FMT_STRING_DATA: number of bytes excluding trailing zero for all others: 1=success; 0 = empty; -1 = error

on exit *line_ptr points to the next byte after the last entered

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MolfileSaveCopy()

int MolfileSaveCopy	(	INCHI_IOSTREAM *	inp_file,
		long	fPtrStart,
		long	fPtrEnd,
		FILE *	outfile,
		long	num
	)

Copy MOL-formatted data of SDF record or Molfile to another file.

Parameters

inp_file	Pointer to the input file stream.
fPtrStart	File pointer position to start copying from.
fPtrEnd	File pointer position to stop copying at.
outfile	Pointer to the output file stream.
num	Structure number to write in the header line.

Returns

last position of the output file stream.

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MolfileStrnread()

int MolfileStrnread	(	char *	dest,
		char *	source,
		int	len,
		char **	first_space
	)

Read a string from a source buffer into a destination buffer.

Parameters

dest	Pointer to the destination buffer.
source	Pointer to the source buffer.
len	Length of the string to read.
first_space	Pointer to a variable that will receive the address of the first space character in the source buffer.

Returns

number of actually processed bytes excluding zero terminator.

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