#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"
#include "stb_sprintf.h"

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Functions
static int	get_actual_atom_number (int index, int n, int orig, int fin)

int	MolfileV3000Init (MOL_FMT_CTAB ctab, char pStrErr)
	Initialize V3000 connection table in MOL file data structure.

int	DeleteMolfileV3000Info (MOL_FMT_v3000 *v3000)
	Free memory allocated for V3000 specific data in the MOL file data structure.

char *	inchi_fgetsLf_V3000 (char line, INCHI_IOSTREAM inp_stream)
	Read a line from the input file stream, handling V3000 line continuations: Extended version of inchi_fgetsLf which is able of reading concatenated lines (ending with '-') of V3000 Molfile. Also removes "M V30 " prefix" and normalizes the rest of string.

int	MolfileV3000ReadField (void data, int data_type, char *line_ptr)
	Extract the 'data' in specified mol file field at given text position 'line_ptr'.

int	MolfileV3000ReadKeyword (char key, char *line_ptr)
	Read keyword from the specified line.

int	MolfileV3000ReadCTABBeginAndCountsLine (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, char *pStrErr)
	Read V3000 head (begin and counts line) of in MOL file data structure from input file stream.

int	MolfileV3000ReadSGroup (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 Sgroup information from the input file stream into the MOL file data structure.

int	MolfileV3000Read3DBlock (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 3D constraints block in MOL file data structure from input file stream.

int	MolfileV3000ReadCollections (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 collections block in MOL file data structure from input file stream.

int	MolfileV3000ReadAtomsBlock (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 atoms block in MOL file data structure from input file stream.

int	MolfileV3000ReadBondsBlock (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 bonds block in MOL file data structure from input file stream.

int	MolfileV3000ReadTailOfCTAB (MOL_FMT_CTAB ctab, INCHI_IOSTREAM inp_file, int err, char *pStrErr)
	Read V3000 tail (haptic bonds, stereo collections, Sgroups, 3D constraints, collections, end line) in to the MOL file data structure from input file stream.

int	MolfileV3000ReadHapticBond (MOL_FMT_CTAB ctab, char line_ptr, int num_list, char pStrErr)
	Read V3000 haptic bond information from the input line.

int	MolfileV3000ReadStereoCollection (MOL_FMT_CTAB ctab, char line_ptr, int num_list, char pStrErr)
	Read V3000 stereo collection information from the input line.

int	get_V3000_input_line_to_strbuf (INCHI_IOS_STRING buf, INCHI_IOSTREAM inp_stream)
	Get a V3000 input line and store it in a string buffer.

Function Documentation

◆ DeleteMolfileV3000Info()

int DeleteMolfileV3000Info ( MOL_FMT_v3000 * v3000 )

Free memory allocated for V3000 specific data in the MOL file data structure.

Parameters

v3000 Pointer to the V3000 specific data structure to free.

Returns: 0.

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◆ get_actual_atom_number()

int get_actual_atom_number	(	int	index,
		int	n,
		int *	orig,
		int *	fin
	)

static

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◆ get_V3000_input_line_to_strbuf()

int get_V3000_input_line_to_strbuf	(	INCHI_IOS_STRING *	buf,
		INCHI_IOSTREAM *	inp_stream
	)

Get a V3000 input line and store it in a string buffer.

Parameters

buf	Pointer to the string buffer to store the line.
inp_stream	Pointer to the input file stream.

Returns: Length of buffer stored on success, -1 on failure.

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◆ inchi_fgetsLf_V3000()

char * inchi_fgetsLf_V3000	(	char *	line,
		INCHI_IOSTREAM *	inp_stream
	)

Read a line from the input file stream, handling V3000 line continuations: Extended version of inchi_fgetsLf which is able of reading concatenated lines (ending with '-') of V3000 Molfile. Also removes "M V30 " prefix" and normalizes the rest of string.

Parameters

line	Pointer to the buffer to store the read line.
inp_stream	Pointer to the input file stream.

Returns: Pointer to the read line, or NULL on end of file or error.

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◆ MolfileV3000Init()

int MolfileV3000Init	(	MOL_FMT_CTAB *	ctab,
		char *	pStrErr
	)

Initialize V3000 connection table in MOL file data structure.

Parameters

ctab	Pointer to the connection table data structure.
pStrErr	Pointer to the error string buffer.

Returns: 0 on success, -1 on failure.

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◆ MolfileV3000Read3DBlock()

int MolfileV3000Read3DBlock	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 3D constraints block in MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0: Success (no error encountered, 3D block read correctly) 1: Error (e.g., missing "END 3D" marker, or other parsing errors)

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◆ MolfileV3000ReadAtomsBlock()

int MolfileV3000ReadAtomsBlock	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 atoms block in MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0 on success, -1 on failure.

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◆ MolfileV3000ReadBondsBlock()

int MolfileV3000ReadBondsBlock	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 bonds block in MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0: Success (no error, bonds block read correctly), 1: Error: No V3000 Bond block start marker ("BEGIN BOND" missing), 2: Error: Cannot read V3000 bond block line (input line missing or unreadable), 4: Error: Cannot interpret V3000 bond block line (parsing failure) Negative values: If the end-of-data marker ($$$$) is encountered, err is set to -abs(err) (e.g., -1, -2, -4) Other values: If the end marker ("END BOND") is missing, err is set to 1

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◆ MolfileV3000ReadCollections()

int MolfileV3000ReadCollections	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 collections block in MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0: Success (collections block read and parsed correctly) 7: Error in reading or interpreting V3000 collection lines (parsing failure, unexpected format, missing required fields, etc.)

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◆ MolfileV3000ReadCTABBeginAndCountsLine()

int MolfileV3000ReadCTABBeginAndCountsLine	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		char *	pStrErr
	)

Read V3000 head (begin and counts line) of in MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
pStrErr	Pointer to the error string buffer.

Returns: 0 on success, -1 on failure.

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◆ MolfileV3000ReadField()

int MolfileV3000ReadField	(	void *	data,
		int	data_type,
		char **	line_ptr
	)

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

Parameters

data	Pointer to the destination buffer.
data_type	Type of the data to read. E.g. MOL_FMT_STRING_DATA, MOL_FMT_CHAR_INT_DATA, etc.
line_ptr	Pointer to the line buffer.

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

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◆ MolfileV3000ReadHapticBond()

int MolfileV3000ReadHapticBond	(	MOL_FMT_CTAB *	ctab,
		char **	line_ptr,
		int **	num_list,
		char *	pStrErr
	)

Read V3000 haptic bond information from the input line.

Parameters

ctab	Pointer to the connection table data structure.
line_ptr	Pointer to the line buffer.
num_list	Pointer to the list of numbers.
pStrErr	Pointer to the error string buffer.

Returns: Positive integer (nread > 0): Success; number of bytes/fields read from the haptic bond block. 0: No data read (rare, usually means nothing was parsed). -1: Error; parsing failed at any step (missing '(', invalid count, allocation failure, field read error, missing "ATTACH=ALL", etc.).

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◆ MolfileV3000ReadKeyword()

int MolfileV3000ReadKeyword	(	char *	key,
		char **	line_ptr
	)

Read keyword from the specified line.

Parameters

key	Pointer to the buffer to store the keyword.
line_ptr	Pointer to the line buffer.

Returns: Length of the keyword on success, -1 on failure.

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◆ MolfileV3000ReadSGroup()

int MolfileV3000ReadSGroup	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 Sgroup information from the input file stream into the MOL file data structure.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0: Success (no error encountered, SGroup read correctly) 1: Error (e.g., missing "END SGROUP" marker, or other parsing errors)

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◆ MolfileV3000ReadStereoCollection()

int MolfileV3000ReadStereoCollection	(	MOL_FMT_CTAB *	ctab,
		char **	line_ptr,
		int **	num_list,
		char *	pStrErr
	)

Read V3000 stereo collection information from the input line.

Parameters

ctab	Pointer to the connection table data structure.
line_ptr	Pointer to the line buffer.
num_list	Pointer to the list of numbers.
pStrErr	Pointer to the error string buffer.

Returns: Positive integer (nread > 0): Success; number of bytes/fields read from the stereo collection block. 0: No data read (rare, usually means nothing was parsed). -1: Error; parsing failed at any step (missing '(', invalid count, allocation failure, field read error, missing "ATTACH=ALL", etc.).

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◆ MolfileV3000ReadTailOfCTAB()

int MolfileV3000ReadTailOfCTAB	(	MOL_FMT_CTAB *	ctab,
		INCHI_IOSTREAM *	inp_file,
		int	err,
		char *	pStrErr
	)

Read V3000 tail (haptic bonds, stereo collections, Sgroups, 3D constraints, collections, end line) in to the MOL file data structure from input file stream.

Parameters

ctab	Pointer to the connection table data structure.
inp_file	Pointer to the input file stream.
err	Error code.
pStrErr	Pointer to the error string buffer.

Returns: 0: Success (no error encountered, tail of CTAB read correctly) 1: Error (e.g., missing "END CTAB" marker, or other parsing errors) 7: Error in reading or interpreting V3000 collection lines 71, 77, etc.: Error codes from sub-blocks (e.g., SGroup, 3DBlock, Collection) plus 70, indicating which sub-block failed Other positive values: Error codes from called functions (e.g., MolfileV3000ReadSGroup, MolfileV3000Read3DBlock, MolfileV3000ReadCollections) plus 70 Negative values: If an end-of-data marker ($$$$) is encountered during an error, the error code may be returned as a negative value (e.g., -1, -7, -71, etc.)

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Functions

Function Documentation

◆ DeleteMolfileV3000Info()

◆ get_actual_atom_number()

◆ get_V3000_input_line_to_strbuf()

◆ inchi_fgetsLf_V3000()

◆ MolfileV3000Init()

◆ MolfileV3000Read3DBlock()

◆ MolfileV3000ReadAtomsBlock()

◆ MolfileV3000ReadBondsBlock()

◆ MolfileV3000ReadCollections()

◆ MolfileV3000ReadCTABBeginAndCountsLine()

◆ MolfileV3000ReadField()

◆ MolfileV3000ReadHapticBond()

◆ MolfileV3000ReadKeyword()

◆ MolfileV3000ReadSGroup()

◆ MolfileV3000ReadStereoCollection()

◆ MolfileV3000ReadTailOfCTAB()