mol_fmt4.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 "ichimain.h"
#include "bcf_s.h"

Include dependency graph for mol_fmt4.c:

Macros
#define	ALIASED_AT(i)   (0 < NUM_ISO_H(at, i))
#define	IS_DEUTERIUM(i)   (!strcmp(at[i].elname, "D") || at[i].iso_atw_diff == 2 && !strcmp(at[i].elname, "H"))
#define	IS_TRITIUM(i)   (!strcmp(at[i].elname, "T") || at[i].iso_atw_diff == 3 && !strcmp(at[i].elname, "H"))
#define	ABNORMAL_ISO(i)   (at[i].iso_atw_diff == 1 || at[i].iso_atw_diff < -3 || at[i].iso_atw_diff > 5)
#define	ABNORMAL_CHG(i)   (abs(at[i].charge) > 3)
#define	ABNORMAL_RAD(i)   (RADICAL_SINGLET <= at[i].radical && at[i].radical <= RADICAL_TRIPLET)
#define	ANY_ISO(i, X)
#define	ANY_CHG(i)   (0 != at[i].charge)
#define	ANY_RAD(i)   (RADICAL_SINGLET <= at[i].radical && at[i].radical <= RADICAL_TRIPLET)
#define	NORMAL_ISO(i, X)   (ANY_ISO(i, X) && !ABNORMAL_ISO(i))
#define	ABNORMAL_AT(i)
#define	ADD_LINE_AT(i)

Enumerations
enum	{   SDF_START , SDF_DATA_HEADER , SDF_DATA_HEADER_NAME , SDF_DATA_HEADER_COMMENT ,   SDF_DATA_HEADER_CAS , SDF_DATA_HEADER_USER , SDF_DATA_LINE , SD_FMT_END_OF_DATA_ITEM ,   SDF_EMPTY_LINE , SD_FMT_END_OF_DATA_BLOCK }

Functions
int	OrigAtData_WriteToSDfileHeaderAndCountThings (const ORIG_ATOM_DATA *inp_at_data, INCHI_IOSTREAM *fcb, const char *name, const char *comment, int bChiralFlag, int bAtomsDT, const char *szLabel, const char *szValue, int *nNumAliasLines, int *nNumChargeLines, int *nNumRadicalLines, int *nNumIsoLines, int *nNumAddLines, int *num_bonds)
int	OrigAtData_WriteToSDfileAtomsBlock (const ORIG_ATOM_DATA *inp_at_data, INCHI_IOSTREAM *fcb, const char *name, const char *comment, int bAtomsDT, const char *szLabel, const char *szValue)
int	OrigAtData_WriteToSDfileBondsBlock (const ORIG_ATOM_DATA *inp_at_data, INCHI_IOSTREAM *fcb, const char *name, const char *comment, const char *szLabel, const char *szValue, INT_ARRAY *written_bond_ends)
int	OrigAtData_WriteToSDfileAdditionalLines (const ORIG_ATOM_DATA *inp_at_data, INCHI_IOSTREAM *fcb, const char *name, const char *comment, int bAtomsDT, const char *szLabel, const char *szValue, int nNumAliasLines, int nNumChargeLines, int nNumRadicalLines, int nNumIsoLines, INT_ARRAY *written_bond_ends)
int	OrigAtData_WriteToSDfilePolymerData (const ORIG_ATOM_DATA *inp_at_data, INCHI_IOSTREAM *fcb, const char *name, const char *comment, const char *szLabel, const char *szValue, INT_ARRAY *written_bond_ends)
int	SDFileSkipExtraData (INCHI_IOSTREAM *inp_file, unsigned long *CAS_num, char *comment, int lcomment, char *name, int lname, int prev_err, const char *pSdfLabel, char *pSdfValue, char *pStrErr, int bNoWarnings)
	Skip extra data in SDF file after the MOL file data.
int	SDFileIdentifyLabel (char *inp_line, const char *pSdfLabel)
	Identify if the given line matches the specified SDF label.
unsigned long	SDFileExtractCASNo (char *line)
	Extract CAS number from the given line.
int	NumLists_Alloc (NUM_LISTS *num_lists, int nlists)
	Allocates memory for a specified number of numeric lists.
int	NumLists_ReAlloc (NUM_LISTS *num_lists)
	Reallocates memory for the numeric lists.
int	NumLists_Append (NUM_LISTS *num_lists, int *list)
	Push new item to the end of array.
void	NumLists_Free (NUM_LISTS *num_lists)
	Frees the memory allocated for the numeric list.
int	IntArray_Alloc (INT_ARRAY *items, int nitems)
	Initializes an INT_ARRAY structure.
int	IntArray_ReAlloc (INT_ARRAY *items)
	Reallocates memory for the INT_ARRAY structure.
int	IntArray_Append (INT_ARRAY *items, int new_item)
	Appends a new item to the INT_ARRAY structure.
int	IntArray_AppendIfAbsent (INT_ARRAY *items, int new_item)
	Appends a new item to the INT_ARRAY structure if it is not already present.
void	IntArray_DebugPrint (INT_ARRAY *items)
	Prints the contents of the INT_ARRAY structure for debugging purposes.
void	IntArray_Reset (INT_ARRAY *items)
	Resets the INT_ARRAY structure to its initial state.
void	IntArray_Free (INT_ARRAY *items)
	Frees the memory allocated for the INT_ARRAY structure.
int	MolFmtSgroup_Create (MOL_FMT_SGROUP **sgroup, int id, int type)
	Allocate new array Sgroup.
void	MolFmtSgroup_Free (MOL_FMT_SGROUP *sgroup)
	Frees the memory allocated for the Sgroup.
int	MolFmtSgroups_Alloc (MOL_FMT_SGROUPS *sgroups, int nsgroups)
	Allocates memory for a specified number of Sgroup objects.
int	MolFmtSgroups_ReAlloc (MOL_FMT_SGROUPS *sgroups)
	Expand array of Sgroups.
int	MolFmtSgroups_Append (MOL_FMT_SGROUPS *sgroups, int id, int type)
	Appends a new Sgroup to the array.
void	MolFmtSgroups_Free (MOL_FMT_SGROUPS *sgroups)
	Frees the memory allocated for the MOL_FMT_SGROUPS list.
int	MolFmtSgroups_GetIndexBySgroupId (int id, MOL_FMT_SGROUPS *sgroups)
	Gets the index of a Sgroup by its ID.
int	OrigAtData_WriteToSDfile (const ORIG_ATOM_DATA *inp_at_data, INCHI_IOSTREAM *fcb, const char *name, const char *comment, int bChiralFlag, int bAtomsDT, const char *szLabel, const char *szValue)
	Write original atom data to SD file.

Variables
static const char	sdf_data_hdr_name [] = "NAME"
static const char	sdf_data_hdr_comm [] = "COMMENT"

Macro Definition Documentation

ABNORMAL_AT

#define ABNORMAL_AT

(

i

)

Value:

                        (at[i].radical || abs(at[i].charge) > 3 || \
                        ABNORMAL_ISO(i))

ABNORMAL_CHG

#define ABNORMAL_CHG

(

i

)

(abs(at[i].charge) > 3)

ABNORMAL_ISO

#define ABNORMAL_ISO

(

i

)

(at[i].iso_atw_diff == 1 || at[i].iso_atw_diff < -3 || at[i].iso_atw_diff > 5)

ABNORMAL_RAD

#define ABNORMAL_RAD

(

i

)

(RADICAL_SINGLET <= at[i].radical && at[i].radical <= RADICAL_TRIPLET)

ADD_LINE_AT

#define ADD_LINE_AT

(

i

)

Value:

                        (at[i].charge ||  \
                        at[i].radical || \
                        at[i].iso_atw_diff && (bAtomsDT ? (at[i].iso_atw_diff != 1 || strcmp(at[i].elname, "H")) : 1))

ALIASED_AT

#define ALIASED_AT

(

i

)

(0 < NUM_ISO_H(at, i))

ANY_CHG

#define ANY_CHG

(

i

)

(0 != at[i].charge)

ANY_ISO

#define ANY_ISO	(		i,
			X
	)

Value:

                          ((X)? (at[i].iso_atw_diff && !IS_DEUTERIUM(i) && !IS_TRITIUM(i)) :\
                          (at[i].iso_atw_diff ||  IS_DEUTERIUM(i) ||  IS_TRITIUM(i)))

ANY_RAD

#define ANY_RAD

(

i

)

(RADICAL_SINGLET <= at[i].radical && at[i].radical <= RADICAL_TRIPLET)

IS_DEUTERIUM

#define IS_DEUTERIUM

(

i

)

(!strcmp(at[i].elname, "D") || at[i].iso_atw_diff == 2 && !strcmp(at[i].elname, "H"))

IS_TRITIUM

#define IS_TRITIUM

(

i

)

(!strcmp(at[i].elname, "T") || at[i].iso_atw_diff == 3 && !strcmp(at[i].elname, "H"))

NORMAL_ISO

#define NORMAL_ISO	(		i,
			X
	)		(ANY_ISO(i, X) && !ABNORMAL_ISO(i))

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
SDF_START
SDF_DATA_HEADER
SDF_DATA_HEADER_NAME
SDF_DATA_HEADER_COMMENT
SDF_DATA_HEADER_CAS
SDF_DATA_HEADER_USER
SDF_DATA_LINE
SD_FMT_END_OF_DATA_ITEM
SDF_EMPTY_LINE
SD_FMT_END_OF_DATA_BLOCK

Function Documentation

IntArray_Alloc()

int IntArray_Alloc	(	INT_ARRAY *	items,
		int	nitems
	)

Initializes an INT_ARRAY structure.

Parameters

items	Pointer to the INT_ARRAY structure to initialize.
nitems	Initial number of items to allocate.

Returns

0 on success, -1 on failure.

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IntArray_Append()

int IntArray_Append	(	INT_ARRAY *	items,
		int	new_item
	)

Appends a new item to the INT_ARRAY structure.

Parameters

items	Pointer to the INT_ARRAY structure to modify.
new_item	The new item to append.

Returns

0 on success, -1 on failure.

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IntArray_AppendIfAbsent()

int IntArray_AppendIfAbsent	(	INT_ARRAY *	items,
		int	new_item
	)

Appends a new item to the INT_ARRAY structure if it is not already present.

Parameters

items	Pointer to the INT_ARRAY structure to modify.
new_item	The new item to append.

Returns

0 on success, -1 on failure.

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IntArray_DebugPrint()

void IntArray_DebugPrint

(

INT_ARRAY *

items

)

Prints the contents of the INT_ARRAY structure for debugging purposes.

Parameters

items

Pointer to the INT_ARRAY structure to print.

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IntArray_Free()

void IntArray_Free

(

INT_ARRAY *

items

)

Frees the memory allocated for the INT_ARRAY structure.

Parameters

items

Pointer to the INT_ARRAY structure to free.

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IntArray_ReAlloc()

int IntArray_ReAlloc

(

INT_ARRAY *

items

)

Reallocates memory for the INT_ARRAY structure.

Parameters

items

Pointer to the INT_ARRAY structure to reallocate.

Returns

0 on success, -1 on failure.

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IntArray_Reset()

void IntArray_Reset

(

INT_ARRAY *

items

)

Resets the INT_ARRAY structure to its initial state.

Parameters

items

Pointer to the INT_ARRAY structure to reset.

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MolFmtSgroup_Create()

int MolFmtSgroup_Create	(	MOL_FMT_SGROUP **	sgroup,
		int	id,
		int	type
	)

Allocate new array Sgroup.

Parameters

sgroup	Pointer to the Sgroup structure to allocate.
id	Sgroup ID.
type	Sgroup type.

Returns

0 on success, -1 on failure.

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MolFmtSgroup_Free()

void MolFmtSgroup_Free

(

MOL_FMT_SGROUP *

sgroup

)

Frees the memory allocated for the Sgroup.

Parameters

sgroup

Pointer to the Sgroup structure to free.

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MolFmtSgroups_Alloc()

int MolFmtSgroups_Alloc	(	MOL_FMT_SGROUPS *	items,
		int	nitems
	)

Allocates memory for a specified number of Sgroup objects.

Parameters

items	Pointer to the MOL_FMT_SGROUPS structure.
nitems	Number of Sgroup objects to allocate.

Returns

0 on success, -1 on failure.

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MolFmtSgroups_Append()

int MolFmtSgroups_Append	(	MOL_FMT_SGROUPS *	items,
		int	id,
		int	type
	)

Appends a new Sgroup to the array.

Parameters

items	Pointer to the MOL_FMT_SGROUPS structure.
id	Sgroup ID.
type	Sgroup type.

Returns

0 on success, -1 on failure.

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MolFmtSgroups_Free()

void MolFmtSgroups_Free

(

MOL_FMT_SGROUPS *

items

)

Frees the memory allocated for the MOL_FMT_SGROUPS list.

Parameters

items

Pointer to the MOL_FMT_SGROUPS structure.

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MolFmtSgroups_GetIndexBySgroupId()

int MolFmtSgroups_GetIndexBySgroupId	(	int	id,
		MOL_FMT_SGROUPS *	items
	)

Gets the index of a Sgroup by its ID.

Parameters

id	Sgroup ID.
items	Pointer to the MOL_FMT_SGROUPS structure.

Returns

Index of the Sgroup on success, -1 on failure.

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MolFmtSgroups_ReAlloc()

int MolFmtSgroups_ReAlloc

(

MOL_FMT_SGROUPS *

items

)

Expand array of Sgroups.

Parameters

items

Pointer to the MOL_FMT_SGROUPS structure.

Returns

0 on success, -1 on failure.

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NumLists_Alloc()

int NumLists_Alloc	(	NUM_LISTS *	num_lists,
		int	nlists
	)

Allocates memory for a specified number of numeric lists.

Parameters

num_lists	Pointer to the NUM_LISTS structure.
nlists	Number of lists to allocate.

Returns

0 on success, -1 on failure.

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NumLists_Append()

int NumLists_Append	(	NUM_LISTS *	num_lists,
		int *	list
	)

Push new item to the end of array.

Parameters

num_lists	Pointer to the NUM_LISTS structure.
list	Pointer to the list of integers to append.

Returns

0 on success, -1 on failure.

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NumLists_Free()

void NumLists_Free

(

NUM_LISTS *

num_lists

)

Frees the memory allocated for the numeric list.

Parameters

num_lists

Pointer to the NUM_LISTS structure.

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NumLists_ReAlloc()

int NumLists_ReAlloc

(

NUM_LISTS *

num_lists

)

Reallocates memory for the numeric lists.

Parameters

num_lists

Pointer to the NUM_LISTS structure.

Returns

0 on success, -1 on failure.

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OrigAtData_WriteToSDfile()

int OrigAtData_WriteToSDfile	(	const ORIG_ATOM_DATA *	inp_at_data,
		INCHI_IOSTREAM *	fcb,
		const char *	name,
		const char *	comment,
		int	bChiralFlag,
		int	bAtomsDT,
		const char *	szLabel,
		const char *	szValue
	)

Write original atom data to SD file.

Parameters

inp_at_data	Pointer to original atom data structure
fcb	File stream to write to
name	Name of the structure
comment	Comment to include
bChiralFlag	Flag indicating for chiral information
bAtomsDT	Flag indicating how H isotopes (D/T) are represented in the SD output
szLabel	SDF label
szValue	SDF value

Returns

int Status code

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OrigAtData_WriteToSDfileAdditionalLines()

int OrigAtData_WriteToSDfileAdditionalLines	(	const ORIG_ATOM_DATA *	inp_at_data,
		INCHI_IOSTREAM *	fcb,
		const char *	name,
		const char *	comment,
		int	bAtomsDT,
		const char *	szLabel,
		const char *	szValue,
		int	nNumAliasLines,
		int	nNumChargeLines,
		int	nNumRadicalLines,
		int	nNumIsoLines,
		INT_ARRAY *	written_bond_ends
	)

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OrigAtData_WriteToSDfileAtomsBlock()

int OrigAtData_WriteToSDfileAtomsBlock	(	const ORIG_ATOM_DATA *	inp_at_data,
		INCHI_IOSTREAM *	fcb,
		const char *	name,
		const char *	comment,
		int	bAtomsDT,
		const char *	szLabel,
		const char *	szValue
	)

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OrigAtData_WriteToSDfileBondsBlock()

int OrigAtData_WriteToSDfileBondsBlock	(	const ORIG_ATOM_DATA *	inp_at_data,
		INCHI_IOSTREAM *	fcb,
		const char *	name,
		const char *	comment,
		const char *	szLabel,
		const char *	szValue,
		INT_ARRAY *	written_bond_ends
	)

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OrigAtData_WriteToSDfileHeaderAndCountThings()

int OrigAtData_WriteToSDfileHeaderAndCountThings	(	const ORIG_ATOM_DATA *	inp_at_data,
		INCHI_IOSTREAM *	fcb,
		const char *	name,
		const char *	comment,
		int	bChiralFlag,
		int	bAtomsDT,
		const char *	szLabel,
		const char *	szValue,
		int *	nNumAliasLines,
		int *	nNumChargeLines,
		int *	nNumRadicalLines,
		int *	nNumIsoLines,
		int *	nNumAddLines,
		int *	num_bonds
	)

Important: Atoms with alias cannot have charge, radical

isotope differences are allowed

Atoms with alias cannot be abnormal.

Abnormal atoms are atoms which need M CHG, M RAD, M ISO

Output aliased atoms if they have implicit D or T

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OrigAtData_WriteToSDfilePolymerData()

int OrigAtData_WriteToSDfilePolymerData	(	const ORIG_ATOM_DATA *	inp_at_data,
		INCHI_IOSTREAM *	fcb,
		const char *	name,
		const char *	comment,
		const char *	szLabel,
		const char *	szValue,
		INT_ARRAY *	written_bond_ends
	)

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SDFileExtractCASNo()

unsigned long SDFileExtractCASNo

(

char *

line

)

Extract CAS number from the given line.

Parameters

line	Pointer to the line containing the CAS number.

Returns

The extracted CAS number, or 0 if not found or invalid.

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SDFileIdentifyLabel()

int SDFileIdentifyLabel	(	char *	inp_line,
		const char *	pSdfLabel
	)

Identify if the given line matches the specified SDF label.

Parameters

inp_line	Pointer to the input line.
pSdfLabel	Pointer to the SDF label to match.

Returns

SDF_DATA_HEADER_USER: The label matches the user-specified label (pSdfLabel). SDF_DATA_HEADER_NAME: The label is "NAME". SDF_DATA_HEADER_COMMENT: The label is "COMMENT". SDF_DATA_HEADER_CAS: The label is "CAS". SDF_DATA_HEADER: The label does not match any of the above (default case).

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SDFileSkipExtraData()

int SDFileSkipExtraData	(	INCHI_IOSTREAM *	inp_file,
		unsigned long *	CAS_num,
		char *	comment,
		int	lcomment,
		char *	name,
		int	lname,
		int	prev_err,
		const char *	pSdfLabel,
		char *	pSdfValue,
		char *	pStrErr,
		int	bNoWarnings
	)

Skip extra data in SDF file after the MOL file data.

Parameters

inp_file	Pointer to the input file stream.
CAS_num	Pointer to the variable to store the CAS number.
comment	Pointer to the buffer to store the comment.
lcomment	Length of the comment buffer.
name	Pointer to the buffer to store the name.
lname	Length of the name buffer.
prev_err	Previous error code.
pSdfLabel	Pointer to the SDF label buffer.
pSdfValue	Pointer to the SDF value buffer.
pStrErr	Pointer to the error string buffer.
bNoWarnings	Flag indicating whether to suppress warnings.

Returns

0: Success; extra SDF data was skipped without errors. 3: Unexpected SData header line (unexpected contents or format). 5: Only blank lines encountered (all lines empty). 9: Error occurred, but successfully bypassed to the next structure ($$$$ marker found); non-fatal, warning issued. Other values: The function may propagate the value of prev_err if set before entering the loop.

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Variable Documentation

sdf_data_hdr_comm

const char sdf_data_hdr_comm[] = "COMMENT"

static

sdf_data_hdr_name

const char sdf_data_hdr_name[] = "NAME"

static