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)
int	SDFileIdentifyLabel (char *inp_line, const char *pSdfLabel)
unsigned long	SDFileExtractCASNo (char *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)

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
	)

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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

)

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SDFileIdentifyLabel()

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

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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
	)

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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