ichimake.c File Reference

#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <locale.h>
#include "mode.h"
#include "ichimake.h"
#include "inchi_api.h"
#include "ichimain.h"
#include "ichister.h"
#include "ichi_io.h"
#include "ichitime.h"
#include "ichi_bns.h"
#include "bcf_s.h"

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Data Structures
struct	tagOrderStruct

Macros
#define	nFirstFmlSegm   DIFS_f_FORMULA
#define	nFirstIsoSegm   DIFS_i_IATOMS

Typedefs
typedef enum tagSp3StereoTypeTmp	SP3_TYPE_TMP
typedef struct tagOrderStruct	OrderStruct

Enumerations
enum	tagSp3StereoTypeTmp {   SP3_NONE = 0 , SP3_ONLY = 1 , SP3_ABS = 2 , SP3_REL = 4 ,   SP3_RAC = 8 , SP3_TYPE = (SP3_ABS | SP3_REL | SP3_RAC) , SP3_ANY = (SP3_ABS | SP3_REL | SP3_RAC | SP3_ONLY) }

Functions
int	inp2spATOM (inp_ATOM *inp_at, int num_inp_at, sp_ATOM *at)
int	GetElementAndCount (const char **f, char *szEl, int *count)
int	CompareHillFormulas (const char *f1, const char *f2)
int	CompareInchiStereo (INChI_Stereo *Stereo1, INCHI_MODE nFlags1, INChI_Stereo *Stereo2, INCHI_MODE nFlags2)
int	CompareReversedStereoINChI (INChI_Stereo *s1, INChI_Stereo *s2)
int	GetAtomOrdNbrInCanonOrd (struct tagCANON_GLOBALS *pCG, inp_ATOM *norm_at, AT_NUMB *nAtomOrdNbr, AT_NUMB *nOrigAtNosInCanonOrd, int num_at)
int	FillOutCanonInfAtom (struct tagCANON_GLOBALS *pCG, inp_ATOM *norm_at, INF_ATOM_DATA *inf_norm_at_data, int init_num_at, int bIsotopic, INChI *pINChI, INChI_Aux *pINChI_Aux, int bAbcNumbers, INCHI_MODE nMode)
int	FillOutOneCanonInfAtom (struct tagCANON_GLOBALS *pCG, inp_ATOM *inp_norm_at, INF_ATOM_DATA *inf_norm_at_data, AT_NUMB *pStereoFlags, int init_num_at, int offset, int offset_H, int bIsotopic, INChI *pINChI, INChI_Aux *pINChI_Aux, int bAbcNumbers, INCHI_MODE nMode)
int	FillOutInputInfAtom (inp_ATOM *inp_at, INF_ATOM_DATA *inf_at_data, int init_num_at, int num_removed_H, int bAdd_DT_to_num_H, int nNumRemovedProtons, NUM_H *nNumRemovedProtonsIsotopic, int bIsotopic, int bAbcNumbers)
int	CheckCanonNumberingCorrectness (int num_atoms, int num_at_tg, sp_ATOM *at, CANON_STAT *pCS, CANON_GLOBALS *pCG, int bTautomeric, char *pStrErrStruct)
static int	CompareDfsDescendants4CT (const void *a1, const void *a2, void *)
int	GetSp3RelRacAbs (const INChI *pINChI, INChI_Stereo *Stereo)
int	CompareReversedStereoINChI2 (INChI_Stereo *s1, INChI_Stereo *s2, ICR *picr)
int	CompareHillFormulasNoH (const char *f1, const char *f2, int *num_H1, int *num_H2)
int	CompareTautNonIsoPartOfINChI (const INChI *i1, const INChI *i2)
int	CompINChITautVsNonTaut (const INCHI_SORT *p1, const INCHI_SORT *p2, int bCompareIsotopic)
	Compare tautomeric vs non-tautomeric information.
int	CompINChILayers (const INCHI_SORT *p1, const INCHI_SORT *p2, char sDifSegs[][DIFS_LENGTH], int bFixTranspChargeBug)
	Compare InChI layers.
int	INChI_SegmentAction (char cDifSegs)
	Action to take per segment (?)
int	MarkUnusedAndEmptyLayers (char sDifSegs[][DIFS_LENGTH])
	Mark unused and empty layers.
int	CompINChI2 (const INCHI_SORT *p1, const INCHI_SORT *p2, int bTaut, int bCompareIsotopic)
	Compares two INChI data structures (qsort)
int	CompINChINonTaut2 (const void *p1, const void *p2)
	Compare function for qsort (normal structure)
int	CompINChITaut2 (const void *p1, const void *p2)
	Compare function for qsort (tautomeric structures)
void	mystrrev (char *p)
	Reverse a string in place.
AT_NUMB *	GetDfsOrder4CT (CANON_GLOBALS *pCG, AT_NUMB *LinearCT, int nLenCT, S_CHAR *nNum_H, int num_atoms, int nCtMode)
int	GetInpStructErrorType (INPUT_PARMS *ip, int err, char *pStrErrStruct, int num_inp_atoms)
	Get the input struct error type.
int	ProcessStructError (INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *log_file, char *pStrErrStruct, int nErrorType, long num_inp, INPUT_PARMS *ip)
int	CompareReversedINChI (INChI *i1, INChI *i2, INChI_Aux *a1, INChI_Aux *a2)
	Compares two InChIs (1)
int	CompareIcr (ICR *picr1, ICR *picr2, INCHI_MODE *pin1, INCHI_MODE *pin2, INCHI_MODE mask)
	Compares results from InChI comparison.
INCHI_MODE	CompareReversedINChI2 (INChI *i1, INChI *i2, INChI_Aux *a1, INChI_Aux *a2, ICR *picr, int *err)
	Compares two InChIs (2)
int	Create_INChI (CANON_GLOBALS *pCG, INCHI_CLOCK *ic, INPUT_PARMS *ip, INChI **ppINChI, INChI_Aux **ppINChI_Aux, ORIG_ATOM_DATA *orig_inp_data, inp_ATOM *inp_at, INP_ATOM_DATA *out_norm_data[2], int num_inp_at, INCHI_MODE nUserMode, INCHI_MODE *pbTautFlags, INCHI_MODE *pbTautFlagsDone, struct tagInchiTime *ulMaxTime, T_GROUP_INFO *ti_out, char *pStrErrStruct)
	Create INChI.

Macro Definition Documentation

nFirstFmlSegm

#define nFirstFmlSegm   DIFS_f_FORMULA

nFirstIsoSegm

#define nFirstIsoSegm   DIFS_i_IATOMS

Typedef Documentation

OrderStruct

typedef struct tagOrderStruct OrderStruct

SP3_TYPE_TMP

typedef enum tagSp3StereoTypeTmp SP3_TYPE_TMP

Enumeration Type Documentation

tagSp3StereoTypeTmp

enum tagSp3StereoTypeTmp

Enumerator
SP3_NONE
SP3_ONLY
SP3_ABS
SP3_REL
SP3_RAC
SP3_TYPE
SP3_ANY

Function Documentation

CheckCanonNumberingCorrectness()

int CheckCanonNumberingCorrectness	(	int	num_atoms,
		int	num_at_tg,
		sp_ATOM *	at,
		CANON_STAT *	pCS,
		CANON_GLOBALS *	pCG,
		int	bTautomeric,
		char *	pStrErrStruct
	)

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CompareDfsDescendants4CT()

static int CompareDfsDescendants4CT ( const void *  a1, const void *  a2, void *  p  )

static

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CompareHillFormulas()

int CompareHillFormulas	(	const char *	f1,
		const char *	f2
	)

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CompareHillFormulasNoH()

int CompareHillFormulasNoH	(	const char *	f1,
		const char *	f2,
		int *	num_H1,
		int *	num_H2
	)

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CompareIcr()

int CompareIcr	(	ICR *	picr1,
		ICR *	picr2,
		INCHI_MODE *	pin1,
		INCHI_MODE *	pin2,
		INCHI_MODE	mask
	)

Compares results from InChI comparison.

Parameters

picr1	Pointer to first comparison results
picr2	Pointer to second comparison results
pin1	Pointer to first InChI mode (never used?)
pin2	Pointer to second InChI mode (never used?)
mask	Either IDIFF_CONSTIT or IDIFF_STEREO

Returns

* int 2 if undefined results, 1 if unequal, 0 if equal, -1 if unequal

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CompareInchiStereo()

int CompareInchiStereo	(	INChI_Stereo *	Stereo1,
		INCHI_MODE	nFlags1,
		INChI_Stereo *	Stereo2,
		INCHI_MODE	nFlags2
	)

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CompareReversedINChI()

int CompareReversedINChI	(	INChI *	i1,
		INChI *	i2,
		INChI_Aux *	a1,
		INChI_Aux *	a2
	)

Compares two InChIs (1)

Parameters

i1	Pointer to first InChI (InChI from reversed struct)
i2	Pointer to second InChI
a1	Pointer to first InChI AuxInfo
a2	Pointer to second InChI AuxInfo

Returns

int 0 if NULL, 1 if one is NULL, >1 if difference in structure

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CompareReversedINChI2()

INCHI_MODE CompareReversedINChI2	(	INChI *	i1,
		INChI *	i2,
		INChI_Aux *	a1,
		INChI_Aux *	a2,
		ICR *	picr,
		int *	err
	)

Compares two InChIs (2)

Parameters

i1	Pointer to first InChI (InChI from reversed struct)
i2	Pointer to second InChI
a1	Pointer to first InChI AuxInfo
a2	Pointer to second InChI AuxInfo
picr	Pointer to comparison results
err	Pointer to error code

Returns

INCHI_MODE Returns code from IDIF

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CompareReversedStereoINChI()

int CompareReversedStereoINChI	(	INChI_Stereo *	s1,
		INChI_Stereo *	s2
	)

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CompareReversedStereoINChI2()

int CompareReversedStereoINChI2	(	INChI_Stereo *	s1,
		INChI_Stereo *	s2,
		ICR *	picr
	)

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CompareTautNonIsoPartOfINChI()

int CompareTautNonIsoPartOfINChI	(	const INChI *	i1,
		const INChI *	i2
	)

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CompINChI2()

int CompINChI2	(	const INCHI_SORT *	p1,
		const INCHI_SORT *	p2,
		int	bTaut,
		int	bCompareIsotopic
	)

Compares two INChI data structures (qsort)

Parameters

p1	Pointer to the first INCHI_SORT data structure
p2	Pointer to the second INCHI_SORT data structure
bTaut	Flag for tautomeric comparison
bCompareIsotopic	Flag for isotopic comparison

Returns

int -1 if *p1 > *p2, return +1 if *p1 < *p2

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CompINChILayers()

int CompINChILayers	(	const INCHI_SORT *	p1,
		const INCHI_SORT *	p2,
		char	sDifSegs[][DIFS_LENGTH],
		int	bFixTranspChargeBug
	)

Compare InChI layers.

Parameters

p1	Pointer to InChI component 1
p2	Pointer to InChI component 2
sDifSegs	Array of different layers
bFixTranspChargeBug	Flag to fix charge bug (?)

Returns

int -1 if *p1 > *p2, return +1 if *p1 < *p2

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CompINChINonTaut2()

int CompINChINonTaut2	(	const void *	p1,
		const void *	p2
	)

Compare function for qsort (normal structure)

Parameters

p1	Pointer to first INCHI_SORT structure
p2	Pointer to second INCHI_SORT structure

Returns

int -1 if *p1 > *p2, return +1 if *p1 < *p2

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CompINChITaut2()

int CompINChITaut2	(	const void *	p1,
		const void *	p2
	)

Compare function for qsort (tautomeric structures)

Parameters

p1	Pointer to first INCHI_SORT structure
p2	Pointer to second INCHI_SORT structure

Returns

int -1 if *p1 > *p2, return +1 if *p1 < *p2

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CompINChITautVsNonTaut()

int CompINChITautVsNonTaut	(	const INCHI_SORT *	p1,
		const INCHI_SORT *	p2,
		int	bCompareIsotopic
	)

Compare tautomeric vs non-tautomeric information.

Parameters

p1	Pointer to the first INCHI_SORT data structure
p2	Pointer to the second INCHI_SORT data structure
bCompareIsotopic	Flag for comparing isotopic non-tautomeric part

Returns

int -1 if *p1 > *p2, return +1 if *p1 < *p2

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Create_INChI()

int Create_INChI	(	struct tagCANON_GLOBALS *	pCG,
		struct tagINCHI_CLOCK *	ic,
		INPUT_PARMS *	ip,
		INChI **	ppINChI,
		INChI_Aux **	ppINChI_Aux,
		ORIG_ATOM_DATA *	orig_inp_data,
		inp_ATOM *	inp_at,
		INP_ATOM_DATA *	inp_norm_data[2],
		int	num_inp_at,
		INCHI_MODE	nUserMode,
		INCHI_MODE *	pbTautFlags,
		INCHI_MODE *	pbTautFlagsDone,
		struct tagInchiTime *	ulMaxTime,
		struct tagTautomerGroupsInfo *	ti_out,
		char *	pStrErrStruct
	)

Create INChI.

Parameters

pCG	Pointer to canonicalization globals data structure
ic	Pointer to InChI clock data structure
ip	Pointer to input parameters
ppINChI	Pointer to INChI data structure
ppINChI_Aux	Pointer to AuxInfo data structure
orig_inp_data	Pointer to original atom data
inp_at	Pointer to atom array
inp_norm_data	Pointer to normalized atom data
num_inp_at	Number of atoms
nUserMode	User mode
pbTautFlags	Tautomer flags
pbTautFlagsDone	Tautomer flags completed
ulMaxTime	Maximum time
ti_out	Tautomer info
pStrErrStruct	Store error or warning messages

Returns

int Status code

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FillOutCanonInfAtom()

int FillOutCanonInfAtom	(	struct tagCANON_GLOBALS *	pCG,
		inp_ATOM *	norm_at,
		INF_ATOM_DATA *	inf_norm_at_data,
		int	init_num_at,
		int	bIsotopic,
		INChI *	pINChI,
		INChI_Aux *	pINChI_Aux,
		int	bAbcNumbers,
		INCHI_MODE	nMode
	)

FillOutInputInfAtom()

int FillOutInputInfAtom	(	inp_ATOM *	inp_at,
		INF_ATOM_DATA *	inf_at_data,
		int	init_num_at,
		int	num_removed_H,
		int	bAdd_DT_to_num_H,
		int	nNumRemovedProtons,
		NUM_H *	nNumRemovedProtonsIsotopic,
		int	bIsotopic,
		int	bAbcNumbers
	)

FillOutOneCanonInfAtom()

int FillOutOneCanonInfAtom	(	struct tagCANON_GLOBALS *	pCG,
		inp_ATOM *	inp_norm_at,
		INF_ATOM_DATA *	inf_norm_at_data,
		AT_NUMB *	pStereoFlags,
		int	init_num_at,
		int	offset,
		int	offset_H,
		int	bIsotopic,
		INChI *	pINChI,
		INChI_Aux *	pINChI_Aux,
		int	bAbcNumbers,
		INCHI_MODE	nMode
	)

GetAtomOrdNbrInCanonOrd()

int GetAtomOrdNbrInCanonOrd	(	struct tagCANON_GLOBALS *	pCG,
		inp_ATOM *	norm_at,
		AT_NUMB *	nAtomOrdNbr,
		AT_NUMB *	nOrigAtNosInCanonOrd,
		int	num_at
	)

GetDfsOrder4CT()

AT_NUMB * GetDfsOrder4CT	(	CANON_GLOBALS *	pCG,
		AT_NUMB *	LinearCT,
		int	nLenCT,
		S_CHAR *	nNum_H,
		int	num_atoms,
		int	nCtMode
	)

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GetElementAndCount()

int GetElementAndCount	(	const char **	f,
		char *	szEl,
		int *	count
	)

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GetInpStructErrorType()

int GetInpStructErrorType	(	INPUT_PARMS *	ip,
		int	err,
		char *	pStrErrStruct,
		int	num_inp_atoms
	)

Get the input struct error type.

Parameters

ip	Pointer to input parameters
err	Error code
pStrErrStruct	Pointer to error string
num_inp_atoms	Number of input atoms

Returns

int Returns type of error

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GetSp3RelRacAbs()

int GetSp3RelRacAbs	(	const INChI *	pINChI,
		INChI_Stereo *	Stereo
	)

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INChI_SegmentAction()

int INChI_SegmentAction

(

char

cDifSegs

)

Action to take per segment (?)

Parameters

cDifSegs

Segment bits

Returns

int Type of segment action (INCHI_SEGM_OMIT, INCHI_SEGM_EMPTY, INCHI_SEGM_FILL)

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inp2spATOM()

int inp2spATOM	(	inp_ATOM *	inp_at,
		int	num_inp_at,
		sp_ATOM *	at
	)

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MarkUnusedAndEmptyLayers()

int MarkUnusedAndEmptyLayers

(

char

sDifSegs[][DIFS_LENGTH]

)

Mark unused and empty layers.

Parameters

sDifSegs

Array of different layers

Returns

int returns 0

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mystrrev()

void mystrrev

(

char *

p

)

Reverse a string in place.

Parameters

p	Pointer to the string to reverse

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ProcessStructError()

int ProcessStructError	(	INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	log_file,
		char *	pStrErrStruct,
		int	nErrorType,
		long	num_inp,
		INPUT_PARMS *	ip
	)

Parameters

out_file	Pointer to output file
log_file	Pointer to log file
pStrErrStruct	Pointer to error string
nErrorType	Error type
num_inp	Number of input structure (?)
ip	Pointer to input parameters

Returns

int Retunrs error type

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