ichirvr4.c File Reference

#include <string.h>
#include "mode.h"
#include "ichitime.h"
#include "ichirvrs.h"
#include "ichicant.h"
#include "ichi_io.h"
#include "ichimake.h"
#include "bcf_s.h"

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Macros
#define	MAX_NUM_CARBON_CHARGE_EDGES   2

Functions
int	ForbidCarbonChargeEdges (BN_STRUCT *pBNS, ALL_TC_GROUPS *pTCGroups, EDGE_LIST *pCarbonChargeEdges, int forbidden_edge_mask)
int	ForbidNintrogenPlus2BondsInSmallRings (BN_STRUCT *pBNS, inp_ATOM *at, int num_at, VAL_AT *pVA, int min_ring_size, ALL_TC_GROUPS *pTCGroups, EDGE_LIST *pNplus2BondsEdges, int forbidden_edge_mask)
int	FixLessHydrogenInFormula (BN_STRUCT *pBNS, BN_DATA *pBD, StrFromINChI *pStruct, inp_ATOM *at, inp_ATOM *at2, inp_ATOM *atf, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, int *pnNumRunBNS, int *pnTotalDelta, int forbidden_edge_mask)
int	FixMoreHydrogenInFormula (BN_STRUCT *pBNS, BN_DATA *pBD, StrFromINChI *pStruct, inp_ATOM *at, inp_ATOM *at2, inp_ATOM *atf, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, int *pnNumRunBNS, int *pnTotalDelta, int forbidden_edge_mask)
int	FixRemoveExtraTautEndpoints (BN_STRUCT *pBNS, BN_DATA *pBD, StrFromINChI *pStruct, inp_ATOM *at, inp_ATOM *at2, inp_ATOM *atf, inp_ATOM *atn, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, ICR *picr, int *pnNumRunBNS, int *pnTotalDelta, int forbidden_edge_mask)
int	FillOutExtraFixedHDataRestr (StrFromINChI *pStruct)
int	FillOutExtraFixedHDataInChI (StrFromINChI *pStruct, INChI *pInChI[])
int	FillOutCMP2FHINCHI (StrFromINChI *pStruct, inp_ATOM *at2, VAL_AT *pVA, INChI *pInChI[], CMP2FHINCHI *pc2i)
int	FillOutCMP2MHINCHI (StrFromINChI *pStruct, ALL_TC_GROUPS *pTCGroups, inp_ATOM *at2, VAL_AT *pVA, INChI *pInChI[], CMP2MHINCHI *pc2i)
int	NormalizeAndCompare (CANON_GLOBALS *pCG, INCHI_CLOCK *ic, ICHICONST INPUT_PARMS *ip, STRUCT_DATA *sd, BN_STRUCT *pBNS, BN_DATA *pBD, StrFromINChI *pStruct, inp_ATOM *at, inp_ATOM *at2, inp_ATOM *at3, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, INChI *pInChI[], long num_inp, int bHasSomeFixedH, int *pnNumRunBNS, int *pnTotalDelta, int forbidden_edge_mask, int forbidden_stereo_edge_mask)
int	CheckAndRefixStereobonds (BN_STRUCT *pBNS, BN_DATA *pBD, StrFromINChI *pStruct, inp_ATOM *at, inp_ATOM *at2, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, int *pnNumRunBNS, int *pnTotalDelta, int forbidden_edge_mask)
int	MoveChargeToRemoveCenerpoints (BN_STRUCT *pBNS, BN_DATA *pBD, StrFromINChI *pStruct, inp_ATOM *at, inp_ATOM *at2, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, int *pnNumRunBNS, int *pnTotalDelta, int forbidden_edge_mask)
int	MakeSingleBondsMetal2ChargedHeteroat (BN_STRUCT *pBNS, BN_DATA *pBD, StrFromINChI *pStruct, inp_ATOM *at, inp_ATOM *at2, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, int *pnNumRunBNS, int *pnTotalDelta, int forbidden_edge_mask)
int	SaltBondsToCoordBonds (BN_STRUCT *pBNS, BN_DATA *pBD, StrFromINChI *pStruct, inp_ATOM *at, inp_ATOM *at2, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, int *pnNumRunBNS, int *pnTotalDelta, int forbidden_edge_mask)
int	RunBnsRestore1 (CANON_GLOBALS *pCG, INCHI_CLOCK *ic, ICHICONST INPUT_PARMS *ip, STRUCT_DATA *sd, BN_STRUCT *pBNS, BN_DATA *pBD, StrFromINChI *pStruct, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, INChI *pInChI[], long num_inp, int bHasSomeFixedH)
int	RestoreAtomMakeBNS (INCHI_CLOCK *ic, CANON_GLOBALS *pCG, ICHICONST INPUT_PARMS *ip, STRUCT_DATA *sd, StrFromINChI *pStruct, int iComponent, int iAtNoOffset, INChI *pInChI[], const char *szCurHdr, long num_inp, int bHasSomeFixedH)
int	OneInChI2Atom (INCHI_CLOCK *ic, CANON_GLOBALS *pCG, ICHICONST INPUT_PARMS *ip_inp, STRUCT_DATA *sd, const char *szCurHdr, long num_inp, StrFromINChI *pStruct, int iComponent, int iAtNoOffset, int bHasSomeFixedH, INChI *pInChI[])
int	MakeProtonComponent (StrFromINChI *pStruct, int iComponent, int num_prot)
int	AddRemProtonsInRestrStruct (INCHI_CLOCK *ic, CANON_GLOBALS *pCG, ICHICONST INPUT_PARMS *ip_inp, STRUCT_DATA *sd, long num_inp, int bHasSomeFixedH, StrFromINChI *pStruct, int num_components, StrFromINChI *pStructR, int num_componentsR, NUM_H *nProtonsToBeRemovedByNormFromRevrs, int *recmet_change_balance)
int	AddRemIsoProtonsInRestrStruct (INCHI_CLOCK *ic, CANON_GLOBALS *pCG, ICHICONST INPUT_PARMS *ip_inp, STRUCT_DATA *sd, long num_inp, int bHasSomeFixedH, StrFromINChI *pStruct, int num_components, StrFromINChI *pStructR, int num_componentsR, NUM_H pProtonBalance[], NUM_H recmet_change_balance[])

Macro Definition Documentation

MAX_NUM_CARBON_CHARGE_EDGES

#define MAX_NUM_CARBON_CHARGE_EDGES   2

Function Documentation

AddRemIsoProtonsInRestrStruct()

int AddRemIsoProtonsInRestrStruct	(	INCHI_CLOCK *	ic,
		CANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip_inp,
		STRUCT_DATA *	sd,
		long	num_inp,
		int	bHasSomeFixedH,
		StrFromINChI *	pStruct,
		int	num_components,
		StrFromINChI *	pStructR,
		int	num_componentsR,
		NUM_H	pProtonBalance[],
		NUM_H	recmet_change_balance[]
	)

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AddRemProtonsInRestrStruct()

int AddRemProtonsInRestrStruct	(	INCHI_CLOCK *	ic,
		CANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip_inp,
		STRUCT_DATA *	sd,
		long	num_inp,
		int	bHasSomeFixedH,
		StrFromINChI *	pStruct,
		int	num_components,
		StrFromINChI *	pStructR,
		int	num_componentsR,
		NUM_H *	nProtonsToBeRemovedByNormFromRevrs,
		int *	recmet_change_balance
	)

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CheckAndRefixStereobonds()

int CheckAndRefixStereobonds	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		inp_ATOM *	at2,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int *	pnNumRunBNS,
		int *	pnTotalDelta,
		int	forbidden_edge_mask
	)

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FillOutCMP2FHINCHI()

int FillOutCMP2FHINCHI	(	StrFromINChI *	pStruct,
		inp_ATOM *	at2,
		VAL_AT *	pVA,
		INChI *	pInChI[],
		CMP2FHINCHI *	pc2i
	)

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FillOutCMP2MHINCHI()

int FillOutCMP2MHINCHI	(	StrFromINChI *	pStruct,
		ALL_TC_GROUPS *	pTCGroups,
		inp_ATOM *	at2,
		VAL_AT *	pVA,
		INChI *	pInChI[],
		CMP2MHINCHI *	pc2i
	)

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FillOutExtraFixedHDataInChI()

int FillOutExtraFixedHDataInChI	(	StrFromINChI *	pStruct,
		INChI *	pInChI[]
	)

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FillOutExtraFixedHDataRestr()

int FillOutExtraFixedHDataRestr

(

StrFromINChI *

pStruct

)

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FixLessHydrogenInFormula()

int FixLessHydrogenInFormula	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		inp_ATOM *	at2,
		inp_ATOM *	atf,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int *	pnNumRunBNS,
		int *	pnTotalDelta,
		int	forbidden_edge_mask
	)

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FixMoreHydrogenInFormula()

int FixMoreHydrogenInFormula	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		inp_ATOM *	at2,
		inp_ATOM *	atf,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int *	pnNumRunBNS,
		int *	pnTotalDelta,
		int	forbidden_edge_mask
	)

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FixRemoveExtraTautEndpoints()

int FixRemoveExtraTautEndpoints	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		inp_ATOM *	at2,
		inp_ATOM *	atf,
		inp_ATOM *	atn,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		ICR *	picr,
		int *	pnNumRunBNS,
		int *	pnTotalDelta,
		int	forbidden_edge_mask
	)

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ForbidCarbonChargeEdges()

int ForbidCarbonChargeEdges	(	BN_STRUCT *	pBNS,
		ALL_TC_GROUPS *	pTCGroups,
		EDGE_LIST *	pCarbonChargeEdges,
		int	forbidden_edge_mask
	)

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ForbidNintrogenPlus2BondsInSmallRings()

int ForbidNintrogenPlus2BondsInSmallRings	(	BN_STRUCT *	pBNS,
		inp_ATOM *	at,
		int	num_at,
		VAL_AT *	pVA,
		int	min_ring_size,
		ALL_TC_GROUPS *	pTCGroups,
		EDGE_LIST *	pNplus2BondsEdges,
		int	forbidden_edge_mask
	)

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MakeProtonComponent()

int MakeProtonComponent	(	StrFromINChI *	pStruct,
		int	iComponent,
		int	num_prot
	)

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MakeSingleBondsMetal2ChargedHeteroat()

int MakeSingleBondsMetal2ChargedHeteroat	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		inp_ATOM *	at2,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int *	pnNumRunBNS,
		int *	pnTotalDelta,
		int	forbidden_edge_mask
	)

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MoveChargeToRemoveCenerpoints()

int MoveChargeToRemoveCenerpoints	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		inp_ATOM *	at2,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int *	pnNumRunBNS,
		int *	pnTotalDelta,
		int	forbidden_edge_mask
	)

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NormalizeAndCompare()

int NormalizeAndCompare	(	CANON_GLOBALS *	pCG,
		INCHI_CLOCK *	ic,
		ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		inp_ATOM *	at2,
		inp_ATOM *	at3,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		INChI *	pInChI[],
		long	num_inp,
		int	bHasSomeFixedH,
		int *	pnNumRunBNS,
		int *	pnTotalDelta,
		int	forbidden_edge_mask,
		int	forbidden_stereo_edge_mask
	)

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OneInChI2Atom()

int OneInChI2Atom	(	INCHI_CLOCK *	ic,
		CANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip_inp,
		STRUCT_DATA *	sd,
		const char *	szCurHdr,
		long	num_inp,
		StrFromINChI *	pStruct,
		int	iComponent,
		int	iAtNoOffset,
		int	bHasSomeFixedH,
		INChI *	pInChI[]
	)

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RestoreAtomMakeBNS()

int RestoreAtomMakeBNS	(	INCHI_CLOCK *	ic,
		CANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		StrFromINChI *	pStruct,
		int	iComponent,
		int	iAtNoOffset,
		INChI *	pInChI[],
		const char *	szCurHdr,
		long	num_inp,
		int	bHasSomeFixedH
	)

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RunBnsRestore1()

int RunBnsRestore1	(	CANON_GLOBALS *	pCG,
		INCHI_CLOCK *	ic,
		ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		StrFromINChI *	pStruct,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		INChI *	pInChI[],
		long	num_inp,
		int	bHasSomeFixedH
	)

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SaltBondsToCoordBonds()

int SaltBondsToCoordBonds	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		inp_ATOM *	at2,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int *	pnNumRunBNS,
		int *	pnTotalDelta,
		int	forbidden_edge_mask
	)

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