ichirvr2.c File Reference

#include <stdlib.h>
#include <string.h>
#include "mode.h"
#include "ichister.h"
#include "ichirvrs.h"
#include "bcf_s.h"

Include dependency graph for ichirvr2.c:

Data Structures
struct	tagMobileHGroups
struct	tagMobileGroupList

Macros
#define	FIX_BOND_ADD_ALLOC   128
#define	INC_EDGE_LIST   16
#define	INC_EDGE_LIST   16
#define	INC_EDGE_LIST   16
#define	IS_C(x)   (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1)

Typedefs
typedef struct tagMobileHGroups	MOBILE_GR
typedef struct tagMobileGroupList	MGROUPS

Functions
void	CopyAt2St (inp_ATOM *at, inp_ATOM_STEREO *st, int num_atoms)
void	CopySt2At (inp_ATOM *at, inp_ATOM_STEREO *st, int num_atoms)
int	RestoreAtomConnectionsSetStereo (StrFromINChI *pStruct, int iComponent, int iAtNoOffset, INChI *pInChI, INChI *pInChIMobH)
int	SetStereoBondTypeFor0DParity (inp_ATOM *at, int i1, int m1)
int	SetStereoBondTypesFrom0DStereo (StrFromINChI *pStruct, INChI *pInChI)
int	CopyBnsToAtom (StrFromINChI *pStruct, BN_STRUCT *pBNS, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, int bAllowZeroBondOrder)
int	CheckBnsConsistency (StrFromINChI *pStruct, BN_STRUCT *pBNS, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, int bNoRad)
int	AddExplicitDeletedH (inp_ATOM *at, int jv, int num_at, int *iDeletedH, int *iH, int nNumDeletedH, int bTwoStereo)
int	bFindCumuleneChain (inp_ATOM *at, AT_NUMB i1, AT_NUMB i2, AT_NUMB nCumulene[], int nMaxLen)
int	set_bond_type (inp_ATOM *at, AT_NUMB i1, AT_NUMB i2, int bType)
int	set_cumulene_0D_parity (inp_ATOM *at, inp_ATOM_STEREO *st, int num_at, int idelH1, int i1, int i2, int idelH2, int parity, int len)
int	set_atom_0D_parity (inp_ATOM *at, inp_ATOM_STEREO *st, int num_at, int num_deleted_H, int i1, int parity)
int	MoveRadToAtomsAddCharges (BN_STRUCT *pBNS, BN_DATA *pBD, StrFromINChI *pStruct, inp_ATOM *at, inp_ATOM *at2, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, int forbidden_mask)
int	AdjustTgroupsToForbiddenEdges2 (BN_STRUCT *pBNS, inp_ATOM *at, VAL_AT *pVA, int num_atoms, int forbidden_mask)
int	RearrangePlusMinusEdgesFlow (BN_STRUCT *pBNS, BN_DATA *pBD, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, int forbidden_edge_mask)
int	IncrementZeroOrderBondsToHeteroat (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	MovePlusFromS2DiaminoCarbon (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	EliminateChargeSeparationOnHeteroatoms (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 forbidden_stereo_edge_mask)
int	RestoreCyanoGroup (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	RestoreIsoCyanoGroup (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	FixMetal_Nminus_Ominus (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	RestoreNNNgroup (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	EliminateNitrogen5Val3Bonds (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	Convert_SIV_to_SVI (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	PlusFromDB_N_DB_O_to_Metal (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	MoveMobileHToAvoidFixedBonds (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	RemoveRadFromMobileHEndpoint (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	RemoveRadFromMobileHEndpointFixH (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	MoveChargeToMakeCenerpoints (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)

Macro Definition Documentation

FIX_BOND_ADD_ALLOC

#define FIX_BOND_ADD_ALLOC   128

INC_EDGE_LIST [1/3]

#define INC_EDGE_LIST   16

INC_EDGE_LIST [2/3]

#define INC_EDGE_LIST   16

INC_EDGE_LIST [3/3]

#define INC_EDGE_LIST   16

IS_C

#define IS_C

(

x

)

(NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1)

Typedef Documentation

MGROUPS

typedef struct tagMobileGroupList MGROUPS

MOBILE_GR

typedef struct tagMobileHGroups MOBILE_GR

Function Documentation

AddExplicitDeletedH()

int AddExplicitDeletedH	(	inp_ATOM *	at,
		int	jv,
		int	num_at,
		int *	iDeletedH,
		int *	iH,
		int	nNumDeletedH,
		int	bTwoStereo
	)

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AdjustTgroupsToForbiddenEdges2()

int AdjustTgroupsToForbiddenEdges2	(	BN_STRUCT *	pBNS,
		inp_ATOM *	at,
		VAL_AT *	pVA,
		int	num_atoms,
		int	forbidden_mask
	)

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bFindCumuleneChain()

int bFindCumuleneChain	(	inp_ATOM *	at,
		AT_NUMB	i1,
		AT_NUMB	i2,
		AT_NUMB	nCumulene[],
		int	nMaxLen
	)

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CheckBnsConsistency()

int CheckBnsConsistency	(	StrFromINChI *	pStruct,
		BN_STRUCT *	pBNS,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int	bNoRad
	)

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Convert_SIV_to_SVI()

int Convert_SIV_to_SVI	(	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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CopyAt2St()

void CopyAt2St	(	inp_ATOM *	at,
		inp_ATOM_STEREO *	st,
		int	num_atoms
	)

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CopyBnsToAtom()

int CopyBnsToAtom	(	StrFromINChI *	pStruct,
		BN_STRUCT *	pBNS,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int	bAllowZeroBondOrder
	)

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CopySt2At()

void CopySt2At	(	inp_ATOM *	at,
		inp_ATOM_STEREO *	st,
		int	num_atoms
	)

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EliminateChargeSeparationOnHeteroatoms()

int EliminateChargeSeparationOnHeteroatoms	(	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	forbidden_stereo_edge_mask
	)

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EliminateNitrogen5Val3Bonds()

int EliminateNitrogen5Val3Bonds	(	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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FixMetal_Nminus_Ominus()

int FixMetal_Nminus_Ominus	(	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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IncrementZeroOrderBondsToHeteroat()

int IncrementZeroOrderBondsToHeteroat	(	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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MoveChargeToMakeCenerpoints()

int MoveChargeToMakeCenerpoints	(	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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MoveMobileHToAvoidFixedBonds()

int MoveMobileHToAvoidFixedBonds	(	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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MovePlusFromS2DiaminoCarbon()

int MovePlusFromS2DiaminoCarbon	(	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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MoveRadToAtomsAddCharges()

int MoveRadToAtomsAddCharges	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		inp_ATOM *	at2,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int	forbidden_mask
	)

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PlusFromDB_N_DB_O_to_Metal()

int PlusFromDB_N_DB_O_to_Metal	(	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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RearrangePlusMinusEdgesFlow()

int RearrangePlusMinusEdgesFlow	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int	forbidden_edge_mask
	)

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RemoveRadFromMobileHEndpoint()

int RemoveRadFromMobileHEndpoint	(	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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RemoveRadFromMobileHEndpointFixH()

int RemoveRadFromMobileHEndpointFixH	(	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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RestoreAtomConnectionsSetStereo()

int RestoreAtomConnectionsSetStereo	(	StrFromINChI *	pStruct,
		int	iComponent,
		int	iAtNoOffset,
		INChI *	pInChI,
		INChI *	pInChIMobH
	)

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RestoreCyanoGroup()

int RestoreCyanoGroup	(	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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RestoreIsoCyanoGroup()

int RestoreIsoCyanoGroup	(	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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RestoreNNNgroup()

int RestoreNNNgroup	(	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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set_atom_0D_parity()

int set_atom_0D_parity	(	inp_ATOM *	at,
		inp_ATOM_STEREO *	st,
		int	num_at,
		int	num_deleted_H,
		int	i1,
		int	parity
	)

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set_bond_type()

int set_bond_type	(	inp_ATOM *	at,
		AT_NUMB	i1,
		AT_NUMB	i2,
		int	bType
	)

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set_cumulene_0D_parity()

int set_cumulene_0D_parity	(	inp_ATOM *	at,
		inp_ATOM_STEREO *	st,
		int	num_at,
		int	idelH1,
		int	i1,
		int	i2,
		int	idelH2,
		int	parity,
		int	len
	)

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SetStereoBondTypeFor0DParity()

int SetStereoBondTypeFor0DParity	(	inp_ATOM *	at,
		int	i1,
		int	m1
	)

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SetStereoBondTypesFrom0DStereo()

int SetStereoBondTypesFrom0DStereo	(	StrFromINChI *	pStruct,
		INChI *	pInChI
	)

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