#include "ichimain.h"
#include "ichiring.h"

Include dependency graph for ichirvrs.h:

This graph shows which files directly or indirectly include this file:

Data Structures
struct	tagXYZCoord

struct	tagStructRestoreMode

struct	tagReversedInChI

struct	tagBfsQueue

struct	tagInpAtomAddParities

struct	tagAtomIonPrperies

struct	tagTCGroup

struct	tagAllTCGroups

struct	tagEdgeList

struct	tagChargeValence

struct	tagChargeChangeCandidate

struct	tagOneComponentRemovedAndExchangeableH

struct	tagRemovedAndExchangeableH

struct	tagInputInChI

struct	tagStructFromInChI

struct	tagVertCapFlow

struct	tagEdgeCapFlow

struct	tagChargeNodes

struct	tagChargeNodeList

struct	tagAtomsCmpTwoFixedH

struct	tagStructCmpTwoFixedH

struct	tagAtomsCmpTwoMobileH

struct	tagStructCmpTwoMobileH

Macros
#define	ICHICONST const

#define	RI_ERR_ALLOC (-1)

#define	RI_ERR_SYNTAX (-2)

#define	RI_ERR_PROGR (-3)

#define	RI_ERR_EOL (-4)

#define	RI_ERR_EOF (0)

#define	RI_ERR_MISMATCH (-9)

#define	NO_VALUE_INT 9999

#define	NOT_READ_INT 9998 /* has not been read yet */

#define	VALUE_OCTET 8 /* number of electrons in a full shell */

#define	INC_EDGE_LIST_DEFAULT 64

#define	BFS_Q_CLEAR (-1)

#define	BFS_Q_FREE (-2)

#define	EXTRACT_STRUCT_NUMBER 1

#define	FIX_STEREO_BOND_ORDER 0 /* 1=> fix stereobonds; treat metal as non-metal if it is stereogenic or has a stereobond */

#define	METAL_FREE_CHARGE_VAL 1 /* 1=> allow free changing charges/valences of metals; initial bond order=0 or 1 */

#define	ALLOW_METAL_BOND_ZERO 1 /* 1=> allow zero flow (bobd order) to metals */

#define	INIT_METAL_BOND_ZERO 0 /* 1=> initialize zero order bond to metals */

#define	INIT_METAL_BOND_FLOW 1 /* 1=> init flow=1, 0 => init. flow = 0 */

#define	I2A_FLAG_FIXEDH 0x0001

#define	I2A_FLAG_RECMET 0x0002

#define	ATYPE_H 1

#define	ATYPE_Na 2

#define	ATYPE_Mg 3

#define	ATYPE_B 4

#define	ATYPE_C 5

#define	ATYPE_N 6

#define	ATYPE_O 7

#define	ATYPE_Cl 8

#define	VAL_BASE ( 1)

#define	VAL_MIN_CHARGE (-1)

#define	VAL_MAX_CHARGE ( 1)

#define	VAL_NUMBER ( 2)

#define	VAL_NEUTR_ORDER (VAL_MAX_CHARGE-VAL_MIN_CHARGE+1)

#define	VAL_LENGTH (VAL_NEUTR_ORDER+1)

#define	VAL_NEGAT_CHARGE 0

#define	VAL_NEUTR_CHARGE 1

#define	VAL_POSIT_CHARGE 2

#define	INI_NUM_TCGROUPS 16

#define	INC_NUM_TCGROUPS 16

#define	EDGE_LIST_CLEAR (-1)

#define	EDGE_LIST_FREE (-2)

#define	BOND_MARK_STEREO 0x10

#define	BOND_TYPE_STEREO (BOND_TYPE_SINGLE \| BOND_MARK_STEREO)

#define	RESET_EDGE_FORBIDDEN_MASK 0

#define	TREAT_ATOM_AS_METAL 99

#define	MY_CONST const

#define	EL_TYPE_O 0x0001

#define	EL_TYPE_S 0x0002

#define	EL_TYPE_N 0x0004

#define	EL_TYPE_P 0x0008

#define	EL_TYPE_C 0x0010

#define	EL_TYPE_X 0x0020 /* any not metal */

#define	EL_TYPE_MASK 0x003f

#define	EL_TYPE_OSt 0x0100 /* terminal -OH, -O(-), -SH, -S(-), ... from fix_special_bonds(...) */

#define	EL_TYPE_PT 0x0200 /* may be a tautomeric endpoint */

#define	MAX_CN_VAL 3

#define	cn_bits_N 1 /* Neutral: charge = 0 */

#define	cn_bits_P 2 /* Plus 1: charge = +1 */

#define	cn_bits_M 4 /* Minus 1: charge = -1 */

#define	cn_bits_shift 3

#define	MAX_NUM_CN_BITS 4

#define	MAKE_CN_BITS(A, B, C, D) (( (( ((D) << cn_bits_shift \| (C)) << cn_bits_shift ) \| (B)) << cn_bits_shift ) \| (A))

#define	cn_bits_PNPN MAKE_CN_BITS(cn_bits_P, cn_bits_N, cn_bits_P, cn_bits_N)

#define	cn_bits_NPNP MAKE_CN_BITS(cn_bits_N, cn_bits_P, cn_bits_N, cn_bits_P)

#define	cn_bits_NPN MAKE_CN_BITS(cn_bits_N, cn_bits_P, cn_bits_N, 0)

#define	cn_bits_PNP MAKE_CN_BITS(cn_bits_P, cn_bits_N, cn_bits_P, 0)

#define	cn_bits_MNP MAKE_CN_BITS(cn_bits_M, cn_bits_N, cn_bits_P, 0)

#define	cn_bits_PNM MAKE_CN_BITS(cn_bits_P, cn_bits_N, cn_bits_M, 0)

#define	cn_bits_EN MAKE_CN_BITS(cn_bits_P \| cn_bits_M, cn_bits_N, 0, 0)

#define	cn_bits_NMN MAKE_CN_BITS(cn_bits_N, cn_bits_M, cn_bits_N, 0)

#define	cn_bits_NE MAKE_CN_BITS(cn_bits_N, cn_bits_P \| cn_bits_M, 0, 0)

#define	cn_bits_NEN MAKE_CN_BITS(cn_bits_N, cn_bits_M \| cn_bits_N, cn_bits_N, 0)

#define	cn_bits_NP MAKE_CN_BITS(cn_bits_N, cn_bits_P, 0, 0)

#define	cn_bits_PN MAKE_CN_BITS(cn_bits_P, cn_bits_N, 0, 0)

#define	cn_bits_NM MAKE_CN_BITS(cn_bits_N, cn_bits_M, 0, 0)

#define	cn_bits_MN MAKE_CN_BITS(cn_bits_M, cn_bits_N, 0, 0)

#define	cn_bits_P_ MAKE_CN_BITS(cn_bits_P, 0, 0, 0)

#define	cn_bits_M_ MAKE_CN_BITS(cn_bits_M, 0, 0, 0)

#define	cn_bits_N_ MAKE_CN_BITS(cn_bits_N, 0, 0, 0)

#define	cn_bits_Me (-1)

#define	cnListIndexMe (17) /* index of {cnMe, cn_bits_Me,... } element of cnList[] */

#define	MAX_DIFF_FIXH 256

#define	MAX_DIFF_MOBH 256

#define	KEEP_METAL_EDGE_FLOW 0 /* counterexample: mdb0-1738.sdf.txt */

#define	MOVE_CHARGES_FROM_HETEREO_TO_METAL 0 /* disabled */

#define	FIX_ADD_PROTON_FOR_ADP 0 /* not used */

Typedefs
typedef struct tagXYZCoord	XYZ_COORD

typedef struct tagStructRestoreMode	SRM

typedef struct tagReversedInChI	REV_INCHI

typedef struct tagBfsQueue	BFS_Q

typedef struct tagInpAtomAddParities	inp_ATOM_STEREO

typedef struct tagAtomIonPrperies	VAL_AT

typedef enum tagTgRestoreFlags	TGRF

typedef struct tagTCGroup	TC_GROUP

typedef enum tagTCGroupTypes	TCGR_TYPE

typedef struct tagAllTCGroups	ALL_TC_GROUPS

typedef struct tagEdgeList	EDGE_LIST

typedef struct tagChargeValence	CHARGE_VAL

typedef struct tagChargeChangeCandidate	CC_CAND

typedef struct tagOneComponentRemovedAndExchangeableH	COMPONENT_REM_PROTONS

typedef struct tagRemovedAndExchangeableH	REM_PROTONS

typedef struct tagInputInChI	InpInChI

typedef struct tagStructFromInChI	StrFromINChI

typedef struct tagVertCapFlow	VCF

typedef struct tagEdgeCapFlow	ECF

typedef struct tagChargeNodes	C_NODE

typedef struct tagChargeNodeList	CN_LIST

typedef struct tagAtomsCmpTwoFixedH	CMP2FHATOMS

typedef struct tagStructCmpTwoFixedH	CMP2FHINCHI

typedef struct tagAtomsCmpTwoMobileH	CMP2MHATOMS

typedef struct tagStructCmpTwoMobileH	CMP2MHINCHI

Enumerations
enum	tagTgRestoreFlags { TGRF_MINUS_FIRST = 1 }

enum	tagTCGroupTypes { TCG_None = -1 , TCG_Plus0 = 0 , TCG_Plus1 , TCG_Minus0 , TCG_Minus1 , TCG_Plus_C0 , TCG_Plus_C1 , TCG_Minus_C0 , TCG_Minus_C1 , TCG_Plus_M0 , TCG_Plus_M1 , TCG_Minus_M0 , TCG_Minus_M1 , TCG_MeFlower0 , TCG_MeFlower1 , TCG_MeFlower2 , TCG_MeFlower3 , TCG_Plus , TCG_Minus , NUM_TCGROUP_TYPES }

Functions
int	OneInChI2Atom (struct tagINCHI_CLOCK ic, struct tagCANON_GLOBALS pCG, ICHICONST INPUT_PARMS ip, STRUCT_DATA sd, const char szCurHdr, long num_inp, StrFromINChI pStruct, int iComponent, int iAtNoOffset, int bHasSomeFixedH, INChI *pInChI[])

int	get_sp_element_type (int nPeriodicNumber, int *nRow)

int	get_bonds_valences (int nPeriodicNum, int bonds_valence, int num_H, VAL_AT *pVA)

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	GetTgroupInfoFromInChI (T_GROUP_INFO ti, inp_ATOM at, AT_NUMB endpoint, INChI pInChI)

int	FillOutpStructEndpointFromInChI (INChI pInChI, AT_NUMB *pEndpoint)

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

int	SetStereoBondTypesFrom0DStereo (StrFromINChI pStruct, INChI pInChI)

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	RestoreAtomMakeBNS (struct tagINCHI_CLOCK ic, struct tagCANON_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	nAddSuperCGroups (ALL_TC_GROUPS *pTCGroups)

int	AddCGroups2TCGBnStruct (BN_STRUCT pBNS, StrFromINChI pStruct, VAL_AT pVA, ALL_TC_GROUPS pTCGroups, int nMaxAddEdges)

int	AddTGroups2TCGBnStruct (BN_STRUCT pBNS, StrFromINChI pStruct, VAL_AT pVA, ALL_TC_GROUPS pTCGroups, int nMaxAddEdges)

BN_STRUCT *	AllocateAndInitTCGBnStruct (StrFromINChI pStruct, VAL_AT pVA, ALL_TC_GROUPS pTCGroups, int nMaxAddAtoms, int nMaxAddEdges, int max_altp, int pNum_changed_bonds)

int	nCountBnsSizes (inp_ATOM at, int num_at, int nAddEdges2eachAtom, int nAddVertices, T_GROUP_INFO ti, VAL_AT pVA, ICHICONST SRM pSrm, ALL_TC_GROUPS *pTCGroups)

int	GetAtomRestoreInfo (struct tagCANON_GLOBALS pCG, inp_ATOM atom, int iat, VAL_AT pVArray, ICHICONST SRM pSrm, int bMobileH, AT_NUMB *endpoint)

int	AddEdgeFlow (int edge_cap, int edge_flow, BNS_EDGE e01, BNS_VERTEX pv0, BNS_VERTEX pv1, int tot_st_cap, int *tot_st_flow)

void	SetEdgeCapFlow (BNS_EDGE *e, int edge_cap, int edge_flow)

void	AddStCapFlow (BNS_VERTEX vert_ficpoint, int tot_st_flow, int *tot_st_cap, int cap, int flow)

void	SetStCapFlow (BNS_VERTEX vert_ficpoint, int tot_st_flow, int *tot_st_cap, int cap, int flow)

int	ConnectSuperCGroup (int nTCG_Plus, int nAddGroups[], int num_add, int pcur_num_vertices, int pcur_num_edges, int tot_st_cap, int tot_st_flow, BN_STRUCT pBNS, ALL_TC_GROUPS pTCGroups)

int	ConnectTwoVertices (BNS_VERTEX p1, BNS_VERTEX p2, BNS_EDGE e, BN_STRUCT pBNS, int bClearEdge)

int	nTautEndpointEdgeCap (inp_ATOM at, VAL_AT pVA, int i)

int	AtomStcapStflow (inp_ATOM atom, VAL_AT pVA, ICHICONST SRM pSrm, int iat, int pnStcap, int pnStflow, EdgeFlow pnMGroupEdgeCap, EdgeFlow *pnMGroupEdgeFlow)

int	BondFlowMaxcapMinorder (inp_ATOM atom, VAL_AT pVA, ICHICONST SRM pSrm, int iat, int ineigh, int pnMaxcap, int pnMinorder, int pbNeedsFlower)

int	clean_charge_val (struct tagCANON_GLOBALS pCG, CHARGE_VAL pChargeVal, int len, inp_ATOM atom, VAL_AT pVA, int iat, int bIsMetal, int bMobileH, AT_NUMB *endpoint)

int	ReallocTCGroups (ALL_TC_GROUPS *pTCGroups, int nAdd)

int	RegisterTCGroup (ALL_TC_GROUPS *pTCGroups, int nGroupType, int nGroupOrdNum, int nVertexCap, int nVertexFlow, int nEdgeCap, int nEdgeFlow, int nNumEdges)

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	RunBnsRestore1 (struct tagCANON_GLOBALS pCG, struct tagINCHI_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	RunBnsRestoreOnce (BN_STRUCT pBNS, BN_DATA pBD, VAL_AT pVA, ALL_TC_GROUPS pTCGroups)

int	nNumEdgesToCnVertex (MY_CONST C_NODE *pCN, int len, int v)

int	ConnectMetalFlower (int pcur_num_vertices, int pcur_num_edges, int tot_st_cap, int tot_st_flow, ICHICONST SRM pSrm, BN_STRUCT pBNS, ALL_TC_GROUPS *pTCGroups)

int	AddRadicalToMetal (int tot_st_cap, int tot_st_flow, ICHICONST SRM pSrm, BN_STRUCT pBNS, ALL_TC_GROUPS *pTCGroups)

int	bMayBeACationInMobileHLayer (inp_ATOM at, VAL_AT pVA, int iat, int bMobileH)

int	MakeOneInChIOutOfStrFromINChI (struct tagCANON_GLOBALS pCG, struct tagINCHI_CLOCK ic, ICHICONST INPUT_PARMS ip, STRUCT_DATA sd, StrFromINChI pStruct, inp_ATOM at2, inp_ATOM at3, ALL_TC_GROUPS pTCGroups)

void	IncrZeroBondsAndClearEndpts (inp_ATOM *at, int num_at, int iComponent)

void	IncrZeroBonds (inp_ATOM *at, int num_at, int iComponent)

void	ClearEndpts (inp_ATOM *at, int num_at)

int	DisplayRestoredComponent (struct tagCANON_GLOBALS pCG, StrFromINChI pStruct, int iComponent, int iAtNoOffset, INChI pInChI, const char szCurHdr)

int	cmp_charge_val (const void a1, const void a2, void *)

int	EvaluateChargeChanges (BN_STRUCT pBNS, VAL_AT pVA, int pnDeltaH, int pnDeltaCharge, int *pnNumVisitedAtoms)

int	RunBnsTestOnce (BN_STRUCT pBNS, BN_DATA pBD, VAL_AT pVA, Vertex pvFirst, Vertex pvLast, int pPathLen, int pnDeltaH, int pnDeltaCharge, int *pnNumVisitedAtoms)

int	comp_cc_cand (const void a1, const void a2)

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)

void	RemoveForbiddenBondFlowBits (BN_STRUCT *pBNS, int forbidden_edge_mask_int)

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

int	AllocEdgeList (EDGE_LIST *pEdges, int nLen)

int	AddToEdgeList (EDGE_LIST *pEdges, int iedge, int nAddLen)

int	RemoveFromEdgeListByIndex (EDGE_LIST *pEdges, int index)

int	RemoveFromEdgeListByValue (EDGE_LIST *pEdges, int iedge)

int	FindInEdgeList (EDGE_LIST *pEdges, int iedge)

int	AllocBfsQueue (BFS_Q *pQ, int num_at, int min_ring_size)

void	RemoveForbiddenEdgeMask (BN_STRUCT pBNS, EDGE_LIST pEdges, int forbidden_edge_mask)

void	SetForbiddenEdgeMask (BN_STRUCT pBNS, EDGE_LIST pEdges, int forbidden_edge_mask)

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

int	ForbidMetalCarbonEdges (BN_STRUCT pBNS, inp_ATOM at, int num_at, VAL_AT pVA, ALL_TC_GROUPS pTCGroups, EDGE_LIST *pMetalCarbonEdges, 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	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	MoveChargeFromHeteroatomsToMetals (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	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	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	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	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	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	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)

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

int	ConnectDisconnectedH (inp_ATOM *at, int num_atoms, int num_deleted_H)

int	DisconnectedConnectedH (inp_ATOM *at, int num_atoms, int num_deleted_H)

int	MakeInChIOutOfStrFromINChI2 (struct tagINCHI_CLOCK ic, struct tagCANON_GLOBALS pCG, ICHICONST INPUT_PARMS ip_inp, STRUCT_DATA sd_inp, StrFromINChI *pStruct, int iComponent, int iAtNoOffset, long num_inp)

int	GetChargeFlowerUpperEdge (BN_STRUCT pBNS, VAL_AT pVA, int nChargeEdge)

int	get_pVA_atom_type (VAL_AT pVA, inp_ATOM at, int iat, int bond_type)

int	NormalizeAndCompare (struct tagCANON_GLOBALS pCG, struct tagINCHI_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	NormalizeStructure (ICHICONST INPUT_PARMS ip, STRUCT_DATA sd, BN_STRUCT pBNS, StrFromINChI pStruct, inp_ATOM at, inp_ATOM at2, VAL_AT pVA, ALL_TC_GROUPS pTCGroups, inp_ATOM at_norm, inp_ATOM at_fixed_bonds_out, T_GROUP_INFO *t_group_info)

int	MakeOneInChIOutOfStrFromINChI2 (struct tagCANON_GLOBALS pCG, struct tagINCHI_CLOCK ic, ICHICONST INPUT_PARMS ip, STRUCT_DATA sd, BN_STRUCT pBNS, StrFromINChI pStruct, inp_ATOM at, inp_ATOM at2, inp_ATOM at3, VAL_AT pVA, ALL_TC_GROUPS pTCGroups, T_GROUP_INFO t_group_info, inp_ATOM at_norm, inp_ATOM *at_prep)

int	FillOutExtraFixedHDataRestr (StrFromINChI *pStruct)

int	FillOutExtraFixedHDataInChI (StrFromINChI pStruct, INChI pInChI[])

int	FixFixedHRestoredStructure (struct tagCANON_GLOBALS pCG, struct tagINCHI_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, T_GROUP_INFO ti, inp_ATOM at_norm, inp_ATOM *at_prep, INChI pInChI[], long num_inp, int bHasSomeFixedH, int pnNumRunBNS, int pnTotalDelta, int forbidden_edge_mask, int forbidden_stereo_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	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	bHas_N_V (inp_ATOM *at2, int num_atoms)

int	GetPlusMinusVertex (BN_STRUCT pBNS, ALL_TC_GROUPS pTCGroups, int bCheckForbiddenPlus, int bCheckForbiddenMinus)

int	FixMobileHRestoredStructure (struct tagCANON_GLOBALS pCG, struct tagINCHI_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, T_GROUP_INFO ppt_group_info, inp_ATOM ppat_norm, inp_ATOM *ppat_prep, INChI pInChI[], long num_inp, int bHasSomeFixedH, int pnNumRunBNS, int pnTotalDelta, int forbidden_edge_mask, int forbidden_stereo_edge_mask)

int	FixRestoredStructureStereo (struct tagCANON_GLOBALS pCG, struct tagINCHI_CLOCK ic, INCHI_MODE cmpInChI, ICR icr, INCHI_MODE cmpInChI2, ICR icr2, 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, T_GROUP_INFO ppt_group_info, inp_ATOM ppat_norm, inp_ATOM *ppat_prep, INChI pInChI[], long num_inp, int pnNumRunBNS, int pnTotalDelta, int forbidden_edge_mask, int forbidden_stereo_edge_mask)

int	AddRemProtonsInRestrStruct (struct tagINCHI_CLOCK ic, struct tagCANON_GLOBALS pCG, ICHICONST INPUT_PARMS ip, STRUCT_DATA sd, long num_inp, int bHasSomeFixedH, StrFromINChI pStruct, int num_components, StrFromINChI pStructR, int num_componentsR, NUM_H pProtonBalance, int recmet_change_balance)

int	AllInchiToStructure (struct tagINCHI_CLOCK ic, struct tagCANON_GLOBALS pCG, ICHICONST INPUT_PARMS ip, STRUCT_DATA sd, long num_inp, char szCurHdr, ICHICONST SRM pSrm, int bReqNonTaut, StrFromINChI pStruct[INCHI_NUM][TAUT_NUM], InpInChI pOneInput)

int	AddProtonAndIsoHBalanceToMobHStruct (struct tagINCHI_CLOCK ic, struct tagCANON_GLOBALS pCG, ICHICONST INPUT_PARMS ip, STRUCT_DATA sd, long num_inp, int bHasSomeFixedH, char szCurHdr, StrFromINChI pStruct[INCHI_NUM][TAUT_NUM], InpInChI *pOneInput)

int	InChI2Atom (struct tagINCHI_CLOCK ic, struct tagCANON_GLOBALS pCG, ICHICONST INPUT_PARMS ip, STRUCT_DATA sd, const char szCurHdr, long num_inp, StrFromINChI pStruct, int iComponent, int iAtNoOffset, int bI2A_Flag, int bHasSomeFixedH, InpInChI *pOneInput)

int	MarkDisconectedIdenticalToReconnected (InpInChI *pOneInput)

void	RemoveFixHInChIIdentical2MobH (InpInChI *pOneInput)

void	SetUpSrm (SRM *pSrm)

void	FreeInputInChI2Struct (InpInChI *pOneInput)

void	FreeStrFromINChI (StrFromINChI *pStruct[INCHI_NUM][TAUT_NUM], int nNumComponents[INCHI_NUM][TAUT_NUM])

int	OldPrintCompareOneOrigInchiToRevInChI (StrFromINChI pStruct, INChI pInChI[TAUT_NUM], int bMobileH, int iComponent, long num_inp, char *szCurHdr)

int	CompareOneOrigInchiToRevInChI (StrFromINChI pStruct, INChI pInChI[TAUT_NUM], int bMobileH, int iComponent, long num_inp, char szCurHdr, COMPONENT_REM_PROTONS nCurRemovedProtons, INCHI_MODE CompareInchiFlags[])

int	CompareTwoPairsOfInChI (INChI pInChI1[TAUT_NUM], INChI pInChI2[TAUT_NUM], int bMobileH, INCHI_MODE CompareInchiFlags[])

INCHI_MODE	CompareReversedINChI3 (INChI i1, INChI i2, INChI_Aux a1, INChI_Aux a2, int *err)

INCHI_MODE	CompareReversedStereoINChI3 (INChI_Stereo s1, INChI_Stereo s2, ICR *picr)

int	CompareAllOrigInchiToRevInChI (StrFromINChI pStruct[INCHI_NUM][TAUT_NUM], InpInChI pOneInput, int bReqNonTaut, long num_inp, char *szCurHdr)

int	CompareAllDisconnectedOrigInchiToRevInChI (StrFromINChI pStruct[INCHI_NUM][TAUT_NUM], InpInChI pOneInput, int bHasSomeFixedH, long num_inp, char *szCurHdr)

int	insertions_sort_AT_NUMB (AT_NUMB *base, int num)

int	AddRemIsoProtonsInRestrStruct (struct tagINCHI_CLOCK ic, struct tagCANON_GLOBALS pCG, ICHICONST INPUT_PARMS ip, 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[])

int	OutputInChIOutOfStrFromINChI (struct tagINCHI_CLOCK ic, struct tagCANON_GLOBALS pCG, ICHICONST INPUT_PARMS ip_inp, STRUCT_DATA sd_inp, long num_inp, int bINChIOutputOptions, INCHI_IOSTREAM pout, INCHI_IOSTREAM plog, InpInChI *pOneInput, int bHasSomeFixedH, unsigned char save_opt_bits)

int	MergeStructureComponents (ICHICONST INPUT_PARMS ip, STRUCT_DATA sd, long num_inp, char szCurHdr, ICHICONST SRM pSrm, int bReqNonTaut, StrFromINChI pStruct[INCHI_NUM][TAUT_NUM], InpInChI pOneInput)

int	AddOneMsg (char szMsg, int used_len, int tot_len, const char szAddMsg, const char *szDelim)

int	FillOutCompareMessage (char *szMsg, int nLenMsg, INCHI_MODE bits[])

void	clear_t_group_info (T_GROUP_INFO *ti)

int	bInpInchiComponentExists (InpInChI *pOneInput, int iINCHI, int bMobileH, int k)

int	bInpInchiComponentDeleted (InpInChI *pOneInput, int iInChI, int bMobileH, int k)

int	bRevInchiComponentExists (StrFromINChI *pStruct, int iInChI, int bMobileH, int k)

int	bRevInchiComponentDeleted (StrFromINChI *pStruct, int iInChI, int bMobileH, int k)

int	DetectInpInchiCreationOptions (InpInChI pOneInput, int bHasReconnected, int bHasMetal, int bHasFixedH, int sFlag, int bTautFlag)

int	DisplayStructureComponents (struct tagCANON_GLOBALS pCG, ICHICONST INPUT_PARMS ip, STRUCT_DATA sd, long num_inp, char szCurHdr, ICHICONST SRM pSrm, int bReqNonTaut, StrFromINChI pStruct[INCHI_NUM][TAUT_NUM], InpInChI *pOneInput)

int	DisplayOneRestoredComponent (struct tagCANON_GLOBALS pCG, StrFromINChI pStruct, inp_ATOM at, int iComponent, int nNumComponents, int bMobileH, const char szCurHdr)

int	DisplayAllRestoredComponents (struct tagCANON_GLOBALS pCG, inp_ATOM at, int num_at, const char *szCurHdr)

int	CountStereoTypes (INChI pInChI, int num_known_SB, int num_known_SC, int num_unk_und_SB, int num_unk_und_SC, int num_SC_PIII, int *num_SC_AsIII)

int	GetNumNeighborsFromInchi (INChI *pInChI, AT_NUMB nAtNumber)

int	bIsUnsatCarbonInASmallRing (inp_ATOM at, VAL_AT pVA, int iat, BFS_Q *pbfsq, int min_ring_size)

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

void	FreeInpInChI (InpInChI *pOneInput)

Variables
const int	cnListNumEl

MY_CONST CN_LIST	cnList []

Macro Definition Documentation

◆ ALLOW_METAL_BOND_ZERO

#define ALLOW_METAL_BOND_ZERO 1 /* 1=> allow zero flow (bobd order) to metals */

◆ ATYPE_B

#define ATYPE_B 4

◆ ATYPE_C

#define ATYPE_C 5

◆ ATYPE_Cl

#define ATYPE_Cl 8

◆ ATYPE_H

#define ATYPE_H 1

◆ ATYPE_Mg

#define ATYPE_Mg 3

◆ ATYPE_N

#define ATYPE_N 6

◆ ATYPE_Na

#define ATYPE_Na 2

◆ ATYPE_O

#define ATYPE_O 7

◆ BFS_Q_CLEAR

#define BFS_Q_CLEAR (-1)

◆ BFS_Q_FREE

#define BFS_Q_FREE (-2)

◆ BOND_MARK_STEREO

#define BOND_MARK_STEREO 0x10

◆ BOND_TYPE_STEREO

#define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO)

◆ cn_bits_EN

#define cn_bits_EN MAKE_CN_BITS(cn_bits_P | cn_bits_M, cn_bits_N, 0, 0)

◆ cn_bits_M

#define cn_bits_M 4 /* Minus 1: charge = -1 */

◆ cn_bits_M_

#define cn_bits_M_ MAKE_CN_BITS(cn_bits_M, 0, 0, 0)

◆ cn_bits_Me

#define cn_bits_Me (-1)

◆ cn_bits_MN

#define cn_bits_MN MAKE_CN_BITS(cn_bits_M, cn_bits_N, 0, 0)

◆ cn_bits_MNP

#define cn_bits_MNP MAKE_CN_BITS(cn_bits_M, cn_bits_N, cn_bits_P, 0)

◆ cn_bits_N

#define cn_bits_N 1 /* Neutral: charge = 0 */

◆ cn_bits_N_

#define cn_bits_N_ MAKE_CN_BITS(cn_bits_N, 0, 0, 0)

◆ cn_bits_NE

#define cn_bits_NE MAKE_CN_BITS(cn_bits_N, cn_bits_P | cn_bits_M, 0, 0)

◆ cn_bits_NEN

#define cn_bits_NEN MAKE_CN_BITS(cn_bits_N, cn_bits_M | cn_bits_N, cn_bits_N, 0)

◆ cn_bits_NM

#define cn_bits_NM MAKE_CN_BITS(cn_bits_N, cn_bits_M, 0, 0)

◆ cn_bits_NMN

#define cn_bits_NMN MAKE_CN_BITS(cn_bits_N, cn_bits_M, cn_bits_N, 0)

◆ cn_bits_NP

#define cn_bits_NP MAKE_CN_BITS(cn_bits_N, cn_bits_P, 0, 0)

◆ cn_bits_NPN

#define cn_bits_NPN MAKE_CN_BITS(cn_bits_N, cn_bits_P, cn_bits_N, 0)

◆ cn_bits_NPNP

#define cn_bits_NPNP MAKE_CN_BITS(cn_bits_N, cn_bits_P, cn_bits_N, cn_bits_P)

◆ cn_bits_P

#define cn_bits_P 2 /* Plus 1: charge = +1 */

◆ cn_bits_P_

#define cn_bits_P_ MAKE_CN_BITS(cn_bits_P, 0, 0, 0)

◆ cn_bits_PN

#define cn_bits_PN MAKE_CN_BITS(cn_bits_P, cn_bits_N, 0, 0)

◆ cn_bits_PNM

#define cn_bits_PNM MAKE_CN_BITS(cn_bits_P, cn_bits_N, cn_bits_M, 0)

◆ cn_bits_PNP

#define cn_bits_PNP MAKE_CN_BITS(cn_bits_P, cn_bits_N, cn_bits_P, 0)

◆ cn_bits_PNPN

#define cn_bits_PNPN MAKE_CN_BITS(cn_bits_P, cn_bits_N, cn_bits_P, cn_bits_N)

◆ cn_bits_shift

#define cn_bits_shift 3

◆ cnListIndexMe

#define cnListIndexMe (17) /* index of {cnMe, cn_bits_Me,... } element of cnList[] */

◆ EDGE_LIST_CLEAR

#define EDGE_LIST_CLEAR (-1)

◆ EDGE_LIST_FREE

#define EDGE_LIST_FREE (-2)

◆ EL_TYPE_C

#define EL_TYPE_C 0x0010

◆ EL_TYPE_MASK

#define EL_TYPE_MASK 0x003f

◆ EL_TYPE_N

#define EL_TYPE_N 0x0004

◆ EL_TYPE_O

#define EL_TYPE_O 0x0001

◆ EL_TYPE_OSt

#define EL_TYPE_OSt 0x0100 /* terminal -OH, -O(-), -SH, -S(-), ... from fix_special_bonds(...) */

◆ EL_TYPE_P

#define EL_TYPE_P 0x0008

◆ EL_TYPE_PT

#define EL_TYPE_PT 0x0200 /* may be a tautomeric endpoint */

◆ EL_TYPE_S

#define EL_TYPE_S 0x0002

◆ EL_TYPE_X

#define EL_TYPE_X 0x0020 /* any not metal */

◆ EXTRACT_STRUCT_NUMBER

#define EXTRACT_STRUCT_NUMBER 1

◆ FIX_ADD_PROTON_FOR_ADP

#define FIX_ADD_PROTON_FOR_ADP 0 /* not used */

◆ FIX_STEREO_BOND_ORDER

#define FIX_STEREO_BOND_ORDER 0 /* 1=> fix stereobonds; treat metal as non-metal if it is stereogenic or has a stereobond */

◆ I2A_FLAG_FIXEDH

#define I2A_FLAG_FIXEDH 0x0001

◆ I2A_FLAG_RECMET

#define I2A_FLAG_RECMET 0x0002

◆ ICHICONST

#define ICHICONST const

◆ INC_EDGE_LIST_DEFAULT

#define INC_EDGE_LIST_DEFAULT 64

◆ INC_NUM_TCGROUPS

#define INC_NUM_TCGROUPS 16

◆ INI_NUM_TCGROUPS

#define INI_NUM_TCGROUPS 16

◆ INIT_METAL_BOND_FLOW

#define INIT_METAL_BOND_FLOW 1 /* 1=> init flow=1, 0 => init. flow = 0 */

◆ INIT_METAL_BOND_ZERO

#define INIT_METAL_BOND_ZERO 0 /* 1=> initialize zero order bond to metals */

◆ KEEP_METAL_EDGE_FLOW

#define KEEP_METAL_EDGE_FLOW 0 /* counterexample: mdb0-1738.sdf.txt */

◆ MAKE_CN_BITS

#define MAKE_CN_BITS	(	A,
		B,
		C,
		D
	)	(( (( ((D) << cn_bits_shift \| (C)) << cn_bits_shift ) \| (B)) << cn_bits_shift ) \| (A))

◆ MAX_CN_VAL

#define MAX_CN_VAL 3

◆ MAX_DIFF_FIXH

#define MAX_DIFF_FIXH 256

◆ MAX_DIFF_MOBH

#define MAX_DIFF_MOBH 256

◆ MAX_NUM_CN_BITS

#define MAX_NUM_CN_BITS 4

◆ METAL_FREE_CHARGE_VAL

#define METAL_FREE_CHARGE_VAL 1 /* 1=> allow free changing charges/valences of metals; initial bond order=0 or 1 */

◆ MOVE_CHARGES_FROM_HETEREO_TO_METAL

#define MOVE_CHARGES_FROM_HETEREO_TO_METAL 0 /* disabled */

◆ MY_CONST

#define MY_CONST const

◆ NO_VALUE_INT

#define NO_VALUE_INT 9999

◆ NOT_READ_INT

#define NOT_READ_INT 9998 /* has not been read yet */

◆ RESET_EDGE_FORBIDDEN_MASK

#define RESET_EDGE_FORBIDDEN_MASK 0

◆ RI_ERR_ALLOC

#define RI_ERR_ALLOC (-1)

◆ RI_ERR_EOF

#define RI_ERR_EOF (0)

◆ RI_ERR_EOL

#define RI_ERR_EOL (-4)

◆ RI_ERR_MISMATCH

#define RI_ERR_MISMATCH (-9)

◆ RI_ERR_PROGR

#define RI_ERR_PROGR (-3)

◆ RI_ERR_SYNTAX

#define RI_ERR_SYNTAX (-2)

◆ TREAT_ATOM_AS_METAL

#define TREAT_ATOM_AS_METAL 99

◆ VAL_BASE

#define VAL_BASE ( 1)

◆ VAL_LENGTH

#define VAL_LENGTH (VAL_NEUTR_ORDER+1)

◆ VAL_MAX_CHARGE

#define VAL_MAX_CHARGE ( 1)

◆ VAL_MIN_CHARGE

#define VAL_MIN_CHARGE (-1)

◆ VAL_NEGAT_CHARGE

#define VAL_NEGAT_CHARGE 0

◆ VAL_NEUTR_CHARGE

#define VAL_NEUTR_CHARGE 1

◆ VAL_NEUTR_ORDER

#define VAL_NEUTR_ORDER (VAL_MAX_CHARGE-VAL_MIN_CHARGE+1)

◆ VAL_NUMBER

#define VAL_NUMBER ( 2)

◆ VAL_POSIT_CHARGE

#define VAL_POSIT_CHARGE 2

◆ VALUE_OCTET

#define VALUE_OCTET 8 /* number of electrons in a full shell */

Typedef Documentation

◆ ALL_TC_GROUPS

typedef struct tagAllTCGroups ALL_TC_GROUPS

◆ BFS_Q

typedef struct tagBfsQueue BFS_Q

◆ C_NODE

typedef struct tagChargeNodes C_NODE

◆ CC_CAND

typedef struct tagChargeChangeCandidate CC_CAND

◆ CHARGE_VAL

typedef struct tagChargeValence CHARGE_VAL

◆ CMP2FHATOMS

typedef struct tagAtomsCmpTwoFixedH CMP2FHATOMS

◆ CMP2FHINCHI

typedef struct tagStructCmpTwoFixedH CMP2FHINCHI

◆ CMP2MHATOMS

typedef struct tagAtomsCmpTwoMobileH CMP2MHATOMS

◆ CMP2MHINCHI

typedef struct tagStructCmpTwoMobileH CMP2MHINCHI

◆ CN_LIST

typedef struct tagChargeNodeList CN_LIST

◆ COMPONENT_REM_PROTONS

typedef struct tagOneComponentRemovedAndExchangeableH COMPONENT_REM_PROTONS

◆ ECF

typedef struct tagEdgeCapFlow ECF

◆ EDGE_LIST

typedef struct tagEdgeList EDGE_LIST

◆ inp_ATOM_STEREO

typedef struct tagInpAtomAddParities inp_ATOM_STEREO

◆ InpInChI

typedef struct tagInputInChI InpInChI

◆ REM_PROTONS

typedef struct tagRemovedAndExchangeableH REM_PROTONS

◆ REV_INCHI

typedef struct tagReversedInChI REV_INCHI

◆ SRM

typedef struct tagStructRestoreMode SRM

◆ StrFromINChI

typedef struct tagStructFromInChI StrFromINChI

◆ TC_GROUP

typedef struct tagTCGroup TC_GROUP

◆ TCGR_TYPE

typedef enum tagTCGroupTypes TCGR_TYPE

◆ TGRF

typedef enum tagTgRestoreFlags TGRF

◆ VAL_AT

typedef struct tagAtomIonPrperies VAL_AT

◆ VCF

typedef struct tagVertCapFlow VCF

◆ XYZ_COORD

typedef struct tagXYZCoord XYZ_COORD

Enumeration Type Documentation

◆ tagTCGroupTypes

enum tagTCGroupTypes

Enumerator
TCG_None
TCG_Plus0
TCG_Plus1
TCG_Minus0
TCG_Minus1
TCG_Plus_C0
TCG_Plus_C1
TCG_Minus_C0
TCG_Minus_C1
TCG_Plus_M0
TCG_Plus_M1
TCG_Minus_M0
TCG_Minus_M1
TCG_MeFlower0
TCG_MeFlower1
TCG_MeFlower2
TCG_MeFlower3
TCG_Plus
TCG_Minus
NUM_TCGROUP_TYPES

◆ tagTgRestoreFlags

enum tagTgRestoreFlags

Enumerator
TGRF_MINUS_FIRST

Function Documentation

◆ AddCGroups2TCGBnStruct()

int AddCGroups2TCGBnStruct	(	BN_STRUCT *	pBNS,
		StrFromINChI *	pStruct,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int	nMaxAddEdges
	)

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◆ AddEdgeFlow()

int AddEdgeFlow	(	int	edge_cap,
		int	edge_flow,
		BNS_EDGE *	e01,
		BNS_VERTEX *	pv0,
		BNS_VERTEX *	pv1,
		int *	tot_st_cap,
		int *	tot_st_flow
	)

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◆ AddExplicitDeletedH()

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

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◆ AddOneMsg()

int AddOneMsg	(	char *	szMsg,
		int	used_len,
		int	tot_len,
		const char *	szAddMsg,
		const char *	szDelim
	)

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◆ AddProtonAndIsoHBalanceToMobHStruct()

int AddProtonAndIsoHBalanceToMobHStruct	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		long	num_inp,
		int	bHasSomeFixedH,
		char *	szCurHdr,
		StrFromINChI *	pStruct[INCHI_NUM][TAUT_NUM],
		InpInChI *	pOneInput
	)

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◆ AddRadicalToMetal()

int AddRadicalToMetal	(	int *	tot_st_cap,
		int *	tot_st_flow,
		ICHICONST SRM *	pSrm,
		BN_STRUCT *	pBNS,
		ALL_TC_GROUPS *	pTCGroups
	)

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◆ AddRemIsoProtonsInRestrStruct()

int AddRemIsoProtonsInRestrStruct	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip,
		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	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		long	num_inp,
		int	bHasSomeFixedH,
		StrFromINChI *	pStruct,
		int	num_components,
		StrFromINChI *	pStructR,
		int	num_componentsR,
		NUM_H *	pProtonBalance,
		int *	recmet_change_balance
	)

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◆ AddStCapFlow()

void AddStCapFlow	(	BNS_VERTEX *	vert_ficpoint,
		int *	tot_st_flow,
		int *	tot_st_cap,
		int	cap,
		int	flow
	)

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◆ AddTGroups2TCGBnStruct()

int AddTGroups2TCGBnStruct	(	BN_STRUCT *	pBNS,
		StrFromINChI *	pStruct,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int	nMaxAddEdges
	)

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◆ AddToEdgeList()

int AddToEdgeList	(	EDGE_LIST *	pEdges,
		int	iedge,
		int	nAddLen
	)

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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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◆ AllInchiToStructure()

int AllInchiToStructure	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		long	num_inp,
		char *	szCurHdr,
		ICHICONST SRM *	pSrm,
		int	bReqNonTaut,
		StrFromINChI *	pStruct[INCHI_NUM][TAUT_NUM],
		InpInChI *	pOneInput
	)

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◆ AllocateAndInitTCGBnStruct()

BN_STRUCT * AllocateAndInitTCGBnStruct	(	StrFromINChI *	pStruct,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		int	nMaxAddAtoms,
		int	nMaxAddEdges,
		int	max_altp,
		int *	pNum_changed_bonds
	)

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◆ AllocBfsQueue()

int AllocBfsQueue	(	BFS_Q *	pQ,
		int	num_at,
		int	min_ring_size
	)

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◆ AllocEdgeList()

int AllocEdgeList	(	EDGE_LIST *	pEdges,
		int	nLen
	)

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◆ AtomStcapStflow()

int AtomStcapStflow	(	inp_ATOM *	atom,
		VAL_AT *	pVA,
		ICHICONST SRM *	pSrm,
		int	iat,
		int *	pnStcap,
		int *	pnStflow,
		EdgeFlow *	pnMGroupEdgeCap,
		EdgeFlow *	pnMGroupEdgeFlow
	)

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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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◆ bHas_N_V()

int bHas_N_V	(	inp_ATOM *	at2,
		int	num_atoms
	)

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◆ bInpInchiComponentDeleted()

int bInpInchiComponentDeleted	(	InpInChI *	pOneInput,
		int	iInChI,
		int	bMobileH,
		int	k
	)

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◆ bInpInchiComponentExists()

int bInpInchiComponentExists	(	InpInChI *	pOneInput,
		int	iINCHI,
		int	bMobileH,
		int	k
	)

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◆ bIsUnsatCarbonInASmallRing()

int bIsUnsatCarbonInASmallRing	(	inp_ATOM *	at,
		VAL_AT *	pVA,
		int	iat,
		BFS_Q *	pbfsq,
		int	min_ring_size
	)

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◆ bMayBeACationInMobileHLayer()

int bMayBeACationInMobileHLayer	(	inp_ATOM *	at,
		VAL_AT *	pVA,
		int	iat,
		int	bMobileH
	)

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◆ BondFlowMaxcapMinorder()

int BondFlowMaxcapMinorder	(	inp_ATOM *	atom,
		VAL_AT *	pVA,
		ICHICONST SRM *	pSrm,
		int	iat,
		int	ineigh,
		int *	pnMaxcap,
		int *	pnMinorder,
		int *	pbNeedsFlower
	)

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◆ bRevInchiComponentDeleted()

int bRevInchiComponentDeleted	(	StrFromINChI *	pStruct,
		int	iInChI,
		int	bMobileH,
		int	k
	)

pStruct->at2 ||

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◆ bRevInchiComponentExists()

int bRevInchiComponentExists	(	StrFromINChI *	pStruct,
		int	iInChI,
		int	bMobileH,
		int	k
	)

pStruct->at2 ||

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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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◆ CheckBnsConsistency()

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

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◆ clean_charge_val()

int clean_charge_val	(	struct tagCANON_GLOBALS *	pCG,
		CHARGE_VAL *	pChargeVal,
		int	len,
		inp_ATOM *	atom,
		VAL_AT *	pVA,
		int	iat,
		int	bIsMetal,
		int	bMobileH,
		AT_NUMB *	endpoint
	)

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◆ clear_t_group_info()

void clear_t_group_info ( T_GROUP_INFO * ti )

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◆ ClearEndpts()

void ClearEndpts	(	inp_ATOM *	at,
		int	num_at
	)

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◆ cmp_charge_val()

int cmp_charge_val	(	const void *	a1,
		const void *	a2,
		void *	p
	)

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◆ comp_cc_cand()

int comp_cc_cand	(	const void *	a1,
		const void *	a2
	)

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◆ CompareAllDisconnectedOrigInchiToRevInChI()

int CompareAllDisconnectedOrigInchiToRevInChI	(	StrFromINChI *	pStruct[INCHI_NUM][TAUT_NUM],
		InpInChI *	pOneInput,
		int	bHasSomeFixedH,
		long	num_inp,
		char *	szCurHdr
	)

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◆ CompareAllOrigInchiToRevInChI()

int CompareAllOrigInchiToRevInChI	(	StrFromINChI *	pStruct[INCHI_NUM][TAUT_NUM],
		InpInChI *	pOneInput,
		int	bReqNonTaut,
		long	num_inp,
		char *	szCurHdr
	)

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◆ CompareOneOrigInchiToRevInChI()

int CompareOneOrigInchiToRevInChI	(	StrFromINChI *	pStruct,
		INChI *	pInChI[TAUT_NUM],
		int	bMobileH,
		int	iComponent,
		long	num_inp,
		char *	szCurHdr,
		COMPONENT_REM_PROTONS *	nCurRemovedProtons,
		INCHI_MODE	CompareInchiFlags[]
	)

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◆ CompareReversedINChI3()

INCHI_MODE CompareReversedINChI3	(	INChI *	i1,
		INChI *	i2,
		INChI_Aux *	a1,
		INChI_Aux *	a2,
		int *	err
	)

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◆ CompareReversedStereoINChI3()

INCHI_MODE CompareReversedStereoINChI3	(	INChI_Stereo *	s1,
		INChI_Stereo *	s2,
		ICR *	picr
	)

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◆ CompareTwoPairsOfInChI()

int CompareTwoPairsOfInChI	(	INChI *	pInChI1[TAUT_NUM],
		INChI *	pInChI2[TAUT_NUM],
		int	bMobileH,
		INCHI_MODE	CompareInchiFlags[]
	)

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◆ ConnectDisconnectedH()

int ConnectDisconnectedH	(	inp_ATOM *	at,
		int	num_atoms,
		int	num_deleted_H
	)

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◆ ConnectMetalFlower()

int ConnectMetalFlower	(	int *	pcur_num_vertices,
		int *	pcur_num_edges,
		int *	tot_st_cap,
		int *	tot_st_flow,
		ICHICONST SRM *	pSrm,
		BN_STRUCT *	pBNS,
		ALL_TC_GROUPS *	pTCGroups
	)

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◆ ConnectSuperCGroup()

int ConnectSuperCGroup	(	int	nTCG_Plus,
		int	nAddGroups[],
		int	num_add,
		int *	pcur_num_vertices,
		int *	pcur_num_edges,
		int *	tot_st_cap,
		int *	tot_st_flow,
		BN_STRUCT *	pBNS,
		ALL_TC_GROUPS *	pTCGroups
	)

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◆ ConnectTwoVertices()

int ConnectTwoVertices	(	BNS_VERTEX *	p1,
		BNS_VERTEX *	p2,
		BNS_EDGE *	e,
		BN_STRUCT *	pBNS,
		int	bClearEdge
	)

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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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◆ CountStereoTypes()

int CountStereoTypes	(	INChI *	pInChI,
		int *	num_known_SB,
		int *	num_known_SC,
		int *	num_unk_und_SB,
		int *	num_unk_und_SC,
		int *	num_SC_PIII,
		int *	num_SC_AsIII
	)

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◆ DetectInpInchiCreationOptions()

int DetectInpInchiCreationOptions	(	InpInChI *	pOneInput,
		int *	bHasReconnected,
		int *	bHasMetal,
		int *	bHasFixedH,
		int *	sFlag,
		int *	bTautFlag
	)

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◆ DisconnectedConnectedH()

int DisconnectedConnectedH	(	inp_ATOM *	at,
		int	num_atoms,
		int	num_deleted_H
	)

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◆ DisplayAllRestoredComponents()

int DisplayAllRestoredComponents	(	struct tagCANON_GLOBALS *	pCG,
		inp_ATOM *	at,
		int	num_at,
		const char *	szCurHdr
	)

◆ DisplayOneRestoredComponent()

int DisplayOneRestoredComponent	(	struct tagCANON_GLOBALS *	pCG,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		int	iComponent,
		int	nNumComponents,
		int	bMobileH,
		const char *	szCurHdr
	)

◆ DisplayRestoredComponent()

int DisplayRestoredComponent	(	struct tagCANON_GLOBALS *	pCG,
		StrFromINChI *	pStruct,
		int	iComponent,
		int	iAtNoOffset,
		INChI *	pInChI,
		const char *	szCurHdr
	)

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◆ DisplayStructureComponents()

int DisplayStructureComponents	(	struct tagCANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		long	num_inp,
		char *	szCurHdr,
		ICHICONST SRM *	pSrm,
		int	bReqNonTaut,
		StrFromINChI *	pStruct[INCHI_NUM][TAUT_NUM],
		InpInChI *	pOneInput
	)

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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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◆ EvaluateChargeChanges()

int EvaluateChargeChanges	(	BN_STRUCT *	pBNS,
		VAL_AT *	pVA,
		int *	pnDeltaH,
		int *	pnDeltaCharge,
		int *	pnNumVisitedAtoms
	)

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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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◆ FillOutCompareMessage()

int FillOutCompareMessage	(	char *	szMsg,
		int	nLenMsg,
		INCHI_MODE	bits[]
	)

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◆ FillOutExtraFixedHDataInChI()

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

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◆ FillOutExtraFixedHDataRestr()

int FillOutExtraFixedHDataRestr ( StrFromINChI * pStruct )

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◆ FillOutpStructEndpointFromInChI()

int FillOutpStructEndpointFromInChI	(	INChI *	pInChI,
		AT_NUMB **	pEndpoint
	)

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◆ FindInEdgeList()

int FindInEdgeList	(	EDGE_LIST *	pEdges,
		int	iedge
	)

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◆ FixAddProtonForADP()

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

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◆ FixFixedHRestoredStructure()

int FixFixedHRestoredStructure	(	struct tagCANON_GLOBALS *	pCG,
		struct tagINCHI_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,
		T_GROUP_INFO **	ti,
		inp_ATOM **	at_norm,
		inp_ATOM **	at_prep,
		INChI *	pInChI[],
		long	num_inp,
		int	bHasSomeFixedH,
		int *	pnNumRunBNS,
		int *	pnTotalDelta,
		int	forbidden_edge_mask,
		int	forbidden_stereo_edge_mask
	)

pc2i->c2at[i].endptInChI &&

at2[iat].num_H &&

(nMobHInChI && nMobHInChI[i] ) &&

(pStruct->fixed_H && pStruct->fixed_H[i]) &&

(nMobHInChI && nMobHInChI[i] ) &&

pc2i->c2at[i].endptRevrs &&

pStruct->endpoint[i] &&

(pStruct->fixed_H && pStruct->fixed_H[i]) &&

pc2i->c2at[i].endptInChI &&

(nMobHInChI && nMobHInChI[i] ) &&

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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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◆ 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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◆ FixMobileHRestoredStructure()

int FixMobileHRestoredStructure	(	struct tagCANON_GLOBALS *	pCG,
		struct tagINCHI_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,
		T_GROUP_INFO **	ppt_group_info,
		inp_ATOM **	ppat_norm,
		inp_ATOM **	ppat_prep,
		INChI *	pInChI[],
		long	num_inp,
		int	bHasSomeFixedH,
		int *	pnNumRunBNS,
		int *	pnTotalDelta,
		int	forbidden_edge_mask,
		int	forbidden_stereo_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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◆ FixRestoredStructureStereo()

int FixRestoredStructureStereo	(	struct tagCANON_GLOBALS *	pCG,
		struct tagINCHI_CLOCK *	ic,
		INCHI_MODE	cmpInChI,
		ICR *	icr,
		INCHI_MODE	cmpInChI2,
		ICR *	icr2,
		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,
		T_GROUP_INFO **	ppt_group_info,
		inp_ATOM **	ppat_norm,
		inp_ATOM **	ppat_prep,
		INChI *	pInChI[],
		long	num_inp,
		int *	pnNumRunBNS,
		int *	pnTotalDelta,
		int	forbidden_edge_mask,
		int	forbidden_stereo_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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◆ ForbidMetalCarbonEdges()

int ForbidMetalCarbonEdges	(	BN_STRUCT *	pBNS,
		inp_ATOM *	at,
		int	num_at,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		EDGE_LIST *	pMetalCarbonEdges,
		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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◆ FreeInpInChI()

void FreeInpInChI ( InpInChI * pOneInput )

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◆ FreeInputInChI2Struct()

void FreeInputInChI2Struct ( InpInChI * pOneInput )

◆ FreeStrFromINChI()

void FreeStrFromINChI	(	StrFromINChI *	pStruct[INCHI_NUM][TAUT_NUM],
		int	nNumComponents[INCHI_NUM][TAUT_NUM]
	)

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◆ get_bonds_valences()

int get_bonds_valences	(	int	nPeriodicNum,
		int	bonds_valence,
		int	num_H,
		VAL_AT *	pVA
	)

◆ get_pVA_atom_type()

int get_pVA_atom_type	(	VAL_AT *	pVA,
		inp_ATOM *	at,
		int	iat,
		int	bond_type
	)

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◆ get_sp_element_type()

int get_sp_element_type	(	int	nPeriodicNumber,
		int *	nRow
	)

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◆ GetAtomRestoreInfo()

int GetAtomRestoreInfo	(	struct tagCANON_GLOBALS *	pCG,
		inp_ATOM *	atom,
		int	iat,
		VAL_AT *	pVArray,
		ICHICONST SRM *	pSrm,
		int	bMobileH,
		AT_NUMB *	endpoint
	)

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◆ GetChargeFlowerUpperEdge()

int GetChargeFlowerUpperEdge	(	BN_STRUCT *	pBNS,
		VAL_AT *	pVA,
		int	nChargeEdge
	)

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◆ GetNumNeighborsFromInchi()

int GetNumNeighborsFromInchi	(	INChI *	pInChI,
		AT_NUMB	nAtNumber
	)

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◆ GetPlusMinusVertex()

int GetPlusMinusVertex	(	BN_STRUCT *	pBNS,
		ALL_TC_GROUPS *	pTCGroups,
		int	bCheckForbiddenPlus,
		int	bCheckForbiddenMinus
	)

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◆ GetTgroupInfoFromInChI()

int GetTgroupInfoFromInChI	(	T_GROUP_INFO *	ti,
		inp_ATOM *	at,
		AT_NUMB *	endpoint,
		INChI *	pInChI
	)

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◆ InChI2Atom()

int InChI2Atom	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		const char *	szCurHdr,
		long	num_inp,
		StrFromINChI *	pStruct,
		int	iComponent,
		int	iAtNoOffset,
		int	bI2A_Flag,
		int	bHasSomeFixedH,
		InpInChI *	pOneInput
	)

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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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◆ IncrZeroBonds()

void IncrZeroBonds	(	inp_ATOM *	at,
		int	num_at,
		int	iComponent
	)

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◆ IncrZeroBondsAndClearEndpts()

void IncrZeroBondsAndClearEndpts	(	inp_ATOM *	at,
		int	num_at,
		int	iComponent
	)

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◆ insertions_sort_AT_NUMB()

int insertions_sort_AT_NUMB	(	AT_NUMB *	base,
		int	num
	)

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◆ MakeInChIOutOfStrFromINChI2()

int MakeInChIOutOfStrFromINChI2	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip_inp,
		STRUCT_DATA *	sd_inp,
		StrFromINChI *	pStruct,
		int	iComponent,
		int	iAtNoOffset,
		long	num_inp
	)

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◆ MakeOneInChIOutOfStrFromINChI()

int MakeOneInChIOutOfStrFromINChI	(	struct tagCANON_GLOBALS *	pCG,
		struct tagINCHI_CLOCK *	ic,
		ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		StrFromINChI *	pStruct,
		inp_ATOM *	at2,
		inp_ATOM *	at3,
		ALL_TC_GROUPS *	pTCGroups
	)

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◆ MakeOneInChIOutOfStrFromINChI2()

int MakeOneInChIOutOfStrFromINChI2	(	struct tagCANON_GLOBALS *	pCG,
		struct tagINCHI_CLOCK *	ic,
		ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		BN_STRUCT *	pBNS,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		inp_ATOM *	at2,
		inp_ATOM *	at3,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		T_GROUP_INFO **	t_group_info,
		inp_ATOM **	at_norm,
		inp_ATOM **	at_prep
	)

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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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◆ MarkDisconectedIdenticalToReconnected()

int MarkDisconectedIdenticalToReconnected ( InpInChI * pOneInput )

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◆ MergeStructureComponents()

int MergeStructureComponents	(	ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		long	num_inp,
		char *	szCurHdr,
		ICHICONST SRM *	pSrm,
		int	bReqNonTaut,
		StrFromINChI *	pStruct[INCHI_NUM][TAUT_NUM],
		InpInChI *	pOneInput
	)

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◆ MoveChargeFromHeteroatomsToMetals()

int MoveChargeFromHeteroatomsToMetals	(	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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◆ 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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◆ 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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◆ nAddSuperCGroups()

int nAddSuperCGroups ( ALL_TC_GROUPS * pTCGroups )

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◆ nCountBnsSizes()

int nCountBnsSizes	(	inp_ATOM *	at,
		int	num_at,
		int	nAddEdges2eachAtom,
		int	nAddVertices,
		T_GROUP_INFO *	ti,
		VAL_AT *	pVA,
		ICHICONST SRM *	pSrm,
		ALL_TC_GROUPS *	pTCGroups
	)

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◆ nNumEdgesToCnVertex()

int nNumEdgesToCnVertex	(	MY_CONST C_NODE *	pCN,
		int	len,
		int	v
	)

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◆ NormalizeAndCompare()

int NormalizeAndCompare	(	struct tagCANON_GLOBALS *	pCG,
		struct tagINCHI_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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◆ NormalizeStructure()

int NormalizeStructure	(	ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		BN_STRUCT *	pBNS,
		StrFromINChI *	pStruct,
		inp_ATOM *	at,
		inp_ATOM *	at2,
		VAL_AT *	pVA,
		ALL_TC_GROUPS *	pTCGroups,
		inp_ATOM *	at_norm,
		inp_ATOM *	at_fixed_bonds_out,
		T_GROUP_INFO *	t_group_info
	)

◆ nTautEndpointEdgeCap()

int nTautEndpointEdgeCap	(	inp_ATOM *	at,
		VAL_AT *	pVA,
		int	i
	)

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◆ OldPrintCompareOneOrigInchiToRevInChI()

int OldPrintCompareOneOrigInchiToRevInChI	(	StrFromINChI *	pStruct,
		INChI *	pInChI[TAUT_NUM],
		int	bMobileH,
		int	iComponent,
		long	num_inp,
		char *	szCurHdr
	)

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◆ OneInChI2Atom()

int OneInChI2Atom	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip,
		STRUCT_DATA *	sd,
		const char *	szCurHdr,
		long	num_inp,
		StrFromINChI *	pStruct,
		int	iComponent,
		int	iAtNoOffset,
		int	bHasSomeFixedH,
		INChI *	pInChI[]
	)

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◆ OutputInChIOutOfStrFromINChI()

int OutputInChIOutOfStrFromINChI	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		ICHICONST INPUT_PARMS *	ip_inp,
		STRUCT_DATA *	sd_inp,
		long	num_inp,
		int	bINChIOutputOptions,
		INCHI_IOSTREAM *	pout,
		INCHI_IOSTREAM *	plog,
		InpInChI *	pOneInput,
		int	bHasSomeFixedH,
		unsigned char	save_opt_bits
	)

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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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◆ ReallocTCGroups()

int ReallocTCGroups	(	ALL_TC_GROUPS *	pTCGroups,
		int	nAdd
	)

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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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◆ RegisterTCGroup()

int RegisterTCGroup	(	ALL_TC_GROUPS *	pTCGroups,
		int	nGroupType,
		int	nGroupOrdNum,
		int	nVertexCap,
		int	nVertexFlow,
		int	nEdgeCap,
		int	nEdgeFlow,
		int	nNumEdges
	)

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◆ RemoveFixHInChIIdentical2MobH()

void RemoveFixHInChIIdentical2MobH ( InpInChI * pOneInput )

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◆ RemoveForbiddenBondFlowBits()

void RemoveForbiddenBondFlowBits	(	BN_STRUCT *	pBNS,
		int	forbidden_edge_mask_int
	)

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◆ RemoveForbiddenEdgeMask()

void RemoveForbiddenEdgeMask	(	BN_STRUCT *	pBNS,
		EDGE_LIST *	pEdges,
		int	forbidden_edge_mask
	)

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◆ RemoveFromEdgeListByIndex()

int RemoveFromEdgeListByIndex	(	EDGE_LIST *	pEdges,
		int	index
	)

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◆ RemoveFromEdgeListByValue()

int RemoveFromEdgeListByValue	(	EDGE_LIST *	pEdges,
		int	iedge
	)

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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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◆ RestoreAtomMakeBNS()

int RestoreAtomMakeBNS	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_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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◆ 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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◆ RunBnsRestore1()

int RunBnsRestore1	(	struct tagCANON_GLOBALS *	pCG,
		struct tagINCHI_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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◆ RunBnsRestoreOnce()

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

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◆ RunBnsTestOnce()

int RunBnsTestOnce	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		VAL_AT *	pVA,
		Vertex *	pvFirst,
		Vertex *	pvLast,
		int *	pPathLen,
		int *	pnDeltaH,
		int *	pnDeltaCharge,
		int *	pnNumVisitedAtoms
	)

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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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◆ 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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◆ SetEdgeCapFlow()

void SetEdgeCapFlow	(	BNS_EDGE *	e,
		int	edge_cap,
		int	edge_flow
	)

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◆ SetForbiddenEdgeMask()

void SetForbiddenEdgeMask	(	BN_STRUCT *	pBNS,
		EDGE_LIST *	pEdges,
		int	forbidden_edge_mask
	)

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◆ SetStCapFlow()

void SetStCapFlow	(	BNS_VERTEX *	vert_ficpoint,
		int *	tot_st_flow,
		int *	tot_st_cap,
		int	cap,
		int	flow
	)

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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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◆ SetUpSrm()

void SetUpSrm ( SRM * pSrm )

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Variable Documentation

◆ cnList

MY_CONST CN_LIST cnList[]

extern

◆ cnListNumEl

const int cnListNumEl

extern

Data Structures

Macros

Typedefs

Enumerations

Functions

Variables

Macro Definition Documentation

◆ ALLOW_METAL_BOND_ZERO

◆ ATYPE_B

◆ ATYPE_C

◆ ATYPE_Cl

◆ ATYPE_H

◆ ATYPE_Mg

◆ ATYPE_N

◆ ATYPE_Na

◆ ATYPE_O

◆ BFS_Q_CLEAR

◆ BFS_Q_FREE

◆ BOND_MARK_STEREO

◆ BOND_TYPE_STEREO

◆ cn_bits_EN

◆ cn_bits_M

◆ cn_bits_M_

◆ cn_bits_Me

◆ cn_bits_MN

◆ cn_bits_MNP

◆ cn_bits_N

◆ cn_bits_N_

◆ cn_bits_NE

◆ cn_bits_NEN

◆ cn_bits_NM

◆ cn_bits_NMN

◆ cn_bits_NP

◆ cn_bits_NPN

◆ cn_bits_NPNP

◆ cn_bits_P

◆ cn_bits_P_

◆ cn_bits_PN

◆ cn_bits_PNM

◆ cn_bits_PNP

◆ cn_bits_PNPN

◆ cn_bits_shift

◆ cnListIndexMe

◆ EDGE_LIST_CLEAR

◆ EDGE_LIST_FREE

◆ EL_TYPE_C

◆ EL_TYPE_MASK

◆ EL_TYPE_N

◆ EL_TYPE_O

◆ EL_TYPE_OSt

◆ EL_TYPE_P

◆ EL_TYPE_PT

◆ EL_TYPE_S

◆ EL_TYPE_X

◆ EXTRACT_STRUCT_NUMBER

◆ FIX_ADD_PROTON_FOR_ADP

◆ FIX_STEREO_BOND_ORDER

◆ I2A_FLAG_FIXEDH

◆ I2A_FLAG_RECMET

◆ ICHICONST

◆ INC_EDGE_LIST_DEFAULT

◆ INC_NUM_TCGROUPS

◆ INI_NUM_TCGROUPS

◆ INIT_METAL_BOND_FLOW

◆ INIT_METAL_BOND_ZERO

◆ KEEP_METAL_EDGE_FLOW

◆ MAKE_CN_BITS

◆ MAX_CN_VAL

◆ MAX_DIFF_FIXH

◆ MAX_DIFF_MOBH

◆ MAX_NUM_CN_BITS

◆ METAL_FREE_CHARGE_VAL

◆ MOVE_CHARGES_FROM_HETEREO_TO_METAL

◆ MY_CONST

◆ NO_VALUE_INT

◆ NOT_READ_INT

◆ RESET_EDGE_FORBIDDEN_MASK

◆ RI_ERR_ALLOC

◆ RI_ERR_EOF

◆ RI_ERR_EOL