#include "incomdef.h"
#include "inpdef.h"

Include dependency graph for ichi_bns.h:

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

Data Structures
struct	BnsEdge

struct	BnsStEdge

struct	BnsVertex

union	BnsAltPath

struct	BalancedNetworkStructure

struct	BalancedNetworkData

struct	BN_AtomsAtTautGroup

struct	tagBNS_FLOW_CHANGES

struct	tagNodeSet

Macros
#define	BN_MAX_ALTP 16

#define	BNS_EDGE_FORBIDDEN_MASK 1

#define	BNS_EDGE_FORBIDDEN_TEMP 2

#define	BNS_EDGE_FORBIDDEN_TEST 4

#define	BNS_VERT_TYPE_ATOM 0x0001

#define	BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */

#define	BNS_VERT_TYPE_TGROUP 0x0004

#define	BNS_VERT_TYPE_C_POINT 0x0008

#define	BNS_VERT_TYPE_C_GROUP 0x0010

#define	BNS_VERT_TYPE_SUPER_TGROUP 0x0020

#define	BNS_VERT_TYPE_TEMP 0x0040

#define	BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */

#define	BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */

#define	BNS_VERT_TYPE_ACID 0x0200 /* only for this type are allowed paths: t_group-atom-c_group_neg (path_TACN) */

#define	BNS_VERT_TYPE_CARBON_GR 0x0400 /* charge of carbon atom; should be used with BNS_VT_C_POS, BNS_VT_C_NEG */

#define	BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */

#define	BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP \| BNS_VERT_TYPE_C_GROUP \| BNS_VERT_TYPE_SUPER_TGROUP)

#define	BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */

#define	BNS_VT_C_NEG (BNS_VERT_TYPE_C_GROUP \| BNS_VERT_TYPE_C_NEGATIVE) /* negative charge group, heteroat */

#define	BNS_VT_C_POS_C (BNS_VT_C_POS \| BNS_VERT_TYPE_CARBON_GR) /* positive charge group, C, Si, Ge, Sn */

#define	BNS_VT_C_NEG_C (BNS_VT_C_NEG \| BNS_VERT_TYPE_CARBON_GR) /* negative charge group, C, Si, Ge, Sn */

#define	BNS_VT_C_POS_M (BNS_VT_C_POS \| BNS_VERT_TYPE_METAL_GR) /* positive charge group, metal */

#define	BNS_VT_C_NEG_M (BNS_VT_C_NEG \| BNS_VERT_TYPE_METAL_GR) /* negative charge group, metal */

#define	BNS_VT_M_GROUP BNS_VERT_TYPE_METAL_GR /* metal-group, flower vertex */

#define	BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP \| BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */

#define	BNS_VT_C_NEG_ALL (BNS_VT_C_POS_ALL \| BNS_VERT_TYPE_C_NEGATIVE) /* supergroup (-) */

#define	BNS_VT_CHRG_STRUCT (BNS_VERT_TYPE__AUX \| BNS_VERT_TYPE_TEMP) /* ChargeStruct vertex */

#define	BNS_VT_YVCONNECTOR BNS_VERT_TYPE__AUX /* group connection */

#define	IS_BNS_VT_C_OR_CSUPER_GR(X) ((X) & BNS_VT_C_POS)

#define	IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP)

#define	IS_BNS_VT_CM_GR(X) (((X) & BNS_VT_C_POS_M) == BNS_VT_C_POS_M) /* metal charge group */

#define	IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */

#define	IS_BNS_VT_YVCONNECTOR(X) (((X) & BNS_VERT_TYPE__AUX) && !((X) & BNS_VERT_TYPE_TEMP))

#define	IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP))

#define	IS_BNS_VT_ATOM(X) ((X) & BNS_VERT_TYPE_ATOM)

#define	BNS_ADD_SUPER_TGROUP 1 /* reserve one more edge for a t-group to connect to a single super-t-group */

#define	NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */

#define	BNS_ADD_ATOMS 2 /* max. number of fictitious atoms to add (except t-gtoups) */

#define	BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */

#define	ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/

#define	ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number

#define	ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number

#define	ALTP_THIS_ATOM_NEIGHBOR(altp, X) (altp)[iALTP_NEIGHBOR+(X)].ineigh[0] /* 0 <= X < path_len */

#define	ALTP_NEXT_ATOM_NEIGHBOR(altp, X) (altp)[iALTP_NEIGHBOR+(X)].ineigh[1]

#define	ALTP_CUR_THIS_ATOM_NEIGHBOR(altp) (altp)[iALTP_NEIGHBOR+ALTP_PATH_LEN(altp)].ineigh[0] /* 0 <= X < path_len */

#define	ALTP_CUR_NEXT_ATOM_NEIGHBOR(altp) (altp)[iALTP_NEIGHBOR+ALTP_PATH_LEN(altp)].ineigh[1]

#define	ALTP_NEXT(altp) (++ALTP_PATH_LEN(altp))

#define	ALTP_PREV(altp) (--ALTP_PATH_LEN(altp))

#define	ALTP_MAY_ADD(altp) (iALTP_NEIGHBOR + (altp)[iALTP_PATH_LEN].number < (altp)[iALTP_MAX_LEN].number)

#define	ALTP_ALLOCATED_LEN(altp) (altp)[iALTP_MAX_LEN].number

#define	ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0]

#define	ALTP_OVERFLOW(altp) (altp)[iALTP_FLOW].flow[1]

#define	Vertex_s 0

#define	Vertex_t 1

#define	NO_VERTEX -2

#define	BLOSSOM_BASE -1

#define	ADD_CAPACITY_RADICAL 1 /* add capacity to radical */

#define	MAX_BOND_EDGE_CAP 2 /* triple bond */

#define	AROM_BOND_EDGE_CAP 1

#define	MAX_TGROUP_EDGE_CAP 2 /* -NH2 provides max. capacity */

#define	EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */

#define	EDGE_FLOW_ST_PATH 0x4000 /* mark: the edge belongs to the augmenting path */

#define	EDGE_FLOW_MASK 0x3fff /* mask for flow */

#define	EDGE_FLOW_PATH 0x4000 /* mark: the edge belongs to the augmenting path */

#define	MAX_AT_FLOW(X)

#define	MAX_ALT_AATG_ARRAY_LEN 127

#define	AATG_MARK_IN_PATH 1 /* atom in path detected by the BNS */

#define	AATG_MARK_WAS_IN_PATH 2 /* found to be in path before next level */

#define	AATG_MARK_MAIN_TYPE 4 /* atom O-"salt" */

#define	AATG_MARK_OTHER_TYPE 8 /* other atom to be tested */

#define	ALT_PATH_MODE_TAUTOM 1

#define	ALT_PATH_MODE_CHARGE 2

#define	ALT_PATH_MODE_4_SALT 3 /* mark alt bonds along the path */

#define	ALT_PATH_MODE_4_SALT2 4 /* mark alt bonds along the path, path to taut. group fict. vertex if exists */

#define	ALT_PATH_MODE_REM2H_CHG 5 /* remove 2 H along alt. path AH-=-BH => A=-=B and change bonds to alternating */

#define	ALT_PATH_MODE_ADD2H_CHG 6 /* add 2 H along alt. path A=-=B => AH-=-BH and change bonds to alternating */

#define	ALT_PATH_MODE_REM2H_TST 7 /* test-remove 2 H along alt. path AH-=-BH => A=-=B; restore changed bonds */

#define	ALT_PATH_MODE_ADD2H_TST 8 /* test-add 2 H along alt. path A=-=B => AH-=-BH; restore changed bonds */

#define	ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */

#define	ALT_PATH_MODE_TAUTOM_KET 10 /* same as ALT_PATH_MODE_TAUTOM, applies to C=-OH or CH-=O; H may be (-) */

#define	ALT_PATH_MODE_TAUTOM_PT_22_00 11

#define	ALT_PATH_MODE_TAUTOM_PT_16_00 12

#define	ALT_PATH_MODE_TAUTOM_PT_06_00 13

#define	ALT_PATH_MODE_TAUTOM_PT_39_00 14

#define	ALT_PATH_MODE_TAUTOM_PT_13_00 15

#define	ALT_PATH_MODE_TAUTOM_PT_18_00 16

#define	BIT_WORD_MASK ((bitWord)~0)

#define	BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */

#define	BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */

#define	BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW \| BNS_EF_RSTR_FLOW)

#define	BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */

#define	BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */

#define	BNS_EF_UPD_RAD_ORI

#define	BNS_EF_SET_NOSTEREO

#define	BNS_EF_UPD_H_CHARGE 64 /* update charges and H-counts according to change flow to c- and t-group vertices */

#define	BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW \| BNS_EF_CHNG_BONDS \| BNS_EF_UPD_RAD_ORI)

#define	BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS \| BNS_EF_SET_NOSTEREO)

#define	BNS_EF_RAD_SRCH 128 /* search for rafical paths closures */

Typedefs
typedef int	Vertex

typedef int	EdgeIndex

typedef int	Edge[2]

typedef int	BNS_IEDGE

typedef int	EdgeFlow

typedef int	VertexFlow

typedef enum tagAltPathConst	ALT_CONST

typedef struct BnsEdge	BNS_EDGE

typedef struct BnsStEdge	BNS_ST_EDGE

typedef struct BnsVertex	BNS_VERTEX

typedef union BnsAltPath	BNS_ALT_PATH

typedef struct BalancedNetworkStructure	BN_STRUCT

typedef enum tagBnsRadSrchMode	BRS_MODE

typedef struct BalancedNetworkData	BN_DATA

typedef struct BN_AtomsAtTautGroup	BN_AATG

typedef struct tagBNS_FLOW_CHANGES	BNS_FLOW_CHANGES

typedef U_SHORT	bitWord

typedef struct tagNodeSet	NodeSet

Enumerations
enum	tagAltPathConst { iALTP_MAX_LEN , iALTP_FLOW , iALTP_PATH_LEN , iALTP_START_ATOM , iALTP_END_ATOM , iALTP_NEIGHBOR , iALTP_HDR_LEN = iALTP_NEIGHBOR }

enum	tagBnsRadSrchMode { RAD_SRCH_NORM = 0 , RAD_SRCH_FROM_FICT = 1 }

Functions
int	NodeSetCreate (struct tagCANON_GLOBALS pCG, NodeSet pSet, int n, int L)

void	NodeSetFree (struct tagCANON_GLOBALS pCG, NodeSet pSet)

int	IsNodeSetEmpty (NodeSet *cur_nodes, int k)

int	DoNodeSetsIntersect (NodeSet *cur_nodes, int k1, int k2)

void	AddNodeSet2ToNodeSet1 (NodeSet *cur_nodes, int k1, int k2)

void	NodeSetFromRadEndpoints (struct tagCANON_GLOBALS pCG, NodeSet cur_nodes, int k, Vertex RadEndpoints[], int num_v)

void	RemoveFromNodeSet (struct tagCANON_GLOBALS pCG, NodeSet cur_nodes, int k, Vertex v[], int num_v)

int	AddNodesToRadEndpoints (struct tagCANON_GLOBALS pCG, NodeSet cur_nodes, int k, Vertex RadEndpoints[], Vertex vRad, int nStart, int nLen)

int	nExists2AtMoveAltPath (struct BalancedNetworkStructure pBNS, struct BalancedNetworkData pBD, struct BN_AtomsAtTautGroup pAATG, inp_ATOM at, int num_atoms, int jj2, int jj1, struct tagSaltChargeCandidate s_candidate, int nNumCandidates, AT_NUMB nForbiddenAtom, int nNumForbiddenAtoms)

int	bExistsAltPath (struct tagCANON_GLOBALS pCG, struct BalancedNetworkStructure pBNS, struct BalancedNetworkData pBD, struct BN_AtomsAtTautGroup pAATG, inp_ATOM *at, int num_atoms, int nVertDoubleBond, int nVertSingleBond, int path_type)

int	bExistsAnyAltPath (struct tagCANON_GLOBALS pCG, struct BalancedNetworkStructure pBNS, struct BalancedNetworkData pBD, inp_ATOM at, int num_atoms, int nVertDoubleBond, int nVertSingleBond, int path_type)

int	AddTGroups2BnStruct (struct tagCANON_GLOBALS pCG, struct BalancedNetworkStructure pBNS, inp_ATOM at, int num_atoms, struct tagTautomerGroupsInfo tgi)

int	AddSuperTGroup2BnStruct (struct BalancedNetworkStructure pBNS, inp_ATOM at, int num_atoms, struct tagTautomerGroupsInfo *tgi)

int	AddCGroups2BnStruct (struct tagCANON_GLOBALS pCG, struct BalancedNetworkStructure pBNS, inp_ATOM at, int num_atoms, struct tagChargeGroupsInfo cgi)

int	ReInitBnStruct (struct BalancedNetworkStructure pBNS, inp_ATOM at, int num_at, int bRemoveGroupsFromAtoms)

int	ReInitBnStructAddGroups (struct tagCANON_GLOBALS pCG, struct BalancedNetworkStructure pBNS, inp_ATOM at, int num_atoms, struct tagTautomerGroupsInfo tgi, struct tagChargeGroupsInfo *cgi)

int	DisconnectTestAtomFromTGroup (struct BalancedNetworkStructure pBNS, int v1, int pv2, BNS_FLOW_CHANGES *fcd)

int	DisconnectTGroupFromSuperTGroup (struct BalancedNetworkStructure pBNS, int v1, int pv1, int pv2, BNS_FLOW_CHANGES fcd)

int	ReconnectTestAtomToTGroup (struct BalancedNetworkStructure pBNS, int v1, int v2, int ie, BNS_FLOW_CHANGES fcd)

int	bIsHardRemHCandidate (inp_ATOM at, int i, int cSubType)

int	RunBalancedNetworkSearch (BN_STRUCT pBNS, BN_DATA pBD, int bChangeFlow)

BN_STRUCT *	AllocateAndInitBnStruct (inp_ATOM at, int num_atoms, int nMaxAddAtoms, int nMaxAddEdges, int max_altp, int num_changed_bonds)

BN_STRUCT *	DeAllocateBnStruct (BN_STRUCT *pBNS)

int	ReInitBnStructAltPaths (BN_STRUCT *pBNS)

int	ReInitBnStructForMoveableAltBondTest (BN_STRUCT pBNS, inp_ATOM at, int num_atoms)

void	ClearAllBnDataVertices (Vertex *v, Vertex value, int size)

void	ClearAllBnDataEdges (Edge *e, Vertex value, int size)

BN_DATA *	DeAllocateBnData (BN_DATA *pBD)

BN_DATA *	AllocateAndInitBnData (int max_num_vertices)

int	ReInitBnData (BN_DATA *pBD)

int	SetForbiddenEdges (BN_STRUCT pBNS, inp_ATOM at, int num_atoms, int edge_forbidden_mask, int nebend, int *ebend)

int	BalancedNetworkSearch (BN_STRUCT pBNS, BN_DATA pBD, int bChangeFlow)

int	SetRadEndpoints (BN_STRUCT pBNS, BN_DATA pBD, BRS_MODE bRadSrchMode)

int	SetRadEndpoints2 (struct tagCANON_GLOBALS pCG, BN_STRUCT pBNS, BN_DATA *pBD, BRS_MODE bRadSrchMode)

int	RemoveRadEndpoints (BN_STRUCT pBNS, BN_DATA pBD, inp_ATOM *at)

int	AddRemoveProtonsRestr (inp_ATOM at, int num_atoms, int num_protons_to_add, int nNumProtAddedByRestr, INCHI_MODE bNormalizationFlags, int num_tg, int nChargeRevrs, int nChargeInChI)

int	AddRemoveIsoProtonsRestr (inp_ATOM *at, int num_atoms, NUM_H num_protons_to_add[], int num_tg)

Macro Definition Documentation

◆ AATG_MARK_IN_PATH

#define AATG_MARK_IN_PATH 1 /* atom in path detected by the BNS */

◆ AATG_MARK_MAIN_TYPE

#define AATG_MARK_MAIN_TYPE 4 /* atom O-"salt" */

◆ AATG_MARK_OTHER_TYPE

#define AATG_MARK_OTHER_TYPE 8 /* other atom to be tested */

◆ AATG_MARK_WAS_IN_PATH

#define AATG_MARK_WAS_IN_PATH 2 /* found to be in path before next level */

◆ ADD_CAPACITY_RADICAL

#define ADD_CAPACITY_RADICAL 1 /* add capacity to radical */

◆ ALT_PATH_MODE_4_SALT

#define ALT_PATH_MODE_4_SALT 3 /* mark alt bonds along the path */

◆ ALT_PATH_MODE_4_SALT2

#define ALT_PATH_MODE_4_SALT2 4 /* mark alt bonds along the path, path to taut. group fict. vertex if exists */

◆ ALT_PATH_MODE_ADD2H_CHG

#define ALT_PATH_MODE_ADD2H_CHG 6 /* add 2 H along alt. path A=-=B => AH-=-BH and change bonds to alternating */

◆ ALT_PATH_MODE_ADD2H_TST

#define ALT_PATH_MODE_ADD2H_TST 8 /* test-add 2 H along alt. path A=-=B => AH-=-BH; restore changed bonds */

◆ ALT_PATH_MODE_CHARGE

#define ALT_PATH_MODE_CHARGE 2

◆ ALT_PATH_MODE_REM2H_CHG

#define ALT_PATH_MODE_REM2H_CHG 5 /* remove 2 H along alt. path AH-=-BH => A=-=B and change bonds to alternating */

◆ ALT_PATH_MODE_REM2H_TST

#define ALT_PATH_MODE_REM2H_TST 7 /* test-remove 2 H along alt. path AH-=-BH => A=-=B; restore changed bonds */

◆ ALT_PATH_MODE_REM_PROTON

#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */

◆ ALT_PATH_MODE_TAUTOM

#define ALT_PATH_MODE_TAUTOM 1

◆ ALT_PATH_MODE_TAUTOM_KET

#define ALT_PATH_MODE_TAUTOM_KET 10 /* same as ALT_PATH_MODE_TAUTOM, applies to C=-OH or CH-=O; H may be (-) */

◆ ALT_PATH_MODE_TAUTOM_PT_06_00

#define ALT_PATH_MODE_TAUTOM_PT_06_00 13

◆ ALT_PATH_MODE_TAUTOM_PT_13_00

#define ALT_PATH_MODE_TAUTOM_PT_13_00 15

◆ ALT_PATH_MODE_TAUTOM_PT_16_00

#define ALT_PATH_MODE_TAUTOM_PT_16_00 12

◆ ALT_PATH_MODE_TAUTOM_PT_18_00

#define ALT_PATH_MODE_TAUTOM_PT_18_00 16

◆ ALT_PATH_MODE_TAUTOM_PT_22_00

#define ALT_PATH_MODE_TAUTOM_PT_22_00 11

◆ ALT_PATH_MODE_TAUTOM_PT_39_00

#define ALT_PATH_MODE_TAUTOM_PT_39_00 14

◆ ALTP_ALLOCATED_LEN

#define ALTP_ALLOCATED_LEN ( altp ) (altp)[iALTP_MAX_LEN].number

◆ ALTP_CUR_NEXT_ATOM_NEIGHBOR

#define ALTP_CUR_NEXT_ATOM_NEIGHBOR ( altp ) (altp)[iALTP_NEIGHBOR+ALTP_PATH_LEN(altp)].ineigh[1]

◆ ALTP_CUR_THIS_ATOM_NEIGHBOR

#define ALTP_CUR_THIS_ATOM_NEIGHBOR ( altp ) (altp)[iALTP_NEIGHBOR+ALTP_PATH_LEN(altp)].ineigh[0] /* 0 <= X < path_len */

◆ ALTP_DELTA

#define ALTP_DELTA ( altp ) (altp)[iALTP_FLOW].flow[0]

◆ ALTP_END_ATOM

#define ALTP_END_ATOM ( altp ) (altp)[iALTP_END_ATOM].number

◆ ALTP_MAY_ADD

#define ALTP_MAY_ADD ( altp ) (iALTP_NEIGHBOR + (altp)[iALTP_PATH_LEN].number < (altp)[iALTP_MAX_LEN].number)

◆ ALTP_NEXT

#define ALTP_NEXT ( altp ) (++ALTP_PATH_LEN(altp))

◆ ALTP_NEXT_ATOM_NEIGHBOR

#define ALTP_NEXT_ATOM_NEIGHBOR	(	altp,
		X
	)	(altp)[iALTP_NEIGHBOR+(X)].ineigh[1]

◆ ALTP_OVERFLOW

#define ALTP_OVERFLOW ( altp ) (altp)[iALTP_FLOW].flow[1]

◆ ALTP_PATH_LEN

#define ALTP_PATH_LEN ( altp ) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/

◆ ALTP_PREV

#define ALTP_PREV ( altp ) (--ALTP_PATH_LEN(altp))

◆ ALTP_START_ATOM

#define ALTP_START_ATOM ( altp ) (altp)[iALTP_START_ATOM].number

◆ ALTP_THIS_ATOM_NEIGHBOR

#define ALTP_THIS_ATOM_NEIGHBOR	(	altp,
		X
	)	(altp)[iALTP_NEIGHBOR+(X)].ineigh[0] /* 0 <= X < path_len */

◆ AROM_BOND_EDGE_CAP

#define AROM_BOND_EDGE_CAP 1

◆ BIT_WORD_MASK

#define BIT_WORD_MASK ((bitWord)~0)

◆ BLOSSOM_BASE

#define BLOSSOM_BASE -1

◆ BN_MAX_ALTP

#define BN_MAX_ALTP 16

◆ BNS_ADD_ATOMS

#define BNS_ADD_ATOMS 2 /* max. number of fictitious atoms to add (except t-gtoups) */

◆ BNS_ADD_EDGES

#define BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */

◆ BNS_ADD_SUPER_TGROUP

#define BNS_ADD_SUPER_TGROUP 1 /* reserve one more edge for a t-group to connect to a single super-t-group */

◆ BNS_EDGE_FORBIDDEN_MASK

#define BNS_EDGE_FORBIDDEN_MASK 1

◆ BNS_EDGE_FORBIDDEN_TEMP

#define BNS_EDGE_FORBIDDEN_TEMP 2

◆ BNS_EDGE_FORBIDDEN_TEST

#define BNS_EDGE_FORBIDDEN_TEST 4

◆ BNS_EF_ALTR_BONDS

#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */

◆ BNS_EF_ALTR_NS

#define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO)

◆ BNS_EF_CHNG_BONDS

#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */

◆ BNS_EF_CHNG_FLOW

#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */

◆ BNS_EF_CHNG_RSTR

#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW)

◆ BNS_EF_RAD_SRCH

#define BNS_EF_RAD_SRCH 128 /* search for rafical paths closures */

◆ BNS_EF_RSTR_FLOW

#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */

◆ BNS_EF_SAVE_ALL

#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI)

◆ BNS_EF_SET_NOSTEREO

#define BNS_EF_SET_NOSTEREO

Value:

32 /* in combination with BNS_EF_ALTR_BONDS only:

ALT12 bond cannot be stereogenic */

◆ BNS_EF_UPD_H_CHARGE

#define BNS_EF_UPD_H_CHARGE 64 /* update charges and H-counts according to change flow to c- and t-group vertices */

◆ BNS_EF_UPD_RAD_ORI

#define BNS_EF_UPD_RAD_ORI

Value:

16 /* update BN flow0 & Atom radical values:

flow0 := flow, radical:=st_cap - st_flow */

◆ BNS_VERT_TYPE__AUX

#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */

◆ BNS_VERT_TYPE_ACID

#define BNS_VERT_TYPE_ACID 0x0200 /* only for this type are allowed paths: t_group-atom-c_group_neg (path_TACN) */

◆ BNS_VERT_TYPE_ANY_GROUP

#define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP)

◆ BNS_VERT_TYPE_ATOM

#define BNS_VERT_TYPE_ATOM 0x0001

◆ BNS_VERT_TYPE_C_GROUP

#define BNS_VERT_TYPE_C_GROUP 0x0010

◆ BNS_VERT_TYPE_C_NEGATIVE

#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */

◆ BNS_VERT_TYPE_C_POINT

#define BNS_VERT_TYPE_C_POINT 0x0008

◆ BNS_VERT_TYPE_CARBON_GR

#define BNS_VERT_TYPE_CARBON_GR 0x0400 /* charge of carbon atom; should be used with BNS_VT_C_POS, BNS_VT_C_NEG */

◆ BNS_VERT_TYPE_ENDPOINT

#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */

◆ BNS_VERT_TYPE_METAL_GR

#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */

◆ BNS_VERT_TYPE_SUPER_TGROUP

#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020

◆ BNS_VERT_TYPE_TEMP

#define BNS_VERT_TYPE_TEMP 0x0040

◆ BNS_VERT_TYPE_TGROUP

#define BNS_VERT_TYPE_TGROUP 0x0004

◆ BNS_VT_C_NEG

#define BNS_VT_C_NEG (BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE) /* negative charge group, heteroat */

◆ BNS_VT_C_NEG_ALL

#define BNS_VT_C_NEG_ALL (BNS_VT_C_POS_ALL | BNS_VERT_TYPE_C_NEGATIVE) /* supergroup (-) */

◆ BNS_VT_C_NEG_C

#define BNS_VT_C_NEG_C (BNS_VT_C_NEG | BNS_VERT_TYPE_CARBON_GR) /* negative charge group, C, Si, Ge, Sn */

◆ BNS_VT_C_NEG_M

#define BNS_VT_C_NEG_M (BNS_VT_C_NEG | BNS_VERT_TYPE_METAL_GR) /* negative charge group, metal */

◆ BNS_VT_C_POS

#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */

◆ BNS_VT_C_POS_ALL

#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */

◆ BNS_VT_C_POS_C

#define BNS_VT_C_POS_C (BNS_VT_C_POS | BNS_VERT_TYPE_CARBON_GR) /* positive charge group, C, Si, Ge, Sn */

◆ BNS_VT_C_POS_M

#define BNS_VT_C_POS_M (BNS_VT_C_POS | BNS_VERT_TYPE_METAL_GR) /* positive charge group, metal */

◆ BNS_VT_CHRG_STRUCT

#define BNS_VT_CHRG_STRUCT (BNS_VERT_TYPE__AUX | BNS_VERT_TYPE_TEMP) /* ChargeStruct vertex */

◆ BNS_VT_M_GROUP

#define BNS_VT_M_GROUP BNS_VERT_TYPE_METAL_GR /* metal-group, flower vertex */

◆ BNS_VT_YVCONNECTOR

#define BNS_VT_YVCONNECTOR BNS_VERT_TYPE__AUX /* group connection */

◆ EDGE_FLOW_MASK

#define EDGE_FLOW_MASK 0x3fff /* mask for flow */

◆ EDGE_FLOW_PATH

#define EDGE_FLOW_PATH 0x4000 /* mark: the edge belongs to the augmenting path */

◆ EDGE_FLOW_ST_MASK

#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */

◆ EDGE_FLOW_ST_PATH

#define EDGE_FLOW_ST_PATH 0x4000 /* mark: the edge belongs to the augmenting path */

◆ IS_BNS_VT_ATOM

#define IS_BNS_VT_ATOM ( X ) ((X) & BNS_VERT_TYPE_ATOM)

◆ IS_BNS_VT_C_GR

#define IS_BNS_VT_C_GR ( X ) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP)

◆ IS_BNS_VT_C_OR_CSUPER_GR

#define IS_BNS_VT_C_OR_CSUPER_GR ( X ) ((X) & BNS_VT_C_POS)

◆ IS_BNS_VT_CHRG_STRUCT

#define IS_BNS_VT_CHRG_STRUCT ( X ) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP))

◆ IS_BNS_VT_CM_GR

#define IS_BNS_VT_CM_GR ( X ) (((X) & BNS_VT_C_POS_M) == BNS_VT_C_POS_M) /* metal charge group */

◆ IS_BNS_VT_M_GR

#define IS_BNS_VT_M_GR ( X ) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */

◆ IS_BNS_VT_YVCONNECTOR

#define IS_BNS_VT_YVCONNECTOR ( X ) (((X) & BNS_VERT_TYPE__AUX) && !((X) & BNS_VERT_TYPE_TEMP))

◆ MAX_ALT_AATG_ARRAY_LEN

#define MAX_ALT_AATG_ARRAY_LEN 127

◆ MAX_AT_FLOW

#define MAX_AT_FLOW ( X )

Value:

                       (((X).chem_bonds_valence - (X).valence)+\
                       ((is_centerpoint_elem((X).el_number)||get_endpoint_valence((X).el_number))?\
                           (((X).radical==RADICAL_DOUBLET)/*+2*((X).radical==RADICAL_TRIPLET)*/):0))

◆ MAX_BOND_EDGE_CAP

#define MAX_BOND_EDGE_CAP 2 /* triple bond */

◆ MAX_TGROUP_EDGE_CAP

#define MAX_TGROUP_EDGE_CAP 2 /* -NH2 provides max. capacity */

◆ NO_VERTEX

#define NO_VERTEX -2

◆ NUM_KINDS_OF_GROUPS

#define NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */

◆ Vertex_s

#define Vertex_s 0

◆ Vertex_t

#define Vertex_t 1

Typedef Documentation

◆ ALT_CONST

typedef enum tagAltPathConst ALT_CONST

◆ bitWord

typedef U_SHORT bitWord

◆ BN_AATG

typedef struct BN_AtomsAtTautGroup BN_AATG

◆ BN_DATA

typedef struct BalancedNetworkData BN_DATA

◆ BN_STRUCT

typedef struct BalancedNetworkStructure BN_STRUCT

◆ BNS_ALT_PATH

typedef union BnsAltPath BNS_ALT_PATH

◆ BNS_EDGE

typedef struct BnsEdge BNS_EDGE

◆ BNS_FLOW_CHANGES

typedef struct tagBNS_FLOW_CHANGES BNS_FLOW_CHANGES

◆ BNS_IEDGE

typedef int BNS_IEDGE

◆ BNS_ST_EDGE

typedef struct BnsStEdge BNS_ST_EDGE

◆ BNS_VERTEX

typedef struct BnsVertex BNS_VERTEX

◆ BRS_MODE

typedef enum tagBnsRadSrchMode BRS_MODE

◆ Edge

typedef int Edge[2]

◆ EdgeFlow

typedef int EdgeFlow

◆ EdgeIndex

typedef int EdgeIndex

◆ NodeSet

typedef struct tagNodeSet NodeSet

◆ Vertex

typedef int Vertex

◆ VertexFlow

typedef int VertexFlow

Enumeration Type Documentation

◆ tagAltPathConst

enum tagAltPathConst

Enumerator
iALTP_MAX_LEN
iALTP_FLOW
iALTP_PATH_LEN
iALTP_START_ATOM
iALTP_END_ATOM
iALTP_NEIGHBOR
iALTP_HDR_LEN

◆ tagBnsRadSrchMode

enum tagBnsRadSrchMode

Enumerator
RAD_SRCH_NORM
RAD_SRCH_FROM_FICT

Function Documentation

◆ AddCGroups2BnStruct()

int AddCGroups2BnStruct	(	struct tagCANON_GLOBALS *	pCG,
		struct BalancedNetworkStructure *	pBNS,
		inp_ATOM *	at,
		int	num_atoms,
		struct tagChargeGroupsInfo *	cgi
	)

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◆ AddNodeSet2ToNodeSet1()

void AddNodeSet2ToNodeSet1	(	NodeSet *	cur_nodes,
		int	k1,
		int	k2
	)

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◆ AddNodesToRadEndpoints()

int AddNodesToRadEndpoints	(	struct tagCANON_GLOBALS *	pCG,
		NodeSet *	cur_nodes,
		int	k,
		Vertex	RadEndpoints[],
		Vertex	vRad,
		int	nStart,
		int	nLen
	)

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◆ AddRemoveIsoProtonsRestr()

int AddRemoveIsoProtonsRestr	(	inp_ATOM *	at,
		int	num_atoms,
		NUM_H	num_protons_to_add[],
		int	num_tg
	)

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◆ AddRemoveProtonsRestr()

int AddRemoveProtonsRestr	(	inp_ATOM *	at,
		int	num_atoms,
		int *	num_protons_to_add,
		int	nNumProtAddedByRestr,
		INCHI_MODE	bNormalizationFlags,
		int	num_tg,
		int	nChargeRevrs,
		int	nChargeInChI
	)

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◆ AddSuperTGroup2BnStruct()

int AddSuperTGroup2BnStruct	(	struct BalancedNetworkStructure *	pBNS,
		inp_ATOM *	at,
		int	num_atoms,
		struct tagTautomerGroupsInfo *	tgi
	)

◆ AddTGroups2BnStruct()

int AddTGroups2BnStruct	(	struct tagCANON_GLOBALS *	pCG,
		struct BalancedNetworkStructure *	pBNS,
		inp_ATOM *	at,
		int	num_atoms,
		struct tagTautomerGroupsInfo *	tgi
	)

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◆ AllocateAndInitBnData()

BN_DATA * AllocateAndInitBnData ( int max_num_vertices )

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◆ AllocateAndInitBnStruct()

BN_STRUCT * AllocateAndInitBnStruct	(	inp_ATOM *	at,
		int	num_atoms,
		int	nMaxAddAtoms,
		int	nMaxAddEdges,
		int	max_altp,
		int *	num_changed_bonds
	)

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◆ BalancedNetworkSearch()

int BalancedNetworkSearch	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		int	bChangeFlow
	)

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◆ bExistsAltPath()

int bExistsAltPath	(	struct tagCANON_GLOBALS *	pCG,
		struct BalancedNetworkStructure *	pBNS,
		struct BalancedNetworkData *	pBD,
		struct BN_AtomsAtTautGroup *	pAATG,
		inp_ATOM *	at,
		int	num_atoms,
		int	nVertDoubleBond,
		int	nVertSingleBond,
		int	path_type
	)

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◆ bExistsAnyAltPath()

int bExistsAnyAltPath	(	struct tagCANON_GLOBALS *	pCG,
		struct BalancedNetworkStructure *	pBNS,
		struct BalancedNetworkData *	pBD,
		inp_ATOM *	at,
		int	num_atoms,
		int	nVertDoubleBond,
		int	nVertSingleBond,
		int	path_type
	)

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◆ bIsHardRemHCandidate()

int bIsHardRemHCandidate	(	inp_ATOM *	at,
		int	i,
		int *	cSubType
	)

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◆ ClearAllBnDataEdges()

void ClearAllBnDataEdges	(	Edge *	e,
		Vertex	value,
		int	size
	)

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◆ ClearAllBnDataVertices()

void ClearAllBnDataVertices	(	Vertex *	v,
		Vertex	value,
		int	size
	)

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◆ DeAllocateBnData()

BN_DATA * DeAllocateBnData ( BN_DATA * pBD )

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◆ DeAllocateBnStruct()

BN_STRUCT * DeAllocateBnStruct ( BN_STRUCT * pBNS )

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◆ DisconnectTestAtomFromTGroup()

int DisconnectTestAtomFromTGroup	(	struct BalancedNetworkStructure *	pBNS,
		int	v1,
		int *	pv2,
		BNS_FLOW_CHANGES *	fcd
	)

◆ DisconnectTGroupFromSuperTGroup()

int DisconnectTGroupFromSuperTGroup	(	struct BalancedNetworkStructure *	pBNS,
		int	v1,
		int *	pv1,
		int *	pv2,
		BNS_FLOW_CHANGES *	fcd
	)

◆ DoNodeSetsIntersect()

int DoNodeSetsIntersect	(	NodeSet *	cur_nodes,
		int	k1,
		int	k2
	)

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◆ IsNodeSetEmpty()

int IsNodeSetEmpty	(	NodeSet *	cur_nodes,
		int	k
	)

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◆ nExists2AtMoveAltPath()

int nExists2AtMoveAltPath	(	struct BalancedNetworkStructure *	pBNS,
		struct BalancedNetworkData *	pBD,
		struct BN_AtomsAtTautGroup *	pAATG,
		inp_ATOM *	at,
		int	num_atoms,
		int	jj2,
		int	jj1,
		struct tagSaltChargeCandidate *	s_candidate,
		int	nNumCandidates,
		AT_NUMB *	nForbiddenAtom,
		int	nNumForbiddenAtoms
	)

◆ NodeSetCreate()

int NodeSetCreate	(	struct tagCANON_GLOBALS *	pCG,
		NodeSet *	pSet,
		int	n,
		int	L
	)

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◆ NodeSetFree()

void NodeSetFree	(	struct tagCANON_GLOBALS *	pCG,
		NodeSet *	pSet
	)

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◆ NodeSetFromRadEndpoints()

void NodeSetFromRadEndpoints	(	struct tagCANON_GLOBALS *	pCG,
		NodeSet *	cur_nodes,
		int	k,
		Vertex	RadEndpoints[],
		int	num_v
	)

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◆ ReconnectTestAtomToTGroup()

int ReconnectTestAtomToTGroup	(	struct BalancedNetworkStructure *	pBNS,
		int	v1,
		int	v2,
		int	ie,
		BNS_FLOW_CHANGES *	fcd
	)

◆ ReInitBnData()

int ReInitBnData ( BN_DATA * pBD )

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◆ ReInitBnStruct()

int ReInitBnStruct	(	struct BalancedNetworkStructure *	pBNS,
		inp_ATOM *	at,
		int	num_at,
		int	bRemoveGroupsFromAtoms
	)

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◆ ReInitBnStructAddGroups()

int ReInitBnStructAddGroups	(	struct tagCANON_GLOBALS *	pCG,
		struct BalancedNetworkStructure *	pBNS,
		inp_ATOM *	at,
		int	num_atoms,
		struct tagTautomerGroupsInfo *	tgi,
		struct tagChargeGroupsInfo *	cgi
	)

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◆ ReInitBnStructAltPaths()

int ReInitBnStructAltPaths ( BN_STRUCT * pBNS )

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◆ ReInitBnStructForMoveableAltBondTest()

int ReInitBnStructForMoveableAltBondTest	(	BN_STRUCT *	pBNS,
		inp_ATOM *	at,
		int	num_atoms
	)

◆ RemoveFromNodeSet()

void RemoveFromNodeSet	(	struct tagCANON_GLOBALS *	pCG,
		NodeSet *	cur_nodes,
		int	k,
		Vertex	v[],
		int	num_v
	)

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◆ RemoveRadEndpoints()

int RemoveRadEndpoints	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		inp_ATOM *	at
	)

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◆ RunBalancedNetworkSearch()

int RunBalancedNetworkSearch	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		int	bChangeFlow
	)

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◆ SetForbiddenEdges()

int SetForbiddenEdges	(	BN_STRUCT *	pBNS,
		inp_ATOM *	at,
		int	num_atoms,
		int	edge_forbidden_mask,
		int	nebend,
		int *	ebend
	)

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◆ SetRadEndpoints()

int SetRadEndpoints	(	BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		BRS_MODE	bRadSrchMode
	)

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◆ SetRadEndpoints2()

int SetRadEndpoints2	(	struct tagCANON_GLOBALS *	pCG,
		BN_STRUCT *	pBNS,
		BN_DATA *	pBD,
		BRS_MODE	bRadSrchMode
	)

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Data Structures

Macros

Typedefs

Enumerations

Functions

Macro Definition Documentation

◆ AATG_MARK_IN_PATH

◆ AATG_MARK_MAIN_TYPE

◆ AATG_MARK_OTHER_TYPE

◆ AATG_MARK_WAS_IN_PATH

◆ ADD_CAPACITY_RADICAL

◆ ALT_PATH_MODE_4_SALT

◆ ALT_PATH_MODE_4_SALT2

◆ ALT_PATH_MODE_ADD2H_CHG

◆ ALT_PATH_MODE_ADD2H_TST

◆ ALT_PATH_MODE_CHARGE

◆ ALT_PATH_MODE_REM2H_CHG

◆ ALT_PATH_MODE_REM2H_TST

◆ ALT_PATH_MODE_REM_PROTON

◆ ALT_PATH_MODE_TAUTOM

◆ ALT_PATH_MODE_TAUTOM_KET

◆ ALT_PATH_MODE_TAUTOM_PT_06_00

◆ ALT_PATH_MODE_TAUTOM_PT_13_00

◆ ALT_PATH_MODE_TAUTOM_PT_16_00

◆ ALT_PATH_MODE_TAUTOM_PT_18_00

◆ ALT_PATH_MODE_TAUTOM_PT_22_00

◆ ALT_PATH_MODE_TAUTOM_PT_39_00

◆ ALTP_ALLOCATED_LEN

◆ ALTP_CUR_NEXT_ATOM_NEIGHBOR

◆ ALTP_CUR_THIS_ATOM_NEIGHBOR

◆ ALTP_DELTA

◆ ALTP_END_ATOM

◆ ALTP_MAY_ADD

◆ ALTP_NEXT

◆ ALTP_NEXT_ATOM_NEIGHBOR

◆ ALTP_OVERFLOW

◆ ALTP_PATH_LEN

◆ ALTP_PREV

◆ ALTP_START_ATOM

◆ ALTP_THIS_ATOM_NEIGHBOR

◆ AROM_BOND_EDGE_CAP

◆ BIT_WORD_MASK

◆ BLOSSOM_BASE

◆ BN_MAX_ALTP

◆ BNS_ADD_ATOMS

◆ BNS_ADD_EDGES

◆ BNS_ADD_SUPER_TGROUP

◆ BNS_EDGE_FORBIDDEN_MASK

◆ BNS_EDGE_FORBIDDEN_TEMP

◆ BNS_EDGE_FORBIDDEN_TEST

◆ BNS_EF_ALTR_BONDS

◆ BNS_EF_ALTR_NS

◆ BNS_EF_CHNG_BONDS

◆ BNS_EF_CHNG_FLOW

◆ BNS_EF_CHNG_RSTR

◆ BNS_EF_RAD_SRCH

◆ BNS_EF_RSTR_FLOW

◆ BNS_EF_SAVE_ALL

◆ BNS_EF_SET_NOSTEREO

◆ BNS_EF_UPD_H_CHARGE

◆ BNS_EF_UPD_RAD_ORI

◆ BNS_VERT_TYPE__AUX

◆ BNS_VERT_TYPE_ACID

◆ BNS_VERT_TYPE_ANY_GROUP

◆ BNS_VERT_TYPE_ATOM

◆ BNS_VERT_TYPE_C_GROUP

◆ BNS_VERT_TYPE_C_NEGATIVE

◆ BNS_VERT_TYPE_C_POINT

◆ BNS_VERT_TYPE_CARBON_GR

◆ BNS_VERT_TYPE_ENDPOINT

◆ BNS_VERT_TYPE_METAL_GR

◆ BNS_VERT_TYPE_SUPER_TGROUP

◆ BNS_VERT_TYPE_TEMP

◆ BNS_VERT_TYPE_TGROUP

◆ BNS_VT_C_NEG

◆ BNS_VT_C_NEG_ALL

◆ BNS_VT_C_NEG_C

◆ BNS_VT_C_NEG_M

◆ BNS_VT_C_POS

◆ BNS_VT_C_POS_ALL