ichican2.c File Reference

#include <stdlib.h>
#include <string.h>
#include <limits.h>
#include <time.h>
#include "mode.h"
#include "ichicano.h"
#include "ichicomn.h"
#include "ichitime.h"
#include "bcf_s.h"

Include dependency graph for ichican2.c:

Data Structures
struct	tagUnorderedPartition
struct	tagCell
struct	tagTransposition
struct	tagCTable
struct	tagkLeast
struct	tagNodeValues

Macros
#define	MAX_CELLS   32766
#define	MAX_NODES   32766
#define	MAX_SET_SIZE   32766 /*16384*/
#define	NORMALLY_ALLOWED_MAX_SET_SIZE   2048
#define	MAX_LAYERS   100
#define	SEPARATE_CANON_CALLS   0
#define	INCHI_CANON_INFINITY   0x7FFF
#define	INCHI_CANON_MIN
#define	EMPTY_CT   0
#define	EMPTY_H_NUMBER   (INCHI_CANON_INFINITY-1)
#define	BASE_H_NUMBER   ((INCHI_CANON_INFINITY-1)/2)
#define	EMPTY_ISO_SORT_KEY   LONG_MAX
#define	CanonGraph01   CanonGraph
#define	CanonGraph02   CanonGraph
#define	CanonGraph03   CanonGraph
#define	CanonGraph04   CanonGraph
#define	CanonGraph05   CanonGraph
#define	CanonGraph06   CanonGraph
#define	CanonGraph07   CanonGraph
#define	CanonGraph08   CanonGraph
#define	CanonGraph09   CanonGraph
#define	CanonGraph10   CanonGraph
#define	CanonGraph11   CanonGraph
#define	CanonGraph12   CanonGraph
#define	QZFIX_OK(X)   ((X)<=0)
#define	ELEM_NAME_LEN   2
#define	FREE_CONTABLE(X)   if (X) {CTableFree( X);inchi_free( X);}
#define	FREE_ARRAY(X)   if (X) inchi_free( X);
#define	FREE_CONTABLE(X)   if (X) {CTableFree( X);inchi_free( X);}
#define	FREE_ARRAY(X)   if (X) inchi_free( X);

Typedefs
typedef AT_NUMB	Node
typedef NEIGH_LIST	Graph
typedef struct tagUnorderedPartition	UnorderedPartition
typedef struct tagCell	Cell
typedef struct tagTransposition	Transposition
typedef struct tagCTable	ConTable
typedef struct tagkLeast	kLeast
typedef struct tagNodeValues	NV

Functions
int	CanonGraph (struct tagINCHI_CLOCK *ic, CANON_GLOBALS *pCG, int n, int n_tg, int n_max, int bDigraph, Graph *G, Partition pi[], AT_RANK *nSymmRank, AT_RANK *nCanonRank, AT_NUMB *nAtomNumberCanon, CANON_DATA *pCD, CANON_COUNTS *pCC, ConTable **pp_zb_rho_inp, ConTable **pp_zb_rho_out, int LargeMolecules)
void	CtPartFill (Graph *G, CANON_DATA *pCD, Partition *p, ConTable *Ct, int k, int n, int n_tg, int n_max)
void	CtPartClear (ConTable *Ct, int k)
void	CtPartINCHI_CANON_INFINITY (ConTable *Ct, S_CHAR *cmp, int k)
int	CtPartCompare (ConTable *Ct1, ConTable *Ct2, S_CHAR *cmp, kLeast *kLeastForLayer, int k, int bOnlyCommon, int bSplitTautCompare)
int	CtFullCompare (ConTable *Ct1, ConTable *Ct2, int bOnlyCommon, int bSplitTautCompare)
void	CtPartCopy (ConTable *Ct1, ConTable *Ct2, int k)
void	CtFullCopy (ConTable *Ct1, ConTable *Ct2)
int	CtFullCompareLayers (kLeast *kLeastForLayer)
int	CtCompareLayersGetFirstDiff (kLeast *kLeast_rho, int nOneAdditionalLayer, int *L_rho, int *I_rho, int *k_rho)
int	CtPartCompareLayers (kLeast *kLeast_rho, int L_rho_fix_prev, int nOneAdditionalLayer)
void	UpdateCompareLayers (kLeast kLeastForLayer[], int hzz)
int	GetOneAdditionalLayer (CANON_DATA *pCD, ConTable *pzb_rho_fix)
void	CleanNumH (NUM_H *NumH, int len)
int	CleanCt (AT_RANK *Ct, int len)
void	CleanIsoSortKeys (AT_ISO_SORT_KEY *isk, int len)
void	MergeCleanIsoSortKeys (AT_ISO_SORT_KEY *isk1, AT_ISO_SORT_KEY *isk2, int len)
int	UnorderedPartitionJoin (UnorderedPartition *p1, UnorderedPartition *p2, int n)
Node	GetUnorderedPartitionMcrNode (UnorderedPartition *p1, Node v)
int	nJoin2Mcrs2 (AT_RANK *nEqArray, AT_RANK n1, AT_RANK n2)
AT_RANK	nGetMcr2 (AT_RANK *nEqArray, AT_RANK n)
int	AllNodesAreInSet (NodeSet *cur_nodes, int lcur_nodes, NodeSet *set, int lset)
void	NodeSetFromVertices (CANON_GLOBALS *pCG, NodeSet *cur_nodes, int l, Node *v, int num_v)
void	CellMakeEmpty (Cell *baseW, int k)
Node	CellGetMinNode (Partition *p, Cell *W, Node v, CANON_DATA *pCD)
int	CellGetNumberOfNodes (Partition *p, Cell *W)
int	CellIntersectWithSet (struct tagCANON_GLOBALS *pCG, Partition *p, Cell *W, NodeSet *Mcr, int l)
int	PartitionColorVertex (CANON_GLOBALS *pCG, Graph *G, Partition *p, Node v, int n, int n_tg, int n_max, int bDigraph, int nNumPrevRanks)
void	PartitionCopy (Partition *To, Partition *From, int n)
int	PartitionSatisfiesLemma_2_25 (Partition *p, int n)
void	PartitionGetTransposition (Partition *pFrom, Partition *pTo, int n, Transposition *gamma)
void	PartitionGetMcrAndFixSet (CANON_GLOBALS *pCG, Partition *p, NodeSet *Mcr, NodeSet *Fix, int n, int l)
int	PartitionGetFirstCell (Partition *p, Cell *baseW, int k, int n)
int	PartitionIsDiscrete (Partition *p, int n)
void	PartitionFree (Partition *p)
int	PartitionCreate (Partition *p, int n)
void	UnorderedPartitionMakeDiscrete (UnorderedPartition *p, int n)
void	UnorderedPartitionFree (UnorderedPartition *p)
int	UnorderedPartitionCreate (UnorderedPartition *p, int n)
void	CTableFree (ConTable *Ct)
int	CTableCreate (ConTable *Ct, int n, CANON_DATA *pCD)
void	TranspositionFree (Transposition *p)
int	TranspositionCreate (Transposition *p, int n)
void	TranspositionGetMcrAndFixSetAndUnorderedPartition (struct tagCANON_GLOBALS *pCG, Transposition *gamma, NodeSet *McrSet, NodeSet *FixSet, int n, int l, UnorderedPartition *p)
void	insertions_sort_NeighList_AT_NUMBERS2 (NEIGH_LIST base, AT_RANK *nRank, AT_RANK max_rj)
int	WriteGraph (Graph *G, int n, int gnum, char *fname, char *fmode)
int	SetInitialRanks2 (int num_atoms, ATOM_INVARIANT2 *pAtomInvariant2, AT_RANK *nNewRank, AT_RANK *nAtomNumber, CANON_GLOBALS *pCG)
void	FillOutAtomInvariant2 (sp_ATOM *at, int num_atoms, int num_at_tg, ATOM_INVARIANT2 *pAtomInvariant, int bIgnoreIsotopic, int bHydrogensInRanks, int bHydrogensFixedInRanks, int bDigraph, int bTautGroupsOnly, T_GROUP_INFO *t_group_info)
int	GetCanonRanking2 (int num_atoms, int num_at_tg, int num_max, int bDigraph, sp_ATOM *at, AT_RANK **pRankStack, int nNumPrevRanks, AT_RANK *nSymmRank, AT_RANK *nCanonRank, NEIGH_LIST *NeighList, AT_RANK *nTempRank, CANON_STAT *pCS)
int	NodeSetCreate (struct tagCANON_GLOBALS *pCG, NodeSet *pSet, int n, int L)
void	NodeSetFree (struct tagCANON_GLOBALS *pCG, NodeSet *pSet)
void	NodeSetFromRadEndpoints (CANON_GLOBALS *pCG, NodeSet *cur_nodes, int k, Vertex RadEndpoints[], int num_v)
void	RemoveFromNodeSet (CANON_GLOBALS *pCG, NodeSet *cur_nodes, int k, Vertex v[], int num_v)
int	DoNodeSetsIntersect (NodeSet *cur_nodes, int k1, int k2)
int	IsNodeSetEmpty (NodeSet *cur_nodes, int k)
void	AddNodeSet2ToNodeSet1 (NodeSet *cur_nodes, int k1, int k2)
int	AddNodesToRadEndpoints (CANON_GLOBALS *pCG, NodeSet *cur_nodes, int k, Vertex RadEndpoints[], Vertex vRad, int nStart, int nLen)
int	SetBitCreate (CANON_GLOBALS *pCG)
int	SetBitFree (CANON_GLOBALS *pCG)
void	DeAllocBCN (BCN *pBCN)
int	GetBaseCanonRanking (INCHI_CLOCK *ic, int num_atoms, int num_at_tg, sp_ATOM *at[], T_GROUP_INFO *t_group_info, ATOM_SIZES s[], BCN *pBCN, struct tagInchiTime *ulTimeOutTime, CANON_GLOBALS *pCG, int bFixIsoFixedH, int LargeMolecules)

Variables
static AT_NUMB	rank_mark_bit
static AT_NUMB	rank_mask_bit

Macro Definition Documentation

BASE_H_NUMBER

#define BASE_H_NUMBER   ((INCHI_CANON_INFINITY-1)/2)

CanonGraph01

#define CanonGraph01   CanonGraph

CanonGraph02

#define CanonGraph02   CanonGraph

CanonGraph03

#define CanonGraph03   CanonGraph

CanonGraph04

#define CanonGraph04   CanonGraph

CanonGraph05

#define CanonGraph05   CanonGraph

CanonGraph06

#define CanonGraph06   CanonGraph

CanonGraph07

#define CanonGraph07   CanonGraph

CanonGraph08

#define CanonGraph08   CanonGraph

CanonGraph09

#define CanonGraph09   CanonGraph

CanonGraph10

#define CanonGraph10   CanonGraph

CanonGraph11

#define CanonGraph11   CanonGraph

CanonGraph12

#define CanonGraph12   CanonGraph

ELEM_NAME_LEN

#define ELEM_NAME_LEN   2

EMPTY_CT

#define EMPTY_CT   0

EMPTY_H_NUMBER

#define EMPTY_H_NUMBER   (INCHI_CANON_INFINITY-1)

EMPTY_ISO_SORT_KEY

#define EMPTY_ISO_SORT_KEY   LONG_MAX

FREE_ARRAY [1/2]

#define FREE_ARRAY

(

X

)

if (X) inchi_free( X);

FREE_ARRAY [2/2]

#define FREE_ARRAY

(

X

)

if (X) inchi_free( X);

FREE_CONTABLE [1/2]

#define FREE_CONTABLE

(

X

)

if (X) {CTableFree( X);inchi_free( X);}

FREE_CONTABLE [2/2]

#define FREE_CONTABLE

(

X

)

if (X) {CTableFree( X);inchi_free( X);}

INCHI_CANON_INFINITY

#define INCHI_CANON_INFINITY   0x7FFF

INCHI_CANON_MIN

#define INCHI_CANON_MIN

MAX_CELLS

#define MAX_CELLS   32766

MAX_LAYERS

#define MAX_LAYERS   100

MAX_NODES

#define MAX_NODES   32766

MAX_SET_SIZE

#define MAX_SET_SIZE   32766 /*16384*/

NORMALLY_ALLOWED_MAX_SET_SIZE

#define NORMALLY_ALLOWED_MAX_SET_SIZE   2048

QZFIX_OK

#define QZFIX_OK

(

X

)

((X)<=0)

SEPARATE_CANON_CALLS

#define SEPARATE_CANON_CALLS   0

Typedef Documentation

Cell

typedef struct tagCell Cell

ConTable

typedef struct tagCTable ConTable

Graph

typedef NEIGH_LIST Graph

kLeast

typedef struct tagkLeast kLeast

Node

typedef AT_NUMB Node

NV

typedef struct tagNodeValues NV

Transposition

typedef struct tagTransposition Transposition

UnorderedPartition

typedef struct tagUnorderedPartition UnorderedPartition

Function Documentation

AddNodeSet2ToNodeSet1()

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

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AddNodesToRadEndpoints()

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

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AllNodesAreInSet()

int AllNodesAreInSet	(	NodeSet *	cur_nodes,
		int	lcur_nodes,
		NodeSet *	set,
		int	lset
	)

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CanonGraph()

int CanonGraph	(	struct tagINCHI_CLOCK *	ic,
		CANON_GLOBALS *	pCG,
		int	n,
		int	n_tg,
		int	n_max,
		int	bDigraph,
		Graph *	G,
		Partition	pi[],
		AT_RANK *	nSymmRank,
		AT_RANK *	nCanonRank,
		AT_NUMB *	nAtomNumberCanon,
		CANON_DATA *	pCD,
		CANON_COUNTS *	pCC,
		ConTable **	pp_zb_rho_inp,
		ConTable **	pp_zb_rho_out,
		int	LargeMolecules
	)

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CellGetMinNode()

Node CellGetMinNode	(	Partition *	p,
		Cell *	W,
		Node	v,
		CANON_DATA *	pCD
	)

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CellGetNumberOfNodes()

int CellGetNumberOfNodes	(	Partition *	p,
		Cell *	W
	)

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CellIntersectWithSet()

int CellIntersectWithSet	(	struct tagCANON_GLOBALS *	pCG,
		Partition *	p,
		Cell *	W,
		NodeSet *	Mcr,
		int	l
	)

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CellMakeEmpty()

void CellMakeEmpty	(	Cell *	baseW,
		int	k
	)

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CleanCt()

int CleanCt	(	AT_RANK *	Ct,
		int	len
	)

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CleanIsoSortKeys()

void CleanIsoSortKeys	(	AT_ISO_SORT_KEY *	isk,
		int	len
	)

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CleanNumH()

void CleanNumH	(	NUM_H *	NumH,
		int	len
	)

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CTableCreate()

int CTableCreate	(	ConTable *	Ct,
		int	n,
		CANON_DATA *	pCD
	)

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CTableFree()

void CTableFree

(

ConTable *

Ct

)

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CtCompareLayersGetFirstDiff()

int CtCompareLayersGetFirstDiff	(	kLeast *	kLeast_rho,
		int	nOneAdditionalLayer,
		int *	L_rho,
		int *	I_rho,
		int *	k_rho
	)

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CtFullCompare()

int CtFullCompare	(	ConTable *	Ct1,
		ConTable *	Ct2,
		int	bOnlyCommon,
		int	bSplitTautCompare
	)

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CtFullCompareLayers()

int CtFullCompareLayers

(

kLeast *

kLeastForLayer

)

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CtFullCopy()

void CtFullCopy	(	ConTable *	Ct1,
		ConTable *	Ct2
	)

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CtPartClear()

void CtPartClear	(	ConTable *	Ct,
		int	k
	)

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CtPartCompare()

int CtPartCompare	(	ConTable *	Ct1,
		ConTable *	Ct2,
		S_CHAR *	cmp,
		kLeast *	kLeastForLayer,
		int	k,
		int	bOnlyCommon,
		int	bSplitTautCompare
	)

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CtPartCompareLayers()

int CtPartCompareLayers	(	kLeast *	kLeast_rho,
		int	L_rho_fix_prev,
		int	nOneAdditionalLayer
	)

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CtPartCopy()

void CtPartCopy	(	ConTable *	Ct1,
		ConTable *	Ct2,
		int	k
	)

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CtPartFill()

void CtPartFill	(	Graph *	G,
		CANON_DATA *	pCD,
		Partition *	p,
		ConTable *	Ct,
		int	k,
		int	n,
		int	n_tg,
		int	n_max
	)

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CtPartINCHI_CANON_INFINITY()

void CtPartINCHI_CANON_INFINITY	(	ConTable *	Ct,
		S_CHAR *	cmp,
		int	k
	)

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DeAllocBCN()

void DeAllocBCN

(

BCN *

pBCN

)

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DoNodeSetsIntersect()

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

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FillOutAtomInvariant2()

void FillOutAtomInvariant2	(	sp_ATOM *	at,
		int	num_atoms,
		int	num_at_tg,
		ATOM_INVARIANT2 *	pAtomInvariant,
		int	bIgnoreIsotopic,
		int	bHydrogensInRanks,
		int	bHydrogensFixedInRanks,
		int	bDigraph,
		int	bTautGroupsOnly,
		T_GROUP_INFO *	t_group_info
	)

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GetBaseCanonRanking()

int GetBaseCanonRanking	(	INCHI_CLOCK *	ic,
		int	num_atoms,
		int	num_at_tg,
		sp_ATOM *	at[],
		T_GROUP_INFO *	t_group_info,
		ATOM_SIZES	s[],
		BCN *	pBCN,
		struct tagInchiTime *	ulTimeOutTime,
		CANON_GLOBALS *	pCG,
		int	bFixIsoFixedH,
		int	LargeMolecules
	)

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GetCanonRanking2()

int GetCanonRanking2	(	int	num_atoms,
		int	num_at_tg,
		int	num_max,
		int	bDigraph,
		sp_ATOM *	at,
		AT_RANK **	pRankStack,
		int	nNumPrevRanks,
		AT_RANK *	nSymmRank,
		AT_RANK *	nCanonRank,
		NEIGH_LIST *	NeighList,
		AT_RANK *	nTempRank,
		CANON_STAT *	pCS
	)

GetOneAdditionalLayer()

int GetOneAdditionalLayer	(	CANON_DATA *	pCD,
		ConTable *	pzb_rho_fix
	)

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GetUnorderedPartitionMcrNode()

Node GetUnorderedPartitionMcrNode	(	UnorderedPartition *	p1,
		Node	v
	)

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insertions_sort_NeighList_AT_NUMBERS2()

void insertions_sort_NeighList_AT_NUMBERS2	(	NEIGH_LIST	base,
		AT_RANK *	nRank,
		AT_RANK	max_rj
	)

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IsNodeSetEmpty()

int IsNodeSetEmpty	(	NodeSet *	cur_nodes,
		int	k
	)

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MergeCleanIsoSortKeys()

void MergeCleanIsoSortKeys	(	AT_ISO_SORT_KEY *	isk1,
		AT_ISO_SORT_KEY *	isk2,
		int	len
	)

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nGetMcr2()

AT_RANK nGetMcr2	(	AT_RANK *	nEqArray,
		AT_RANK	n
	)

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nJoin2Mcrs2()

int nJoin2Mcrs2	(	AT_RANK *	nEqArray,
		AT_RANK	n1,
		AT_RANK	n2
	)

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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	(	CANON_GLOBALS *	pCG,
		NodeSet *	cur_nodes,
		int	k,
		Vertex	RadEndpoints[],
		int	num_v
	)

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NodeSetFromVertices()

void NodeSetFromVertices	(	CANON_GLOBALS *	pCG,
		NodeSet *	cur_nodes,
		int	l,
		Node *	v,
		int	num_v
	)

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PartitionColorVertex()

int PartitionColorVertex	(	CANON_GLOBALS *	pCG,
		Graph *	G,
		Partition *	p,
		Node	v,
		int	n,
		int	n_tg,
		int	n_max,
		int	bDigraph,
		int	nNumPrevRanks
	)

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PartitionCopy()

void PartitionCopy	(	Partition *	To,
		Partition *	From,
		int	n
	)

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PartitionCreate()

int PartitionCreate	(	Partition *	p,
		int	n
	)

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PartitionFree()

void PartitionFree

(

Partition *

p

)

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PartitionGetFirstCell()

int PartitionGetFirstCell	(	Partition *	p,
		Cell *	baseW,
		int	k,
		int	n
	)

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PartitionGetMcrAndFixSet()

void PartitionGetMcrAndFixSet	(	CANON_GLOBALS *	pCG,
		Partition *	p,
		NodeSet *	Mcr,
		NodeSet *	Fix,
		int	n,
		int	l
	)

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PartitionGetTransposition()

void PartitionGetTransposition	(	Partition *	pFrom,
		Partition *	pTo,
		int	n,
		Transposition *	gamma
	)

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PartitionIsDiscrete()

int PartitionIsDiscrete	(	Partition *	p,
		int	n
	)

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PartitionSatisfiesLemma_2_25()

int PartitionSatisfiesLemma_2_25	(	Partition *	p,
		int	n
	)

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RemoveFromNodeSet()

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

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SetBitCreate()

int SetBitCreate

(

CANON_GLOBALS *

pCG

)

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SetBitFree()

int SetBitFree

(

CANON_GLOBALS *

pCG

)

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SetInitialRanks2()

int SetInitialRanks2	(	int	num_atoms,
		ATOM_INVARIANT2 *	pAtomInvariant2,
		AT_RANK *	nNewRank,
		AT_RANK *	nAtomNumber,
		CANON_GLOBALS *	pCG
	)

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TranspositionCreate()

int TranspositionCreate	(	Transposition *	p,
		int	n
	)

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TranspositionFree()

void TranspositionFree

(

Transposition *

p

)

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TranspositionGetMcrAndFixSetAndUnorderedPartition()

void TranspositionGetMcrAndFixSetAndUnorderedPartition	(	struct tagCANON_GLOBALS *	pCG,
		Transposition *	gamma,
		NodeSet *	McrSet,
		NodeSet *	FixSet,
		int	n,
		int	l,
		UnorderedPartition *	p
	)

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UnorderedPartitionCreate()

int UnorderedPartitionCreate	(	UnorderedPartition *	p,
		int	n
	)

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UnorderedPartitionFree()

void UnorderedPartitionFree

(

UnorderedPartition *

p

)

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UnorderedPartitionJoin()

int UnorderedPartitionJoin	(	UnorderedPartition *	p1,
		UnorderedPartition *	p2,
		int	n
	)

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UnorderedPartitionMakeDiscrete()

void UnorderedPartitionMakeDiscrete	(	UnorderedPartition *	p,
		int	n
	)

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UpdateCompareLayers()

void UpdateCompareLayers	(	kLeast	kLeastForLayer[],
		int	hzz
	)

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WriteGraph()

int WriteGraph	(	Graph *	G,
		int	n,
		int	gnum,
		char *	fname,
		char *	fmode
	)

Variable Documentation

rank_mark_bit

AT_NUMB rank_mark_bit

static

rank_mask_bit

AT_NUMB rank_mask_bit

static