ichicomn.h File Reference

#include "ichierr.h"
#include "ichicano.h"

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Data Structures
struct	tagEquNeigh

Macros
#define	tsort   insertions_sort

Typedefs
typedef struct tagEquNeigh	EQ_NEIGH

Functions
int	unpack_iso_sort_key (AT_ISO_SORT_KEY iso_sort_key, S_CHAR *num_1H, S_CHAR *num_2H, S_CHAR *num_3H, S_CHAR *iso_atw_diff)
AT_ISO_SORT_KEY	make_iso_sort_key (int iso_atw_diff, int num_1H, int num_2H, int num_3H)
int	set_atom_iso_sort_keys (int num_at, sp_ATOM *at, T_GROUP_INFO *t_group_info, int *bHasIsotopicInTautomerGroups)
void	insertions_sort_NeighList_AT_NUMBERS (NEIGH_LIST base, AT_RANK *nRank)
int	insertions_sort_NeighList_AT_NUMBERS3 (NEIGH_LIST base, AT_RANK *nRank)
int	insertions_sort_AT_RANK (AT_RANK *base, int num)
void	insertions_sort_NeighListBySymmAndCanonRank (NEIGH_LIST base, const AT_RANK *nSymmRank, const AT_RANK *nCanonRank)
int	CompareNeighListLex (NEIGH_LIST pp1, NEIGH_LIST pp2, const AT_RANK *nRank)
int	CompareNeighListLexUpToMaxRank (NEIGH_LIST pp1, NEIGH_LIST pp2, const AT_RANK *nRank, AT_RANK nMaxAtNeighRank)
int	compare_NeighLists (const NEIGH_LIST *op1, const NEIGH_LIST *op2, void *p)
int	CompNeighborsAT_NUMBER (const void *a1, const void *a2, void *p)
int	comp_AT_RANK (const void *a1, const void *a2, void *)
int	CompRank (const void *a1, const void *a2, void *p)
int	CompRanksOrd (const void *a1, const void *a2, void *p)
int	CompAtomInvariants2Only (const void *a1, const void *a2, void *p)
int	CompAtomInvariants2 (const void *a1, const void *a2, void *p)
int	CompNeighListRanks (const void *a1, const void *a2, void *p)
int	CompNeighListRanksOrd (const void *a1, const void *a2, void *p)
int	CompNeighLists (const void *a1, const void *a2, void *p)
int	CompNeighListsUpToMaxRank (const void *a1, const void *a2, void *p)
int	CompNeighborsRanksCountEql (const void *a1, const void *a2, void *p)
int	CompRanksInvOrd (const void *a1, const void *a2, void *)
int	CompChemElemLex (const void *a1, const void *a2)
int *	iisort (int *list, int num)
NEIGH_LIST *	CreateNeighList (int num_atoms, int num_at_tg, sp_ATOM *at, int bDoubleBondSquare, T_GROUP_INFO *t_group_info)
NEIGH_LIST *	CreateNeighListFromLinearCT (AT_NUMB *LinearCT, int nLenCT, int num_atoms)
void	FreeNeighList (NEIGH_LIST *pp)
int	BreakAllTies (CANON_GLOBALS *pCG, int num_atoms, int num_max, AT_RANK **pRankStack, NEIGH_LIST *NeighList, AT_RANK *nTempRank, CANON_STAT *pCS)
void	switch_ptrs (AT_RANK **p1, AT_RANK **p2)
int	SortedEquInfoToRanks (const AT_RANK *nSymmRank, AT_RANK *nRank, const AT_RANK *nAtomNumber, int num_atoms, int *bChanged)
int	SortedRanksToEquInfo (AT_RANK *nSymmRank, const AT_RANK *nRank, const AT_RANK *nAtomNumber, int num_atoms)
int	SetNewRanksFromNeighLists (CANON_GLOBALS *pCG, int num_atoms, NEIGH_LIST *NeighList, AT_RANK *nRank, AT_RANK *nNewRank, AT_RANK *nAtomNumber, int bUseAltSort, int(*comp)(const void *, const void *, void *))
int	SetNewRanksFromNeighLists3 (CANON_GLOBALS *pCG, int num_atoms, NEIGH_LIST *NeighList, AT_RANK *nRank, AT_RANK *nNewRank, AT_RANK *nAtomNumber)
int	SetNewRanksFromNeighLists4 (CANON_GLOBALS *pCG, int num_atoms, NEIGH_LIST *NeighList, AT_RANK *nRank, AT_RANK *nNewRank, AT_RANK *nAtomNumber, AT_RANK nMaxAtRank)
void	SortNeighListsBySymmAndCanonRank (int num_atoms, NEIGH_LIST *NeighList, const AT_RANK *nSymmRank, const AT_RANK *nCanonRank)
int	SortNeighLists2 (int num_atoms, AT_RANK *nRank, NEIGH_LIST *NeighList, AT_RANK *nAtomNumber)
int	DifferentiateRanks2 (CANON_GLOBALS *pCG, int num_atoms, NEIGH_LIST *NeighList, int nNumCurrRanks, AT_RANK *pnCurrRank, AT_RANK *pnPrevRank, AT_RANK *nAtomNumber, long *lNumIter, int bUseAltSort)
int	DifferentiateRanks3 (CANON_GLOBALS *pCG, int num_atoms, NEIGH_LIST *NeighList, int nNumCurrRanks, AT_RANK *pnCurrRank, AT_RANK *pnPrevRank, AT_RANK *nAtomNumber, long *lNumIter)
int	DifferentiateRanks4 (CANON_GLOBALS *pCG, int num_atoms, NEIGH_LIST *NeighList, int nNumCurrRanks, AT_RANK *pnCurrRank, AT_RANK *pnPrevRank, AT_RANK *nAtomNumber, AT_RANK nMaxAtRank, long *lNumIter)
int	DifferentiateRanksBasic (CANON_GLOBALS *pCG, int num_atoms, NEIGH_LIST *NeighList, int nNumCurrRanks, AT_RANK *pnCurrRank, AT_RANK *pnPrevRank, AT_RANK *nAtomNumber, long *lNumIter, int bUseAltSort)
int	parity_of_mapped_atom2 (CANON_GLOBALS *pCG, int from_at, int to_at, const sp_ATOM *at, EQ_NEIGH *pEN, const AT_RANK *nCanonRankFrom, const AT_RANK *nRankFrom, const AT_RANK *nRankTo)
int	parity_of_mapped_half_bond (int from_at, int to_at, int from_neigh, int to_neigh, sp_ATOM *at, EQ_NEIGH *pEN, const AT_RANK *nCanonRankFrom, const AT_RANK *nRankFrom, const AT_RANK *nRankTo)
int	HalfStereoBondParity (sp_ATOM *at, int at_no1, int i_sb_neigh, const AT_RANK *nRank)
int	NumberOfTies (AT_RANK **pRankStack1, AT_RANK **pRankStack2, int length, int at_no1, int at_no2, AT_RANK *nNewRank, int *bAddStack, int *bMapped1)
int	map_an_atom2 (CANON_GLOBALS *pCG, int num_atoms, int num_max, int at_no1, int at_no2, AT_RANK *nTempRank, int nNumMappedRanks, int *pnNewNumMappedRanks, CANON_STAT *pCS, NEIGH_LIST *NeighList, AT_RANK **pRankStack1, AT_RANK **pRankStack2, int *bAddStack)
int	ClearPreviousMappings (AT_RANK **pRankStack1)
int	SetOneStereoBondIllDefParity (sp_ATOM *at, int jc, int k, int new_parity)
int	RemoveOneStereoBond (sp_ATOM *at, int jc, int k)
int	RemoveOneStereoCenter (sp_ATOM *at, int jc)
int	RemoveCalculatedNonStereo (CANON_GLOBALS *pCG, sp_ATOM *at, int num_atoms, int num_at_tg, AT_RANK **pRankStack1, AT_RANK **pRankStack2, AT_RANK *nTempRank, NEIGH_LIST *NeighList, const AT_RANK *nSymmRank, AT_RANK *nCanonRank, AT_RANK *nAtomNumberCanon, CANON_STAT *pCS, int vABParityUnknown)
int	might_change_other_atom_parity (sp_ATOM *at, int num_atoms, int at_no, AT_RANK *nRank2, AT_RANK *nRank1)
int	map_stereo_bonds4 (struct tagINCHI_CLOCK *ic, CANON_GLOBALS *pCG, sp_ATOM *at, int num_atoms, int num_at_tg, int num_max, int bAllene, const AT_RANK *nCanonRankFrom, const AT_RANK *nAtomNumberCanonFrom, AT_RANK *nCanonRankTo, const AT_RANK *nSymmRank, AT_RANK **pRankStack1, AT_RANK **pRankStack2, AT_RANK *nTempRank, int nNumMappedRanksInput, AT_RANK *nSymmStereo, NEIGH_LIST *NeighList, CANON_STAT *pCS, CUR_TREE *cur_tree, int nNumMappedBonds, int vABParityUnknown)
int	map_stereo_atoms4 (struct tagINCHI_CLOCK *ic, CANON_GLOBALS *pCG, sp_ATOM *at, int num_atoms, int num_at_tg, int num_max, const AT_RANK *nCanonRankFrom, const AT_RANK *nAtomNumberCanonFrom, AT_RANK *nCanonRankTo, const AT_RANK *nSymmRank, AT_RANK **pRankStack1, AT_RANK **pRankStack2, AT_RANK *nTempRank, int nNumMappedRanksInput, AT_RANK *nSymmStereo, NEIGH_LIST *NeighList, CANON_STAT *pCS, CUR_TREE *cur_tree, int nNumMappedAtoms, int vABParityUnknown)
int	CurTreeAlloc (CUR_TREE *cur_tree, int num_atoms)
int	CurTreeReAlloc (CUR_TREE *cur_tree)
void	CurTreeFree (CUR_TREE *cur_tree)
int	CurTreeAddRank (CUR_TREE *cur_tree, AT_NUMB rank)
int	CurTreeRemoveLastRank (CUR_TREE *cur_tree)
int	CurTreeReplaceLastRank (CUR_TREE *cur_tree, AT_NUMB rank)
int	CurTreeFindTheRankPos (CUR_TREE *cur_tree, AT_NUMB rank)
int	CurTreeGetPos (CUR_TREE *cur_tree)
int	CurTreeSetPos (CUR_TREE *cur_tree, int len)
int	CurTreeAddAtom (CUR_TREE *cur_tree, int at_no)
int	CurTreeRemoveLastAtom (CUR_TREE *cur_tree)
int	CurTreeIsLastRank (CUR_TREE *cur_tree, AT_NUMB rank)
int	CurTreeIsLastAtomEqu (CUR_TREE *cur_tree, int at_no, AT_NUMB *nSymmStereo)
int	CurTreeRemoveIfLastAtom (CUR_TREE *cur_tree, int at_no)
int	CurTreeRemoveLastRankIfNoAtoms (CUR_TREE *cur_tree)
void	CurTreeKeepLastAtomsOnly (CUR_TREE *cur_tree, int tpos, int shift)
void	SetUseAtomForStereo (S_CHAR *bAtomUsedForStereo, sp_ATOM *at, int num_atoms)
int	nJoin2Mcrs (AT_RANK *nEqArray, AT_RANK n1, AT_RANK n2)
AT_RANK	nGetMcr (AT_RANK *nEqArray, AT_RANK n)
int	bUniqueAtNbrFromMappingRank (AT_RANK **pRankStack, AT_RANK nAtRank, AT_NUMB *nAtNumber)
int	Next_SB_At_CanonRanks2 (AT_RANK *canon_rank1, AT_RANK *canon_rank2, AT_RANK *canon_rank1_min, AT_RANK *canon_rank2_min, int *bFirstTime, S_CHAR *bAtomUsedForStereo, const ppAT_RANK pRankStack1, const ppAT_RANK pRankStack2, const AT_RANK *nCanonRankFrom, const AT_RANK *nAtomNumberCanonFrom, const sp_ATOM *at, int num_atoms, int bAllene)
int	Next_SC_At_CanonRank2 (AT_RANK *canon_rank1, AT_RANK *canon_rank1_min, int *bFirstTime, S_CHAR *bAtomUsedForStereo, const ppAT_RANK pRankStack1, const ppAT_RANK pRankStack2, const AT_RANK *nAtomNumberCanonFrom, int num_atoms)
int	NextStereoParity2Test (int *stereo_bond_parity, int *sb_parity_calc, int nNumBest, int nNumWorse, int nNumUnkn, int nNumUndf, int nNumCalc, int vABParityUnknown)
int	All_SB_Same (AT_RANK canon_rank1, AT_RANK canon_rank2, const ppAT_RANK pRankStack1, const ppAT_RANK pRankStack2, const AT_RANK *nAtomNumberCanonFrom, sp_ATOM *at)
int	All_SC_Same (AT_RANK canon_rank1, const ppAT_RANK pRankStack1, const ppAT_RANK pRankStack2, const AT_RANK *nAtomNumberCanonFrom, const sp_ATOM *at)
int	CompareLinCtStereoDoubleToValues (AT_STEREO_DBLE *LinearCTStereoDble, AT_RANK at_rank_canon1, AT_RANK at_rank_canon2, U_CHAR bond_parity)
int	CompareLinCtStereoAtomToValues (AT_STEREO_CARB *LinearCTStereoCarb, AT_RANK at_rank_canon1, U_CHAR parity)
int	CompareLinCtStereoDble (AT_STEREO_DBLE *LinearCTStereoDble1, int nLenLinearCTStereoDble1, AT_STEREO_DBLE *LinearCTStereoDble2, int nLenLinearCTStereoDble2)
int	CompareLinCtStereoCarb (AT_STEREO_CARB *LinearCTStereoCarb1, int nLenLinearCTStereoCarb1, AT_STEREO_CARB *LinearCTStereoCarb2, int nLenLinearCTStereoCarb2)
int	CompareLinCtStereo (AT_STEREO_DBLE *LinearCTStereoDble1, int nLenLinearCTStereoDble1, AT_STEREO_CARB *LinearCTStereoCarb1, int nLenLinearCTStereoCarb1, AT_STEREO_DBLE *LinearCTStereoDble2, int nLenLinearCTStereoDble2, AT_STEREO_CARB *LinearCTStereoCarb2, int nLenLinearCTStereoCarb2)
int	UnmarkNonStereo (CANON_GLOBALS *pCG, sp_ATOM *at, int num_atoms, const AT_RANK *nRank, const AT_RANK *nAtomNumber, int bIsotopic)
int	FillSingleStereoDescriptors (CANON_GLOBALS *pCG, sp_ATOM *at, int i, int num_trans, const AT_RANK *nRank, AT_STEREO_CARB *LinearCTStereoCarb, int *nStereoCarbLen, int nMaxStereoCarbLen, AT_STEREO_DBLE *LinearCTStereoDble, int *nStereoDbleLen, int nMaxStereoDbleLen, int bAllene)
void	SwitchAtomStereoAndIsotopicStereo (sp_ATOM *at, int num_atoms, int *bSwitched)
void	SetCtToIsotopicStereo (CANON_STAT *pCS, CANON_STAT *pCS2)
void	SetCtToNonIsotopicStereo (CANON_STAT *pCS, CANON_STAT *pCS2)
int	FillAllStereoDescriptors (CANON_GLOBALS *pCG, sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank, const AT_RANK *nAtomNumberCanon, CANON_STAT *pCS)
int	FillOutStereoParities (sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank, const AT_RANK *nAtomNumberCanon, const AT_RANK *nRank, const AT_RANK *nAtomNumber, CANON_STAT *pCS, CANON_GLOBALS *pCG, int bIsotopic)
int	InvertStereo (sp_ATOM *at, int num_at_tg, AT_RANK *nCanonRank, AT_RANK *nAtomNumberCanon, CANON_STAT *pCS, int bInvertLinearCTStereo)
int	find_atoms_with_parity (sp_ATOM *at, S_CHAR *visited, int from_atom, int cur_atom)
int	GetStereoNeighborPos (sp_ATOM *at, int iAt1, int iAt2)
int	GetStereoBondParity (sp_ATOM *at, int i, int n, AT_RANK *nRank)
int	GetStereoCenterParity (CANON_GLOBALS *pCG, sp_ATOM *at, int i, AT_RANK *nRank)
int	GetPermutationParity (CANON_GLOBALS *pCG, sp_ATOM *at, AT_RANK nAvoidNeighbor, AT_RANK *nCanonRank)

Macro Definition Documentation

tsort

#define tsort   insertions_sort

Typedef Documentation

EQ_NEIGH

typedef struct tagEquNeigh EQ_NEIGH

Function Documentation

All_SB_Same()

int All_SB_Same	(	AT_RANK	canon_rank1,
		AT_RANK	canon_rank2,
		const ppAT_RANK	pRankStack1,
		const ppAT_RANK	pRankStack2,
		const AT_RANK *	nAtomNumberCanonFrom,
		sp_ATOM *	at
	)

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All_SC_Same()

int All_SC_Same	(	AT_RANK	canon_rank1,
		const ppAT_RANK	pRankStack1,
		const ppAT_RANK	pRankStack2,
		const AT_RANK *	nAtomNumberCanonFrom,
		const sp_ATOM *	at
	)

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BreakAllTies()

int BreakAllTies	(	CANON_GLOBALS *	pCG,
		int	num_atoms,
		int	num_max,
		AT_RANK **	pRankStack,
		NEIGH_LIST *	NeighList,
		AT_RANK *	nTempRank,
		CANON_STAT *	pCS
	)

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bUniqueAtNbrFromMappingRank()

int bUniqueAtNbrFromMappingRank	(	AT_RANK **	pRankStack,
		AT_RANK	nAtRank,
		AT_NUMB *	nAtNumber
	)

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ClearPreviousMappings()

int ClearPreviousMappings

(

AT_RANK **

pRankStack1

)

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comp_AT_RANK()

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

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compare_NeighLists()

int compare_NeighLists	(	const NEIGH_LIST *	op1,
		const NEIGH_LIST *	op2,
		void *	p
	)

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CompareLinCtStereo()

int CompareLinCtStereo	(	AT_STEREO_DBLE *	LinearCTStereoDble1,
		int	nLenLinearCTStereoDble1,
		AT_STEREO_CARB *	LinearCTStereoCarb1,
		int	nLenLinearCTStereoCarb1,
		AT_STEREO_DBLE *	LinearCTStereoDble2,
		int	nLenLinearCTStereoDble2,
		AT_STEREO_CARB *	LinearCTStereoCarb2,
		int	nLenLinearCTStereoCarb2
	)

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CompareLinCtStereoAtomToValues()

int CompareLinCtStereoAtomToValues	(	AT_STEREO_CARB *	LinearCTStereoCarb,
		AT_RANK	at_rank_canon1,
		U_CHAR	parity
	)

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CompareLinCtStereoCarb()

int CompareLinCtStereoCarb	(	AT_STEREO_CARB *	LinearCTStereoCarb1,
		int	nLenLinearCTStereoCarb1,
		AT_STEREO_CARB *	LinearCTStereoCarb2,
		int	nLenLinearCTStereoCarb2
	)

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CompareLinCtStereoDble()

int CompareLinCtStereoDble	(	AT_STEREO_DBLE *	LinearCTStereoDble1,
		int	nLenLinearCTStereoDble1,
		AT_STEREO_DBLE *	LinearCTStereoDble2,
		int	nLenLinearCTStereoDble2
	)

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CompareLinCtStereoDoubleToValues()

int CompareLinCtStereoDoubleToValues	(	AT_STEREO_DBLE *	LinearCTStereoDble,
		AT_RANK	at_rank_canon1,
		AT_RANK	at_rank_canon2,
		U_CHAR	bond_parity
	)

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CompareNeighListLex()

int CompareNeighListLex	(	NEIGH_LIST	pp1,
		NEIGH_LIST	pp2,
		const AT_RANK *	nRank
	)

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CompareNeighListLexUpToMaxRank()

int CompareNeighListLexUpToMaxRank	(	NEIGH_LIST	pp1,
		NEIGH_LIST	pp2,
		const AT_RANK *	nRank,
		AT_RANK	nMaxAtNeighRank
	)

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CompAtomInvariants2()

int CompAtomInvariants2	(	const void *	a1,
		const void *	a2,
		void *	p
	)

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CompAtomInvariants2Only()

int CompAtomInvariants2Only	(	const void *	a1,
		const void *	a2,
		void *	p
	)

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CompChemElemLex()

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

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CompNeighborsAT_NUMBER()

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

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CompNeighborsRanksCountEql()

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

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CompNeighListRanks()

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

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CompNeighListRanksOrd()

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

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CompNeighLists()

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

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CompNeighListsUpToMaxRank()

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

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CompRank()

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

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CompRanksInvOrd()

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

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CompRanksOrd()

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

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CreateNeighList()

NEIGH_LIST * CreateNeighList	(	int	num_atoms,
		int	num_at_tg,
		sp_ATOM *	at,
		int	bDoubleBondSquare,
		T_GROUP_INFO *	t_group_info
	)

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CreateNeighListFromLinearCT()

NEIGH_LIST * CreateNeighListFromLinearCT	(	AT_NUMB *	LinearCT,
		int	nLenCT,
		int	num_atoms
	)

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CurTreeAddAtom()

int CurTreeAddAtom	(	CUR_TREE *	cur_tree,
		int	at_no
	)

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CurTreeAddRank()

int CurTreeAddRank	(	CUR_TREE *	cur_tree,
		AT_NUMB	rank
	)

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CurTreeAlloc()

int CurTreeAlloc	(	CUR_TREE *	cur_tree,
		int	num_atoms
	)

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CurTreeFindTheRankPos()

int CurTreeFindTheRankPos	(	CUR_TREE *	cur_tree,
		AT_NUMB	rank
	)

CurTreeFree()

void CurTreeFree

(

CUR_TREE *

cur_tree

)

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CurTreeGetPos()

int CurTreeGetPos

(

CUR_TREE *

cur_tree

)

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CurTreeIsLastAtomEqu()

int CurTreeIsLastAtomEqu	(	CUR_TREE *	cur_tree,
		int	at_no,
		AT_NUMB *	nSymmStereo
	)

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CurTreeIsLastRank()

int CurTreeIsLastRank	(	CUR_TREE *	cur_tree,
		AT_NUMB	rank
	)

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CurTreeKeepLastAtomsOnly()

void CurTreeKeepLastAtomsOnly	(	CUR_TREE *	cur_tree,
		int	tpos,
		int	shift
	)

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CurTreeReAlloc()

int CurTreeReAlloc

(

CUR_TREE *

cur_tree

)

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CurTreeRemoveIfLastAtom()

int CurTreeRemoveIfLastAtom	(	CUR_TREE *	cur_tree,
		int	at_no
	)

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CurTreeRemoveLastAtom()

int CurTreeRemoveLastAtom

(

CUR_TREE *

cur_tree

)

CurTreeRemoveLastRank()

int CurTreeRemoveLastRank

(

CUR_TREE *

cur_tree

)

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CurTreeRemoveLastRankIfNoAtoms()

int CurTreeRemoveLastRankIfNoAtoms

(

CUR_TREE *

cur_tree

)

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CurTreeReplaceLastRank()

int CurTreeReplaceLastRank	(	CUR_TREE *	cur_tree,
		AT_NUMB	rank
	)

CurTreeSetPos()

int CurTreeSetPos	(	CUR_TREE *	cur_tree,
		int	len
	)

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DifferentiateRanks2()

int DifferentiateRanks2	(	CANON_GLOBALS *	pCG,
		int	num_atoms,
		NEIGH_LIST *	NeighList,
		int	nNumCurrRanks,
		AT_RANK *	pnCurrRank,
		AT_RANK *	pnPrevRank,
		AT_RANK *	nAtomNumber,
		long *	lNumIter,
		int	bUseAltSort
	)

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DifferentiateRanks3()

int DifferentiateRanks3	(	CANON_GLOBALS *	pCG,
		int	num_atoms,
		NEIGH_LIST *	NeighList,
		int	nNumCurrRanks,
		AT_RANK *	pnCurrRank,
		AT_RANK *	pnPrevRank,
		AT_RANK *	nAtomNumber,
		long *	lNumIter
	)

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DifferentiateRanks4()

int DifferentiateRanks4	(	CANON_GLOBALS *	pCG,
		int	num_atoms,
		NEIGH_LIST *	NeighList,
		int	nNumCurrRanks,
		AT_RANK *	pnCurrRank,
		AT_RANK *	pnPrevRank,
		AT_RANK *	nAtomNumber,
		AT_RANK	nMaxAtRank,
		long *	lNumIter
	)

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DifferentiateRanksBasic()

int DifferentiateRanksBasic	(	CANON_GLOBALS *	pCG,
		int	num_atoms,
		NEIGH_LIST *	NeighList,
		int	nNumCurrRanks,
		AT_RANK *	pnCurrRank,
		AT_RANK *	pnPrevRank,
		AT_RANK *	nAtomNumber,
		long *	lNumIter,
		int	bUseAltSort
	)

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FillAllStereoDescriptors()

int FillAllStereoDescriptors	(	CANON_GLOBALS *	pCG,
		sp_ATOM *	at,
		int	num_atoms,
		const AT_RANK *	nCanonRank,
		const AT_RANK *	nAtomNumberCanon,
		CANON_STAT *	pCS
	)

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FillOutStereoParities()

int FillOutStereoParities	(	sp_ATOM *	at,
		int	num_atoms,
		const AT_RANK *	nCanonRank,
		const AT_RANK *	nAtomNumberCanon,
		const AT_RANK *	nRank,
		const AT_RANK *	nAtomNumber,
		CANON_STAT *	pCS,
		CANON_GLOBALS *	pCG,
		int	bIsotopic
	)

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FillSingleStereoDescriptors()

int FillSingleStereoDescriptors	(	CANON_GLOBALS *	pCG,
		sp_ATOM *	at,
		int	i,
		int	num_trans,
		const AT_RANK *	nRank,
		AT_STEREO_CARB *	LinearCTStereoCarb,
		int *	nStereoCarbLen,
		int	nMaxStereoCarbLen,
		AT_STEREO_DBLE *	LinearCTStereoDble,
		int *	nStereoDbleLen,
		int	nMaxStereoDbleLen,
		int	bAllene
	)

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find_atoms_with_parity()

int find_atoms_with_parity	(	sp_ATOM *	at,
		S_CHAR *	visited,
		int	from_atom,
		int	cur_atom
	)

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FreeNeighList()

void FreeNeighList

(

NEIGH_LIST *

pp

)

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GetPermutationParity()

int GetPermutationParity	(	CANON_GLOBALS *	pCG,
		sp_ATOM *	at,
		AT_RANK	nAvoidNeighbor,
		AT_RANK *	nCanonRank
	)

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GetStereoBondParity()

int GetStereoBondParity	(	sp_ATOM *	at,
		int	i,
		int	n,
		AT_RANK *	nRank
	)

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GetStereoCenterParity()

int GetStereoCenterParity	(	CANON_GLOBALS *	pCG,
		sp_ATOM *	at,
		int	i,
		AT_RANK *	nRank
	)

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GetStereoNeighborPos()

int GetStereoNeighborPos	(	sp_ATOM *	at,
		int	iAt1,
		int	iAt2
	)

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HalfStereoBondParity()

int HalfStereoBondParity	(	sp_ATOM *	at,
		int	at_no1,
		int	i_sb_neigh,
		const AT_RANK *	nRank
	)

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iisort()

int * iisort	(	int *	list,
		int	num
	)

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insertions_sort_AT_RANK()

int insertions_sort_AT_RANK	(	AT_RANK *	base,
		int	num
	)

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insertions_sort_NeighList_AT_NUMBERS()

void insertions_sort_NeighList_AT_NUMBERS	(	NEIGH_LIST	base,
		AT_RANK *	nRank
	)

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insertions_sort_NeighList_AT_NUMBERS3()

int insertions_sort_NeighList_AT_NUMBERS3	(	NEIGH_LIST	base,
		AT_RANK *	nRank
	)

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insertions_sort_NeighListBySymmAndCanonRank()

void insertions_sort_NeighListBySymmAndCanonRank	(	NEIGH_LIST	base,
		const AT_RANK *	nSymmRank,
		const AT_RANK *	nCanonRank
	)

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InvertStereo()

int InvertStereo	(	sp_ATOM *	at,
		int	num_at_tg,
		AT_RANK *	nCanonRank,
		AT_RANK *	nAtomNumberCanon,
		CANON_STAT *	pCS,
		int	bInvertLinearCTStereo
	)

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make_iso_sort_key()

AT_ISO_SORT_KEY make_iso_sort_key	(	int	iso_atw_diff,
		int	num_1H,
		int	num_2H,
		int	num_3H
	)

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map_an_atom2()

int map_an_atom2	(	CANON_GLOBALS *	pCG,
		int	num_atoms,
		int	num_max,
		int	at_no1,
		int	at_no2,
		AT_RANK *	nTempRank,
		int	nNumMappedRanks,
		int *	pnNewNumMappedRanks,
		CANON_STAT *	pCS,
		NEIGH_LIST *	NeighList,
		AT_RANK **	pRankStack1,
		AT_RANK **	pRankStack2,
		int *	bAddStack
	)

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map_stereo_atoms4()

int map_stereo_atoms4	(	struct tagINCHI_CLOCK *	ic,
		CANON_GLOBALS *	pCG,
		sp_ATOM *	at,
		int	num_atoms,
		int	num_at_tg,
		int	num_max,
		const AT_RANK *	nCanonRankFrom,
		const AT_RANK *	nAtomNumberCanonFrom,
		AT_RANK *	nCanonRankTo,
		const AT_RANK *	nSymmRank,
		AT_RANK **	pRankStack1,
		AT_RANK **	pRankStack2,
		AT_RANK *	nTempRank,
		int	nNumMappedRanksInput,
		AT_RANK *	nSymmStereo,
		NEIGH_LIST *	NeighList,
		CANON_STAT *	pCS,
		CUR_TREE *	cur_tree,
		int	nNumMappedAtoms,
		int	vABParityUnknown
	)

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map_stereo_bonds4()

int map_stereo_bonds4	(	struct tagINCHI_CLOCK *	ic,
		CANON_GLOBALS *	pCG,
		sp_ATOM *	at,
		int	num_atoms,
		int	num_at_tg,
		int	num_max,
		int	bAllene,
		const AT_RANK *	nCanonRankFrom,
		const AT_RANK *	nAtomNumberCanonFrom,
		AT_RANK *	nCanonRankTo,
		const AT_RANK *	nSymmRank,
		AT_RANK **	pRankStack1,
		AT_RANK **	pRankStack2,
		AT_RANK *	nTempRank,
		int	nNumMappedRanksInput,
		AT_RANK *	nSymmStereo,
		NEIGH_LIST *	NeighList,
		CANON_STAT *	pCS,
		CUR_TREE *	cur_tree,
		int	nNumMappedBonds,
		int	vABParityUnknown
	)

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might_change_other_atom_parity()

int might_change_other_atom_parity	(	sp_ATOM *	at,
		int	num_atoms,
		int	at_no,
		AT_RANK *	nRank2,
		AT_RANK *	nRank1
	)

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Next_SB_At_CanonRanks2()

int Next_SB_At_CanonRanks2	(	AT_RANK *	canon_rank1,
		AT_RANK *	canon_rank2,
		AT_RANK *	canon_rank1_min,
		AT_RANK *	canon_rank2_min,
		int *	bFirstTime,
		S_CHAR *	bAtomUsedForStereo,
		const ppAT_RANK	pRankStack1,
		const ppAT_RANK	pRankStack2,
		const AT_RANK *	nCanonRankFrom,
		const AT_RANK *	nAtomNumberCanonFrom,
		const sp_ATOM *	at,
		int	num_atoms,
		int	bAllene
	)

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Next_SC_At_CanonRank2()

int Next_SC_At_CanonRank2	(	AT_RANK *	canon_rank1,
		AT_RANK *	canon_rank1_min,
		int *	bFirstTime,
		S_CHAR *	bAtomUsedForStereo,
		const ppAT_RANK	pRankStack1,
		const ppAT_RANK	pRankStack2,
		const AT_RANK *	nAtomNumberCanonFrom,
		int	num_atoms
	)

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NextStereoParity2Test()

int NextStereoParity2Test	(	int *	stereo_bond_parity,
		int *	sb_parity_calc,
		int	nNumBest,
		int	nNumWorse,
		int	nNumUnkn,
		int	nNumUndf,
		int	nNumCalc,
		int	vABParityUnknown
	)

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nGetMcr()

AT_RANK nGetMcr	(	AT_RANK *	nEqArray,
		AT_RANK	n
	)

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nJoin2Mcrs()

int nJoin2Mcrs	(	AT_RANK *	nEqArray,
		AT_RANK	n1,
		AT_RANK	n2
	)

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NumberOfTies()

int NumberOfTies	(	AT_RANK **	pRankStack1,
		AT_RANK **	pRankStack2,
		int	length,
		int	at_no1,
		int	at_no2,
		AT_RANK *	nNewRank,
		int *	bAddStack,
		int *	bMapped1
	)

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parity_of_mapped_atom2()

int parity_of_mapped_atom2	(	CANON_GLOBALS *	pCG,
		int	from_at,
		int	to_at,
		const sp_ATOM *	at,
		EQ_NEIGH *	pEN,
		const AT_RANK *	nCanonRankFrom,
		const AT_RANK *	nRankFrom,
		const AT_RANK *	nRankTo
	)

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parity_of_mapped_half_bond()

int parity_of_mapped_half_bond	(	int	from_at,
		int	to_at,
		int	from_neigh,
		int	to_neigh,
		sp_ATOM *	at,
		EQ_NEIGH *	pEN,
		const AT_RANK *	nCanonRankFrom,
		const AT_RANK *	nRankFrom,
		const AT_RANK *	nRankTo
	)

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RemoveCalculatedNonStereo()

int RemoveCalculatedNonStereo	(	CANON_GLOBALS *	pCG,
		sp_ATOM *	at,
		int	num_atoms,
		int	num_at_tg,
		AT_RANK **	pRankStack1,
		AT_RANK **	pRankStack2,
		AT_RANK *	nTempRank,
		NEIGH_LIST *	NeighList,
		const AT_RANK *	nSymmRank,
		AT_RANK *	nCanonRank,
		AT_RANK *	nAtomNumberCanon,
		CANON_STAT *	pCS,
		int	vABParityUnknown
	)

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RemoveOneStereoBond()

int RemoveOneStereoBond	(	sp_ATOM *	at,
		int	jc,
		int	k
	)

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RemoveOneStereoCenter()

int RemoveOneStereoCenter	(	sp_ATOM *	at,
		int	jc
	)

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set_atom_iso_sort_keys()

int set_atom_iso_sort_keys	(	int	num_at,
		sp_ATOM *	at,
		T_GROUP_INFO *	t_group_info,
		int *	bHasIsotopicInTautomerGroups
	)

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SetCtToIsotopicStereo()

void SetCtToIsotopicStereo	(	CANON_STAT *	pCS,
		CANON_STAT *	pCS2
	)

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SetCtToNonIsotopicStereo()

void SetCtToNonIsotopicStereo	(	CANON_STAT *	pCS,
		CANON_STAT *	pCS2
	)

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SetNewRanksFromNeighLists()

int SetNewRanksFromNeighLists	(	CANON_GLOBALS *	pCG,
		int	num_atoms,
		NEIGH_LIST *	NeighList,
		AT_RANK *	nRank,
		AT_RANK *	nNewRank,
		AT_RANK *	nAtomNumber,
		int	bUseAltSort,
		int(*)(const void *, const void *, void *)	comp
	)

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SetNewRanksFromNeighLists3()

int SetNewRanksFromNeighLists3	(	CANON_GLOBALS *	pCG,
		int	num_atoms,
		NEIGH_LIST *	NeighList,
		AT_RANK *	nRank,
		AT_RANK *	nNewRank,
		AT_RANK *	nAtomNumber
	)

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SetNewRanksFromNeighLists4()

int SetNewRanksFromNeighLists4	(	CANON_GLOBALS *	pCG,
		int	num_atoms,
		NEIGH_LIST *	NeighList,
		AT_RANK *	nRank,
		AT_RANK *	nNewRank,
		AT_RANK *	nAtomNumber,
		AT_RANK	nMaxAtRank
	)

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SetOneStereoBondIllDefParity()

int SetOneStereoBondIllDefParity	(	sp_ATOM *	at,
		int	jc,
		int	k,
		int	new_parity
	)

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SetUseAtomForStereo()

void SetUseAtomForStereo	(	S_CHAR *	bAtomUsedForStereo,
		sp_ATOM *	at,
		int	num_atoms
	)

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SortedEquInfoToRanks()

int SortedEquInfoToRanks	(	const AT_RANK *	nSymmRank,
		AT_RANK *	nRank,
		const AT_RANK *	nAtomNumber,
		int	num_atoms,
		int *	bChanged
	)

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SortedRanksToEquInfo()

int SortedRanksToEquInfo	(	AT_RANK *	nSymmRank,
		const AT_RANK *	nRank,
		const AT_RANK *	nAtomNumber,
		int	num_atoms
	)

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SortNeighLists2()

int SortNeighLists2	(	int	num_atoms,
		AT_RANK *	nRank,
		NEIGH_LIST *	NeighList,
		AT_RANK *	nAtomNumber
	)

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SortNeighListsBySymmAndCanonRank()

void SortNeighListsBySymmAndCanonRank	(	int	num_atoms,
		NEIGH_LIST *	NeighList,
		const AT_RANK *	nSymmRank,
		const AT_RANK *	nCanonRank
	)

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switch_ptrs()

void switch_ptrs	(	AT_RANK **	p1,
		AT_RANK **	p2
	)

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SwitchAtomStereoAndIsotopicStereo()

void SwitchAtomStereoAndIsotopicStereo	(	sp_ATOM *	at,
		int	num_atoms,
		int *	bSwitched
	)

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UnmarkNonStereo()

int UnmarkNonStereo	(	CANON_GLOBALS *	pCG,
		sp_ATOM *	at,
		int	num_atoms,
		const AT_RANK *	nRank,
		const AT_RANK *	nAtomNumber,
		int	bIsotopic
	)

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unpack_iso_sort_key()

int unpack_iso_sort_key	(	AT_ISO_SORT_KEY	iso_sort_key,
		S_CHAR *	num_1H,
		S_CHAR *	num_2H,
		S_CHAR *	num_3H,
		S_CHAR *	iso_atw_diff
	)