ichimap2.c File Reference

#include <stdlib.h>
#include <string.h>
#include "mode.h"
#include "ichicomn.h"
#include "bcf_s.h"

Include dependency graph for ichimap2.c:

Macros
#define	MAP_MODE_STD   0 /* Standard approach: switch 2 neighbors */
#define	MAP_MODE_C2v   1 /* Check for C2v reflection leading to parity inversion */
#define	MAP_MODE_C2   2 /* Check for C2 rotation preserving parities */
#define	MAP_MODE_S4   3 /* Check for S4 rotation/reflection leading to parity inversion */
#define	MAX_OTHER_NEIGH   2
#define	NEIGH_MODE_RING   1
#define	NEIGH_MODE_CHAIN   2
#define	CHECKING_STEREOCENTER   1
#define	CHECKING_STEREOBOND   2
#define	COMP_STEREO_SUCCESS   1
#define	NOT_WELL_DEF_UNKN   2
#define	NOT_WELL_DEF_UNDF   4
#define	PARITY_IMPOSSIBLE   999

Functions
void	DeAllocateForNonStereoRemoval (AT_RANK **nAtomNumberCanon1, AT_RANK **nAtomNumberCanon2, NEIGH_LIST **nl, NEIGH_LIST **nl1, NEIGH_LIST **nl2, AT_RANK **nVisited1, AT_RANK **nVisited2)
int	AllocateForNonStereoRemoval (sp_ATOM *at, int num_atoms, const AT_RANK *nSymmRank, AT_RANK *nCanonRank, AT_RANK **nAtomNumberCanon1, AT_RANK **nAtomNumberCanon2, NEIGH_LIST **nl, NEIGH_LIST **nl1, NEIGH_LIST **nl2, AT_RANK **nVisited1, AT_RANK **nVisited2)
AT_RANK	GetMinNewRank (AT_RANK *nAtomRank, AT_RANK *nAtomNumb, AT_RANK nRank1)
int	BreakNeighborsTie (CANON_GLOBALS *pCG, sp_ATOM *at, int num_atoms, int num_at_tg, int ib, int ia, AT_RANK *neigh_num, int in1, int in2, int mode, AT_RANK **pRankStack1, AT_RANK **pRankStack2, AT_RANK *nTempRank, NEIGH_LIST *NeighList, const AT_RANK *nSymmRank, AT_RANK *nCanonRank, NEIGH_LIST *nl1, NEIGH_LIST *nl2, long *lNumIter)
int	CheckNextSymmNeighborsAndBonds (sp_ATOM *at, AT_RANK cur1, AT_RANK cur2, AT_RANK n1, AT_RANK n2, AT_RANK *nAvoidCheckAtom, AT_RANK *nVisited1, AT_RANK *nVisited2, AT_RANK *nVisitOrd1, AT_RANK *nVisitOrd2, const AT_RANK *nRank1, const AT_RANK *nRank2)
int	CreateCheckSymmPaths (sp_ATOM *at, AT_RANK prev1, AT_RANK cur1, AT_RANK prev2, AT_RANK cur2, AT_RANK *nAvoidCheckAtom, AT_RANK *nVisited1, AT_RANK *nVisited2, AT_RANK *nVisitOrd1, AT_RANK *nVisitOrd2, NEIGH_LIST *nl1, NEIGH_LIST *nl2, const AT_RANK *nRank1, const AT_RANK *nRank2, AT_RANK *nCanonRank, AT_RANK *nLength, int *bParitiesInverted, int mode)
int	CalculatedPathsParitiesAreIdentical (CANON_GLOBALS *pCG, sp_ATOM *at, int num_atoms, const AT_RANK *nSymmRank, AT_RANK *nCanonRank, AT_RANK *nAtomNumberCanon, AT_RANK *nAtomNumberCanon1, AT_RANK *nAtomNumberCanon2, AT_RANK *nVisited1, AT_RANK *nVisited2, AT_RANK prev_sb_neigh, AT_RANK cur, AT_RANK next1, AT_RANK next2, int nNeighMode, int bParitiesInverted, int mode, CANON_STAT *pCS, int vABParityUnknown)
int	RemoveCalculatedNonStereoBondParities (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, AT_RANK *nCanonRank, const AT_RANK *nSymmRank, AT_RANK *nAtomNumberCanon, AT_RANK *nAtomNumberCanon1, AT_RANK *nAtomNumberCanon2, NEIGH_LIST *nl, NEIGH_LIST *nl1, NEIGH_LIST *nl2, AT_RANK *nVisited1, AT_RANK *nVisited2, CANON_STAT *pCS, int vABParityUnknown)
int	RemoveCalculatedNonStereoCenterParities (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, AT_RANK *nCanonRank, const AT_RANK *nSymmRank, AT_RANK *nAtomNumberCanon, AT_RANK *nAtomNumberCanon1, AT_RANK *nAtomNumberCanon2, NEIGH_LIST *nl, NEIGH_LIST *nl1, NEIGH_LIST *nl2, AT_RANK *nVisited1, AT_RANK *nVisited2, CANON_STAT *pCS, int vABParityUnknown)
int	SortNeighLists3 (int num_atoms, AT_RANK *nRank, NEIGH_LIST *NeighList, AT_RANK *nAtomNumber)
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)
void	switch_ptrs (AT_RANK **p1, AT_RANK **p2)
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)
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 *))
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	NumberOfTies (AT_RANK **pRankStack1, AT_RANK **pRankStack2, int length, int at_no1, int at_no2, AT_RANK *nNewRank, int *bAddStack, int *bMapped1)
int	HalfStereoBondParity (sp_ATOM *at, int at_no1, int i_sb_neigh, const AT_RANK *nRank)
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	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	ClearPreviousMappings (AT_RANK **pRankStack1)
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	might_change_other_atom_parity (sp_ATOM *at, int num_atoms, int at_no, AT_RANK *nRank2, AT_RANK *nRank1)
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)

Macro Definition Documentation

CHECKING_STEREOBOND

#define CHECKING_STEREOBOND   2

CHECKING_STEREOCENTER

#define CHECKING_STEREOCENTER   1

COMP_STEREO_SUCCESS

#define COMP_STEREO_SUCCESS   1

MAP_MODE_C2

#define MAP_MODE_C2   2 /* Check for C2 rotation preserving parities */

MAP_MODE_C2v

#define MAP_MODE_C2v   1 /* Check for C2v reflection leading to parity inversion */

MAP_MODE_S4

#define MAP_MODE_S4   3 /* Check for S4 rotation/reflection leading to parity inversion */

MAP_MODE_STD

#define MAP_MODE_STD   0 /* Standard approach: switch 2 neighbors */

MAX_OTHER_NEIGH

#define MAX_OTHER_NEIGH   2

NEIGH_MODE_CHAIN

#define NEIGH_MODE_CHAIN   2

NEIGH_MODE_RING

#define NEIGH_MODE_RING   1

NOT_WELL_DEF_UNDF

#define NOT_WELL_DEF_UNDF   4

NOT_WELL_DEF_UNKN

#define NOT_WELL_DEF_UNKN   2

PARITY_IMPOSSIBLE

#define PARITY_IMPOSSIBLE   999

Function Documentation

AllocateForNonStereoRemoval()

int AllocateForNonStereoRemoval	(	sp_ATOM *	at,
		int	num_atoms,
		const AT_RANK *	nSymmRank,
		AT_RANK *	nCanonRank,
		AT_RANK **	nAtomNumberCanon1,
		AT_RANK **	nAtomNumberCanon2,
		NEIGH_LIST **	nl,
		NEIGH_LIST **	nl1,
		NEIGH_LIST **	nl2,
		AT_RANK **	nVisited1,
		AT_RANK **	nVisited2
	)

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BreakNeighborsTie()

int BreakNeighborsTie	(	CANON_GLOBALS *	pCG,
		sp_ATOM *	at,
		int	num_atoms,
		int	num_at_tg,
		int	ib,
		int	ia,
		AT_RANK *	neigh_num,
		int	in1,
		int	in2,
		int	mode,
		AT_RANK **	pRankStack1,
		AT_RANK **	pRankStack2,
		AT_RANK *	nTempRank,
		NEIGH_LIST *	NeighList,
		const AT_RANK *	nSymmRank,
		AT_RANK *	nCanonRank,
		NEIGH_LIST *	nl1,
		NEIGH_LIST *	nl2,
		long *	lNumIter
	)

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CalculatedPathsParitiesAreIdentical()

int CalculatedPathsParitiesAreIdentical	(	CANON_GLOBALS *	pCG,
		sp_ATOM *	at,
		int	num_atoms,
		const AT_RANK *	nSymmRank,
		AT_RANK *	nCanonRank,
		AT_RANK *	nAtomNumberCanon,
		AT_RANK *	nAtomNumberCanon1,
		AT_RANK *	nAtomNumberCanon2,
		AT_RANK *	nVisited1,
		AT_RANK *	nVisited2,
		AT_RANK	prev_sb_neigh,
		AT_RANK	cur,
		AT_RANK	next1,
		AT_RANK	next2,
		int	nNeighMode,
		int	bParitiesInverted,
		int	mode,
		CANON_STAT *	pCS,
		int	vABParityUnknown
	)

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CheckNextSymmNeighborsAndBonds()

int CheckNextSymmNeighborsAndBonds	(	sp_ATOM *	at,
		AT_RANK	cur1,
		AT_RANK	cur2,
		AT_RANK	n1,
		AT_RANK	n2,
		AT_RANK *	nAvoidCheckAtom,
		AT_RANK *	nVisited1,
		AT_RANK *	nVisited2,
		AT_RANK *	nVisitOrd1,
		AT_RANK *	nVisitOrd2,
		const AT_RANK *	nRank1,
		const AT_RANK *	nRank2
	)

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ClearPreviousMappings()

int ClearPreviousMappings

(

AT_RANK **

pRankStack1

)

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CreateCheckSymmPaths()

int CreateCheckSymmPaths	(	sp_ATOM *	at,
		AT_RANK	prev1,
		AT_RANK	cur1,
		AT_RANK	prev2,
		AT_RANK	cur2,
		AT_RANK *	nAvoidCheckAtom,
		AT_RANK *	nVisited1,
		AT_RANK *	nVisited2,
		AT_RANK *	nVisitOrd1,
		AT_RANK *	nVisitOrd2,
		NEIGH_LIST *	nl1,
		NEIGH_LIST *	nl2,
		const AT_RANK *	nRank1,
		const AT_RANK *	nRank2,
		AT_RANK *	nCanonRank,
		AT_RANK *	nLength,
		int *	bParitiesInverted,
		int	mode
	)

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DeAllocateForNonStereoRemoval()

void DeAllocateForNonStereoRemoval	(	AT_RANK **	nAtomNumberCanon1,
		AT_RANK **	nAtomNumberCanon2,
		NEIGH_LIST **	nl,
		NEIGH_LIST **	nl1,
		NEIGH_LIST **	nl2,
		AT_RANK **	nVisited1,
		AT_RANK **	nVisited2
	)

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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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GetMinNewRank()

AT_RANK GetMinNewRank	(	AT_RANK *	nAtomRank,
		AT_RANK *	nAtomNumb,
		AT_RANK	nRank1
	)

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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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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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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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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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RemoveCalculatedNonStereoBondParities()

int RemoveCalculatedNonStereoBondParities	(	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,
		AT_RANK *	nCanonRank,
		const AT_RANK *	nSymmRank,
		AT_RANK *	nAtomNumberCanon,
		AT_RANK *	nAtomNumberCanon1,
		AT_RANK *	nAtomNumberCanon2,
		NEIGH_LIST *	nl,
		NEIGH_LIST *	nl1,
		NEIGH_LIST *	nl2,
		AT_RANK *	nVisited1,
		AT_RANK *	nVisited2,
		CANON_STAT *	pCS,
		int	vABParityUnknown
	)

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RemoveCalculatedNonStereoCenterParities()

int RemoveCalculatedNonStereoCenterParities	(	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,
		AT_RANK *	nCanonRank,
		const AT_RANK *	nSymmRank,
		AT_RANK *	nAtomNumberCanon,
		AT_RANK *	nAtomNumberCanon1,
		AT_RANK *	nAtomNumberCanon2,
		NEIGH_LIST *	nl,
		NEIGH_LIST *	nl1,
		NEIGH_LIST *	nl2,
		AT_RANK *	nVisited1,
		AT_RANK *	nVisited2,
		CANON_STAT *	pCS,
		int	vABParityUnknown
	)

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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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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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SortNeighLists3()

int SortNeighLists3	(	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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