ichimain.h File Reference

#include "strutil.h"
#include "ichicomn.h"

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Data Structures
struct	tagLine
struct	tagStructData
struct	tagINCHI_OUT_CTL
struct	tagPOSEContext

Macros
#define	ESC_KEY   27
#define	INCHI_SEGM_BUFLEN   524288
#define	PRINT_INCHI_MAX_TAG_LEN   64
#define	COMP_ORIG_0_MAIN   0x0001
#define	COMP_ORIG_0_RECN   0x0002
#define	COMP_PREP_0_MAIN   0x0004
#define	COMP_PREP_0_RECN   0x0008
#define	COMP_ORIG_1_MAIN   0x0010
#define	COMP_ORIG_1_RECN   0x0020
#define	PERMAXATOMS   32767
#define	BYTE(X)   ((unsigned char *)(X))

Typedefs
typedef struct tagLine	SEGM_LINE
typedef struct tagStructData	STRUCT_DATA
typedef struct tagINCHI_OUT_CTL	INCHI_OUT_CTL
typedef struct tagPOSEContext	POSEContext
typedef enum MAIN_LOOP_ACTION	MAIN_LOOP_ACTION

Enumerations
enum	MAIN_LOOP_ACTION { DO_NEXT_STEP , DO_BREAK_MAIN_LOOP , DO_EXIT_FUNCTION , DO_CONTINUE_MAIN_LOOP }

Functions
int	rrand (int m)
void	shuffle (void *obj, size_t nmemb, size_t size)
int	POSEContext_Init (POSEContext *context, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits)
void	POSEContext_Free (POSEContext *context)
void	POSEContext_DebugPrint (POSEContext *context)
int	ProcessSingleInputFile (int argc, char *argv[])
int	ProcessMultipleInputFiles (int argc, char *argv[])
int	ReadCommandLineParms (int argc, const char *argv[], INPUT_PARMS *ip, char *szSdfDataValue, unsigned long *ulDisplTime, int bReleaseVersion, INCHI_IOSTREAM *log_file)
void	HelpCommandLineParms (INCHI_IOSTREAM *f)
int	OpenFiles (FILE **inp_file, FILE **out_file, FILE **log_file, FILE **prb_file, INPUT_PARMS *ip)
int	PrintInputParms (INCHI_IOSTREAM *log_file, INPUT_PARMS *ip)
int	SortAndPrintINChI (struct tagCANON_GLOBALS *pCG, INCHI_IOSTREAM *out_file, INCHI_IOS_STRING *strbuf, INCHI_IOSTREAM *log_file, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, COMP_ATOM_DATA composite_norm_data[INCHI_NUM][TAUT_NUM+1], ORIG_STRUCT *pOrigStruct, int num_components[INCHI_NUM], int num_non_taut[INCHI_NUM], int num_taut[INCHI_NUM], INCHI_MODE bTautFlags[INCHI_NUM], INCHI_MODE bTautFlagsDone[INCHI_NUM], NORM_CANON_FLAGS *pncFlags, long num_inp, PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM], int *pSortPrintINChIFlags, unsigned char save_opt_bits)
void	FreeAllINChIArrays (PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM], int num_components[2])
void	FreeINChIArrays (PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, int num_components)
int	ReadTheStructure (struct tagINCHI_CLOCK *ic, STRUCT_DATA *sd, INPUT_PARMS *ip, INCHI_IOSTREAM *inp_file, ORIG_ATOM_DATA *orig_inp_data, int inp_index, int *out_index)
int	TreatErrorsInReadTheStructure (STRUCT_DATA *sd, INPUT_PARMS *ip, int nLogMask, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, long *num_inp)
int	GetOneComponent (struct tagINCHI_CLOCK *ic, STRUCT_DATA *sd, INPUT_PARMS *ip, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INP_ATOM_DATA *inp_cur_data, ORIG_ATOM_DATA *orig_inp_data, int i, long num_inp)
int	CreateOneComponentINChI (struct tagCANON_GLOBALS *pCG, struct tagINCHI_CLOCK *ic, STRUCT_DATA *sd, INPUT_PARMS *ip, INP_ATOM_DATA *inp_cur_data, ORIG_ATOM_DATA *orig_inp_data, PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, int iINChI, int i, long num_inp, INP_ATOM_DATA **inp_norm_data, NORM_CANON_FLAGS *pncFlags, INCHI_IOSTREAM *log_file)
int	TreatErrorsInCreateOneComponentINChI (STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, int i, long num_inp, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file)
int	TreatCreateINChIWarning (STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, long num_inp, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file)
int	GetProcessingWarningsOneComponentInChI (INChI *cur_INChI[], INP_ATOM_DATA **inp_norm_data, STRUCT_DATA *sd, int bNoWarnings)
int	GetTheNextRecordOfInputFile (struct tagINCHI_CLOCK *ic, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *plog, INCHI_IOSTREAM *pout, INCHI_IOSTREAM *pprb, ORIG_ATOM_DATA *orig_inp_data, long *num_inp, STRUCT_FPTRS *pStructPtrs, int *nRet, int *have_err_in_GetOneStructure, long *num_err, int output_error_inchi)
int	CalcAndPrintINCHIAndINCHIKEY (struct tagINCHI_CLOCK *ic, CANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *plog, INCHI_IOSTREAM *pout, INCHI_IOSTREAM *pprb, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long *num_inp, STRUCT_FPTRS *pStructPtrs, int *nRet, int have_err_in_GetOneStructure, long *num_err, int output_error_inchi, INCHI_IOS_STRING *strbuf, unsigned long *pulTotalProcessingTime, char *pLF, char *pTAB, char *ikey, int silent)
int	GetOneStructure (struct tagINCHI_CLOCK *ic, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, long *num_inp, STRUCT_FPTRS *struct_fptrs)
int	ProcessOneStructure (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *pCG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits)
int	ProcessOneStructureEx (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *pCG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits)
int	PreprocessPolymerCRUData (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits, char **sinchi, char **saux)
int	OAD_ProcessOneStructureNoEdits (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits, int *n_pzz, char **sinchi, char **saux)
int	OAD_ProcessOneStructure105Plus (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits, char **sinchi, char **saux)
int	ValidateAndPreparePolymerAndPseudoatoms (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, INCHI_IOS_STRING *strbuf, unsigned char save_opt_bits, int *mind_polymers)
int	CreateOneStructureINChI (struct tagCANON_GLOBALS *pCG, struct tagINCHI_CLOCK *ic, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], int iINChI, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, COMP_ATOM_DATA composite_norm_data2[][TAUT_NUM+1], long num_inp, INCHI_IOS_STRING *strbuf, NORM_CANON_FLAGS *pncFlags)
int	PreprocessOneStructure (struct tagINCHI_CLOCK *ic, STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data)
int	RepeatedlyRenumberAtomsAndRecalcINCHI (struct tagINCHI_CLOCK *ic, CANON_GLOBALS *CG, STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *plog, INCHI_IOSTREAM *pout, INCHI_IOSTREAM *pprb, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long *num_inp, STRUCT_FPTRS *pStructPtrs, int *nRet, int have_err_in_GetOneStructure, long *num_err, int output_error_inchi, INCHI_IOS_STRING *strbuf, unsigned long *pulTotalProcessingTime, char *pLF, char *pTAB, long int nrepeat)
int	bIsStructChiral (PINChI2 *pINChI2[INCHI_NUM], int num_components[])
int	OrigAtData_Duplicate (ORIG_ATOM_DATA *new_orig_atom, ORIG_ATOM_DATA *orig_atom)
void	OrigAtData_Permute (ORIG_ATOM_DATA *permuted, ORIG_ATOM_DATA *saved, int *numbers)
int	OrigAtData_RemoveAtom (ORIG_ATOM_DATA *orig_at_data, int iatom)
int	OrigAtData_AddSingleStereolessBond (int this_atom, int other_atom, inp_ATOM *at, int *num_inp_bonds)
int	OrigAtData_AddBond (int this_atom, int other_atom, inp_ATOM *at, int bond_type, int bond_stereo, int *num_bonds)
int	OrigAtData_RemoveBond (int this_atom, int other_atom, inp_ATOM *at, int *bond_type, int *bond_stereo, int *num_inp_bonds)
int	OrigAtData_RemoveHalfBond (int this_atom, int other_atom, inp_ATOM *at, int *bond_type, int *bond_stereo)
int	OrigAtData_IncreaseBondOrder (int this_atom, int other_atom, inp_ATOM *at)
int	OrigAtData_DecreaseBondOrder (int this_atom, int other_atom, inp_ATOM *at)
int	OrigAtData_SaveMolfile (ORIG_ATOM_DATA *orig_inp_data, STRUCT_DATA *sd, INPUT_PARMS *ip, long num_inp, INCHI_IOSTREAM *out_file)
void	OrigAtData_DebugTrace (ORIG_ATOM_DATA *at_data)
int	OAD_StructureEdits_Apply (STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_at_data, OAD_StructureEdits *ed, int *ret)
void	OAD_CollectFragmentBondsAndAtoms (ORIG_ATOM_DATA *at_data, int nforbidden, int *forbidden_orig, int *n_fragbonds, int **fragbonds, int *n_fragatoms, int *fragatoms, int *err, char *pStrErr)
void	winchi_calc_inchikey (int ret, int *ikflag, INPUT_PARMS *ip, INCHI_IOSTREAM *out_file, INCHI_IOSTREAM *log_file)
int	Inp_Atom_GetBondType (inp_ATOM *at, int iatom1, int iatom2)
int	OrigStruct_FillOut (struct tagCANON_GLOBALS *pCG, ORIG_ATOM_DATA *orig_inp_data, ORIG_STRUCT *pOrigStruct, STRUCT_DATA *sd)
void	OrigStruct_Free (ORIG_STRUCT *pOrigStruct)
int	ReadWriteInChI (struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *pCG, INCHI_IOSTREAM *pInp, INCHI_IOSTREAM *pOut, INCHI_IOSTREAM *pLog, INPUT_PARMS *ip_inp, STRUCT_DATA *sd_inp, inp_ATOM **at, int *num_at, int *num_bonds, OAD_Polymer **polymer, OAD_V3000 **v3000, char *szMsg, int nMsgLen, unsigned long WarningFlags[2][2])
int	CompareHillFormulasNoH (const char *f1, const char *f2, int *num_H1, int *num_H2)
int	CreateCompositeNormAtom (COMP_ATOM_DATA *composite_norm_data, INP_ATOM_DATA2 *all_inp_norm_data, int num_components)
void	EditINCHI_HidePolymerZz (INCHI_IOSTREAM *out, int n_pzz, int n_zy)
void	SplitTime (unsigned long ulTotalTime, int *hours, int *minutes, int *seconds, int *mseconds)
void	set_line_separators (int bINChIOutputOptions, char **pLF, char **pTAB)
void	save_command_line (int argc, char *argv[], INCHI_IOSTREAM *plog)
void	emit_empty_inchi (INPUT_PARMS *ip, long num_inp, char *pLF, char *pTAB, INCHI_IOSTREAM *pout)

Macro Definition Documentation

BYTE

#define BYTE

(

X

)

((unsigned char *)(X))

COMP_ORIG_0_MAIN

#define COMP_ORIG_0_MAIN   0x0001

COMP_ORIG_0_RECN

#define COMP_ORIG_0_RECN   0x0002

COMP_ORIG_1_MAIN

#define COMP_ORIG_1_MAIN   0x0010

COMP_ORIG_1_RECN

#define COMP_ORIG_1_RECN   0x0020

COMP_PREP_0_MAIN

#define COMP_PREP_0_MAIN   0x0004

COMP_PREP_0_RECN

#define COMP_PREP_0_RECN   0x0008

ESC_KEY

#define ESC_KEY   27

INCHI_SEGM_BUFLEN

#define INCHI_SEGM_BUFLEN   524288

PERMAXATOMS

#define PERMAXATOMS   32767

PRINT_INCHI_MAX_TAG_LEN

#define PRINT_INCHI_MAX_TAG_LEN   64

Typedef Documentation

INCHI_OUT_CTL

typedef struct tagINCHI_OUT_CTL INCHI_OUT_CTL

MAIN_LOOP_ACTION

typedef enum MAIN_LOOP_ACTION MAIN_LOOP_ACTION

POSEContext

typedef struct tagPOSEContext POSEContext

SEGM_LINE

typedef struct tagLine SEGM_LINE

STRUCT_DATA

typedef struct tagStructData STRUCT_DATA

Enumeration Type Documentation

MAIN_LOOP_ACTION

enum MAIN_LOOP_ACTION

Enumerator
DO_NEXT_STEP
DO_BREAK_MAIN_LOOP
DO_EXIT_FUNCTION
DO_CONTINUE_MAIN_LOOP

Function Documentation

bIsStructChiral()

int bIsStructChiral	(	PINChI2 *	pINChI2[INCHI_NUM],
		int	num_components[]
	)

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CalcAndPrintINCHIAndINCHIKEY()

int CalcAndPrintINCHIAndINCHIKEY	(	struct tagINCHI_CLOCK *	ic,
		CANON_GLOBALS *	CG,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		PINChI2 *	pINChI[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux[INCHI_NUM],
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	plog,
		INCHI_IOSTREAM *	pout,
		INCHI_IOSTREAM *	pprb,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data,
		long *	num_inp,
		STRUCT_FPTRS *	pStructPtrs,
		int *	nRet,
		int	have_err_in_GetOneStructure,
		long *	num_err,
		int	output_error_inchi,
		INCHI_IOS_STRING *	strbuf,
		unsigned long *	pulTotalProcessingTime,
		char *	pLF,
		char *	pTAB,
		char *	ikey,
		int	silent
	)

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CompareHillFormulasNoH()

int CompareHillFormulasNoH	(	const char *	f1,
		const char *	f2,
		int *	num_H1,
		int *	num_H2
	)

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CreateCompositeNormAtom()

int CreateCompositeNormAtom	(	COMP_ATOM_DATA *	composite_norm_data,
		INP_ATOM_DATA2 *	all_inp_norm_data,
		int	num_components
	)

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CreateOneComponentINChI()

int CreateOneComponentINChI	(	struct tagCANON_GLOBALS *	pCG,
		struct tagINCHI_CLOCK *	ic,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		INP_ATOM_DATA *	inp_cur_data,
		ORIG_ATOM_DATA *	orig_inp_data,
		PINChI2 *	pINChI,
		PINChI_Aux2 *	pINChI_Aux,
		int	iINChI,
		int	i,
		long	num_inp,
		INP_ATOM_DATA **	inp_norm_data,
		NORM_CANON_FLAGS *	pncFlags,
		INCHI_IOSTREAM *	log_file
	)

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CreateOneStructureINChI()

int CreateOneStructureINChI	(	struct tagCANON_GLOBALS *	pCG,
		struct tagINCHI_CLOCK *	ic,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		PINChI2 *	pINChI2[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux2[INCHI_NUM],
		int	iINChI,
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data,
		COMP_ATOM_DATA	composite_norm_data2[][TAUT_NUM+1],
		long	num_inp,
		INCHI_IOS_STRING *	strbuf,
		NORM_CANON_FLAGS *	pncFlags
	)

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EditINCHI_HidePolymerZz()

void EditINCHI_HidePolymerZz	(	INCHI_IOSTREAM *	out,
		int	n_pzz,
		int	n_zy
	)

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emit_empty_inchi()

void emit_empty_inchi	(	INPUT_PARMS *	ip,
		long	num_inp,
		char *	pLF,
		char *	pTAB,
		INCHI_IOSTREAM *	pout
	)

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FreeAllINChIArrays()

void FreeAllINChIArrays	(	PINChI2 *	pINChI[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux[INCHI_NUM],
		int	num_components[2]
	)

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FreeINChIArrays()

void FreeINChIArrays	(	PINChI2 *	pINChI,
		PINChI_Aux2 *	pINChI_Aux,
		int	num_components
	)

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GetOneComponent()

int GetOneComponent	(	struct tagINCHI_CLOCK *	ic,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INP_ATOM_DATA *	inp_cur_data,
		ORIG_ATOM_DATA *	orig_inp_data,
		int	i,
		long	num_inp
	)

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GetOneStructure()

int GetOneStructure	(	struct tagINCHI_CLOCK *	ic,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file,
		ORIG_ATOM_DATA *	orig_inp_data,
		long *	num_inp,
		STRUCT_FPTRS *	struct_fptrs
	)

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GetProcessingWarningsOneComponentInChI()

int GetProcessingWarningsOneComponentInChI	(	INChI *	cur_INChI[],
		INP_ATOM_DATA **	inp_norm_data,
		STRUCT_DATA *	sd,
		int	bNoWarnings
	)

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GetTheNextRecordOfInputFile()

int GetTheNextRecordOfInputFile	(	struct tagINCHI_CLOCK *	ic,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	plog,
		INCHI_IOSTREAM *	pout,
		INCHI_IOSTREAM *	pprb,
		ORIG_ATOM_DATA *	orig_inp_data,
		long *	num_inp,
		STRUCT_FPTRS *	pStructPtrs,
		int *	nRet,
		int *	have_err_in_GetOneStructure,
		long *	num_err,
		int	output_error_inchi
	)

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HelpCommandLineParms()

void HelpCommandLineParms

(

INCHI_IOSTREAM *

f

)

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Inp_Atom_GetBondType()

int Inp_Atom_GetBondType	(	inp_ATOM *	at,
		int	iatom1,
		int	iatom2
	)

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OAD_CollectFragmentBondsAndAtoms()

void OAD_CollectFragmentBondsAndAtoms	(	ORIG_ATOM_DATA *	at_data,
		int	nforbidden,
		int *	forbidden_orig,
		int *	n_fragbonds,
		int **	fragbonds,
		int *	n_fragatoms,
		int *	fragatoms,
		int *	err,
		char *	pStrErr
	)

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OAD_ProcessOneStructure105Plus()

int OAD_ProcessOneStructure105Plus	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	CG,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		PINChI2 *	pINChI2[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux2[INCHI_NUM],
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data,
		long	num_inp,
		INCHI_IOS_STRING *	strbuf,
		unsigned char	save_opt_bits,
		char **	sinchi,
		char **	saux
	)

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OAD_ProcessOneStructureNoEdits()

int OAD_ProcessOneStructureNoEdits	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	CG,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		PINChI2 *	pINChI2[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux2[INCHI_NUM],
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data,
		long	num_inp,
		INCHI_IOS_STRING *	strbuf,
		unsigned char	save_opt_bits,
		int *	n_pzz,
		char **	sinchi,
		char **	saux
	)

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OAD_StructureEdits_Apply()

int OAD_StructureEdits_Apply	(	STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		ORIG_ATOM_DATA *	orig_at_data,
		OAD_StructureEdits *	ed,
		int *	ret
	)

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OpenFiles()

int OpenFiles	(	FILE **	inp_file,
		FILE **	out_file,
		FILE **	log_file,
		FILE **	prb_file,
		INPUT_PARMS *	ip
	)

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OrigAtData_AddBond()

int OrigAtData_AddBond	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at,
		int	bond_type,
		int	bond_stereo,
		int *	num_bonds
	)

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OrigAtData_AddSingleStereolessBond()

int OrigAtData_AddSingleStereolessBond	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at,
		int *	num_inp_bonds
	)

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OrigAtData_DebugTrace()

void OrigAtData_DebugTrace

(

ORIG_ATOM_DATA *

at_data

)

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OrigAtData_DecreaseBondOrder()

int OrigAtData_DecreaseBondOrder	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at
	)

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OrigAtData_Duplicate()

int OrigAtData_Duplicate	(	ORIG_ATOM_DATA *	new_orig_atom,
		ORIG_ATOM_DATA *	orig_atom
	)

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OrigAtData_IncreaseBondOrder()

int OrigAtData_IncreaseBondOrder	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at
	)

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OrigAtData_Permute()

void OrigAtData_Permute	(	ORIG_ATOM_DATA *	permuted,
		ORIG_ATOM_DATA *	saved,
		int *	numbers
	)

OrigAtData_RemoveAtom()

int OrigAtData_RemoveAtom	(	ORIG_ATOM_DATA *	orig_at_data,
		int	iatom
	)

OrigAtData_RemoveBond()

int OrigAtData_RemoveBond	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at,
		int *	bond_type,
		int *	bond_stereo,
		int *	num_inp_bonds
	)

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OrigAtData_RemoveHalfBond()

int OrigAtData_RemoveHalfBond	(	int	this_atom,
		int	other_atom,
		inp_ATOM *	at,
		int *	bond_type,
		int *	bond_stereo
	)

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OrigAtData_SaveMolfile()

int OrigAtData_SaveMolfile	(	ORIG_ATOM_DATA *	orig_inp_data,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		long	num_inp,
		INCHI_IOSTREAM *	out_file
	)

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OrigStruct_FillOut()

int OrigStruct_FillOut	(	struct tagCANON_GLOBALS *	pCG,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_STRUCT *	pOrigStruct,
		STRUCT_DATA *	sd
	)

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OrigStruct_Free()

void OrigStruct_Free

(

ORIG_STRUCT *

pOrigStruct

)

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POSEContext_DebugPrint()

void POSEContext_DebugPrint

(

POSEContext *

context

)

POSEContext_Free()

void POSEContext_Free

(

POSEContext *

context

)

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POSEContext_Init()

int POSEContext_Init	(	POSEContext *	context,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		PINChI2 *	pINChI2[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux2[INCHI_NUM],
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data,
		long	num_inp,
		INCHI_IOS_STRING *	strbuf,
		unsigned char	save_opt_bits
	)

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PreprocessOneStructure()

int PreprocessOneStructure	(	struct tagINCHI_CLOCK *	ic,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data
	)

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PreprocessPolymerCRUData()

int PreprocessPolymerCRUData	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	CG,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		PINChI2 *	pINChI2[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux2[INCHI_NUM],
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data,
		long	num_inp,
		INCHI_IOS_STRING *	strbuf,
		unsigned char	save_opt_bits,
		char **	sinchi,
		char **	saux
	)

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PrintInputParms()

int PrintInputParms	(	INCHI_IOSTREAM *	log_file,
		INPUT_PARMS *	ip
	)

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ProcessMultipleInputFiles()

int ProcessMultipleInputFiles	(	int	argc,
		char *	argv[]
	)

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ProcessOneStructure()

int ProcessOneStructure	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		PINChI2 *	pINChI2[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux2[INCHI_NUM],
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data,
		long	num_inp,
		INCHI_IOS_STRING *	strbuf,
		unsigned char	save_opt_bits
	)

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ProcessOneStructureEx()

int ProcessOneStructureEx	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		PINChI2 *	pINChI2[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux2[INCHI_NUM],
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data,
		long	num_inp,
		INCHI_IOS_STRING *	strbuf,
		unsigned char	save_opt_bits
	)

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ProcessSingleInputFile()

int ProcessSingleInputFile	(	int	argc,
		char *	argv[]
	)

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ReadCommandLineParms()

int ReadCommandLineParms	(	int	argc,
		const char *	argv[],
		INPUT_PARMS *	ip,
		char *	szSdfDataValue,
		unsigned long *	ulDisplTime,
		int	bReleaseVersion,
		INCHI_IOSTREAM *	log_file
	)

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ReadTheStructure()

int ReadTheStructure	(	struct tagINCHI_CLOCK *	ic,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		INCHI_IOSTREAM *	inp_file,
		ORIG_ATOM_DATA *	orig_inp_data,
		int	inp_index,
		int *	out_index
	)

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ReadWriteInChI()

int ReadWriteInChI	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG,
		INCHI_IOSTREAM *	pInp,
		INCHI_IOSTREAM *	pOut,
		INCHI_IOSTREAM *	pLog,
		INPUT_PARMS *	ip_inp,
		STRUCT_DATA *	sd_inp,
		inp_ATOM **	at,
		int *	num_at,
		int *	num_bonds,
		OAD_Polymer **	polymer,
		OAD_V3000 **	v3000,
		char *	szMsg,
		int	nMsgLen,
		unsigned long	WarningFlags[2][2]
	)

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RepeatedlyRenumberAtomsAndRecalcINCHI()

int RepeatedlyRenumberAtomsAndRecalcINCHI	(	struct tagINCHI_CLOCK *	ic,
		CANON_GLOBALS *	CG,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		PINChI2 *	pINChI[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux[INCHI_NUM],
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	plog,
		INCHI_IOSTREAM *	pout,
		INCHI_IOSTREAM *	pprb,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data,
		long *	num_inp,
		STRUCT_FPTRS *	pStructPtrs,
		int *	nRet,
		int	have_err_in_GetOneStructure,
		long *	num_err,
		int	output_error_inchi,
		INCHI_IOS_STRING *	strbuf,
		unsigned long *	pulTotalProcessingTime,
		char *	pLF,
		char *	pTAB,
		long int	nrepeat
	)

rrand()

int rrand

(

int

m

)

save_command_line()

void save_command_line	(	int	argc,
		char *	argv[],
		INCHI_IOSTREAM *	plog
	)

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set_line_separators()

void set_line_separators	(	int	bINChIOutputOptions,
		char **	pLF,
		char **	pTAB
	)

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shuffle()

void shuffle	(	void *	obj,
		size_t	nmemb,
		size_t	size
	)

SortAndPrintINChI()

int SortAndPrintINChI	(	struct tagCANON_GLOBALS *	pCG,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOS_STRING *	strbuf,
		INCHI_IOSTREAM *	log_file,
		INPUT_PARMS *	ip,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data,
		COMP_ATOM_DATA	composite_norm_data[INCHI_NUM][TAUT_NUM+1],
		ORIG_STRUCT *	pOrigStruct,
		int	num_components[INCHI_NUM],
		int	num_non_taut[INCHI_NUM],
		int	num_taut[INCHI_NUM],
		INCHI_MODE	bTautFlags[INCHI_NUM],
		INCHI_MODE	bTautFlagsDone[INCHI_NUM],
		NORM_CANON_FLAGS *	pncFlags,
		long	num_inp,
		PINChI2 *	pINChI[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux[INCHI_NUM],
		int *	pSortPrintINChIFlags,
		unsigned char	save_opt_bits
	)

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SplitTime()

void SplitTime	(	unsigned long	ulTotalTime,
		int *	hours,
		int *	minutes,
		int *	seconds,
		int *	mseconds
	)

TreatCreateINChIWarning()

int TreatCreateINChIWarning	(	STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		ORIG_ATOM_DATA *	orig_inp_data,
		long	num_inp,
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file
	)

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TreatErrorsInCreateOneComponentINChI()

int TreatErrorsInCreateOneComponentINChI	(	STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		ORIG_ATOM_DATA *	orig_inp_data,
		int	i,
		long	num_inp,
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file
	)

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TreatErrorsInReadTheStructure()

int TreatErrorsInReadTheStructure	(	STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		int	nLogMask,
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file,
		ORIG_ATOM_DATA *	orig_inp_data,
		long *	num_inp
	)

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ValidateAndPreparePolymerAndPseudoatoms()

int ValidateAndPreparePolymerAndPseudoatoms	(	struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	CG,
		STRUCT_DATA *	sd,
		INPUT_PARMS *	ip,
		char *	szTitle,
		PINChI2 *	pINChI2[INCHI_NUM],
		PINChI_Aux2 *	pINChI_Aux2[INCHI_NUM],
		INCHI_IOSTREAM *	inp_file,
		INCHI_IOSTREAM *	log_file,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	prb_file,
		ORIG_ATOM_DATA *	orig_inp_data,
		ORIG_ATOM_DATA *	prep_inp_data,
		long	num_inp,
		INCHI_IOS_STRING *	strbuf,
		unsigned char	save_opt_bits,
		int *	mind_polymers
	)

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winchi_calc_inchikey()

void winchi_calc_inchikey	(	int	ret,
		int *	ikflag,
		INPUT_PARMS *	ip,
		INCHI_IOSTREAM *	out_file,
		INCHI_IOSTREAM *	log_file
	)

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