runichi2.c File Reference

#include <stdlib.h>
#include <string.h>
#include <stdarg.h>
#include <errno.h>
#include <limits.h>
#include <math.h>
#include <ctype.h>
#include "mode.h"
#include "ichitime.h"
#include "ichister.h"
#include "ichimain.h"
#include "ichi_io.h"
#include "mol_fmt.h"
#include "inchi_api.h"
#include "readinch.h"
#include "inchi_gui.h"
#include "ichirvrs.h"
#include "bcf_s.h"

Include dependency graph for runichi2.c:

Data Structures
struct	tagModSCenterInfo
struct	tagDiylFrag

Typedefs
typedef struct tagModSCenterInfo	ModSCenterInfo
typedef struct tagDiylFrag	DiylFrag

Functions
static DiylFrag *	DiylFrag_New (int na, int e1nd, int end2, char *s)
static void	DiylFrag_Free (DiylFrag *pfrag)
static void	DiylFrag_MakeSignature (DiylFrag *pfrag, int nxc, int *xc, int *tmp)
static int	DiylFrag_Diff (DiylFrag *pfrag1, DiylFrag *pfrag2)
static void	DiylFrag_DebugTrace (DiylFrag *pfrag)
static int	NDefStereoBonds (inp_ATOM *at, int iatom, int bOnlyPointedEndMatters)
static void	ModSCenter_Init (ModSCenterInfo *scinfo, inp_ATOM *at, int iatom)
static void	ModSCenter_AddTo (ModSCenterInfo *scinfo, int iadd)
static void	ModSCenter_DelFrom (ModSCenterInfo *scinfo, int idel)
static int	ModSCenter_IsChanged (ModSCenterInfo *scinfo, inp_ATOM *at)
static int	GetFrameShiftInfoFrom105PlusInChI (char *sinchi, int *alist, int max_crossing)
static int	analyze_CRU_folding (ORIG_ATOM_DATA *orig_at_data, int iunit, int n_all_bkb, int *all_bkb, int nxclasses, int *xc, OAD_StructureEdits *ed)
static int	count_colors_in_sequence (int *entries, int n_entries, int max_distinct, int *counts)
static int	len_repeating_subsequence (int *color, int *color2, int n)
int	GetOneStructure (INCHI_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	GetOneComponent (INCHI_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	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	InchiToOrigAtom (INCHI_IOSTREAM *inp_molfile, ORIG_ATOM_DATA *orig_at_data, int bMergeAllInputStructures, int bGetOrigCoord, int bDoNotAddH, int vABParityUnknown, INPUT_TYPE nInputType, char *pSdfLabel, char *pSdfValue, unsigned long *lSdfId, INCHI_MODE *pInpAtomFlags, int *err, char *pStrErr)
int	bIsSameBond (int a1, int a2, int b1, int b2)
int	extract_orig_nums_from_auxinfo_string (char *saux, int *orig)
int	extract_nonstereo_eq_classes_from_auxinfo_string (char *saux, int nat, int *orig, int *nclasses, int *eclass, int *eclass_by_origs)
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	OAD_StructureEdits_Init (OAD_StructureEdits *ed)
void	OAD_StructureEdits_Clear (OAD_StructureEdits *ed)
void	OAD_StructureEdits_DebugPrint (OAD_StructureEdits *ed)
int	OAD_Polymer_PrepareFoldCRUEdits (ORIG_ATOM_DATA *orig_at_data, char *sinchi_noedits, char *saux_noedits, char *sinchi, char *saux, OAD_StructureEdits *ed)
int	OAD_Polymer_PrepareFrameShiftEdits (ORIG_ATOM_DATA *orig_at_data, char *sinchi, char *saux, OAD_StructureEdits *ed)

Variables
int	ec_opp [MAX_ATOMS]
int	ec_cano_opp [MAX_ATOMS]
int	at_stereo_mark_orig_opp [MAX_ATOMS]
int	xc_opp [MAX_ATOMS]

Typedef Documentation

DiylFrag

typedef struct tagDiylFrag DiylFrag

ModSCenterInfo

typedef struct tagModSCenterInfo ModSCenterInfo

Function Documentation

analyze_CRU_folding()

int analyze_CRU_folding ( ORIG_ATOM_DATA *  orig_at_data, int  iunit, int  n_all_bkb, int *  all_bkb, int  nxclasses, int *  xc, OAD_StructureEdits *  ed  )

static

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bIsSameBond()

int bIsSameBond	(	int	a1,
		int	a2,
		int	b1,
		int	b2
	)

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count_colors_in_sequence()

int count_colors_in_sequence ( int *  entries, int  n_entries, int  max_distinct, int *  counts  )

static

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DiylFrag_DebugTrace()

void DiylFrag_DebugTrace ( DiylFrag *  pfrag )

static

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DiylFrag_Diff()

int DiylFrag_Diff ( DiylFrag *  pfrag1, DiylFrag *  pfrag2  )

static

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DiylFrag_Free()

void DiylFrag_Free ( DiylFrag *  pfrag )

static

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DiylFrag_MakeSignature()

void DiylFrag_MakeSignature ( DiylFrag *  pfrag, int  nxc, int *  xc, int *  tmp  )

static

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DiylFrag_New()

DiylFrag * DiylFrag_New ( int  na, int  e1nd, int  end2, char *  s  )

static

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extract_nonstereo_eq_classes_from_auxinfo_string()

int extract_nonstereo_eq_classes_from_auxinfo_string	(	char *	saux,
		int	nat,
		int *	orig,
		int *	nclasses,
		int *	eclass,
		int *	eclass_by_origs
	)

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extract_orig_nums_from_auxinfo_string()

int extract_orig_nums_from_auxinfo_string	(	char *	saux,
		int *	orig
	)

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GetFrameShiftInfoFrom105PlusInChI()

static int GetFrameShiftInfoFrom105PlusInChI ( char *  sinchi, int *  alist, int  max_crossing  )

static

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GetOneComponent()

int GetOneComponent	(	INCHI_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	(	INCHI_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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InchiToOrigAtom()

int InchiToOrigAtom	(	INCHI_IOSTREAM *	inp_molfile,
		ORIG_ATOM_DATA *	orig_at_data,
		int	bMergeAllInputStructures,
		int	bGetOrigCoord,
		int	bDoNotAddH,
		int	vABParityUnknown,
		INPUT_TYPE	nInputType,
		char *	pSdfLabel,
		char *	pSdfValue,
		unsigned long *	lSdfId,
		INCHI_MODE *	pInpAtomFlags,
		int *	err,
		char *	pStrErr
	)

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len_repeating_subsequence()

int len_repeating_subsequence ( int *  color, int *  color2, int  n  )

static

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ModSCenter_AddTo()

void ModSCenter_AddTo ( ModSCenterInfo *  scinfo, int  iadd  )

static

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ModSCenter_DelFrom()

void ModSCenter_DelFrom ( ModSCenterInfo *  scinfo, int  idel  )

static

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ModSCenter_Init()

void ModSCenter_Init ( ModSCenterInfo *  scinfo, inp_ATOM *  at, int  iatom  )

static

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ModSCenter_IsChanged()

int ModSCenter_IsChanged ( ModSCenterInfo *  scinfo, inp_ATOM *  at  )

static

!! TUT NADO NE TAK base2 tot, kogo net v new_nbr new_base2 - tot, kogo net v nbr

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NDefStereoBonds()

int NDefStereoBonds ( inp_ATOM *  at, int  iatom, int  bOnlyPointedEndMatters  )

static

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OAD_Polymer_PrepareFoldCRUEdits()

int OAD_Polymer_PrepareFoldCRUEdits	(	ORIG_ATOM_DATA *	orig_at_data,
		char *	sinchi_noedits,
		char *	saux_noedits,
		char *	sinchi,
		char *	saux,
		OAD_StructureEdits *	ed
	)

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OAD_Polymer_PrepareFrameShiftEdits()

int OAD_Polymer_PrepareFrameShiftEdits	(	ORIG_ATOM_DATA *	orig_at_data,
		char *	sinchi,
		char *	saux,
		OAD_StructureEdits *	ed
	)

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OAD_StructureEdits_Clear()

void OAD_StructureEdits_Clear

(

OAD_StructureEdits *

ed

)

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OAD_StructureEdits_DebugPrint()

void OAD_StructureEdits_DebugPrint

(

OAD_StructureEdits *

ed

)

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OAD_StructureEdits_Init()

int OAD_StructureEdits_Init

(

OAD_StructureEdits *

ed

)

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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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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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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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Variable Documentation

at_stereo_mark_orig_opp

int at_stereo_mark_orig_opp[MAX_ATOMS]

ec_cano_opp

int ec_cano_opp[MAX_ATOMS]

ec_opp

int ec_opp[MAX_ATOMS]

xc_opp

int xc_opp[MAX_ATOMS]