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)
static int	BuildPolymerCrossingBondEndpointMask (INP_ATOM_DATA *inp_cur_data, const ORIG_ATOM_DATA *orig_inp_data, const INPUT_PARMS *ip, int component_number)
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)
	Convert InChI representation to original atom data.
int	bIsSameBond (int a1, int a2, int b1, int b2)
	Check if two bonds are the same.
int	extract_orig_nums_from_auxinfo_string (char *saux, int *orig)
	Parse AuxInfostring and get a list of original atom numbers orig[cano_num].
int	extract_nonstereo_eq_classes_from_auxinfo_string (char *saux, int nat, int *orig, int *nclasses, int *eclass, int *eclass_by_origs)
	Parse AuxInfostring and get non-stereo equivalence classes.
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)
	Initialize structure edits.
void	OAD_StructureEdits_Clear (OAD_StructureEdits *ed)
	Clear structure edits.
void	OAD_StructureEdits_DebugPrint (OAD_StructureEdits *ed)
	Debug print structure edits.
int	OAD_Polymer_PrepareFoldCRUEdits (ORIG_ATOM_DATA *orig_at_data, char *sinchi_noedits, char *saux_noedits, char *sinchi, char *saux, OAD_StructureEdits *ed)
	Prepare CRU edits for polymer data structure (prepare CRU fold edits as suggested by the strings with preliminary generated interim (1.05+ flavoured) InChI and AuxInfo)
int	OAD_Polymer_PrepareFrameShiftEdits (ORIG_ATOM_DATA *orig_at_data, char *sinchi, char *saux, OAD_StructureEdits *ed)
	Prepare frame shift edits for polymer data structure (prepare frame shift edits as suggested by the strings with preliminary generated interim (1.05+ flavoured) InChI and AuxInfo)

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
	)

Check if two bonds are the same.

Parameters

a1	Atom a1 index
a2	Atom a2 index
b1	Atom b1 index
b2	Atom b2 index

Returns

int Returns 1 if bonds (a1,a2) and (b1,b2) are the same, -1 if atoms swapped, 0 if not the same

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BuildPolymerCrossingBondEndpointMask()

static int BuildPolymerCrossingBondEndpointMask ( INP_ATOM_DATA *  inp_cur_data, const ORIG_ATOM_DATA *  orig_inp_data, const INPUT_PARMS *  ip, int  component_number  )

static

@nnuk

Build a component-local mask of polymer crossing-bond endpoints.

The polymer crossing-bond list (OAD_PolymerUnit.blist) uses whole-structure, 1-based atom numbering, whereas inp_cur_data contains only atoms from the selected connected component. ExtractConnectedComponent() preserves the original atom order within the component, allowing the corresponding local atom index to be reconstructed.

The mask is later consulted by remove_terminal_HDT() to preserve explicit H/D/T atoms that participate in polymer crossing bonds.

Parameters

inp_cur_data	chemical structure information for the current component
orig_inp_data	chemical structure information for the whole structure
ip	input parameters
component_number	number of component in the chemical structure

Returns

Return 0 on success or when no mask is required; return -1 on allocation failure.

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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 *	have_eclass_info,
		int *	eclass,
		int *	eclass_by_origs
	)

Parse AuxInfostring and get non-stereo equivalence classes.

Parameters

saux	Pointer to AuxInfo string
nat	Number of atoms
orig	Pointer to array of original atom numbers
have_eclass_info	Pointer to output flag indicating if equivalence class info is present
eclass	Pointer to output array of equivalence classes by canonical atom number
eclass_by_origs	Pointer to output array of equivalence classes by original atom number

Returns

int Status code

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extract_orig_nums_from_auxinfo_string()

int extract_orig_nums_from_auxinfo_string	(	char *	saux,
		int *	orig
	)

Parse AuxInfostring and get a list of original atom numbers orig[cano_num].

Parameters

saux	Pointer to AuxInfo string
orig	Pointer to output array of original atom numbers

Returns

int Status code

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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 *	infile,
		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
	)

Convert InChI representation to original atom data.

Parameters

infile	Input file stream
orig_at_data	Pointer to original atom data structure to be filled
bMergeAllInputStructures	Flag indicating whether to merge all input structures
bGetOrigCoord	Flag indicating whether to get original coordinates
bDoNotAddH	Flag indicating whether to avoid adding hydrogens
vABParityUnknown	Flag indicating whether to treat vAB parity as unknown
nInputType	Input type
pSdfLabel	Pointer to SDF label
pSdfValue	Pointer to SDF value
lSdfId	Pointer to SDF ID
pInpAtomFlags	Pointer to input atom flags
err	Pointer to error code
pStrErr	Pointer to error string

Returns

int Status code

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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
	)

Prepare CRU edits for polymer data structure (prepare CRU fold edits as suggested by the strings with preliminary generated interim (1.05+ flavoured) InChI and AuxInfo)

Parameters

orig_at_data	Pointer to original atom data structure
sinchi_noedits	Pointer to InChI string without edits
saux_noedits	Pointer to auxiliary InChI string without edits
sinchi	Pointer to InChI string with edits
saux	Pointer to auxiliary InChI string with edits
ed	Pointer to structure edits to be filled

Returns

int Status code

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OAD_Polymer_PrepareFrameShiftEdits()

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

Prepare frame shift edits for polymer data structure (prepare frame shift edits as suggested by the strings with preliminary generated interim (1.05+ flavoured) InChI and AuxInfo)

Parameters

orig_at_data	Pointer to original atom data structure
sinchi	Pointer to InChI string with edits
saux	Pointer to auxiliary InChI string with edits
ed	Pointer to structure edits to be filled

Returns

int Status code

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OAD_StructureEdits_Clear()

void OAD_StructureEdits_Clear

(

OAD_StructureEdits *

ed

)

Clear structure edits.

Parameters

ed	Pointer to structure edits

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OAD_StructureEdits_DebugPrint()

void OAD_StructureEdits_DebugPrint

(

OAD_StructureEdits *

ed

)

Debug print structure edits.

Parameters

ed	Pointer to structure edits

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OAD_StructureEdits_Init()

int OAD_StructureEdits_Init

(

OAD_StructureEdits *

ed

)

Initialize structure edits.

Parameters

ed	Pointer to structure edits

Returns

int Error status code

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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]