ichiread.c File Reference

#include <string.h>
#include <ctype.h>
#include <limits.h>
#include <locale.h>
#include "mode.h"
#include "ichierr.h"
#include "ichi.h"
#include "ichitime.h"
#include "ichidrp.h"
#include "inpdef.h"
#include "util.h"
#include "strutil.h"
#include "ichi_io.h"
#include "ichimain.h"
#include "extr_ct.h"
#include "ichitaut.h"
#include "ichister.h"
#include "ichisize.h"
#include "ichiring.h"
#include "ichinorm.h"
#include "ichicant.h"
#include "ichirvrs.h"
#include "mol_fmt.h"
#include "bcf_s.h"

Include dependency graph for ichiread.c:

Data Structures
struct	tagOneLinkedBond
struct	tagLinkedBonds
struct	tagInchiReadErrMsg
struct	tagNumElem

Macros
#define	SEGM_LINE_ADD   128
#define	LINKED_BOND_ADD   128
#define	SEG_END   '/'
#define	INCHI_INP_EOL(X)   ((X)=='\n' || (X)=='\r' || (X)=='\t')
#define	INCHI_TOKEN   "/\n\r\t\\"
#define	IST_HAPPENED_IN_RECMET   100
#define	NSTRLEN   524288
#define	MAX_MSG_LEN   512
#define	MAX_MSG_BUF_LEN   128
#define	nNum_H(ICOMPONENT)   ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed)
#define	LAST_AT_LEN   256

Typedefs
typedef struct tagOneLinkedBond	ONE_LINKED_BOND
typedef struct tagLinkedBonds	LINKED_BONDS
typedef enum tagModeProtonIsoExchgH	MODE_PIXH
typedef enum tagInChI_STATE	INCHI_STATE
typedef struct tagInchiReadErrMsg	INCHI_READ_ERR_MSG
typedef enum tagCopySegmentType	COPY_SEG_TYPE
typedef struct tagNumElem	NUM_ELEM
typedef enum tagAuxInfoState	AUX_INFO_STATE

Enumerations
enum	tagModeProtonIsoExchgH {   MODE_PIXH_UNDEFINED , MODE_PIXH_ADD_TO_FIRST , MODE_PIXH_ADD_TO_EACH , MODE_PIXH_ADD_A_PIXH_COMPONENT ,   MODE_PIXH_KEEP_TOTALS }
enum	tagInChI_STATE {   IST_MOBILE_H_FORMULA , IST_MOBILE_H_CONNECTIONS , IST_MOBILE_H , IST_MOBILE_H_CHARGE ,   IST_MOBILE_H_PROTONS , IST_MOBILE_H_SP2 , IST_MOBILE_H_SP3 , IST_MOBILE_H_SP3_M ,   IST_MOBILE_H_SP3_S , IST_MOBILE_H_ISO_LAYER_FORK , IST_MOBILE_H_ISO_ATOMS , IST_MOBILE_H_ISO_EXCH_H ,   IST_MOBILE_H_ISO_SP2 , IST_MOBILE_H_ISO_SP3 , IST_MOBILE_H_ISO_SP3_M , IST_MOBILE_H_ISO_SP3_S ,   IST_FIXED_H_LAYER_FORK , IST_FIXED_H_FORMULA , IST_FIXED_H , IST_FIXED_H_CHARGE ,   IST_FIXED_H_SP2 , IST_FIXED_H_SP3 , IST_FIXED_H_SP3_M , IST_FIXED_H_SP3_S ,   IST_FIXED_H_PERMUTATION , IST_FIXED_H_ISO_LAYER_FORK , IST_FIXED_H_ISO_ATOMS , IST_FIXED_H_ISO_LAYER ,   IST_FIXED_H_ISO_SP2 , IST_FIXED_H_ISO_SP3 , IST_FIXED_H_ISO_SP3_M , IST_FIXED_H_ISO_SP3_S ,   IST_FIXED_H_ISO_PERMUTATION , IST_RECONNECTED_LAYER_FORK , IST_RECONNECTED_FORMULA , IST_MATERIAL_BALANCE_ERROR ,   IST_MOBILE_H_POLYMER , IST_END = -1 }
enum	tagCopySegmentType {   CPY_SP2 , CPY_SP3 , CPY_SP3_M , CPY_SP3_S ,   CPY_ISO_AT }
enum	tagAuxInfoState {   AST_VERSION , AST_MOBILE_H_NUMBERS , AST_MOBILE_H_ATOM_EQ , AST_MOBILE_H_GROUP_EQ ,   AST_MOBILE_H_SP3_INV , AST_MOBILE_H_SP3_INV_NUMBERS , AST_MOBILE_H_ISO_LAYER_FORK , AST_MOBILE_H_ISO_NUMBERS ,   AST_MOBILE_H_ISO_ATOM_EQ , AST_MOBILE_H_ISO_GROUP_EQ , AST_MOBILE_H_ISO_SP3_INV , AST_MOBILE_H_ISO_SP3_INV_NUMBERS ,   AST_FIXED_H_LAYER_FORK , AST_FIXED_H_NUMBERS , AST_FIXED_H_ATOM_EQ , AST_FIXED_H_SP3_INV ,   AST_FIXED_H_SP3_INV_NUMBERS , AST_FIXED_H_ISO_LAYER_FORK , AST_FIXED_H_ISO_NUMBERS , AST_FIXED_H_ISO_ATOM_EQ ,   AST_FIXED_H_ISO_SP3_INV , AST_FIXED_H_ISO_SP3_INV_NUMBERS , AST_REVERSE_INFO_CRV , AST_REVERSE_INFO_ATOMS ,   AST_REVERSE_INFO_BONDS , AST_REVERSE_INFO_XYZ , AST_RECONNECTED_LAYER_FORK , AST_RECONNECTED_LAYER_NUMBERS }

Functions
int	InChILine2Data (INCHI_IOSTREAM *pInp, SEGM_LINE *pLine, char **pStr, int *pState, int *nErr, INChI *pInpInChI[INCHI_NUM][TAUT_NUM], int nNumComponents[INCHI_NUM][TAUT_NUM], REM_PROTONS nNumProtons[INCHI_NUM][TAUT_NUM], int s[INCHI_NUM][TAUT_NUM][2], int bReadCoord, int bInchi2Struct, INCHI_MODE nMode, int *bStdFormat, int *input_has_save_opt, unsigned char *input_save_opt_bits, OAD_Polymer **ppolymer, OAD_V3000 **pv3000)
static int	GetInChIFormulaNumH (INChI *pInChI, int *nNumH)
static int	GetInChINumH (INChI *pInChI, int *nNumH)
static int	GetInChIIsoH (INChI *pInChI, int nNumIsotopicH[NUM_H_ISOTOPES])
static int	getInChIChar (INCHI_IOSTREAM *pInp)
static int	AddInChIChar (INCHI_IOSTREAM *pInp, SEGM_LINE *Line, const char *pszToken)
static int	AddLinkedBond (AT_NUMB at1, AT_NUMB at2, AT_NUMB num_at, LINKED_BONDS *pLB)
static int	bInChIHasReconnectedMetal (INChI *pInChI)
static int	SetProtonsAndXchgIsoH (int bInChI2Structure, int bReqSplitOutputInChI, int bReqProtonsForEachComponent, int bReqNonTaut, int bReqStereo, int num_components[INCHI_NUM], MODE_PIXH nModeProtonIsoExchgH[INCHI_NUM], InpInChI *OneInput)
static int	SetHillFormFromInChI (InpInChI *OneInput)
static int	nGetInChISegment (INCHI_IOSTREAM *pInp, SEGM_LINE *Line, const char *pszToken)
static int	CopySegment (INChI *pInChITo, INChI *pInChIFrom, int StereoType, int bIsotopicTo, int bIsotopicFrom)
static int	nFillOutProtonMobileH (INChI *pInChI)
static int	nProtonCopyIsotopicInfo (INChI *pInChI_to, INChI *pInChI_from)
static int	CopyAtomNumbers (INChI *pInChI_To, int bIsoTo, INChI *pInChI_From, int bIsoFrom)
static int	ParseSegmentFormula (const char *str, int bMobileH, INChI *pInpInChI[], int nNumComponents[], int *na_total)
static int	ParseSegmentConnections (const char *str, int bMobileH, INChI **pInpInChI, int *pnNumComponents, int *pbAbc, int *nb_total)
static int	ParseSegmentMobileH (const char *str, int bMobileH, INChI *pInpInChI[], int pnNumComponents[], int *pbAbc)
static int	ParseSegmentCharge (const char *str, int bMobileH, INChI *pInpInChI[], int nNumComponents[])
static int	ParseSegmentProtons (const char *str, int bMobileH, REM_PROTONS nNumProtons[], int nNumComponents[])
static int	ParseSegmentPolymer (const char *str, int bMobileH, REM_PROTONS nNumProtons[], int nNumComponents[], int na_total, int nb_total, int bInchi2Struct, OAD_Polymer **ppPolymer, OAD_V3000 **ppV3000)
static int	ParseSegmentSp2 (const char *str, int bMobileH, INChI *pInpInChI[], int nNumComponents[], int state, int *pbAbc)
static int	ParseSegmentSp3 (const char *str, int bMobileH, INChI *pInpInChI[], int ppnNumComponents[], int state, int *pbAbc)
static int	SegmentSp3CreateEmpty (const char *str, int bMobileH, INChI *pInpInChI[], int nNumComponents, int state, int *pbAbc)
static int	SegmentSp3StoreStereoCenters (int *pbAbc, const char *pStart, const char *pEnd, int pInChI_iComponent_nNumberOfAtoms, INChI_Stereo *PStereo_0)
static int	SegmentSp3ProcessAbbreviation (int *mpy_component, int iComponent, int nNumComponents, int val, const char *q, int state, int *pbAbc, int bMobileH, int nCpyType, INChI *pInChI, INChI *pInpInChI_ALT_TAUT_bMobileH)
static int	SegmentSp3CopyMultiplierCovered (int mpy_component, int iComponent, INChI *pInpInChI, int bIso, int nCpyType)
static int	ParseSegmentSp3m (const char *str, int bMobileH, INChI *pInpInChI[], int nNumComponents[], int state)
static int	bIsSp3LayerNotEmpty (INChI *pInpInChI[], int bMobileH, int bIso, int nNumComponents)
static int	ParseSegmentSp3s (const char *str, int bMobileH, INChI *pInpInChI[], int s[TAUT_NUM][2], int ppnNumComponents[], int state)
static int	ParseSegmentIsoAtoms (const char *str, int bMobileH, INChI *pInpInChI[], int nNumComponents[], int state, int *pbAbc)
static int	ParseSegmentIsoExchgH (const char *str, int bMobileH, REM_PROTONS nNumProtons[], int nNumComponents[], int state, int *pbAbc)
static int	ParseSegmentPerm (const char *str, int bMobileH, INChI *pInpInChI[], int ppnNumComponents[], int state, int *pbAbc)
static int	ReadInChILine (INCHI_IOSTREAM *pInp, SEGM_LINE *pLine, char **pStr, int *pState, INChI *pInpInChI[INCHI_NUM][TAUT_NUM], int nNumComponents[INCHI_NUM][TAUT_NUM], REM_PROTONS nNumProtons[INCHI_NUM][TAUT_NUM], int s[INCHI_NUM][TAUT_NUM][2], int *input_is_stdinchi, int *input_has_save_opt, unsigned char *input_save_opt_bits, int bInchi2Struct, OAD_Polymer **ppolymer, OAD_V3000 **pv3000)
int	ReadInChICoord (INCHI_IOSTREAM *pInp, SEGM_LINE *pLine, int *pState, INChI *pInpInChI[INCHI_NUM][TAUT_NUM], int nNumComponents[INCHI_NUM][TAUT_NUM])
static int	OutputInChIAsRequested (struct tagCANON_GLOBALS *pCG, INCHI_IOSTREAM *pOut, INCHI_IOSTREAM *pLog, ICHICONST INPUT_PARMS *ip_inp, STRUCT_DATA *sd_inp, InpInChI *OneInput, int num_components[INCHI_NUM], MODE_PIXH nModeProtonIsoExchgH[INCHI_NUM], long num_inp, unsigned char save_opt_bits)
static int	ParseAuxSegmentVersion (const char *str, int bMobileH, INChI *pInpInChI[], int ppnNumComponents[], int state)
static int	ParseAuxSegmentNumbers (const char *str, int bMobileH, INChI *pInpInChI[], int ppnNumComponents[], int state, int *pbAbc)
static int	ParseAuxSegmentAtomEqu (const char *str, int bMobileH, INChI *pInpInChI[], int ppnNumComponents[], int state)
static int	ParseAuxSegmentGroupEqu (const char *str, int bMobileH, INChI *pInpInChI[], int ppnNumComponents[], int state)
static int	ParseAuxSegmentSp3Inv (const char *str, int bMobileH, INChI *pInpInChI[], int ppnNumComponents[], int state)
static int	ParseAuxSegmentSp3InvNumbers (const char *str, int bMobileH, INChI *pInpInChI[], int ppnNumComponents[], int state)
static int	ParseAuxSegmentReverseCRV (const char *str, int state)
static int	ParseAuxSegmentReverseAtoms (const char *str, int state)
static int	ParseAuxSegmentReverseBonds (const char *str, int state)
static int	ParseAuxSegmentReverseXYZ (const char *str, XYZ_COORD **ppXYZ, int state)
static int	AddAuxSegmentCoord (int nRet, XYZ_COORD *pXYZ, int nLenXYZ, INChI *pInpInChI[INCHI_NUM][TAUT_NUM], int nNumComponents[INCHI_NUM][TAUT_NUM])
static void	getInchiStateReadErr (int stat, char *szMsg)
static const char *	getInchiErrName (int nErr)
static int	extract_from_inchi_string (char *sinchi, InpInChI *OneInput)
const char *	ParseSegmentReadDelimitedNumbers (const char *str, const char *pEnd, INT_ARRAY *numlist, char c_delim, char c_stop, int *ret)
void	PrepareSaveOptBits (INPUT_PARMS *ip, INCHI_IOSTREAM *pLog, const long num_inp, const char *szCurHdr, int input_has_save_opt, unsigned char input_save_opt_bits, unsigned char *save_opt_bits)
void	TreatErrorsInReadInChIString (int nReadStatus, int nErr, int pState, INPUT_PARMS *ip, INCHI_IOSTREAM *pOut, INCHI_IOSTREAM *pLog, long *num_inp, long *num_errors, long *num_processed, char **pstrHdr, char **pszCurHdr, InpInChI *pOneInput)
int	ConvertInChI2Struct (ICHICONST INPUT_PARMS *ip_inp, INPUT_PARMS *ip, InpInChI *pOneInput, inp_ATOM **at, int *num_at, OAD_Polymer **polymer, OAD_V3000 **v3000, INCHI_IOSTREAM *pOut, INCHI_IOSTREAM *pLog, STRUCT_DATA *sd, int num_components[INCHI_NUM], MODE_PIXH nModeProtonIsoExchgH[INCHI_NUM], char **pszCurHdr, char *szMsg, int nMsgLen, char szMessage[MAX_MSG_LEN], int nInitLenMessage, int nMessageLen, int input_is_stdinchi, int bHasSomeReconnected, int bHasSomeFixedH, int bHasMetal, int nModeFlagsStereo, int bTautFlags, int bReqNonTaut, unsigned long WarningFlags[2][2], long num_inp, long *num_errors, unsigned char save_opt_bits, inchiTime *pulTStart, long *ulProcessingTime, struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *pCG)
int	ConvertInChI2InChI (INPUT_PARMS *ip, InpInChI *pOneInput, INCHI_IOSTREAM *pOut, INCHI_IOSTREAM *pLog, STRUCT_DATA *sd, int num_components[INCHI_NUM], MODE_PIXH nModeProtonIsoExchgH[INCHI_NUM], char **pszCurHdr, long num_inp, long *num_errors, unsigned char save_opt_bits, inchiTime *pulTStart, long *ulProcessingTime, struct tagINCHI_CLOCK *ic, struct tagCANON_GLOBALS *pCG)
int	DetectAndExposePolymerInternals (INCHI_IOSTREAM *is)
int	DetectHiddenPolymerStuff (char *tmpstr, int tmpstrlen, int *ninsert, int *insert_pos, int insert_lead_offset, int *nstars)
int	ReadWriteInChI (INCHI_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	GetNumNeighborsFromInchi (INChI *pInChI, AT_NUMB nAtNumber)
int	CountStereoTypes (INChI *pInChI, int *num_known_SB, int *num_known_SC, int *num_unk_und_SB, int *num_unk_und_SC, int *num_SC_PIII, int *num_SC_AsIII)
int	bInpInchiComponentExists (InpInChI *pOneInput, int iInChI, int bMobileH, int k)
int	bInpInchiComponentDeleted (InpInChI *pOneInput, int iInChI, int bMobileH, int k)
int	bRevInchiComponentExists (StrFromINChI *pStruct, int iInChI, int bMobileH, int k)
int	bRevInchiComponentDeleted (StrFromINChI *pStruct, int iInChI, int bMobileH, int k)
int	DetectInpInchiCreationOptions (InpInChI *pOneInput, int *bHasReconnected, int *bHasMetal, int *bHasFixedH, int *nModeFlagsStereo, int *bTautFlagsStereo)
int	insertions_sort_AT_NUMB (AT_NUMB *base, int num)
int	extract_stereo_info_from_inchi_string (char *sinchi, int nat, int *orig, int *at_stereo_mark_orig)
int	extract_all_backbone_bonds_from_inchi_string (char *sinchi, int *n_all_bkb_orig, int *orig, int *all_bkb_orig)

Variables
ICHICONST INCHI_READ_ERR_MSG	irErrMsg []

Macro Definition Documentation

INCHI_INP_EOL

#define INCHI_INP_EOL

(

X

)

((X)=='\n' || (X)=='\r' || (X)=='\t')

INCHI_TOKEN

#define INCHI_TOKEN   "/\n\r\t\\"

IST_HAPPENED_IN_RECMET

#define IST_HAPPENED_IN_RECMET   100

LAST_AT_LEN

#define LAST_AT_LEN   256

LINKED_BOND_ADD

#define LINKED_BOND_ADD   128

MAX_MSG_BUF_LEN

#define MAX_MSG_BUF_LEN   128

MAX_MSG_LEN

#define MAX_MSG_LEN   512

nNum_H

#define nNum_H

(

ICOMPONENT

)

((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed)

NSTRLEN

#define NSTRLEN   524288

SEG_END

#define SEG_END   '/'

SEGM_LINE_ADD

#define SEGM_LINE_ADD   128

Typedef Documentation

AUX_INFO_STATE

typedef enum tagAuxInfoState AUX_INFO_STATE

COPY_SEG_TYPE

typedef enum tagCopySegmentType COPY_SEG_TYPE

INCHI_READ_ERR_MSG

typedef struct tagInchiReadErrMsg INCHI_READ_ERR_MSG

INCHI_STATE

typedef enum tagInChI_STATE INCHI_STATE

LINKED_BONDS

typedef struct tagLinkedBonds LINKED_BONDS

MODE_PIXH

typedef enum tagModeProtonIsoExchgH MODE_PIXH

NUM_ELEM

typedef struct tagNumElem NUM_ELEM

ONE_LINKED_BOND

typedef struct tagOneLinkedBond ONE_LINKED_BOND

Enumeration Type Documentation

tagAuxInfoState

enum tagAuxInfoState

Enumerator
AST_VERSION
AST_MOBILE_H_NUMBERS
AST_MOBILE_H_ATOM_EQ
AST_MOBILE_H_GROUP_EQ
AST_MOBILE_H_SP3_INV
AST_MOBILE_H_SP3_INV_NUMBERS
AST_MOBILE_H_ISO_LAYER_FORK
AST_MOBILE_H_ISO_NUMBERS
AST_MOBILE_H_ISO_ATOM_EQ
AST_MOBILE_H_ISO_GROUP_EQ
AST_MOBILE_H_ISO_SP3_INV
AST_MOBILE_H_ISO_SP3_INV_NUMBERS
AST_FIXED_H_LAYER_FORK
AST_FIXED_H_NUMBERS
AST_FIXED_H_ATOM_EQ
AST_FIXED_H_SP3_INV
AST_FIXED_H_SP3_INV_NUMBERS
AST_FIXED_H_ISO_LAYER_FORK
AST_FIXED_H_ISO_NUMBERS
AST_FIXED_H_ISO_ATOM_EQ
AST_FIXED_H_ISO_SP3_INV
AST_FIXED_H_ISO_SP3_INV_NUMBERS
AST_REVERSE_INFO_CRV
AST_REVERSE_INFO_ATOMS
AST_REVERSE_INFO_BONDS
AST_REVERSE_INFO_XYZ
AST_RECONNECTED_LAYER_FORK
AST_RECONNECTED_LAYER_NUMBERS

tagCopySegmentType

enum tagCopySegmentType

Enumerator
CPY_SP2
CPY_SP3
CPY_SP3_M
CPY_SP3_S
CPY_ISO_AT

tagInChI_STATE

enum tagInChI_STATE

Enumerator
IST_MOBILE_H_FORMULA
IST_MOBILE_H_CONNECTIONS
IST_MOBILE_H
IST_MOBILE_H_CHARGE
IST_MOBILE_H_PROTONS
IST_MOBILE_H_SP2
IST_MOBILE_H_SP3
IST_MOBILE_H_SP3_M
IST_MOBILE_H_SP3_S
IST_MOBILE_H_ISO_LAYER_FORK
IST_MOBILE_H_ISO_ATOMS
IST_MOBILE_H_ISO_EXCH_H
IST_MOBILE_H_ISO_SP2
IST_MOBILE_H_ISO_SP3
IST_MOBILE_H_ISO_SP3_M
IST_MOBILE_H_ISO_SP3_S
IST_FIXED_H_LAYER_FORK
IST_FIXED_H_FORMULA
IST_FIXED_H
IST_FIXED_H_CHARGE
IST_FIXED_H_SP2
IST_FIXED_H_SP3
IST_FIXED_H_SP3_M
IST_FIXED_H_SP3_S
IST_FIXED_H_PERMUTATION
IST_FIXED_H_ISO_LAYER_FORK
IST_FIXED_H_ISO_ATOMS
IST_FIXED_H_ISO_LAYER
IST_FIXED_H_ISO_SP2
IST_FIXED_H_ISO_SP3
IST_FIXED_H_ISO_SP3_M
IST_FIXED_H_ISO_SP3_S
IST_FIXED_H_ISO_PERMUTATION
IST_RECONNECTED_LAYER_FORK
IST_RECONNECTED_FORMULA
IST_MATERIAL_BALANCE_ERROR
IST_MOBILE_H_POLYMER
IST_END

tagModeProtonIsoExchgH

enum tagModeProtonIsoExchgH

Enumerator
MODE_PIXH_UNDEFINED
MODE_PIXH_ADD_TO_FIRST
MODE_PIXH_ADD_TO_EACH
MODE_PIXH_ADD_A_PIXH_COMPONENT
MODE_PIXH_KEEP_TOTALS

Function Documentation

AddAuxSegmentCoord()

int AddAuxSegmentCoord ( int  nRet, XYZ_COORD *  pXYZ, int  nLenXYZ, INChI *  pInpInChI[INCHI_NUM][TAUT_NUM], int  nNumComponents[INCHI_NUM][TAUT_NUM]  )

static

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AddInChIChar()

int AddInChIChar ( INCHI_IOSTREAM *  pInp, SEGM_LINE *  Line, const char *  pszToken  )

static

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AddLinkedBond()

int AddLinkedBond ( AT_NUMB  at1, AT_NUMB  at2, AT_NUMB  num_at, LINKED_BONDS *  pLB  )

static

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bInChIHasReconnectedMetal()

int bInChIHasReconnectedMetal ( INChI *  pInChI )

static

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bInpInchiComponentDeleted()

int bInpInchiComponentDeleted	(	InpInChI *	pOneInput,
		int	iInChI,
		int	bMobileH,
		int	k
	)

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bInpInchiComponentExists()

int bInpInchiComponentExists	(	InpInChI *	pOneInput,
		int	iInChI,
		int	bMobileH,
		int	k
	)

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bIsSp3LayerNotEmpty()

int bIsSp3LayerNotEmpty ( INChI *  pInpInChI[], int  bMobileH, int  bIso, int  nNumComponents  )

static

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bRevInchiComponentDeleted()

int bRevInchiComponentDeleted	(	StrFromINChI *	pStruct,
		int	iInChI,
		int	bMobileH,
		int	k
	)

pStruct->at2 ||

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bRevInchiComponentExists()

int bRevInchiComponentExists	(	StrFromINChI *	pStruct,
		int	iInChI,
		int	bMobileH,
		int	k
	)

pStruct->at2 ||

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ConvertInChI2InChI()

int ConvertInChI2InChI	(	INPUT_PARMS *	ip,
		InpInChI *	pOneInput,
		INCHI_IOSTREAM *	pOut,
		INCHI_IOSTREAM *	pLog,
		STRUCT_DATA *	sd,
		int	num_components[INCHI_NUM],
		MODE_PIXH	nModeProtonIsoExchgH[INCHI_NUM],
		char **	pszCurHdr,
		long	num_inp,
		long *	num_errors,
		unsigned char	save_opt_bits,
		inchiTime *	pulTStart,
		long *	ulProcessingTime,
		struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG
	)

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ConvertInChI2Struct()

int ConvertInChI2Struct	(	ICHICONST INPUT_PARMS *	ip_inp,
		INPUT_PARMS *	ip,
		InpInChI *	pOneInput,
		inp_ATOM **	at,
		int *	num_at,
		OAD_Polymer **	polymer,
		OAD_V3000 **	v3000,
		INCHI_IOSTREAM *	pOut,
		INCHI_IOSTREAM *	pLog,
		STRUCT_DATA *	sd,
		int	num_components[INCHI_NUM],
		MODE_PIXH	nModeProtonIsoExchgH[INCHI_NUM],
		char **	pszCurHdr,
		char *	szMsg,
		int	nMsgLen,
		char	szMessage[MAX_MSG_LEN],
		int	nInitLenMessage,
		int	nMessageLen,
		int	input_is_stdinchi,
		int	bHasSomeReconnected,
		int	bHasSomeFixedH,
		int	bHasMetal,
		int	nModeFlagsStereo,
		int	bTautFlags,
		int	bReqNonTaut,
		unsigned long	WarningFlags[2][2],
		long	num_inp,
		long *	num_errors,
		unsigned char	save_opt_bits,
		inchiTime *	pulTStart,
		long *	ulProcessingTime,
		struct tagINCHI_CLOCK *	ic,
		struct tagCANON_GLOBALS *	pCG
	)

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CopyAtomNumbers()

int CopyAtomNumbers ( INChI *  pInChI_To, int  bIsoTo, INChI *  pInChI_From, int  bIsoFrom  )

static

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CopySegment()

int CopySegment ( INChI *  pInChITo, INChI *  pInChIFrom, int  StereoType, int  bIsotopicTo, int  bIsotopicFrom  )

static

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CountStereoTypes()

int CountStereoTypes	(	INChI *	pInChI,
		int *	num_known_SB,
		int *	num_known_SC,
		int *	num_unk_und_SB,
		int *	num_unk_und_SC,
		int *	num_SC_PIII,
		int *	num_SC_AsIII
	)

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DetectAndExposePolymerInternals()

int DetectAndExposePolymerInternals

(

INCHI_IOSTREAM *

is

)

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DetectHiddenPolymerStuff()

int DetectHiddenPolymerStuff	(	char *	tmpstr,
		int	tmpstrlen,
		int *	ninsert,
		int *	insert_pos,
		int	insert_lead_offset,
		int *	nstars
	)

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DetectInpInchiCreationOptions()

int DetectInpInchiCreationOptions	(	InpInChI *	pOneInput,
		int *	bHasReconnected,
		int *	bHasMetal,
		int *	bHasFixedH,
		int *	nModeFlagsStereo,
		int *	bTautFlagsStereo
	)

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extract_all_backbone_bonds_from_inchi_string()

int extract_all_backbone_bonds_from_inchi_string	(	char *	sinchi,
		int *	n_all_bkb_orig,
		int *	orig,
		int *	all_bkb_orig
	)

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extract_from_inchi_string()

int extract_from_inchi_string ( char *  sinchi, InpInChI *  OneInput  )

static

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extract_stereo_info_from_inchi_string()

int extract_stereo_info_from_inchi_string	(	char *	sinchi,
		int	nat,
		int *	orig,
		int *	at_stereo_mark_orig
	)

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getInChIChar()

int getInChIChar ( INCHI_IOSTREAM *  pInp )

static

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getInchiErrName()

const char * getInchiErrName ( int  nErr )

static

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GetInChIFormulaNumH()

int GetInChIFormulaNumH ( INChI *  pInChI, int *  nNumH  )

static

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GetInChIIsoH()

int GetInChIIsoH ( INChI *  pInChI, int  nNumIsotopicH[NUM_H_ISOTOPES]  )

static

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GetInChINumH()

int GetInChINumH ( INChI *  pInChI, int *  nNumH  )

static

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getInchiStateReadErr()

void getInchiStateReadErr ( int  stat, char *  szMsg  )

static

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GetNumNeighborsFromInchi()

int GetNumNeighborsFromInchi	(	INChI *	pInChI,
		AT_NUMB	nAtNumber
	)

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InChILine2Data()

int InChILine2Data	(	INCHI_IOSTREAM *	pInp,
		SEGM_LINE *	pLine,
		char **	pStr,
		int *	pState,
		int *	nErr,
		INChI *	pInpInChI[INCHI_NUM][TAUT_NUM],
		int	nNumComponents[INCHI_NUM][TAUT_NUM],
		REM_PROTONS	nNumProtons[INCHI_NUM][TAUT_NUM],
		int	s[INCHI_NUM][TAUT_NUM][2],
		int	bReadCoord,
		int	bInchi2Struct,
		INCHI_MODE	nMode,
		int *	bStdFormat,
		int *	input_has_save_opt,
		unsigned char *	input_save_opt_bits,
		OAD_Polymer **	ppolymer,
		OAD_V3000 **	pv3000
	)

(pInChI_Alt && pInChI_Alt->Stereo && pInChI_Alt->Stereo->nNumberOfStereoCenters) &&

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insertions_sort_AT_NUMB()

int insertions_sort_AT_NUMB	(	AT_NUMB *	base,
		int	num
	)

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nFillOutProtonMobileH()

int nFillOutProtonMobileH ( INChI *  pInChI )

static

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nGetInChISegment()

int nGetInChISegment ( INCHI_IOSTREAM *  pInp, SEGM_LINE *  Line, const char *  pszToken  )

static

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nProtonCopyIsotopicInfo()

int nProtonCopyIsotopicInfo ( INChI *  pInChI_to, INChI *  pInChI_from  )

static

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OutputInChIAsRequested()

int OutputInChIAsRequested ( struct tagCANON_GLOBALS *  pCG, INCHI_IOSTREAM *  pOut, INCHI_IOSTREAM *  pLog, ICHICONST INPUT_PARMS *  ip_inp, STRUCT_DATA *  sd_inp, InpInChI *  OneInput, int  num_components[INCHI_NUM], MODE_PIXH  nModeProtonIsoExchgH[INCHI_NUM], long  num_inp, unsigned char  save_opt_bits  )

static

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ParseAuxSegmentAtomEqu()

int ParseAuxSegmentAtomEqu ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  ppnNumComponents[], int  state  )

static

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ParseAuxSegmentGroupEqu()

int ParseAuxSegmentGroupEqu ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  ppnNumComponents[], int  state  )

static

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ParseAuxSegmentNumbers()

int ParseAuxSegmentNumbers ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  ppnNumComponents[], int  state, int *  pbAbc  )

static

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ParseAuxSegmentReverseAtoms()

int ParseAuxSegmentReverseAtoms ( const char *  str, int  state  )

static

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ParseAuxSegmentReverseBonds()

int ParseAuxSegmentReverseBonds ( const char *  str, int  state  )

static

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ParseAuxSegmentReverseCRV()

int ParseAuxSegmentReverseCRV ( const char *  str, int  state  )

static

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ParseAuxSegmentReverseXYZ()

int ParseAuxSegmentReverseXYZ ( const char *  str, XYZ_COORD **  ppXYZ, int  state  )

static

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ParseAuxSegmentSp3Inv()

int ParseAuxSegmentSp3Inv ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  ppnNumComponents[], int  state  )

static

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ParseAuxSegmentSp3InvNumbers()

int ParseAuxSegmentSp3InvNumbers ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  ppnNumComponents[], int  state  )

static

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ParseAuxSegmentVersion()

int ParseAuxSegmentVersion ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  ppnNumComponents[], int  state  )

static

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ParseSegmentCharge()

int ParseSegmentCharge ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  nNumComponents[]  )

static

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ParseSegmentConnections()

int ParseSegmentConnections ( const char *  str, int  bMobileH, INChI **  pInpInChI, int *  pnNumComponents, int *  pbAbc, int *  nb_total  )

static

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ParseSegmentFormula()

int ParseSegmentFormula ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  nNumComponents[], int *  na_total  )

static

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ParseSegmentIsoAtoms()

int ParseSegmentIsoAtoms ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  nNumComponents[], int  state, int *  pbAbc  )

static

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ParseSegmentIsoExchgH()

int ParseSegmentIsoExchgH ( const char *  str, int  bMobileH, REM_PROTONS  nNumProtons[], int  nNumComponents[], int  state, int *  pbAbc  )

static

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ParseSegmentMobileH()

int ParseSegmentMobileH ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  pnNumComponents[], int *  pbAbc  )

static

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ParseSegmentPerm()

int ParseSegmentPerm ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  ppnNumComponents[], int  state, int *  pbAbc  )

static

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ParseSegmentPolymer()

int ParseSegmentPolymer ( const char *  str, int  bMobileH, REM_PROTONS  nNumProtons[], int  nNumComponents[], int  na_total, int  nb_total, int  bInchi2Struct, OAD_Polymer **  ppPolymer, OAD_V3000 **  ppV3000  )

static

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ParseSegmentProtons()

int ParseSegmentProtons ( const char *  str, int  bMobileH, REM_PROTONS  nNumProtons[], int  nNumComponents[]  )

static

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ParseSegmentReadDelimitedNumbers()

const char * ParseSegmentReadDelimitedNumbers	(	const char *	str,
		const char *	pEnd,
		INT_ARRAY *	numlist,
		char	c_delim,
		char	c_stop,
		int *	ret
	)

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ParseSegmentSp2()

int ParseSegmentSp2 ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  nNumComponents[], int  state, int *  pbAbc  )

static

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ParseSegmentSp3()

int ParseSegmentSp3 ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  ppnNumComponents[], int  state, int *  pbAbc  )

static

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ParseSegmentSp3m()

int ParseSegmentSp3m ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  nNumComponents[], int  state  )

static

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ParseSegmentSp3s()

int ParseSegmentSp3s ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  s[TAUT_NUM][2], int  ppnNumComponents[], int  state  )

static

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PrepareSaveOptBits()

void PrepareSaveOptBits	(	INPUT_PARMS *	ip,
		INCHI_IOSTREAM *	pLog,
		const long	num_inp,
		const char *	szCurHdr,
		int	input_has_save_opt,
		unsigned char	input_save_opt_bits,
		unsigned char *	save_opt_bits
	)

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ReadInChICoord()

int ReadInChICoord	(	INCHI_IOSTREAM *	pInp,
		SEGM_LINE *	pLine,
		int *	pState,
		INChI *	pInpInChI[INCHI_NUM][TAUT_NUM],
		int	nNumComponents[INCHI_NUM][TAUT_NUM]
	)

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ReadInChILine()

int ReadInChILine ( INCHI_IOSTREAM *  pInp, SEGM_LINE *  pLine, char **  pStr, int *  pState, INChI *  pInpInChI[INCHI_NUM][TAUT_NUM], int  nNumComponents[INCHI_NUM][TAUT_NUM], REM_PROTONS  nNumProtons[INCHI_NUM][TAUT_NUM], int  s[INCHI_NUM][TAUT_NUM][2], int *  input_is_stdinchi, int *  input_has_save_opt, unsigned char *  input_save_opt_bits, int  bInchi2Struct, OAD_Polymer **  ppolymer, OAD_V3000 **  pv3000  )

static

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ReadWriteInChI()

int ReadWriteInChI	(	INCHI_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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SegmentSp3CopyMultiplierCovered()

static int SegmentSp3CopyMultiplierCovered ( int  mpy_component, int  iComponent, INChI *  pInpInChI, int  bIso, int  nCpyType  )

static

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SegmentSp3CreateEmpty()

static int SegmentSp3CreateEmpty ( const char *  str, int  bMobileH, INChI *  pInpInChI[], int  nNumComponents, int  state, int *  pbAbc  )

static

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SegmentSp3ProcessAbbreviation()

static int SegmentSp3ProcessAbbreviation ( int *  mpy_component, int  iComponent, int  nNumComponents, int  val, const char *  q, int  state, int *  pbAbc, int  bMobileH, int  nCpyType, INChI *  pInChI, INChI *  pInpInChI_ALT_TAUT_bMobileH  )

static

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SegmentSp3StoreStereoCenters()

static int SegmentSp3StoreStereoCenters ( int *  pbAbc, const char *  pStart, const char *  pEnd, int  pInChI_iComponent_nNumberOfAtoms, INChI_Stereo *  PStereo_0  )

static

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SetHillFormFromInChI()

int SetHillFormFromInChI ( InpInChI *  OneInput )

static

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SetProtonsAndXchgIsoH()

int SetProtonsAndXchgIsoH ( int  bInChI2Structure, int  bReqSplitOutputInChI, int  bReqProtonsForEachComponent, int  bReqNonTaut, int  bReqStereo, int  num_components[INCHI_NUM], MODE_PIXH  nModeProtonIsoExchgH[INCHI_NUM], InpInChI *  OneInput  )

static

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TreatErrorsInReadInChIString()

void TreatErrorsInReadInChIString	(	int	nReadStatus,
		int	nErr,
		int	pState,
		INPUT_PARMS *	ip,
		INCHI_IOSTREAM *	pOut,
		INCHI_IOSTREAM *	pLog,
		long *	num_inp,
		long *	num_errors,
		long *	num_processed,
		char **	pstrHdr,
		char **	pszCurHdr,
		InpInChI *	pOneInput
	)

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Variable Documentation

irErrMsg

ICHICONST INCHI_READ_ERR_MSG irErrMsg[]