#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)
	Extract stereo information from InChI string.

int	extract_all_backbone_bonds_from_inchi_string (char sinchi, int n_all_bkb_orig, int orig, int all_bkb_orig)
	Extract all backbone bonds from InChI string.

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
	)

Extract all backbone bonds from InChI string.

Parameters

sinchi	Pointer to InChI string
n_all_bkb_orig	Pointer to number of all backbone bonds
orig	Pointer to array of original atom numbers
all_bkb_orig	Pointer to output array of all backbone bonds by original atom numbers

Returns: int Status code

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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
	)

Extract stereo information from InChI string.

Parameters

sinchi	Pointer to InChI string
nat	Number of atoms
orig	Pointer to array of original atom numbers
at_stereo_mark	Pointer to output array of stereo marks for atoms

Returns: int Status code

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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[]

Data Structures

Macros

Typedefs

Enumerations

Functions

Variables

Macro Definition Documentation

◆ INCHI_INP_EOL

◆ INCHI_TOKEN

◆ IST_HAPPENED_IN_RECMET

◆ LAST_AT_LEN

◆ LINKED_BOND_ADD

◆ MAX_MSG_BUF_LEN

◆ MAX_MSG_LEN

◆ nNum_H

◆ NSTRLEN

◆ SEG_END

◆ SEGM_LINE_ADD

Typedef Documentation

◆ AUX_INFO_STATE

◆ COPY_SEG_TYPE

◆ INCHI_READ_ERR_MSG

◆ INCHI_STATE

◆ LINKED_BONDS

◆ MODE_PIXH

◆ NUM_ELEM

◆ ONE_LINKED_BOND

Enumeration Type Documentation

◆ tagAuxInfoState

◆ tagCopySegmentType

◆ tagInChI_STATE

◆ tagModeProtonIsoExchgH

Function Documentation

◆ AddAuxSegmentCoord()

◆ AddInChIChar()

◆ AddLinkedBond()

◆ bInChIHasReconnectedMetal()

◆ bInpInchiComponentDeleted()

◆ bInpInchiComponentExists()

◆ bIsSp3LayerNotEmpty()

◆ bRevInchiComponentDeleted()

◆ bRevInchiComponentExists()

◆ ConvertInChI2InChI()

◆ ConvertInChI2Struct()

◆ CopyAtomNumbers()

◆ CopySegment()

◆ CountStereoTypes()

◆ DetectAndExposePolymerInternals()

◆ DetectHiddenPolymerStuff()

◆ DetectInpInchiCreationOptions()

◆ extract_all_backbone_bonds_from_inchi_string()

◆ extract_from_inchi_string()

◆ extract_stereo_info_from_inchi_string()

◆ getInChIChar()

◆ getInchiErrName()

◆ GetInChIFormulaNumH()

◆ GetInChIIsoH()

◆ GetInChINumH()

◆ getInchiStateReadErr()

◆ GetNumNeighborsFromInchi()

◆ InChILine2Data()

◆ insertions_sort_AT_NUMB()

◆ nFillOutProtonMobileH()

◆ nGetInChISegment()

◆ nProtonCopyIsotopicInfo()

◆ OutputInChIAsRequested()

◆ ParseAuxSegmentAtomEqu()

◆ ParseAuxSegmentGroupEqu()

◆ ParseAuxSegmentNumbers()

◆ ParseAuxSegmentReverseAtoms()

◆ ParseAuxSegmentReverseBonds()

◆ ParseAuxSegmentReverseCRV()

◆ ParseAuxSegmentReverseXYZ()

◆ ParseAuxSegmentSp3Inv()

◆ ParseAuxSegmentSp3InvNumbers()

◆ ParseAuxSegmentVersion()

◆ ParseSegmentCharge()

◆ ParseSegmentConnections()

◆ ParseSegmentFormula()

◆ ParseSegmentIsoAtoms()