/* * International Chemical Identifier (InChI) * Version 1 * Software version 1.04 * September 9, 2011 * * The InChI library and programs are free software developed under the * auspices of the International Union of Pure and Applied Chemistry (IUPAC). * Originally developed at NIST. Modifications and additions by IUPAC * and the InChI Trust. * * IUPAC/InChI-Trust Licence No.1.0 for the * International Chemical Identifier (InChI) Software version 1.04 * Copyright (C) IUPAC and InChI Trust Limited * * This library is free software; you can redistribute it and/or modify it * under the terms of the IUPAC/InChI Trust InChI Licence No.1.0, * or any later version. * * Please note that this library is distributed WITHOUT ANY WARRANTIES * whatsoever, whether expressed or implied. See the IUPAC/InChI Trust * Licence for the International Chemical Identifier (InChI) Software * version 1.04, October 2011 ("IUPAC/InChI-Trust InChI Licence No.1.0") * for more details. * * You should have received a copy of the IUPAC/InChI Trust InChI * Licence No. 1.0 with this library; if not, please write to: * * The InChI Trust * c/o FIZ CHEMIE Berlin * * Franklinstrasse 11 * 10587 Berlin * GERMANY * * or email to: ulrich@inchi-trust.org. * */ #ifndef __STRUTIL_H__ #define __STRUTIL_H__ #ifndef COMPILE_ALL_CPP #ifdef __cplusplus extern "C" { #endif #endif /* forward declaration */ struct tagTautomerGroupsInfo; int ExtractConnectedComponent(inp_ATOM *at, int num_at, int component_number, inp_ATOM *component_at ); int SetConnectedComponentNumber(inp_ATOM *at, int num_at, int component_number ); INChI *Alloc_INChI(inp_ATOM *at, int num_at, int *found_num_bonds, int *found_num_isotopic, int nAllocMode ); int Free_INChI(INChI **ppINChI); int Free_INChI_Members(INChI *pINChI); int Free_INChI_Stereo( INChI_Stereo *pINChI_Stereo ); INChI_Aux *Alloc_INChI_Aux(int num_at, int num_isotopic_atoms, int nAllocMode, int bOrigData ); int Free_INChI_Aux(INChI_Aux **ppINChI_Aux ); int Create_INChI(INChI **ppINChI, INChI_Aux **ppINChI_Aux, ORIG_ATOM_DATA *orig_inp_data, inp_ATOM *inp_at, INP_ATOM_DATA *inp_norm_data[2], int num_inp_at, INCHI_MODE nUserMode, INCHI_MODE *pbTautFlags, INCHI_MODE *pbTautFlagsDone, struct tagInchiTime *ulMaxTime, struct tagTautomerGroupsInfo *ti_out, char *pStrErrStruct); int FillOutInfAtom(inp_ATOM *norm_at, INF_ATOM_DATA *inf_norm_at_data, int init_num_at, int num_removed_H, int bAdd_DT_to_num_H, int nNumRemovedProtons, NUM_H *nNumRemovedProtonsIsotopic, int bIsotopic, INChI *pINChI, INChI_Aux *pINChI_Aux, int bAbcNumbers, INCHI_MODE nMode ); int FillOutCompositeCanonInfAtom(COMP_ATOM_DATA *composite_norm_data, INF_ATOM_DATA *inf_norm_at_data, int bIsotopic, int bTautomeric, PINChI2 *pINChI2, PINChI_Aux2 *pINChI_Aux2, int bAbcNumbers, INCHI_MODE nMode); #if ( FIX_DALKE_BUGS == 1 ) char *AllocateAndFillHillFormula(INChI *pINChI ); #endif typedef enum tagInchiDiffBits { IDIF_PROBLEM = 0x00000001, /* severe: at least one InChI does not exist */ IDIF_NUM_AT = 0x00000001, /* severe: different number of atoms in the skeleton */ IDIF_ATOMS = 0x00000001, /* severe: diiferent types of skeleton atoms */ IDIF_NUM_EL = 0x00000001, /* severe: formulas differ in another element */ IDIF_CON_LEN = 0x00000001, /* severe: different connection table lengths */ IDIF_CON_TBL = 0x00000001, /* severe: different connection tables */ IDIF_POSITION_H = 0x00000002, /* difference in non-taut (Mobile-H) or all H (Fixed-H) location/number */ IDIF_MORE_FH = 0x00000004, /* extra fixed H */ IDIF_LESS_FH = 0x00000008, /* missing fixed H */ IDIF_MORE_H = 0x00000010, /* formulas differ in number of H */ IDIF_LESS_H = 0x00000020, /* formulas differ in number of H */ /*IDIF_TAUT_LEN = 0x00000008,*/ /* different lengths of tautomer lists */ IDIF_NO_TAUT = 0x00000040, /* restored structure has no taut groups while the original InChI has some */ IDIF_WRONG_TAUT = 0x00000080, /* restored has tautomerism while the original does not have it */ IDIF_SINGLE_TG = 0x00000100, /* restored has 1 taut. group while the original InChI has multiple tg */ IDIF_MULTIPLE_TG = 0x00000200, /* restored has multiple tg while the original InChI has only one tg */ IDIF_NUM_TG = 0x00000400, /* different number of tautomeric groups */ /*IDIF_LESS_TG_ENDP = 0x00000200,*/ /* restores structure has less taut. endpoints */ /*IDIF_MORE_TG_ENDP = 0x00000400,*/ /* restores structure has more taut. endpoints */ IDIF_EXTRA_TG_ENDP = 0x00000800, /* extra tautomeric endpoint(s) in restored structure */ IDIF_MISS_TG_ENDP = 0x00001000, /* one or more tg endpoint is not in the restored structure */ IDIF_DIFF_TG_ENDP = 0x00002000, /* lists of tg endpoints are different */ IDIF_TG = 0x00004000, /* different tautomeric groups */ IDIF_NUM_ISO_AT = 0x00008000, /* ?severe: restored struct. has different number of isotopic atoms */ IDIF_ISO_AT = 0x00010000, /* ?severe: restored struct. has different locations/isotopes of isotopic atoms */ IDIF_CHARGE = 0x00020000, /* restored structure has different charge */ IDIF_REM_PROT = 0x00040000, /* proton(s) removed/added from the restored structure */ IDIF_REM_ISO_H = 0x00080000, /* isotopic H removed */ IDIF_SC_INV = 0x00100000, /* restores structure has different inversion stereocenter mark */ IDIF_SC_PARITY = 0x00200000, /* restored structure has stereoatoms or allenes with different parity */ IDIF_SC_EXTRA_UNDF = 0x00400000, /* restored structure has extra undefined stereocenter(s) */ IDIF_SC_EXTRA = 0x00800000, /* restored structure has extra stereocenter(s) */ IDIF_SC_MISS_UNDF = 0x01000000, /* restored structure has not some undefined stereocenter(s) */ IDIF_SC_MISS = 0x02000000, /* restored structure has not some stereocenters that are not undefined */ IDIF_SB_PARITY = 0x04000000, /* restored structure has stereobonds or cumulenes with different parity */ IDIF_SB_EXTRA_UNDF = 0x08000000, /* restored structure has extra undefined stereobond(s) */ IDIF_SB_EXTRA = 0x10000000, /* restored structure has extra stereobond(s) */ IDIF_SB_MISS_UNDF = 0x20000000, /* restored structure has not some undefined stereocenters */ IDIF_SB_MISS = 0x40000000 /* restored structure has not some stereobonds that are not undefined */ } IDIF; #define IDIFF_SB (IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF | IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS) #define IDIFF_SC (IDIF_SC_PARITY | IDIF_SC_EXTRA_UNDF | IDIF_SC_EXTRA | IDIF_SC_MISS_UNDF | IDIF_SC_MISS) #define IDIFF_CONSTIT (IDIF_POSITION_H | IDIF_MORE_FH | IDIF_LESS_FH | IDIF_MORE_H | IDIF_LESS_H |\ IDIF_NO_TAUT | IDIF_WRONG_TAUT | IDIF_SINGLE_TG | IDIF_MULTIPLE_TG | \ IDIF_NUM_TG | IDIF_EXTRA_TG_ENDP | IDIF_MISS_TG_ENDP | IDIF_TG | \ IDIF_NUM_ISO_AT | IDIF_ISO_AT | IDIF_CHARGE | IDIF_REM_PROT | IDIF_REM_ISO_H |\ IDIF_DIFF_TG_ENDP) #define IDIFF_STEREO (IDIF_SC_INV | IDIF_SC_PARITY | IDIF_SC_EXTRA_UNDF | IDIF_SC_EXTRA | \ IDIF_SC_MISS_UNDF | IDIF_SC_MISS | IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF |\ IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS) /*************************************************************************************/ #define ICR_MAX_ENDP_IN1_ONLY 32 #define ICR_MAX_ENDP_IN2_ONLY 32 #define ICR_MAX_DIFF_FIXED_H 32 #define ICR_MAX_SB_IN1_ONLY 32 #define ICR_MAX_SB_IN2_ONLY 32 #define ICR_MAX_SC_IN1_ONLY 32 #define ICR_MAX_SC_IN2_ONLY 32 #define ICR_MAX_SB_UNDF 32 #define ICR_MAX_SC_UNDF 32 typedef struct tagInChICompareResults { INCHI_MODE flags; int tot_num_H1; int tot_num_H2; int num_taut_H1; int num_taut_H2; int num_taut_M1; int num_taut_M2; /* 1 => InChI from reversed struct. 2 => input InChI */ AT_NUMB endp_in1_only[ICR_MAX_ENDP_IN1_ONLY]; /* endpoint canonical number = index+1 */ int num_endp_in1_only; AT_NUMB endp_in2_only[ICR_MAX_ENDP_IN2_ONLY]; /* endpoint canonical number = index+1 */ int num_endp_in2_only; AT_NUMB diff_pos_H_at[ICR_MAX_DIFF_FIXED_H]; /* non-tautomeric H */ S_CHAR diff_pos_H_nH[ICR_MAX_DIFF_FIXED_H]; int num_diff_pos_H; AT_NUMB fixed_H_at1_more[ICR_MAX_DIFF_FIXED_H]; /* extra fixed_H */ S_CHAR fixed_H_nH1_more[ICR_MAX_DIFF_FIXED_H]; int num_fixed_H1_more; AT_NUMB fixed_H_at2_more[ICR_MAX_DIFF_FIXED_H]; /* missed fixed_H */ S_CHAR fixed_H_nH2_more[ICR_MAX_DIFF_FIXED_H]; int num_fixed_H2_more; AT_NUMB sc_in1_only[ICR_MAX_SC_IN1_ONLY]; int num_sc_in1_only; AT_NUMB sc_in2_only[ICR_MAX_SC_IN2_ONLY]; int num_sc_in2_only; AT_NUMB sb_in1_only[ICR_MAX_SB_IN1_ONLY]; int num_sb_in1_only; AT_NUMB sb_in2_only[ICR_MAX_SB_IN2_ONLY]; int num_sb_in2_only; AT_NUMB sb_undef_in1_only[ICR_MAX_SC_UNDF]; int num_sb_undef_in1_only; AT_NUMB sb_undef_in2_only[ICR_MAX_SC_UNDF]; int num_sb_undef_in2_only; AT_NUMB sc_undef_in1_only[ICR_MAX_SB_UNDF]; int num_sc_undef_in1_only; AT_NUMB sc_undef_in2_only[ICR_MAX_SB_UNDF]; int num_sc_undef_in2_only; } ICR; /* tagInChICompareResults */ INCHI_MODE CompareReversedINChI2(INChI *i1 /* InChI from reversed struct */, INChI *i2 /* input InChI */, INChI_Aux *a1, INChI_Aux *a2, ICR *picr, int *err ); int CompareIcr(ICR *picr1, ICR *picr2, INCHI_MODE *pin1, INCHI_MODE *pin2, INCHI_MODE mask ); int CompareReversedINChI(INChI *i1, INChI *i2, INChI_Aux *a1, INChI_Aux *a2 ); const char *CompareReversedInchiMsg(int code); #define EQL_EXISTS 1 #define EQL_SP3 2 #define EQL_SP3_INV 4 #define EQL_SP2 8 int Eql_INChI_Stereo(INChI_Stereo *s1, int eql1, INChI_Stereo *s2, int eql2, int bRelRac ); int Eql_INChI_Isotopic(INChI *i1, INChI *i2 ); #define EQL_EQU 0 #define EQL_EQU_TG 1 #define EQL_EQU_ISO 2 int Eql_INChI_Aux_Equ(INChI_Aux *a1, int eql1, INChI_Aux *a2, int eql2 ); #define EQL_NUM 0 #define EQL_NUM_INV 1 #define EQL_NUM_ISO 2 int Eql_INChI_Aux_Num(INChI_Aux *a1, int eql1, INChI_Aux *a2, int eql2 ); int bHasEquString(AT_NUMB *LinearCT, int nLenCT ); int CompINChINonTaut2(const void *p1, const void *p2); int CompINChITaut2(const void *p1, const void *p2); int CompINChI2(const INCHI_SORT *p1, const INCHI_SORT *p2, int bTaut, int bCompareIsotopic); int CompINChITautVsNonTaut(const INCHI_SORT *p1, const INCHI_SORT *p2, int bCompareIsotopic); typedef enum tagDiffINChISegments { /* r = repetitive, n = non-repetitive */ DIFS_f_FORMULA, /* 0 r; fixed-H <-> mobile-H */ DIFS_c_CONNECT, /* 1 n; connection table; mobile-H only */ DIFS_h_H_ATOMS, /* 2 n; hydrogen atoms: mobile-H and Fixed-H; have different meanings */ DIFS_q_CHARGE, /* 3 r; charge; fixed-H <-> mobile-H */ DIFS_p_PROTONS, /* 4 n; protons; mobile-H only */ DIFS_b_SBONDS, /* 5 r: stereobonds: fixed-H <-> mobile-H * isotopic <-> non-isotopic */ DIFS_t_SATOMS, /* 6 r: stereoatoms: fixed-H <-> mobile-H * isotopic <-> non-isotopic */ DIFS_m_SP3INV, /* 7 r: stereo-abs-inv: fixed-H <-> mobile-H * isotopic <-> non-isotopic */ DIFS_s_STYPE, /* 8 r: stereo-type: fixed-H <-> mobile-H * isotopic <-> non-isotopic */ DIFS_i_IATOMS, /* 9 r: isotopic atoms: fixed-H <-> mobile-H * isotopic <-> non-isotopic */ DIFS_o_TRANSP, /* 10 n: Fixed-H transposition */ DIFS_idf_LENGTH, /* 11 length of the array relevant to the INChI Identifier */ /* later elements referring to AuxInfo may be added */ DIFS_LENGTH = DIFS_idf_LENGTH /* length of the array */ } DIF_SEGMENTS; typedef enum tagDiffINChILayers { DIFL_M, /* 0 main layer */ DIFL_MI, /* 1 main isotopic */ DIFL_F, /* 2 fixed-H */ DIFL_FI, /* 3 fixed-H isotopic */ DIFL_LENGTH /* number of layers */ } DIF_LAYERS; /* Value meaning */ typedef enum tagMarkDiff { DIFV_BOTH_EMPTY = 0, /* both this and the component in the preceding namesake segment are empty */ DIFV_EQL2PRECED = 1, /* equal to the component in the preceding namesake segment */ DIFV_NEQ2PRECED = 2, /* different from the component in the preceding namesake segment */ DIFV_IS_EMPTY = 4, /* is empty while the preceding namesake segment is not empty */ DIFV_FI_EQ_MI = 8, /* FI stereo component is equal to the component in the MI namesake segment */ /* while M and F components are empty */ /* decision_F = bitmask: bits that should not be present */ /* decision_T = bitmask: at least one of the bits should be present */ /* decision = true if( !( BITS & decision_F ) && ( BITS & decision_F ) ) */ DIFV_OUTPUT_EMPTY_T = (DIFV_IS_EMPTY), /* bits present for empty segment output */ DIFV_OUTPUT_EMPTY_F = (DIFV_EQL2PRECED | DIFV_NEQ2PRECED | DIFV_FI_EQ_MI), /* bits NOT present */ DIFV_OUTPUT_OMIT_F = (DIFV_NEQ2PRECED | DIFV_IS_EMPTY), /* bits NOT present for omitting */ DIFV_OUTPUT_FILL_T = (DIFV_EQL2PRECED | DIFV_NEQ2PRECED | DIFV_FI_EQ_MI) } DIF_VALUES; typedef enum tagINChISegmAction { INCHI_SEGM_OMIT = 0, INCHI_SEGM_FILL = 1, /* the value is used in str_LineEnd() */ INCHI_SEGM_EMPTY = 2 /* the value is used in str_LineEnd() */ } INCHI_SEGM_ACTION; int CompINChILayers(const INCHI_SORT *p1, const INCHI_SORT *p2, char sDifSegs[][DIFS_LENGTH], int bFixTranspChargeBug ); int MarkUnusedAndEmptyLayers( char sDifSegs[][DIFS_LENGTH] ); int INChI_SegmentAction( char cDifSegs ); #define FLAG_SORT_PRINT_TRANSPOS_BAS 1 /* transposition in the main InChI layer */ #define FLAG_SORT_PRINT_TRANSPOS_REC 2 /* transposition in the reconnected InChI layer */ #define FLAG_SORT_PRINT_NO_NFIX_H_BAS 4 /* no fixed H non-isotopic in the main InChI layer */ #define FLAG_SORT_PRINT_NO_NFIX_H_REC 8 /* no fixed H non-isotopic in the reconnected InChI layer */ #define FLAG_SORT_PRINT_NO_IFIX_H_BAS 16 /* no fixed H isotopic in the main InChI layer */ #define FLAG_SORT_PRINT_NO_IFIX_H_REC 32 /* no fixed H isotopic in the the reconnected InChI layer */ #define FLAG_SORT_PRINT_ReChI_PREFIX 64 /* Output ReChI instead of InChI */ int OutputINChI1(char *pStr, int nStrLen, INCHI_SORT *pINChISortTautAndNonTaut2[][TAUT_NUM], int iINChI, ORIG_STRUCT *pOrigStruct, int bDisconnectedCoord, int bOutputType, int bINChIOutputOptions, int bXml, int bAbcNumbers,int bCtPredecessors, int bNoStructLabels, int num_components2[], int num_non_taut2[], int num_taut2[], INCHI_IOSTREAM *output_file, INCHI_IOSTREAM *log_file, int num_input_struct, const char *szSdfLabel, const char *szSdfValue, long lSdfId, int *pSortPrintINChIFlags, unsigned char save_opt_bits); int OutputINChI2(char *pStr, int nStrLen, INCHI_SORT *pINChISortTautAndNonTaut2[][TAUT_NUM], int iINChI, ORIG_STRUCT *pOrigStruct, int bDisconnectedCoord, int bOutputType, int bINChIOutputOptions, int bXml, int bAbcNumbers,int bCtPredecessors, int bNoStructLabels, int num_components2[], int num_non_taut2[], int num_taut2[], INCHI_IOSTREAM *output_file, INCHI_IOSTREAM *log_file, int num_input_struct, const char *szSdfLabel, const char *szSdfValue, long lSdfId, int *pSortPrintINChIFlags, unsigned char save_opt_bits); int SaveEquComponentsInfoAndSortOrder(int iINChI, INCHI_SORT *pINChISort[TAUT_NUM], int *num_components, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, COMP_ATOM_DATA composite_norm_data[TAUT_NUM], int bCompareComponents ); int OutputINChIXmlRootStartTag( INCHI_IOSTREAM *output_file ); int OutputINChIXmlRootEndTag( INCHI_IOSTREAM *output_file ); int OutputINChIXmlError( INCHI_IOSTREAM *output_file, char *pStr, int nStrLen, int ind, /*int nErrorNumber,*/ char *szErrorText, int bError ); int OutputINChIPlainError( INCHI_IOSTREAM *output_file, char *pStr, int nStrLen, char *pErrorText, int bError ); int OutputINChIXmlStructStartTag( INCHI_IOSTREAM *output_file, char *pStr, int ind /* indent*/, int nStrLen, int bNoStructLabels, int num_input_struct, const char *szSdfLabel, const char *szSdfValue ); int OutputINChIXmlStructEndTag( INCHI_IOSTREAM *output_file, char *pStr, int nStrLen, int ind ); int GetInpStructErrorType(INPUT_PARMS *ip, int err, char *pStrErrStruct, int num_inp_atoms ); int ProcessStructError( INCHI_IOSTREAM *output_file, INCHI_IOSTREAM *log_file, /*int err,*/ char *pStrErrStruct, int nErrorType, int *bXmlStructStarted, long num_inp, INPUT_PARMS *ip, char *pStr, int nStrLen ); int bNumHeterAtomHasIsotopicH( inp_ATOM *atom, int num_atoms ); int WriteToSDfile( const INP_ATOM_DATA *inp_at_data, INCHI_IOSTREAM* fcb, const char* name, const char* comment, const char *szLabel, const char *szValue ); int WriteOrigAtomDataToSDfile( const ORIG_ATOM_DATA *inp_at_data, INCHI_IOSTREAM * fcb, const char* name, const char* comment, int bChiral, int bAtomsDT, const char *szLabel, const char *szValue); int bIsMetalSalt( inp_ATOM *at, int i ); extern const char gsMissing[]; extern const char gsEmpty[]; extern const char gsSpace[]; extern const char gsEqual[]; /* #define gsMissing "is missing" #define gsEmpty "" #define gsSpace " " #define gsEqual "=" */ /* format string for SDF_LBL_VAL(L,V): %s%s%s%s (four strings) */ /*#define SDF_LBL_VAL(L,V) ((L)&&(L)[0])?gsSpace:gsEmpty, ((L)&&(L)[0])?L:gsEmpty, ((L)&&(L)[0])? (((V)&&(V)[0])?gsEqual:gsSpace):gsEmpty, ((L)&&(L)[0])?((V)&&(V)[0]?V:gsMissing):gsEmpty*/ #define SDF_LBL_VAL(L,V) ((L)&&(L)[0])?gsSpace:gsEmpty, ((L)&&(L)[0])?L:gsEmpty, ((L)&&(L)[0])? (((V)&&(V)[0])?gsEqual:gsSpace):gsEmpty, ((V)&&(V)[0])?V:((L)&&(L)[0])?gsMissing:gsEmpty #ifndef COMPILE_ALL_CPP #ifdef __cplusplus } #endif #endif #endif /* __STRUTIL_H__ */