/* * 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. * */ int DetectInputINChIFileType(FILE **inp_file, INPUT_PARMS *ip, const char *fmode); void HelpCommandLineParmsReduced(INCHI_IOSTREAM *f); /*****************************************************************************************/ int ReadCommandLineParms(int argc, const char *argv[], INPUT_PARMS *ip, char *szSdfDataValue, unsigned long *ulDisplTime, int bReleaseVersion, INCHI_IOSTREAM *log_file) { int i, k, c; const char *q; unsigned long ul; int nFontSize = -9; int nMode = 0; int nReleaseMode = nMode | (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO); #if ( MIN_SB_RING_SIZE > 0 ) int nMinDbRinSize = MIN_SB_RING_SIZE, mdbr=0; #endif /*int bNotRecognized=0;*/ char szNameSuffix[32], szOutputPath[512]; int bNameSuffix, bOutputPath; int bMergeAllInputStructures; int bDisconnectSalts = (DISCONNECT_SALTS==1); int bDoNotAddH = 0; int bVer1Options = 1; int bReconnectCoord = (RECONNECT_METALS==1); int bDisconnectCoord = (DISCONNECT_METALS==1); #ifdef TARGET_LIB_FOR_WINCHI /* int bVer1Options = 0; int bReconnectCoord = 1; int bDisconnectCoord = 1; */ int is_gui = 1; int bINChIOutputOptions = INCHI_OUT_EMBED_REC; /* embed reconnected & output full aux info */ int bCompareComponents = CMP_COMPONENTS; #else /* int bVer1Options = 1; int bReconnectCoord = (RECONNECT_METALS==1); int bDisconnectCoord = (DISCONNECT_METALS==1); */ int is_gui = 0; int bINChIOutputOptions = ((EMBED_REC_METALS_INCHI==1)? INCHI_OUT_EMBED_REC : 0); /*| INCHI_OUT_NO_AUX_INFO INCHI_OUT_SHORT_AUX_INFO*/ int bCompareComponents = 0; #endif int bDisconnectCoordChkVal = (CHECK_METAL_VALENCE == 1); int bMovePositiveCharges = (MOVE_CHARGES==1); int bAcidTautomerism = (DISCONNECT_SALTS==1)? (TEST_REMOVE_S_ATOMS==1? 2:1):0; int bUnchargedAcidTaut = (CHARGED_SALTS_ONLY==0); int bMergeSaltTGroups = (DISCONNECT_SALTS==1); int bDisplayCompositeResults = 0; #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU) INCHI_MODE bVer1DefaultMode = VER103_DEFAULT_MODE; const char *ext[MAX_NUM_PATHS+1]; const char *pArg; double t; int bRecognizedOption; int bDisplay = 0; int bNoStructLabels = 0; int bOutputMolfileOnly = 0; int bOutputMolfileDT = 0; int bOutputMolfileSplit = 0; int bForcedChiralFlag = 0; #if ( READ_INCHI_STRING == 1 ) int bDisplayIfRestoreWarnings = 0; #endif #ifdef TARGET_LIB_FOR_WINCHI int bXml = INCHI_OUT_XML; #else int bXml = INCHI_OUT_PLAIN_TEXT; #endif int bTgFlagVariableProtons = 1; int bTgFlagHardAddRenProtons = 1; #ifdef STEREO_WEDGE_ONLY int bPointedEdgeStereo = STEREO_WEDGE_ONLY; /* NEWPS TG_FLAG_POINTED_EDGE_STEREO*/ #endif #if ( FIX_ADJ_RAD == 1 ) int bFixAdjacentRad = 0; #endif int bAddPhosphineStereo = 1; int bAddArsineStereo = 1; int bFixSp3bug = 1; int bFixFB2 = 1; int bKetoEnolTaut = 0; int b15TautNonRing = 0; int bStdFormat = 1; int bHashKey = 0; int bHashXtra1 = 0; int bHashXtra2 = 0; ext[0] = ".mol"; ext[1] = bVer1Options? ".txt" : ".ich"; ext[2] = ".log"; ext[3] = ".prb"; ext[4] = ""; #if ( MAX_NUM_PATHS < 4 ) #error Wrong initialization #endif /* init table parms */ memset(ip, 0, sizeof(*ip)); /* default are standard InChI generation options */ bVer1DefaultMode &= ~REQ_MODE_BASIC; /* "FIXEDH - OFF" */ bReconnectCoord = 0; /* "RECMET - OFF" */ bPointedEdgeStereo = 1; /* "NEWPS" */ ip->bFixNonUniformDraw = 1; /* "FNUD" */ #ifndef COMPILE_ANSI_ONLY strcpy( ip->tdp.ReqShownFoundTxt[ilSHOWN], "Shown" ); ip->dp.sdp.tdp = &ip->tdp; ip->dp.pdp = &ip->pdp; #endif memset( szNameSuffix, 0, sizeof(szNameSuffix) ); bNameSuffix = 0; memset(szOutputPath, 0, sizeof(szOutputPath) ); bOutputPath = 0; bMergeAllInputStructures = 0; *ulDisplTime = 0; #ifdef TARGET_API_LIB ip->msec_MaxTime = 0; /* milliseconds, default = unlimited in libinchi */ #else ip->msec_MaxTime = 60000; /* milliseconds, default = 60 sec */ #endif if ( bReleaseVersion ) { /* normal */ /*ip->bINChIOutputOptions |= INCHI_OUT_PLAIN_TEXT;*/ /*ip->bXml = 1;*/ ip->bAbcNumbers = 0; ip->bCtPredecessors = 0; /* -- testing -- ip->bXml = 0; ip->bAbcNumbers = 1; */ } else { /*bXml = INCHI_OUT_PLAIN_TEXT;*/ nReleaseMode = 0; } if ( bVer1Options ) { bNameSuffix = 1; szNameSuffix[0] = '\0'; } /* Parse */ for ( i = 1; i < argc; i ++ ) { /* if ( !(bVer1Options & 1) && INCHI_OPTION_PREFX == argv[i][0] && INCHI_OPTION_PREFX != argv[i][1] ) */ if ( is_gui && INCHI_OPTION_PREFX == argv[i][0] && INCHI_OPTION_PREFX != argv[i][1] ) { /*=== parsing TARGET_LIB_FOR_WINCHI GUI (and v. 0.9xx Beta)options ===*/ pArg = argv[i]+1; /*--- Input options ---*/ if ( !stricmp( pArg, "INPAUX" )) { if (INPUT_NONE == ip->nInputType) ip->nInputType = INPUT_INCHI_PLAIN; } else if ( INPUT_NONE == ip->nInputType && (!memicmp( pArg, "SDF", 3 )) && ( pArg[3] == ':' ) ) { k = 0; mystrncpy( ip->szSdfDataHeader, pArg+4, MAX_SDF_HEADER+1 ); LtrimRtrim( ip->szSdfDataHeader, &k ); if ( k ) { ip->pSdfLabel = ip->szSdfDataHeader; ip->pSdfValue = szSdfDataValue; ip->nInputType = INPUT_SDFILE; } else { ip->pSdfLabel = NULL; ip->pSdfValue = NULL; ip->nInputType = INPUT_MOLFILE; } } else if ( INPUT_NONE == ip->nInputType && !stricmp( pArg, "MOL" ) ) { ip->nInputType = INPUT_MOLFILE; } else if ( INPUT_NONE == ip->nInputType && !stricmp( pArg, "SDF" ) ) { ip->nInputType = INPUT_MOLFILE; } #if ( ADD_CMLPP == 1 ) else if ( INPUT_NONE == ip->nInputType && !stricmp( pArg, "CML" ) ) { /* CMLfile label */ ip->nInputType = INPUT_CMLFILE; } #endif else if ( !memicmp( pArg, "START:", 6 ) ) { ip->first_struct_number = strtol(pArg+6, NULL, 10); } else if ( !memicmp( pArg, "END:", 4 ) ) { ip->last_struct_number = strtol(pArg+4, NULL, 10); } #ifdef BUILD_WITH_ENG_OPTIONS else if ( !memicmp( pArg, "RSB:", 4 ) ) { mdbr = (int)strtol(pArg+4, NULL, 10); } else if ( !memicmp( pArg, "DISCONSALT:", 11 ) ) { bDisconnectSalts = (0 != strtol(pArg+11, NULL, 10)); } else if ( !memicmp( pArg, "DISCONMETAL:", 12 ) ) { bDisconnectCoord = (0 != strtol(pArg+12, NULL, 10)); } else if ( !memicmp( pArg, "RECONMETAL:", 11 ) ) { bReconnectCoord = (0 != strtol(pArg+11, NULL, 10)); } else if ( !memicmp( pArg, "DISCONMETALCHKVAL:", 18 ) ) { bDisconnectCoordChkVal = (0 != strtol(pArg+18, NULL, 10)); } else if ( !memicmp( pArg, "MOVEPOS:", 8 ) ) { bMovePositiveCharges = (0 != strtol(pArg+8, NULL, 10)); } else if ( !memicmp( pArg, "MERGESALTTG:", 12 ) ) { bMergeSaltTGroups = (0 != strtol(pArg+12, NULL, 10)); } else if ( !memicmp( pArg, "UNCHARGEDACIDS:", 15) ) { bUnchargedAcidTaut = (0 != strtol(pArg+15, NULL, 16));; } else if ( !memicmp( pArg, "ACIDTAUT:", 9 ) ) { bAcidTautomerism = c = (int)strtol(pArg+9, NULL, 10); if ( 0 <= c && c <= 2 ) bAcidTautomerism = c; /*else bNotRecognized = 2*bReleaseVersion;*/ } #endif /*--- Output options ---*/ #if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) ) else if ( !stricmp( pArg, "Tabbed" ) ) { bXml |= INCHI_OUT_TABBED_OUTPUT; } #endif else if ( !stricmp( pArg, "NOLABELS" ) ) { bNoStructLabels = 1; } else if ( !stricmp( pArg, "SAVEOPT" ) ) { bINChIOutputOptions |= INCHI_OUT_SAVEOPT; } else if ( !stricmp( pArg, "AUXNONE" ) ) { /* no aux. info */ bINChIOutputOptions |= INCHI_OUT_NO_AUX_INFO; /* no aux info */ bINChIOutputOptions &= ~INCHI_OUT_SHORT_AUX_INFO; } #if ( defined(BUILD_WITH_ENG_OPTIONS) || defined(TARGET_LIB_FOR_WINCHI) ) else if ( !stricmp( pArg, "SDFID" ) ) { ip->bGetSdfileId = 1; } else if ( !stricmp( pArg, "XML" ) ) { bXml &= ~INCHI_OUT_PLAIN_TEXT; bXml |= INCHI_OUT_XML; /*bNotRecognized = 2*bReleaseVersion;*/ } else if ( !stricmp( pArg, "PLAIN" ) ) { bXml |= INCHI_OUT_PLAIN_TEXT; bXml &= ~INCHI_OUT_XML; } else if ( !stricmp( pArg, "ANNPLAIN" ) ) { bXml |= INCHI_OUT_PLAIN_TEXT_COMMENTS; bXml &= ~INCHI_OUT_XML_TEXT_COMMENTS; } else if ( !stricmp( pArg, "ANNXML" ) ) { bXml |= INCHI_OUT_XML_TEXT_COMMENTS; bXml &= ~INCHI_OUT_PLAIN_TEXT_COMMENTS; } else if ( !memicmp( pArg, "AUXINFO:", 8 ) && isdigit(UCINT pArg[8]) ) { k = strtol(pArg+8, NULL, 10); if ( k == 0 ) { bINChIOutputOptions |= INCHI_OUT_NO_AUX_INFO; /* no aux info */ bINChIOutputOptions &= ~INCHI_OUT_SHORT_AUX_INFO; } else if ( k == 1 ) { bINChIOutputOptions &= ~(INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO); /* include full aux info */ } else if ( k == 2 ) { bINChIOutputOptions &= ~INCHI_OUT_NO_AUX_INFO; /* include short aux info */ bINChIOutputOptions |= INCHI_OUT_SHORT_AUX_INFO; } else { bINChIOutputOptions = k; /* override everything */ } } else if ( !stricmp( pArg, "MERGE" ) ) { bMergeAllInputStructures = 1; } else if ( !stricmp( pArg, "PGO" ) ) { ip->bSaveAllGoodStructsAsProblem = 1; } else if ( !stricmp( pArg, "DCR" ) ) { bDisplayCompositeResults = 1; } else if ( !stricmp( pArg, "DSB" ) ) { nMode |= REQ_MODE_NO_ALT_SBONDS; } else if ( !stricmp( pArg, "NOHDR" ) ) { bNoStructLabels = 1; } else if ( !stricmp( pArg, "NoVarH" ) ) { bTgFlagVariableProtons = 0; } #endif /* BUILD_WITH_ENG_OPTIONS */ /*--- All modes (std and non-std InChI) structure perception options ---*/ else if ( !stricmp( pArg, "SNON" ) ) { bVer1DefaultMode &= ~REQ_MODE_STEREO; nMode &= ~(REQ_MODE_RACEMIC_STEREO | REQ_MODE_RELATIVE_STEREO | REQ_MODE_CHIR_FLG_STEREO); } else if ( !stricmp( pArg, "NEWPSOFF" ) ) { bPointedEdgeStereo = 0; } else if ( !stricmp( pArg, "DONOTADDH" ) ) { bDoNotAddH = 1; } /* Non-standard */ #ifndef USE_STDINCHI_API /* Non-std InChI structure perception options */ else if ( !stricmp( pArg, "SREL" ) ) { if ( nMode & REQ_MODE_RACEMIC_STEREO ) { nMode ^= REQ_MODE_RACEMIC_STEREO; } if ( nMode & REQ_MODE_CHIR_FLG_STEREO ) { nMode ^= REQ_MODE_CHIR_FLG_STEREO; } nMode |= REQ_MODE_RELATIVE_STEREO; nMode |= REQ_MODE_STEREO; bStdFormat = 0; } else if ( !stricmp( pArg, "SRAC" ) ) { if ( nMode & REQ_MODE_RELATIVE_STEREO ) { nMode ^= REQ_MODE_RELATIVE_STEREO; } if ( nMode & REQ_MODE_CHIR_FLG_STEREO ) { nMode ^= REQ_MODE_CHIR_FLG_STEREO; } nMode |= REQ_MODE_RACEMIC_STEREO; nMode |= REQ_MODE_STEREO; bStdFormat = 0; } else if ( !stricmp( pArg, "SUCF" ) ) { if ( nMode & REQ_MODE_RELATIVE_STEREO ) { nMode ^= REQ_MODE_RELATIVE_STEREO; } if ( nMode & REQ_MODE_RACEMIC_STEREO ) { nMode ^= REQ_MODE_RACEMIC_STEREO; } nMode |= REQ_MODE_CHIR_FLG_STEREO; /* stereo defined by the Chiral flag */ nMode |= REQ_MODE_STEREO; bStdFormat = 0; } else if ( !stricmp( pArg, "ChiralFlagON" ) ) { /* used only with /SUCF */ /* NB: do not toggle off bStdFormat! (if necessary SUCF will do) */ bForcedChiralFlag &= ~FLAG_SET_INP_AT_NONCHIRAL; bForcedChiralFlag |= FLAG_SET_INP_AT_CHIRAL; } else if ( !stricmp( pArg, "ChiralFlagOFF" ) ) { /* used only with /SUCF */ /* NB: do not toggle off bStdFormat! (if necessary SUCF will do) */ bForcedChiralFlag &= ~FLAG_SET_INP_AT_CHIRAL; bForcedChiralFlag |= FLAG_SET_INP_AT_NONCHIRAL; } /*--- Non-std InChI creation options ---*/ else if ( !stricmp( pArg, "SUU" ) ) { /* include omitted undef/unknown stereo */ bVer1DefaultMode &= ~(REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU); bStdFormat = 0; } else if ( !stricmp( pArg, "SLUUD" ) ) { /* make labels for unknown and undefined stereo different */ bVer1DefaultMode |= REQ_MODE_DIFF_UU_STEREO; bStdFormat = 0; } /* FixedH */ else if ( !stricmp( pArg, "FIXEDH" ) ) { bVer1DefaultMode |= REQ_MODE_BASIC; /* tautomeric */ bStdFormat = 0; } /* RecMet */ else if ( !stricmp( pArg, "RECMET" ) ) { /* reconnect metals */ bReconnectCoord = 1; bStdFormat = 0; } #if ( KETO_ENOL_TAUT == 1 ) else if ( !stricmp( pArg, "KET" ) ) { bKetoEnolTaut = 1; bStdFormat = 0; } #endif #if ( TAUT_15_NON_RING == 1 ) else if ( !stricmp( pArg, "15T" ) ) { b15TautNonRing = 1; bStdFormat = 0; } #endif #endif /*--- Generation options ---*/ /* InChIKey/InChI hash */ else if ( !stricmp( pArg, "Key" ) ) { bHashKey = 1; } else if ( !stricmp( pArg, "XHash1" ) ) { bHashXtra1 = 1; } else if ( !stricmp( pArg, "XHash2" ) ) { bHashXtra2 = 1; } /*--- (engineering) Undo bug/draw fixes options ---*/ #ifdef BUILD_WITH_ENG_OPTIONS else if ( !stricmp( pArg, "FixSp3bugOFF" ) ) { bFixSp3bug = 0; bStdFormat = 0; } else if ( !stricmp( pArg, "FBOFF" ) ) { bFixSp3bug = 0; bStdFormat = 0; } else if ( !stricmp( pArg, "FB2OFF" ) ) { bFixFB2 = 0; bStdFormat = 0; } else if ( !stricmp( pArg, "SPXYZOFF" ) ) { bAddPhosphineStereo = 0; bStdFormat = 0; } else if ( !stricmp( pArg, "SASXYZOFF" ) ) { bAddArsineStereo = 0; bStdFormat = 0; } else if ( !stricmp( pArg, "FNUDOFF" ) ) { ip->bFixNonUniformDraw = 0; bStdFormat = 0; } /*--- (hidden) Old structure-perception and InChI creation options ---*/ /*--- (engineering) Old structure-perception and InChI creation options ---*/ else if ( !stricmp( pArg, "NOUUSB" ) ) { nMode |= REQ_MODE_SB_IGN_ALL_UU; bStdFormat = 0; } else if ( !stricmp( pArg, "NOUUSC" ) ) { nMode |= REQ_MODE_SC_IGN_ALL_UU; bStdFormat = 0; } #if ( FIX_ADJ_RAD == 1 ) else if ( !stricmp( pArg, "FixRad" ) ) { bFixAdjacentRad = 1; bStdFormat = 0; } #endif #if ( UNDERIVATIZE == 1 ) else if ( !stricmp( pArg, "DoDRV" ) ) { ip->bUnderivatize = 1; bStdFormat = 0; } #endif #if ( RING2CHAIN == 1 ) else if ( !stricmp( pArg, "DoR2C" ) ) { ip->bRing2Chain = 1; bStdFormat = 0; } #endif #if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 ) else if ( !stricmp( pArg, "DoneOnly" ) ) { ip->bIngnoreUnchanged = 1; bStdFormat = 0; } #endif else if ( !stricmp( pArg, "NoADP" ) ) { bTgFlagHardAddRenProtons = 0; bStdFormat = 0; } else if ( !memicmp( pArg, "DISCONSALT:", 11 ) ) { bDisconnectSalts = (0 != strtol(pArg+11, NULL, 10)); bStdFormat = 0; } else if ( !memicmp( pArg, "DISCONMETAL:", 12 ) ) { bDisconnectCoord = (0 != strtol(pArg+12, NULL, 10)); bStdFormat = 0; } else if ( !memicmp( pArg, "RECONMETAL:", 11 ) ) { bReconnectCoord = (0 != strtol(pArg+11, NULL, 10)); bStdFormat = 0; } else if ( !memicmp( pArg, "DISCONMETALCHKVAL:", 18 ) ) { bDisconnectCoordChkVal = (0 != strtol(pArg+18, NULL, 10)); bStdFormat = 0; } else if ( !memicmp( pArg, "MOVEPOS:", 8 ) ) { bMovePositiveCharges = (0 != strtol(pArg+8, NULL, 10)); bStdFormat = 0; } else if ( !memicmp( pArg, "MERGESALTTG:", 12 ) ) { bMergeSaltTGroups = (0 != strtol(pArg+12, NULL, 10)); bStdFormat = 0; } else if ( !memicmp( pArg, "UNCHARGEDACIDS:", 15) ) { bUnchargedAcidTaut = (0 != strtol(pArg+15, NULL, 16)); bStdFormat = 0; } else if ( !memicmp( pArg, "ACIDTAUT:", 9 ) ) { bAcidTautomerism = c = (int)strtol(pArg+9, NULL, 10); if ( 0 <= c && c <= 2 ) bAcidTautomerism = c; /*else bNotRecognized = 2*bReleaseVersion;*/ bStdFormat = 0; } /*--- (hidden) Old output and other options ---*/ else if ( !memicmp( pArg, "O:", 2 ) ) { bNameSuffix = 1; strncpy(szNameSuffix, pArg+2, sizeof(szNameSuffix)-1); } else if ( !memicmp( pArg, "OP:", 3 ) ) { bOutputPath = 1; strncpy(szOutputPath, pArg+3, sizeof(szOutputPath)-1); } else if ( !stricmp( pArg, "ALT" ) ) { ip->bAbcNumbers = 1; bStdFormat = 0; } else if ( !stricmp( pArg, "SCT" ) ) { ip->bCtPredecessors = 1; bStdFormat = 0; } else if ( !stricmp( pArg, "CMP" ) ) { bCompareComponents = CMP_COMPONENTS; } else if ( !stricmp( pArg, "CMPNONISO" ) ) { bCompareComponents = CMP_COMPONENTS | CMP_COMPONENTS_NONISO; } else if ( !stricmp( pArg, "PW" ) ) { ip->bSaveWarningStructsAsProblem = 1; } #endif /* BUILD_WITH_ENG_OPTIONS */ else { /*for ( k = 0; c=pArg[k]; k ++ )*/ k = 0; c=pArg[k]; /* prohibit multiple option concatenations, strict syntax check 2008-11-05 DT */ { c = toupper( c ); switch ( c ) { case 'D': bDisplay |= 1; if ( (pArg[k+1] == 'C' || pArg[k+1] == 'c') && !pArg[k+2] ) { bDisplay |= 1; k++; ip->bDisplayEachComponentINChI = 1; } else if ( !pArg[k+1] ) { bDisplay |= 1; } break; case 'W': if ( pArg[k+1] == 'D' ) { /* restore Display Time functionality */ c = 'D'; k ++; } t = strtod( pArg+k+1, (char**)&q ); /* cast deliberately discards 'const' qualifier */ if ( q > pArg+k+1 && errno == ERANGE || t < 0.0 || t*1000.0 > (double)ULONG_MAX) { ul = 0; } else { ul = (unsigned long)(t*1000.0); } if ( /*q > pArg+k &&*/ !*q ) { k = q - pArg - 1; /* k will be incremented by the for() cycle */ switch( c ) { case 'D': *ulDisplTime = ul; break; case 'W': ip->msec_MaxTime = ul; break; } } break; case 'F': c = (int)strtol( pArg+k+1, (char**)&q, 10 ); /* cast deliberately discards 'const' qualifier */ if ( q > pArg+k && !*q ) { k = q - pArg - 1; if ( abs(c) > 5 ) { nFontSize = -c; /* font size 5 or less is too small */ } } break; default: if ( !pArg[k+1] ) { switch ( c ) { case 'B': nMode |= REQ_MODE_BASIC; nReleaseMode = 0; /*bNotRecognized = bReleaseVersion;*/ bStdFormat = 0; break; case 'T': nMode |= REQ_MODE_TAUT; nReleaseMode = 0; /*bNotRecognized = bReleaseVersion;*/ break; case 'I': nMode |= REQ_MODE_ISO; nReleaseMode = 0; /*bNotRecognized = bReleaseVersion;*/ break; case 'N': nMode |= REQ_MODE_NON_ISO; nReleaseMode = 0; bStdFormat = 0; /*bNotRecognized = bReleaseVersion;*/ break; case 'S': nMode |= REQ_MODE_STEREO; nReleaseMode = 0; /*bNotRecognized = bReleaseVersion;*/ break; case 'E': if ( nReleaseMode & REQ_MODE_STEREO ) { nReleaseMode ^= REQ_MODE_STEREO; bStdFormat = 0; } break; #ifndef TARGET_LIB_FOR_WINCHI default: inchi_ios_eprint(log_file, "Unrecognized option: \"%c\".\n", c); #endif } } #ifndef TARGET_LIB_FOR_WINCHI else { inchi_ios_eprint(log_file, "Unrecognized option: \"%c\".\n", c); } #endif } /* if ( bNotRecognized && bNotRecognized == bReleaseVersion ) { inchi_ios_eprint(stderr, "Unrecognized option: \"%c\".\n", c); bNotRecognized = 0; } */ } } /* if ( bNotRecognized && bNotRecognized == 2*bReleaseVersion ) { inchi_ios_eprint(stderr, "Unrecognized option: \"%s\".\n", argv[i]); bNotRecognized = 0; } */ } /*=== end of parsing TARGET_LIB_FOR_WINCHI GUI (and v. 0.9xx Beta)options ===*/ else if ( (bVer1Options & 1) && INCHI_OPTION_PREFX == argv[i][0] && argv[i][1] ) { /*=== parsing stand-alone/library InChI options ===*/ pArg = argv[i] + 1; bRecognizedOption = 2; bVer1Options += 2; /* always on: REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO */ #ifdef CML_DEBUG printf ("1 argv %d %s\n", i, argv[i]); #endif /*--- Input options ---*/ if ( !stricmp( pArg, "STDIO" ) ) { bNameSuffix = 0; } else if ( !stricmp( pArg, "INPAUX" )) { if (INPUT_NONE == ip->nInputType) ip->nInputType = INPUT_INCHI_PLAIN; } else if ( /* INPUT_NONE == ip->nInputType &&*/ !memicmp( pArg, "SDF:", 4 ) ) { /* SDfile label */ k = 0; mystrncpy( ip->szSdfDataHeader, pArg+4, MAX_SDF_HEADER+1 ); LtrimRtrim( ip->szSdfDataHeader, &k ); if ( k ) { ip->pSdfLabel = ip->szSdfDataHeader; ip->pSdfValue = szSdfDataValue; if ( INPUT_NONE == ip->nInputType ) { ip->nInputType = INPUT_SDFILE; } } else { ip->pSdfLabel = NULL; ip->pSdfValue = NULL; if ( INPUT_NONE == ip->nInputType ) { ip->nInputType = INPUT_MOLFILE; } } } #if ( ADD_CMLPP == 1 ) else if ( INPUT_NONE == ip->nInputType && !stricmp( pArg, "CML" ) ) { /* CMLfile label */ ip->nInputType = INPUT_CMLFILE; } #endif else if ( !memicmp( pArg, "START:", 6 ) ) { ip->first_struct_number = strtol(pArg+6, NULL, 10); } else if ( !memicmp( pArg, "END:", 4 ) ) { ip->last_struct_number = strtol(pArg+4, NULL, 10); } #ifdef BUILD_WITH_ENG_OPTIONS else if ( !memicmp( pArg, "RSB:", 4 )) { mdbr = (int)strtol(pArg+4, NULL, 10); } #endif /*--- Output options ---*/ #if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) ) else if ( !stricmp( pArg, "Tabbed" ) ) { bXml |= INCHI_OUT_TABBED_OUTPUT; } #endif else if ( !stricmp( pArg, "NOLABELS" ) ) { bNoStructLabels = 1; } else if ( !stricmp( pArg, "SAVEOPT" ) ) { bINChIOutputOptions |= INCHI_OUT_SAVEOPT; } else if ( !stricmp( pArg, "AUXNONE" ) ) { /* no aux. info */ bINChIOutputOptions |= INCHI_OUT_NO_AUX_INFO; /* no aux info */ bINChIOutputOptions &= ~INCHI_OUT_SHORT_AUX_INFO; } else if ( !stricmp( pArg, "OUTPUTSDF" ) ) { /* output SDfile */ bOutputMolfileOnly = 1; } else if ( !stricmp( pArg, "SdfAtomsDT" ) ) { /* output isotopes H as D and T in SDfile */ bOutputMolfileDT = 1; } else if ( !stricmp( pArg, "D" ) ) { /* display the structures */ bDisplay |= 1; } else if ( !memicmp( pArg, "F", 1 ) && (c = (int)strtol( pArg+1, (char**)&q, 10 ), q > pArg+1) ) { nFontSize = -c; /* struct. display font size */ } else if ( !stricmp( pArg, "EQU" ) ) { bCompareComponents = CMP_COMPONENTS; } /*--- All modes (std and non-std InChI) structure perception options ---*/ else if ( !stricmp( pArg, "SNON" ) ) { bVer1DefaultMode &= ~REQ_MODE_STEREO; /* no stereo */ nMode &= ~(REQ_MODE_RACEMIC_STEREO | REQ_MODE_RELATIVE_STEREO | REQ_MODE_CHIR_FLG_STEREO); } else if ( !stricmp( pArg, "NEWPSOFF" ) ) { bPointedEdgeStereo = 0; } else if ( !stricmp( pArg, "DONOTADDH" ) ) { bDoNotAddH = 1; } /* Non-standard */ #ifndef USE_STDINCHI_API /* Non-std InChI structure perception options */ else if ( !stricmp( pArg, "SREL" ) ) { bVer1DefaultMode |= REQ_MODE_STEREO; /* relative stereo */ nMode &= ~(REQ_MODE_RACEMIC_STEREO | REQ_MODE_CHIR_FLG_STEREO); nMode |= REQ_MODE_RELATIVE_STEREO; bStdFormat = 0; } else if ( !stricmp( pArg, "SRAC" ) ) { /* REQ_MODE_CHIR_FLG_STEREO */ bVer1DefaultMode |= REQ_MODE_STEREO; /* racemic stereo */ nMode &= ~(REQ_MODE_RELATIVE_STEREO | REQ_MODE_CHIR_FLG_STEREO); nMode |= REQ_MODE_RACEMIC_STEREO; bStdFormat = 0; } else if ( !stricmp( pArg, "SUCF" ) ) { bVer1DefaultMode |= REQ_MODE_STEREO; /* stereo defined by the Chiral flag */ nMode &= ~(REQ_MODE_RELATIVE_STEREO | REQ_MODE_RACEMIC_STEREO); nMode |= REQ_MODE_CHIR_FLG_STEREO; bStdFormat = 0; } else if ( !stricmp( pArg, "ChiralFlagON" ) ) { /* used only with /SUCF */ /* NB: do not toggle off bStdFormat! (if necessary SUCF will do) */ bForcedChiralFlag &= ~FLAG_SET_INP_AT_NONCHIRAL; bForcedChiralFlag |= FLAG_SET_INP_AT_CHIRAL; } else if ( !stricmp( pArg, "ChiralFlagOFF" ) ) { /* used only with /SUCF */ /* NB: do not toggle off bStdFormat! (if necessary SUCF will do) */ bForcedChiralFlag &= ~FLAG_SET_INP_AT_CHIRAL; bForcedChiralFlag |= FLAG_SET_INP_AT_NONCHIRAL; } /*--- Non-std InChI creation options ---*/ /* Stereo */ else if ( !stricmp( pArg, "SUU" ) ) { /* include omitted undef/unknown stereo */ bVer1DefaultMode &= ~(REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU); bStdFormat = 0; } else if ( !stricmp( pArg, "SLUUD" ) ) { /* Make labels for unknown and undefined stereo different */ bVer1DefaultMode |= REQ_MODE_DIFF_UU_STEREO; bStdFormat = 0; } /* FixedH */ else if ( !stricmp( pArg, "FIXEDH" ) ) { bVer1DefaultMode |= REQ_MODE_BASIC; /* tautomeric */ bStdFormat = 0; } /* RecMet */ else if ( !stricmp( pArg, "RECMET" ) ) { /* reconnect metals */ bReconnectCoord = 1; bStdFormat = 0; } #if ( KETO_ENOL_TAUT == 1 ) else if ( !stricmp( pArg, "KET" ) ) { bKetoEnolTaut = 1; bStdFormat = 0; } #endif #if ( TAUT_15_NON_RING == 1 ) else if ( !stricmp( pArg, "15T" ) ) { b15TautNonRing = 1; bStdFormat = 0; } #endif #endif /*--- Generation options ---*/ else if ( !memicmp( pArg, "W", 1 ) && (t = strtod( pArg+1, (char**)&q ), q > pArg+1) ) { if ( errno == ERANGE || t < 0.0 || t*1000.0 > (double)ULONG_MAX) { ul = 0; } else { ul = (unsigned long)(t*1000.0); /* max. time per structure */ } ip->msec_MaxTime = ul; } else if ( !stricmp( pArg, "WarnOnEmptyStructure" ) ) { ip->bAllowEmptyStructure = 1; } /* InChIKey/InChI hash */ else if ( !stricmp( pArg, "Key" ) ) { bHashKey = 1; } else if ( !stricmp( pArg, "XHash1" ) ) { bHashXtra1 = 1; } else if ( !stricmp( pArg, "XHash2" ) ) { bHashXtra2 = 1; } /*--- Conversion modes ---*/ #if ( READ_INCHI_STRING == 1 ) else if ( !stricmp( pArg, "InChI2InChI" ) ) { /* Read InChI Identifiers and output InChI Identifiers */ ip->nInputType = INPUT_INCHI; ip->bReadInChIOptions |= READ_INCHI_OUTPUT_INCHI; ip->bReadInChIOptions &= ~READ_INCHI_TO_STRUCTURE; } else if ( !stricmp( pArg, "InChI2Struct" ) ) { /* Split InChI Identifiers into components */ ip->bReadInChIOptions |= READ_INCHI_TO_STRUCTURE; ip->bReadInChIOptions &= ~READ_INCHI_OUTPUT_INCHI; ip->nInputType = INPUT_INCHI; } #ifdef BUILD_WITH_ENG_OPTIONS else if ( !stricmp( pArg, "KeepBalanceP" ) ) { /* When spliting InChI Identifiers into components: */ /* If MobileH output then add p to each component; */ /* Otherwise add one more component containing balance */ /* of protons and exchangeable isotopic H */ ip->bReadInChIOptions |= READ_INCHI_KEEP_BALANCE_P; bStdFormat = 0; } #endif #endif /*--- (engineering) Undo bug/draw fixes options ---*/ #ifdef BUILD_WITH_ENG_OPTIONS else if ( !stricmp( pArg, "FixSp3bugOFF" ) ) { bFixSp3bug = 0; bStdFormat = 0; } else if ( !stricmp( pArg, "FBOFF" ) ) { bFixSp3bug = 0; bStdFormat = 0; } else if ( !stricmp( pArg, "FB2OFF" ) ) { bFixFB2 = 0; bStdFormat = 0; } else if ( !stricmp( pArg, "SPXYZOFF" ) ) { bAddPhosphineStereo = 0; bStdFormat = 0; } else if ( !stricmp( pArg, "SASXYZOFF" ) ) { bAddArsineStereo = 0; bStdFormat = 0; } else if ( !stricmp( pArg, "FNUDOFF" ) ) { ip->bFixNonUniformDraw = 0; bStdFormat = 0; } /*--- (engineering) Old structure-perception and InChI creation options ---*/ #if ( FIX_ADJ_RAD == 1 ) else if ( !stricmp( pArg, "FixRad" ) ) { bFixAdjacentRad = 1; bStdFormat = 0; } #endif #if ( UNDERIVATIZE == 1 ) else if ( !stricmp( pArg, "DoDRV" ) ) { ip->bUnderivatize = 1; bStdFormat = 0; } #endif #if ( RING2CHAIN == 1 ) else if ( !stricmp( pArg, "DoR2C" ) ) { ip->bRing2Chain = 1; bStdFormat = 0; } #endif #if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 ) else if ( !stricmp( pArg, "DoneOnly" ) ) { ip->bIngnoreUnchanged = 1; bStdFormat = 0; } #endif else if ( !memicmp( pArg, "MOVEPOS:", 8 ) ) { bMovePositiveCharges = (0 != strtol(pArg+8, NULL, 10)); bStdFormat = 0; } else if ( !stricmp( pArg, "NoADP" ) ) { bTgFlagHardAddRenProtons = 0; bStdFormat = 0; } /* Tautomer perception off */ else if ( !stricmp( pArg, "EXACT" ) ) { bVer1DefaultMode |= REQ_MODE_BASIC; bStdFormat = 0; } else if ( !stricmp( pArg, "ONLYRECSALT" ) ) { /* do not disconnect salts */ bDisconnectSalts = 0; bStdFormat = 0; } else if ( !stricmp( pArg, "ONLYEXACT" ) || !stricmp( pArg, "ONLYFIXEDH" ) ) { bVer1DefaultMode |= REQ_MODE_BASIC; bVer1DefaultMode &= ~REQ_MODE_TAUT; bStdFormat = 0; } else if ( !stricmp( pArg, "ONLYNONISO" ) ) { bVer1DefaultMode |= REQ_MODE_NON_ISO; bVer1DefaultMode &= ~REQ_MODE_ISO; bStdFormat = 0; } else if ( !stricmp( pArg, "TAUT" ) ) { bVer1DefaultMode &= ~REQ_MODE_BASIC; bVer1DefaultMode |= REQ_MODE_TAUT; } else if ( !stricmp( pArg, "ONLYRECMET" ) ) { /* do not disconnect metals */ bDisconnectCoord = 0; bStdFormat = 0; } /*--- (hidden) Old output and other options ---*/ else if ( !stricmp( pArg, "SdfSplit" ) ) { /* Split single Molfiles into disconnected components */ bOutputMolfileSplit = 1; } else if ( !stricmp( pArg, "DCR" ) ) { bDisplayCompositeResults = 1; } else if ( !stricmp( pArg, "AUXFULL" ) || !stricmp( pArg, "AUXMAX" ) ) { /* full aux info */ bINChIOutputOptions &= ~(INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO); /* include short aux info */ } else if ( !stricmp( pArg, "AUXMIN" ) ) { /* minimal aux info */ bINChIOutputOptions &= ~INCHI_OUT_NO_AUX_INFO; /* include short aux info */ bINChIOutputOptions |= INCHI_OUT_SHORT_AUX_INFO; } #if ( READ_INCHI_STRING == 1 ) else if ( !stricmp( pArg, "DDSRC" ) ) { bDisplayIfRestoreWarnings = 1; /* InChI->Structure debugging: Display Debug Structure Restore Components */ } #endif else if ( !stricmp( pArg, "NoVarH" ) ) { bTgFlagVariableProtons = 0; } else if ( !stricmp( pArg, "FULL" ) ) { bVer1DefaultMode = VER103_DEFAULT_MODE; nMode = 0; bReconnectCoord = 1; /* full output */ bINChIOutputOptions = ((EMBED_REC_METALS_INCHI==1)? INCHI_OUT_EMBED_REC : 0) | INCHI_OUT_SHORT_AUX_INFO; ip->bCtPredecessors = 0; ip->bAbcNumbers = 0; bXml |= INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS; bXml &= ~(INCHI_OUT_XML | INCHI_OUT_XML_TEXT_COMMENTS); } else if ( !stricmp( pArg, "MIN" ) ) { bVer1DefaultMode = VER103_DEFAULT_MODE; nMode = 0; bReconnectCoord = 1; /* minimal output */ bINChIOutputOptions = ((EMBED_REC_METALS_INCHI==1)? INCHI_OUT_EMBED_REC : 0) | INCHI_OUT_NO_AUX_INFO; /* minimal compressed output */ ip->bCtPredecessors = 1; ip->bAbcNumbers = 1; bXml |= INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS; bXml &= ~(INCHI_OUT_XML | INCHI_OUT_XML_TEXT_COMMENTS); } else if ( !stricmp( pArg, "COMPRESS" ) ) { ip->bAbcNumbers = 1; ip->bCtPredecessors = 1; /* compressed output */ } #if ( READ_INCHI_STRING == 1 ) else if ( !stricmp( pArg, "InChI2InChI" ) ) { /* Read InChI Identifiers and output InChI Identifiers */ ip->nInputType = INPUT_INCHI; ip->bReadInChIOptions |= READ_INCHI_OUTPUT_INCHI; ip->bReadInChIOptions &= ~READ_INCHI_TO_STRUCTURE; } else if ( !stricmp( pArg, "SplitInChI" ) ) { /* Split InChI Identifiers into components */ ip->bReadInChIOptions |= READ_INCHI_SPLIT_OUTPUT; } #endif else if ( !stricmp( pArg, "MOLFILENUMBER" ) ) { ip->bGetMolfileNumber |= 1; } else if ( !stricmp( pArg, "OutputPLAIN" ) ) { bXml |= INCHI_OUT_PLAIN_TEXT; bXml &= ~INCHI_OUT_XML; } else if ( !stricmp( pArg, "OutputXML" ) ) { bXml |= INCHI_OUT_XML; bXml &= ~INCHI_OUT_PLAIN_TEXT; } else if ( !stricmp( pArg, "OutputANNPLAIN" ) ) { bXml |= INCHI_OUT_PLAIN_TEXT_COMMENTS; bXml &= ~INCHI_OUT_XML_TEXT_COMMENTS; bXml |= INCHI_OUT_WINCHI_WINDOW; /* debug */ } else if ( !stricmp( pArg, "OutputANNXML" ) ) { bXml |= INCHI_OUT_XML_TEXT_COMMENTS; bXml &= ~INCHI_OUT_PLAIN_TEXT_COMMENTS; } else if ( !stricmp( pArg, "ONLYEXACT" ) || !stricmp( pArg, "ONLYFIXEDH" ) ) { bVer1DefaultMode |= REQ_MODE_BASIC; bVer1DefaultMode &= ~REQ_MODE_TAUT; } else if ( !stricmp( pArg, "ONLYNONISO" ) ) { bVer1DefaultMode |= REQ_MODE_NON_ISO; bVer1DefaultMode &= ~REQ_MODE_ISO; } else if ( !stricmp( pArg, "TAUT" ) ) { bVer1DefaultMode &= ~REQ_MODE_BASIC; bVer1DefaultMode |= REQ_MODE_TAUT; } else if ( !stricmp( pArg, "ONLYRECMET" ) ) { /* do not disconnect metals */ bDisconnectCoord = 0; } else if ( !stricmp( pArg, "ONLYRECSALT" ) ) { /* do not disconnect salts */ bDisconnectSalts = 0; } else if ( !memicmp( pArg, "MOVEPOS:", 8 ) ) { /* added -- 2010-03-01 DT */ bMovePositiveCharges = (0 != strtol(pArg+8, NULL, 10)); } else if ( !memicmp( pArg, "RSB:", 4 )) { mdbr = (int)strtol(pArg+4, NULL, 10); } else if ( !stricmp( pArg, "EQU" ) ) { bCompareComponents = CMP_COMPONENTS; } else if ( !stricmp( pArg, "EQUNONISO" ) ) { bCompareComponents = CMP_COMPONENTS | CMP_COMPONENTS_NONISO; } else if ( !memicmp( pArg, "OP:", 3 ) ) { bOutputPath = 1; strncpy(szOutputPath, pArg+3, sizeof(szOutputPath)-1); } #endif /* BUILD_WITH_ENG_OPTIONS */ /* Display unrecognized option */ else { bRecognizedOption = 0; #ifndef TARGET_LIB_FOR_WINCHI inchi_ios_eprint(log_file, "Unrecognized option: \"%s\".\n", pArg); #endif } bVer1Options |= bRecognizedOption; } /*=== end of parsing stand-alone/library InChI options ===*/ else if ( ip->num_paths < MAX_NUM_PATHS ) { char *sz; if ( argv[i] && argv[i][0] ) { if ( sz = (char*) inchi_malloc( (strlen(argv[i]) + 1)*sizeof(sz[0])) ) { strcpy( sz, argv[i] ); } #ifdef CML_DEBUG printf ("1 path %d argv %d %s\n", ip -> num_paths, i, argv [i]); #endif ip->path[ip->num_paths++] = sz; } } } /* for ( i = 1; i < argc; i ++ ) */ if ( bHashKey != 0 ) /* Suppress InChIKey calculation if: compressed output OR Inchi2Struct OR Inchi2Inchi */ { if ( (ip->bAbcNumbers ==1) && (ip->bCtPredecessors == 1) ) { #ifndef TARGET_LIB_FOR_WINCHI inchi_ios_eprint(log_file, "Terminating: generation of InChIKey is not available with 'Compress' option\n"); return -1; #endif bHashKey = 0; } if ( ip->nInputType == INPUT_INCHI ) { #ifndef TARGET_LIB_FOR_WINCHI inchi_ios_eprint(log_file, "Terminating: generation of InChIKey is not available in InChI conversion mode\n"); return -1; #endif bHashKey = 0; } else if ( bOutputMolfileOnly == 1 ) { #ifndef TARGET_LIB_FOR_WINCHI inchi_ios_eprint(log_file, "Terminating: generation of InChIKey is not available with 'OutputSDF' option\n"); return -1; #endif bHashKey = 0; } } if ( bNameSuffix || bOutputPath ) { const char *p = NULL; char *r = NULL; char *sz; int len; const char szNUL[] = "NUL"; /* fix for AMD processor: use const char[] instead of just "NUL" constant 2008-11-5 DT */ /* find the 1st path */ for ( i = 0; i < MAX_NUM_PATHS; i ++ ) { if ( !p && ip->path[i] && ip->path[i][0] ) { p = ip->path[i]; break; } } /* fix output path */ if ( bOutputPath && szOutputPath[0] && p ) { /* remove last slash */ len = strlen(szOutputPath); if ( len > 0 && szOutputPath[len-1] != INCHI_PATH_DELIM ) { szOutputPath[len++] = INCHI_PATH_DELIM; szOutputPath[len] = '\0'; } if ( len > 0 && (r = (char *)strrchr( p, INCHI_PATH_DELIM ) ) && r[1] ) { strcat( szOutputPath, r+1 ); p = szOutputPath; } } /* add missing paths */ for ( i = 0; p && i < MAX_NUM_PATHS; i ++ ) { /* fix for AMD processor: changed order 2008-11-5 DT */ if ( !ip->path[i] || !ip->path[i][0] ) { len = strlen( p ) + strlen(szNameSuffix) + strlen( ext[i] ); if ( sz = (char*) inchi_malloc( (len+1)*sizeof(sz[0]) ) ) { strcpy( sz, p ); strcat( sz, szNameSuffix ); strcat( sz, ext[i] ); ip->num_paths++; ip->path[i] =sz; } } else if ( !stricmp( ip->path[i], szNUL ) ) { inchi_free( (char *)ip->path[i] ); /* cast deliberately const qualifier */ ip->path[i] = NULL; } } } #if ( READ_INCHI_STRING == 1 ) if ( INPUT_INCHI == ip->nInputType ) { bCompareComponents = 0; /*bDisplayCompositeResults = 0;*/ #if ( I2S_MODIFY_OUTPUT == 1 ) if ( !(ip->bReadInChIOptions & READ_INCHI_TO_STRUCTURE ) ) #endif { bOutputMolfileOnly = 0; /*bNoStructLabels = 1;*/ bINChIOutputOptions |= INCHI_OUT_NO_AUX_INFO; bINChIOutputOptions &= ~INCHI_OUT_SHORT_AUX_INFO; bINChIOutputOptions &= ~INCHI_OUT_ONLY_AUX_INFO; } ip->bDisplayIfRestoreWarnings = bDisplayIfRestoreWarnings; if ( !(bINChIOutputOptions & (INCHI_OUT_SDFILE_ONLY | /* not in bINChIOutputOptions yet */ INCHI_OUT_XML | /* not in bINChIOutputOptions yet */ INCHI_OUT_PLAIN_TEXT | /* not in bINChIOutputOptions yet */ INCHI_OUT_PLAIN_TEXT_COMMENTS | /* not in bINChIOutputOptions yet */ INCHI_OUT_XML_TEXT_COMMENTS /* not in bINChIOutputOptions yet */ ) ) #if ( I2S_MODIFY_OUTPUT == 1 ) && !bOutputMolfileOnly && !(bXml & (INCHI_OUT_XML | INCHI_OUT_XML_TEXT_COMMENTS | INCHI_OUT_PLAIN_TEXT | INCHI_OUT_XML_TEXT_COMMENTS)) #endif ) { bINChIOutputOptions |= INCHI_OUT_PLAIN_TEXT; } } #endif if ( bVer1Options ) { nMode |= bVer1DefaultMode; } else if ( bReleaseVersion ) { nMode |= nReleaseMode; } #if ( defined(COMPILE_ANSI_ONLY) || defined(TARGET_LIB_FOR_WINCHI) ) if ( bCompareComponents && !(bDisplay & 1) ) { bCompareComponents = 0; } #endif /* Save original options */ /* nOrigMode = nMode; */ #ifndef COMPILE_ANSI_ONLY ip->dp.sdp.nFontSize = nFontSize; ip->dp.sdp.ulDisplTime = *ulDisplTime; ip->bDisplay = bDisplay; #ifdef TARGET_LIB_FOR_WINCHI ip->bDisplayCompositeResults = bDisplay; #else ip->bDisplayCompositeResults = bDisplayCompositeResults; #endif #else ip->bDisplayEachComponentINChI = 0; bCompareComponents = 0; #endif ip->bMergeAllInputStructures = bMergeAllInputStructures; ip->bDoNotAddH = bDoNotAddH; /* set default options */ if ( !nMode || nMode == REQ_MODE_STEREO ) { /* requested all output */ nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO); } else { if ( !(nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) ) { nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT); } if ( (nMode & REQ_MODE_STEREO) && !(nMode & (REQ_MODE_ISO | REQ_MODE_NON_ISO)) ) { nMode |= (REQ_MODE_ISO | REQ_MODE_NON_ISO); } } /* if the user requested isotopic then unconditionally add non-isotopic output. */ if ( nMode & REQ_MODE_ISO ) { nMode |= REQ_MODE_NON_ISO; } #if ( MIN_SB_RING_SIZE > 0 ) if ( mdbr ) { nMinDbRinSize = mdbr; } nMode |= (nMinDbRinSize << REQ_MODE_MIN_SB_RING_SHFT) & REQ_MODE_MIN_SB_RING_MASK; #endif /* input file */ if ( ip->nInputType == INPUT_NONE && ip->num_paths > 0 ) { ip->nInputType = INPUT_MOLFILE; /* default */ #if ( ADD_CMLPP == 1 ) { const char *p; if ( ip->path[0] && ( p = strrchr(ip->path[0], '.' ) ) && !stricmp( p, ".cml") ) { ip->nInputType = INPUT_CMLFILE; } } #endif } ip->nMode = nMode; if ( (bCompareComponents & CMP_COMPONENTS) && (nMode & REQ_MODE_BASIC) ) { bCompareComponents |= CMP_COMPONENTS_NONTAUT; /* compare non-tautomeric */ } ip->bCompareComponents = bCompareComponents; ip->bINChIOutputOptions = bINChIOutputOptions | (bOutputMolfileOnly? INCHI_OUT_SDFILE_ONLY : 0); if ( bOutputMolfileOnly ) { bXml &= ~(INCHI_OUT_XML | INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS | INCHI_OUT_XML_TEXT_COMMENTS | INCHI_OUT_TABBED_OUTPUT); #if ( SDF_OUTPUT_DT == 1 ) ip->bINChIOutputOptions |= bOutputMolfileDT? INCHI_OUT_SDFILE_ATOMS_DT : 0; ip->bINChIOutputOptions |= bOutputMolfileSplit? INCHI_OUT_SDFILE_SPLIT : 0; #endif } if ( bXml & INCHI_OUT_XML ) { bXml &= ~(INCHI_OUT_PLAIN_TEXT | INCHI_OUT_XML_TEXT_COMMENTS | INCHI_OUT_TABBED_OUTPUT); } #ifdef TARGET_LIB_FOR_WINCHI if ( !(bDisplay & 1) ) { bXml &= ~(INCHI_OUT_PLAIN_TEXT_COMMENTS | INCHI_OUT_XML_TEXT_COMMENTS); /* do not ouput comments in wINChI text file results */ } else { bXml |= INCHI_OUT_WINCHI_WINDOW; } #endif ip->bINChIOutputOptions |= bXml; ip->bNoStructLabels = bNoStructLabels; if ( bForcedChiralFlag ) { ip->bChiralFlag = bForcedChiralFlag; } /*******************************************/ /* tautomeric/salts settings */ /*******************************************/ ip->bTautFlags = 0; /* initialize */ ip->bTautFlagsDone = 0; /* initialize */ /* find regular tautomerism */ ip->bTautFlags |= TG_FLAG_TEST_TAUT__ATOMS; /* disconnect salts */ ip->bTautFlags |= bDisconnectSalts? TG_FLAG_DISCONNECT_SALTS : 0; /* if possible find long-range H/(-) taut. on =C-OH, >C=O */ ip->bTautFlags |= bAcidTautomerism? TG_FLAG_TEST_TAUT__SALTS : 0; /* allow long-range movement of N(+), P(+) charges */ ip->bTautFlags |= bMovePositiveCharges? TG_FLAG_MOVE_POS_CHARGES : 0; /* multi-attachement long-range H/(-) taut. on =C-OH, >C=O */ ip->bTautFlags |= (bAcidTautomerism > 1)? TG_FLAG_TEST_TAUT2_SALTS : 0; /* (debug) allow to find long-range H-only tautomerism on =C-OH, >C=O */ ip->bTautFlags |= (bUnchargedAcidTaut==1)? TG_FLAG_ALLOW_NO_NEGTV_O : 0; /* merge =C-OH and >C=O containing t-groups and other =C-OH groups */ ip->bTautFlags |= bMergeSaltTGroups? TG_FLAG_MERGE_TAUT_SALTS : 0; ip->bTautFlags |= bDisconnectCoord? TG_FLAG_DISCONNECT_COORD : 0; ip->bTautFlags |=(bDisconnectCoord && bReconnectCoord)? TG_FLAG_RECONNECT_COORD : 0; ip->bTautFlags |= bDisconnectCoordChkVal? TG_FLAG_CHECK_VALENCE_COORD : 0; ip->bTautFlags |= bTgFlagVariableProtons? TG_FLAG_VARIABLE_PROTONS : 0; ip->bTautFlags |= bTgFlagHardAddRenProtons? TG_FLAG_HARD_ADD_REM_PROTONS : 0; ip->bTautFlags |= bKetoEnolTaut? TG_FLAG_KETO_ENOL_TAUT : 0; ip->bTautFlags |= b15TautNonRing? TG_FLAG_1_5_TAUT : 0; #ifdef STEREO_WEDGE_ONLY ip->bTautFlags |= bPointedEdgeStereo? TG_FLAG_POINTED_EDGE_STEREO : 0; #endif #if ( FIX_ADJ_RAD == 1 ) ip->bTautFlags |= bFixAdjacentRad? TG_FLAG_FIX_ADJ_RADICALS : 0; #endif ip->bTautFlags |= bAddPhosphineStereo? TG_FLAG_PHOSPHINE_STEREO : 0; ip->bTautFlags |= bAddArsineStereo? TG_FLAG_ARSINE_STEREO : 0; ip->bTautFlags |= bFixSp3bug? TG_FLAG_FIX_SP3_BUG : 0; if (bFixFB2) { #if ( FIX_ISO_FIXEDH_BUG == 1 ) ip->bTautFlags |= TG_FLAG_FIX_ISO_FIXEDH_BUG; /* accomodate FIX_ISO_FIXEDH_BUG */ #endif #if ( FIX_TERM_H_CHRG_BUG == 1 ) ip->bTautFlags |= TG_FLAG_FIX_TERM_H_CHRG_BUG; /* accomodate FIX_TERM_H_CHRG_BUG */ #endif #if ( FIX_TRANSPOSITION_CHARGE_BUG == 1 ) ip->bINChIOutputOptions |= INCHI_OUT_FIX_TRANSPOSITION_CHARGE_BUG; #endif } if ( !ip->nInputType ) ip->nInputType = INPUT_MOLFILE; /* Check if /SNon requested turn OFF SUU/SLUUD */ if ( ! (ip->nMode & REQ_MODE_STEREO) ) { ip->nMode &= ~REQ_MODE_DIFF_UU_STEREO; ip->nMode &= ~(REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU); } /* Standard InChI ? */ if (bStdFormat) { ip->bINChIOutputOptions |= INCHI_OUT_STDINCHI; } /* InChIKey ? */ if ( !bHashKey ) ip->bCalcInChIHash = INCHIHASH_NONE; else ip->bCalcInChIHash = INCHIHASH_KEY; /* Extension(s) to hash (in non-std mode only) ? */ if ( !bHashKey ) { if ( (bHashXtra1!=0) || (bHashXtra2!=0) ) inchi_ios_eprint(log_file, "Hash extension(s) not generated: InChIKey not requested"); } else { if ( bHashXtra1 ) { if ( bHashXtra2 ) ip->bCalcInChIHash = INCHIHASH_KEY_XTRA1_XTRA2; else ip->bCalcInChIHash = INCHIHASH_KEY_XTRA1; } else if ( bHashXtra2 ) { ip->bCalcInChIHash = INCHIHASH_KEY_XTRA2; } } return 0; } /*******************************************************************/ int PrintInputParms( INCHI_IOSTREAM *log_file, INPUT_PARMS *ip ) { INCHI_MODE nMode = ip->nMode; int k; int bStdFormat = 1; int first=1; #ifdef TARGET_LIB_FOR_WINCHI int bInChI2Struct = 0; /* as of December 2008, winchi-1 does not convert InChI to structure */ #else int bInChI2Struct = (ip->bReadInChIOptions & READ_INCHI_TO_STRUCTURE) && ip->nInputType == INPUT_INCHI; #endif if ( !(ip->bINChIOutputOptions & INCHI_OUT_STDINCHI) ) bStdFormat = 0; /* some stereo */ if ( ! (nMode & REQ_MODE_STEREO) ) { inchi_ios_eprint( log_file, "Using specific structure perception features:\n"); first = 0; inchi_ios_eprint( log_file, " Stereo OFF\n"); } else { if ( ! (TG_FLAG_POINTED_EDGE_STEREO & ip->bTautFlags) ) { if (first) { inchi_ios_eprint( log_file, "Using specific structure perception features:\n"); first = 0; } inchi_ios_eprint( log_file, " Both ends of wedge point to stereocenters\n"); } } if ( ip->bDoNotAddH ) { if (first) inchi_ios_eprint( log_file, "Using specific structure perception features:\n"); inchi_ios_eprint( log_file, " Do not add H\n"); } /* Generation/conversion indicator */ if (bStdFormat) { if ( !(ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) && !bInChI2Struct ) inchi_ios_eprint( log_file, "Generating standard InChI\n" ); #if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) && !defined(TARGET_EXE_USING_API) ) /* effective only in command line program InChI or stdInChI */ else if ( bInChI2Struct ) inchi_ios_eprint( log_file, "Converting InChI(s) to structure(s) in %s\n", (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY)? "MOL format" : "aux. info format" ); #endif } else inchi_ios_eprint( log_file, "Generating non-standard InChI with the options: \n" ); /* SDfile output */ if ( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY ) { inchi_ios_eprint( log_file, "Output SDfile only without stereochemical information and atom coordinates%s\n", (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ATOMS_DT)? "\n(write H isotopes as D, T)":"" ); } /* Fixed/Mobile H */ if (!bStdFormat) { if( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT )) == (REQ_MODE_BASIC | REQ_MODE_TAUT) ) inchi_ios_eprint( log_file, " Mobile H Perception OFF (include FixedH layer)\n" ); else if( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT )) == (REQ_MODE_TAUT) ) inchi_ios_eprint( log_file, " Mobile H Perception ON (omit FixedH layer)\n" ); else if( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT )) == (REQ_MODE_BASIC) ) inchi_ios_eprint( log_file, " Mobile H ignored\n" ); else inchi_ios_eprint( log_file, " Undefined Mobile H mode\n" ); if ( (ip->bTautFlags & TG_FLAG_VARIABLE_PROTONS) ) if ( !(ip->bTautFlags & TG_FLAG_HARD_ADD_REM_PROTONS) ) inchi_ios_eprint( log_file, " Disabled Aggressive (De)protonation\n" ); #if ( FIND_RING_SYSTEMS != 1 ) inchi_ios_eprint( log_file, " %s5-, 6-, 7-memb. ring taut. ignored\n", i?"; ":""); #endif /* RecMet */ if ( ip->bTautFlags & TG_FLAG_DISCONNECT_COORD ) { if ( ip->bTautFlags & TG_FLAG_RECONNECT_COORD ) inchi_ios_eprint( log_file, " Include bonds to metals\n"); else inchi_ios_eprint( log_file, " Do not reconnect metals (omit RecMet layer)\n"); } else inchi_ios_eprint( log_file, " Do not disconnect metals\n"); /* isotopic - always ON, output disabled. 09-17-2009*/ /* if ( nMode & REQ_MODE_ISO ) inchi_ios_eprint( log_file, " Isotopic ON\n"); else if ( nMode & REQ_MODE_NON_ISO ) inchi_ios_eprint( log_file, " Isotopic OFF\n"); */ #if ( FIX_ADJ_RAD == 1 ) if ( ip->bTautFlags & TG_FLAG_FIX_ADJ_RADICALS ) inchi_ios_eprint( log_file, "Fix Adjacent Radicals\n" ); #endif /* stereo */ if ( nMode & REQ_MODE_STEREO ) { inchi_ios_eprint( log_file, " %s%s%s%sStereo ON\n", ( nMode & REQ_MODE_NOEQ_STEREO )? "Slow ":"", ( nMode & REQ_MODE_REDNDNT_STEREO )? "Redund. ":"", ( nMode & REQ_MODE_NO_ALT_SBONDS)? "No AltBond ":"", ( nMode & REQ_MODE_RACEMIC_STEREO)? "Racemic " : ( nMode & REQ_MODE_RELATIVE_STEREO)? "Relative " : ( nMode & REQ_MODE_CHIR_FLG_STEREO)? "Chiral Flag " : "Absolute " ); if ( 0 == (nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) inchi_ios_eprint( log_file, " Include undefined/unknown stereogenic centers and bonds\n"); else if ( REQ_MODE_SC_IGN_ALL_UU == (nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) inchi_ios_eprint( log_file, " Omit undefined/unknown stereogenic centers\n"); else if ( REQ_MODE_SB_IGN_ALL_UU == (nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) inchi_ios_eprint( log_file, " Omit undefined/unknown stereogenic bonds\n"); else /*case REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU*/ inchi_ios_eprint( log_file, " Omit undefined/unknown stereogenic centers and bonds\n"); if ( 0 != (nMode & REQ_MODE_DIFF_UU_STEREO) ) { inchi_ios_eprint( log_file, " Make labels for unknown and undefined stereo different\n"); } #if ( defined(MIN_SB_RING_SIZE) && MIN_SB_RING_SIZE > 0 ) k = (ip->nMode & REQ_MODE_MIN_SB_RING_MASK) >> REQ_MODE_MIN_SB_RING_SHFT; if ( bRELEASE_VERSION != 1 || k != MIN_SB_RING_SIZE ) { if ( k >= 3 ) inchi_ios_eprint( log_file, " Min. stereobond ring size: %d\n", k ); else inchi_ios_eprint( log_file, " Min. stereobond ring size: NONE\n" ); } #endif } /* stereo */ } /* !bStdFormat */ if ( !bStdFormat ) { if ( TG_FLAG_KETO_ENOL_TAUT & ip->bTautFlags) inchi_ios_eprint( log_file, " Account for keto-enol tautomerism\n"); else inchi_ios_eprint( log_file, " Do not account for keto-enol tautomerism\n"); if ( TG_FLAG_1_5_TAUT & ip->bTautFlags) inchi_ios_eprint( log_file, " Account for 1,5-tautomerism\n"); else inchi_ios_eprint( log_file, " Do not account for 1,5-tautomerism\n"); #ifdef BUILD_WITH_ENG_OPTIONS if ( TG_FLAG_PHOSPHINE_STEREO & ip->bTautFlags ) inchi_ios_eprint( log_file, " Include phosphine stereochemistry\n"); else inchi_ios_eprint( log_file, " Do not include phosphine stereochemistry\n"); if ( TG_FLAG_ARSINE_STEREO & ip->bTautFlags ) inchi_ios_eprint( log_file, " Include arsine stereochemistry\n"); else inchi_ios_eprint( log_file, " Do not include arsine stereochemistry\n"); if ( ! (TG_FLAG_FIX_SP3_BUG & ip->bTautFlags) ) inchi_ios_eprint( log_file, " Turned OFF fix of bug leading to missing or undefined sp3 parity\n"); if ( !(TG_FLAG_FIX_ISO_FIXEDH_BUG & ip->bTautFlags) ) inchi_ios_eprint( log_file, " Turned OFF bug-fixes found after v.1.02b release\n"); if ( !(ip->bFixNonUniformDraw) ) inchi_ios_eprint( log_file, " Turned OFF fixes of non-uniform drawing issues\n"); if ( ! (TG_FLAG_MOVE_POS_CHARGES & ip->bTautFlags) ) inchi_ios_eprint( log_file, " MovePos turned OFF\n"); #endif } /* !bStdFormat */ if ( ip->bCalcInChIHash != INCHIHASH_NONE ) { if (bStdFormat) inchi_ios_eprint( log_file, "Generating standard InChIKey\n"); else inchi_ios_eprint( log_file, "Generating InChIKey\n"); if ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1 ) inchi_ios_eprint( log_file, "Generating hash extension (1st block)\n"); else if ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA2 ) inchi_ios_eprint( log_file, "Generating hash extension (2nd block)\n"); else if ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1_XTRA2 ) inchi_ios_eprint( log_file, "Generating hash extension (two blocks)\n"); } if ( ip->bINChIOutputOptions & INCHI_OUT_SAVEOPT ) { inchi_ios_eprint( log_file, "Saving InChI creation options" ); if ( bStdFormat ) { inchi_ios_eprint( log_file, " suppressed for standard InChI" ); /* NB: actual suppression takes place on InChI serialization */ /* (as on e.g. Inchi2Inchi conversion it may appear that we create non-std */ /* InChI instead of standard one) */ } inchi_ios_eprint( log_file, "\n" ); } if ( ip->bAllowEmptyStructure ) inchi_ios_eprint( log_file, "Issue warning on empty structure\n" ); /* Input */ if ( ip->nInputType ) { inchi_ios_eprint( log_file, "Input format: %s", ip->nInputType == INPUT_MOLFILE? "MOLfile" : ip->nInputType == INPUT_SDFILE? "SDfile" : ip->nInputType == INPUT_CMLFILE? "CMLfile" : #if ( READ_INCHI_STRING == 1 ) ip->nInputType == INPUT_INCHI? "InChI (plain identifier)" : #endif ip->nInputType == INPUT_INCHI_XML? "InChI AuxInfo (xml)" : ip->nInputType == INPUT_INCHI_PLAIN? "InChI AuxInfo (plain)" : "Unknown" ); if ( (ip->nInputType == INPUT_MOLFILE || ip->nInputType == INPUT_SDFILE) && ip->bGetMolfileNumber ) inchi_ios_eprint( log_file, " (attempting to read Molfile number)" ); inchi_ios_eprint( log_file, "\n"); } if ( ip->szSdfDataHeader[0] && ip->nInputType != INPUT_SDFILE ) inchi_ios_eprint( log_file, " SDfile data header: \"%s\"\n", ip->szSdfDataHeader); /* Output */ inchi_ios_eprint( log_file, "Output format: %s%s\n", (ip->bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT)? "Plain text" : (ip->bINChIOutputOptions & INCHI_OUT_XML)? "XML": ((ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) && bInChI2Struct )? "SDfile only (without stereochemical info and atom coordinates)" : ((ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) && !bInChI2Struct)? "SDfile only" : "Unknown", ((ip->bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT) && (ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT))? ", tabbed":""); #if ( bRELEASE_VERSION == 1 ) if ( ip->bCtPredecessors || ip->bAbcNumbers ) { if ( ip->bCtPredecessors && ip->bAbcNumbers ) inchi_ios_eprint( log_file, "Representation: Compressed\n"); else inchi_ios_eprint( log_file, "Connection table: %s, %s\n", ip->bCtPredecessors? "Predecessor_numbers(closures)":"Canon_numbers(branching, ring closures)", ip->bAbcNumbers? "Shorter alternative":"Numerical"); } #else if ( (bRELEASE_VERSION != 1) || ip->bCtPredecessors || ip->bAbcNumbers ) inchi_ios_eprint( log_file, "Connection table: %s, %s\n", ip->bCtPredecessors? "Predecessor_numbers(closures)":"Canon_numbers(branching, ring closures)", ip->bAbcNumbers? "Shorter alternative":"Numerical"); else inchi_ios_eprint( log_file, "Representation: Numerical"); #endif if ( !(ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) ) { if( ip->bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO ) inchi_ios_eprint( log_file, "Aux. info suppressed\n"); else if ( ip->bINChIOutputOptions & INCHI_OUT_SHORT_AUX_INFO ) inchi_ios_eprint( log_file, "Minimal Aux. info\n"); else inchi_ios_eprint( log_file, "Full Aux. info\n"); } if ( ip->msec_MaxTime ) { unsigned long seconds = ip->msec_MaxTime/1000; unsigned long milliseconds = (ip->msec_MaxTime%1000); inchi_ios_eprint( log_file, "Timeout per structure: %lu.%03lu sec\n", seconds, milliseconds); } else inchi_ios_eprint( log_file, "No timeout"); inchi_ios_eprint( log_file, "Up to %d atoms per structure\n", MAX_ATOMS); if ( ip->first_struct_number > 1 ) inchi_ios_eprint( log_file, "Skipping %ld structure%s\n", ip->first_struct_number-1, ip->first_struct_number==2? "":"s" ); if ( ip->last_struct_number > 0 ) inchi_ios_eprint( log_file, "Terminate after structure #%ld\n", ip->last_struct_number ); if ( ip->bSaveWarningStructsAsProblem && ip->path[3] && ip->path[3][0] ) inchi_ios_eprint( log_file, "Saving warning structures into the problem file\n"); if ( ip->bSaveAllGoodStructsAsProblem && ip->path[3] && ip->path[3][0] ) inchi_ios_eprint( log_file, "Saving only all good structures into the problem file\n"); /* Report debug modes */ #if ( bRELEASE_VERSION != 1 ) inchi_ios_eprint( log_file, "Release version = NO\n"); #endif #if ( TRACE_MEMORY_LEAKS == 1 && defined(_DEBUG) ) inchi_ios_eprint( log_file, "Tracing memory leaks (SLOW)\n"); #endif inchi_ios_eprint( log_file, "\n" ); #if ( bRELEASE_VERSION != 1 ) #if ( FIND_RING_SYSTEMS == 1 ) inchi_ios_eprint( log_file, "Find ring systems=Y\nTautomers:\n" ); inchi_ios_eprint( log_file, " 4-pyridinol=%s\n", TAUT_4PYRIDINOL_RINGS==1? "Y":"N"); inchi_ios_eprint( log_file, " pyrazole=%s\n", TAUT_PYRAZOLE_RINGS==1? "Y":"N"); inchi_ios_eprint( log_file, " tropolone=%s\n", TAUT_TROPOLONE_7==1? "Y":"N"); inchi_ios_eprint( log_file, " tropolone-5=%s\n", TAUT_TROPOLONE_5==1? "Y":"N"); inchi_ios_eprint( log_file, "Only chain attachments to tautomeric rings=%s\n", TAUT_RINGS_ATTACH_CHAIN==1? "Y":"N"); #endif if ( ip->bGetSdfileId ) inchi_ios_eprint( log_file, "Extracting SDfile IDs\n"); inchi_ios_eprint( log_file, "\nDbg: MOVE_CHARGES=%d\n", 0!=(ip->bTautFlags&TG_FLAG_MOVE_POS_CHARGES)); inchi_ios_eprint( log_file, " REPLACE_ALT_WITH_TAUT=%d; NEUTRALIZE_ENDPOINTS=%d; BNS_PROTECT_FROM_TAUT=%d\n", REPLACE_ALT_WITH_TAUT, NEUTRALIZE_ENDPOINTS, BNS_PROTECT_FROM_TAUT); inchi_ios_eprint( log_file, " DISCONNECT_SALTS=%d; TEST_TAUT_SALTS=%d; TEST_TAUT2_SALTS=%d\n", 0!=(ip->bTautFlags&TG_FLAG_DISCONNECT_SALTS), 0!=(ip->bTautFlags&TG_FLAG_TEST_TAUT__SALTS), 0!=(ip->bTautFlags&TG_FLAG_TEST_TAUT2_SALTS)); inchi_ios_eprint( log_file, " CHARGED_ACID_TAUT_ONLY=%d MERGE_TAUT_SALTS=%d\n", 0==(ip->bTautFlags&TG_FLAG_ALLOW_NO_NEGTV_O), 0!=(ip->bTautFlags&TG_FLAG_MERGE_TAUT_SALTS)); inchi_ios_eprint( log_file, " DISCONNECT_COORD=%d\n", 0!=(ip->bTautFlags&TG_FLAG_DISCONNECT_COORD) ); #if ( TEST_RENUMB_ATOMS == 1 ) inchi_ios_eprint( log_file, "\nDbg: TEST_RENUMB_ATOMS=%d; TEST_RENUMB_NEIGH=%d; TEST_RENUMB_SWITCH=%d\n", TEST_RENUMB_ATOMS, TEST_RENUMB_NEIGH, TEST_RENUMB_SWITCH ); inchi_ios_eprint( log_file, " TEST_RENUMB_ATOMS_SAVE_LONGEST=%d\n", TEST_RENUMB_ATOMS_SAVE_LONGEST); #endif #endif /* ( bRELEASE_VERSION != 1 ) */ return 0; } /************************************************************************************/ void HelpCommandLineParms( INCHI_IOSTREAM *f ) { if ( !f ) return; #if ( bRELEASE_VERSION == 1 ) inchi_ios_print_nodisplay( f, #ifdef TARGET_EXE_USING_API "%s ver %s%s.\n\nUsage:\ninchi_main inputFile [outputFile [logFile [problemFile]]] [%coption[ %coption...]]\n", INCHI_NAME, INCHI_VERSION, TARGET_ID_STRING, INCHI_OPTION_PREFX, INCHI_OPTION_PREFX); #else "%s ver %s%s.\n\nUsage:\ninchi-%s inputFile [outputFile [logFile [problemFile]]] [%coption [%coption...]]\n", INCHI_NAME, INCHI_VERSION, TARGET_ID_STRING, INCHI_VERSION, INCHI_OPTION_PREFX, INCHI_OPTION_PREFX); #if ( BUILD_WITH_AMI == 1 ) inchi_ios_print_nodisplay( f, "inchi-%s inputFiles... %cAMI [%coption[ %coption...]]\n", INCHI_VERSION, INCHI_OPTION_PREFX, INCHI_OPTION_PREFX, INCHI_OPTION_PREFX); #endif #endif inchi_ios_print_nodisplay( f, "\nOptions:\n"); inchi_ios_print_nodisplay( f, "\nInput\n"); inchi_ios_print_nodisplay( f, " STDIO Use standard input/output streams\n"); inchi_ios_print_nodisplay( f, " InpAux Input structures in %s default aux. info format\n (for use with STDIO)\n", INCHI_NAME); inchi_ios_print_nodisplay( f, " SDF:DataHeader Read from the input SDfile the ID under this DataHeader\n"); #if ( ADD_CMLPP == 1 ) inchi_ios_print_nodisplay( f, " CML Input in CML format (default for input file .CML extension)\n"); #endif /* inchi_ios_print_nodisplay( f, " START:n Skip structures up to n-th one\n"); inchi_ios_print_nodisplay( f, " END:m Skip structures after m-th one\n"); */ #if ( BUILD_WITH_AMI == 1 ) inchi_ios_print_nodisplay( f, " AMI Allow multiple input files (wildcards supported)\n"); #endif inchi_ios_print_nodisplay( f, "Output\n"); inchi_ios_print_nodisplay( f, " AuxNone Omit auxiliary information (default: Include)\n"); inchi_ios_print_nodisplay( f, " SaveOpt Save custom InChI creation options (non-standard InChI)\n"); inchi_ios_print_nodisplay( f, " NoLabels Omit structure number, DataHeader and ID from %s output\n", INCHI_NAME); inchi_ios_print_nodisplay( f, " Tabbed Separate structure number, %s, and AuxInfo with tabs\n", INCHI_NAME); /*inchi_ios_print_nodisplay( f, " Compress Compressed output\n"); */ /*inchi_ios_print_nodisplay( f, " FULL Standard set of options for Full Verbose Output\n");*/ /*inchi_ios_print_nodisplay( f, " MIN Standard set of options for Minimal Concise Output\n");*/ #if ( defined(_WIN32) && defined(_MSC_VER) && !defined(COMPILE_ANSI_ONLY) && !defined(TARGET_API_LIB) ) inchi_ios_print_nodisplay( f, " D Display the structures\n"); inchi_ios_print_nodisplay( f, " EQU Display sets of identical components\n"); inchi_ios_print_nodisplay( f, " Fnumber Set display Font size in number of points\n"); #endif /*inchi_ios_print_nodisplay( f, " PLAIN Plain text output (Default: XML format)\n");*/ inchi_ios_print_nodisplay( f, " OutputSDF Convert %s created with default aux. info to SDfile\n", INCHI_NAME); #if ( SDF_OUTPUT_DT == 1 ) inchi_ios_print_nodisplay( f, " SdfAtomsDT Output Hydrogen Isotopes to SDfile as Atoms D and T\n"); #endif #if ( BUILD_WITH_AMI == 1 ) inchi_ios_print_nodisplay( f, " AMIOutStd Write output to stdout (in AMI mode)\n"); inchi_ios_print_nodisplay( f, " AMILogStd Write log to stderr (in AMI mode)\n"); inchi_ios_print_nodisplay( f, " AMIPrbNone Suppress creation of problem files (in AMI mode)\n"); #endif inchi_ios_print_nodisplay( f, "Structure perception\n"); inchi_ios_print_nodisplay( f, " SNon Exclude stereo (default: include absolute stereo)\n"); inchi_ios_print_nodisplay( f, " NEWPSOFF Both ends of wedge point to stereocenters (default: a narrow end)\n"); inchi_ios_print_nodisplay( f, " DoNotAddH All H are explicit (default: add H according to usual valences)\n"); #ifndef USE_STDINCHI_API inchi_ios_print_nodisplay( f, "Stereo perception modifiers (non-standard InChI)\n"); inchi_ios_print_nodisplay( f, " SRel Relative stereo\n"); inchi_ios_print_nodisplay( f, " SRac Racemic stereo\n"); inchi_ios_print_nodisplay( f, " SUCF Use Chiral Flag: On means Absolute stereo, Off - Relative\n"); inchi_ios_print_nodisplay( f, "Customizing InChI creation (non-standard InChI)\n"); inchi_ios_print_nodisplay( f, " SUU Always include omitted unknown/undefined stereo\n"); inchi_ios_print_nodisplay( f, " SLUUD Make labels for unknown and undefined stereo different\n"); inchi_ios_print_nodisplay( f, " RecMet Include reconnected metals results\n"); inchi_ios_print_nodisplay( f, " FixedH Include Fixed H layer\n"); inchi_ios_print_nodisplay( f, " KET Account for keto-enol tautomerism (experimental)\n"); inchi_ios_print_nodisplay( f, " 15T Account for 1,5-tautomerism (experimental)\n"); #endif inchi_ios_print_nodisplay( f, "Generation\n"); inchi_ios_print_nodisplay( f, " Wnumber Set time-out per structure in seconds; W0 means unlimited\n"); inchi_ios_print_nodisplay( f, " WarnOnEmptyStructure Warn and produce empty %s for empty structure\n", INCHI_NAME); inchi_ios_print_nodisplay( f, " Key Generate InChIKey\n"); inchi_ios_print_nodisplay( f, " XHash1 Generate hash extension (to 256 bits) for 1st block of InChIKey\n"); inchi_ios_print_nodisplay( f, " XHash2 Generate hash extension (to 256 bits) for 2nd block of InChIKey\n"); inchi_ios_print_nodisplay( f, "Conversion\n"); #ifdef TARGET_EXE_USING_API inchi_ios_print_nodisplay( f, " InChI2InChI Test mode: Mol/SDfile->%s->%s\n", INCHI_NAME, INCHI_NAME); inchi_ios_print_nodisplay( f, " InChI2Struct Test mode: Mol/SDfile->%s->Structure->(%s+AuxInfo)\n", INCHI_NAME, INCHI_NAME); #else inchi_ios_print_nodisplay( f, " InChI2InChI Convert %s string(s) into %s string(s)\n", INCHI_NAME, INCHI_NAME); inchi_ios_print_nodisplay( f, " InChI2Struct Convert InChI string(s) to structure(s) in InChI aux.info format\n"); #endif #ifdef BUILD_WITH_ENG_OPTIONS #if 0 inchi_ios_print_nodisplay( f, "Engineering options (for testing only)\n"); inchi_ios_print_nodisplay( f, " NoADP Disable Aggressive Deprotonation\n"); #if ( FIX_ADJ_RAD == 1 ) inchi_ios_print_nodisplay( f, " FixRad Fix Adjacent Radicals\n"); #endif inchi_ios_print_nodisplay( f, " SPXYZOFF Do not include Phosphines Stereochemistry\n"); inchi_ios_print_nodisplay( f, " SAsXYZOFF Do not include Arsines Stereochemistry\n"); inchi_ios_print_nodisplay( f, " FBOFF Do not fix bug leading to missing or undefined sp3 parity\n" ); inchi_ios_print_nodisplay( f, " FB2OFF Do not fix bugs found after v.1.02b release\n" ); inchi_ios_print_nodisplay( f, " FNUDOFF Do not fix non-uniform drawing issues\n" ); #endif #endif /* breleaseversion<1 #else inchi_ios_print_nodisplay( f, "%s ver %s. Special testing version 12-12-2002.\n", INCHI_NAME, INCHI_VERSION); inchi_ios_print_nodisplay( f, "\nUsage:\ncINChI09b inputFile [outputFile [logFile [problemFile]]] [%coption[ %coption...]]\n", INCHI_OPTION_PREFX, INCHI_OPTION_PREFX); inchi_ios_print_nodisplay( f, "\nOptions:\n"); inchi_ios_print_nodisplay( f, "\tB Basic\n"); inchi_ios_print_nodisplay( f, "\tT basic Tautomeric\n"); inchi_ios_print_nodisplay( f, "\tI Isotopic\n"); inchi_ios_print_nodisplay( f, "\tN Non-isotopic\n"); inchi_ios_print_nodisplay( f, "\tS Stereo\n"); inchi_ios_print_nodisplay( f, "\tE Exclude Stereo\n"); inchi_ios_print_nodisplay( f, "\tD Display the structures\n"); inchi_ios_print_nodisplay( f, "\tALT produce shorter ALTernative representation (Abc)\n"); inchi_ios_print_nodisplay( f, "\tSCT produce shorter connection table representation\n"); inchi_ios_print_nodisplay( f, "\tXML output in xml format\n"); inchi_ios_print_nodisplay( f, "\tPLAIN output in plain format\n"); inchi_ios_print_nodisplay( f, "\tMERGE Merge all MOLfiles from the input file into one compound\n"); inchi_ios_print_nodisplay( f, "\tWnumber time-out per structure in seconds, W0 means unlimited\n"); inchi_ios_print_nodisplay( f, "\tFnumber set display Font size, points\n"); inchi_ios_print_nodisplay( f, "\tSREL Relative Stereo\n"); inchi_ios_print_nodisplay( f, "\tSRAC Racemic Stereo\n"); inchi_ios_print_nodisplay( f, "\tNOUUSB Omit stereobonds if all are unknown/undefined\n"); inchi_ios_print_nodisplay( f, "\tNOUUSC Omit stereocenters if all are unknown/undefined\n"); inchi_ios_print_nodisplay( f, "\tSS Slow Stereo: do not use stereo equivalence\n"); inchi_ios_print_nodisplay( f, "\tRS Do not test for Redundant Stereo elements\n"); inchi_ios_print_nodisplay( f, "\tPW Save warning structures in the problems file\n"); inchi_ios_print_nodisplay( f, "\tPGO Save only all good structures in the problems file\n"); inchi_ios_print_nodisplay( f, "\tDSB Double Stereo Bonds only (ignore alternating bonds stereo)\n"); inchi_ios_print_nodisplay( f, "\tRSB:n Min Ring Size for detecting for Stereo Bonds (n=1 => all)\n"); inchi_ios_print_nodisplay( f, "\tAUXINFO:0 do not output auxiliary information (default:1)\n"); inchi_ios_print_nodisplay( f, "\tDISCONSALT:0 do not disconnect salts (default:1)\n"); inchi_ios_print_nodisplay( f, "\tDISCONMETAL:0 do not disconnect metals (default:1)\n"); inchi_ios_print_nodisplay( f, "\tDISCONMETALCHKVAL:1 do not disconnect if typical valence (default:0)\n"); inchi_ios_print_nodisplay( f, "\tRECONMETAL:0 do not reconnect metals (default:1)\n"); inchi_ios_print_nodisplay( f, "\tMOVEPOS:0 do not check moveable positive charges (default:1)\n"); inchi_ios_print_nodisplay( f, "\tACIDTAUT:n n=1: one H/(-) tautomerism, 2: more (deflt), 0:none\n"); inchi_ios_print_nodisplay( f, "\tMERGESALTTG:1 merge salt t-groups (default), 0: do not merge\n"); inchi_ios_print_nodisplay( f, "\tUNCHARGEDACIDS:1 Apply salt (acid) tautomerism in neutral species\n"); inchi_ios_print_nodisplay( f, "\tO:[suffix] Open all 4 files adding suffix to the inputFile name\n"); inchi_ios_print_nodisplay( f, "\tOP:outputpath Set output path\n"); inchi_ios_print_nodisplay( f, "\tMOL input file is a MOLfile (default)\n"); inchi_ios_print_nodisplay( f, "\tSDF[:DataHeader] Include SDfile data for the header into the results\n"); inchi_ios_print_nodisplay( f, "\tSDFID extract CAS r.n. in addition to requested SDfile data\n"); inchi_ios_print_nodisplay( f, "\tSTART:number Start at the given structure ordering number\n"); inchi_ios_print_nodisplay( f, "\tEND:number Terminate after the given structure ordering number\n"); */ #endif } /*^^^ */ /************************************************************************************/ void HelpCommandLineParmsReduced( INCHI_IOSTREAM *f ) { if ( !f ) return; #if ( bRELEASE_VERSION == 1 ) /*^^^ */ inchi_ios_print_nodisplay( f, #ifdef TARGET_EXE_USING_API "%s ver %s%s.\n\nUsage:\ninchi_main inputFile [outputFile [logFile [problemFile]]] [%coption[ %coption...]]\n", INCHI_NAME, INCHI_VERSION, TARGET_ID_STRING, INCHI_OPTION_PREFX, INCHI_OPTION_PREFX); #else "%s ver %s%s.\n\nUsage:\nc%s-%s inputFile [outputFile [logFile [problemFile]]] [%coption[ %coption...]]\n", INCHI_NAME, INCHI_VERSION, TARGET_ID_STRING, INCHI_NAME, INCHI_VERSION, INCHI_OPTION_PREFX, INCHI_OPTION_PREFX); #endif /*^^^ */ inchi_ios_print_nodisplay( f, "\nOptions:\n"); inchi_ios_print_nodisplay( f, "\nInput\n"); inchi_ios_print_nodisplay( f, " STDIO Use standard input/output streams\n"); inchi_ios_print_nodisplay( f, " InpAux Input structures in %s default aux. info format\n (for use with STDIO)\n", INCHI_NAME); inchi_ios_print_nodisplay( f, " SDF:DataHeader Read from the input SDfile the ID under this DataHeader\n"); #if ( ADD_CMLPP == 1 ) inchi_ios_print_nodisplay( f, " CML Input in CML format (default for input file .CML extension)\n"); #endif /* inchi_ios_print_nodisplay( f, " START:n Skip structures up to n-th one\n"); inchi_ios_print_nodisplay( f, " END:m Skip structures after m-th one\n"); */ #if ( BUILD_WITH_AMI == 1 ) inchi_ios_print_nodisplay( f, " AMI Allow multiple input files (wildcards supported)\n"); #endif inchi_ios_print_nodisplay( f, "Output\n"); inchi_ios_print_nodisplay( f, " AuxNone Omit auxiliary information (default: Include)\n"); inchi_ios_print_nodisplay( f, " SaveOpt Save custom InChI creation options (non-standard InChI)\n"); inchi_ios_print_nodisplay( f, " NoLabels Omit structure number, DataHeader and ID from %s output\n", INCHI_NAME); inchi_ios_print_nodisplay( f, " Tabbed Separate structure number, %s, and AuxInfo with tabs\n", INCHI_NAME); /* inchi_ios_print_nodisplay( f, " Compress Compressed output\n"); */ #if ( defined(_WIN32) && defined(_MSC_VER) && !defined(COMPILE_ANSI_ONLY) && !defined(TARGET_API_LIB) ) inchi_ios_print_nodisplay( f, " D Display the structures\n"); inchi_ios_print_nodisplay( f, " EQU Display sets of identical components\n"); inchi_ios_print_nodisplay( f, " Fnumber Set display Font size in number of points\n"); #endif inchi_ios_print_nodisplay( f, " OutputSDF Convert %s created with default aux. info to SDfile\n", INCHI_NAME); #if ( SDF_OUTPUT_DT == 1 ) inchi_ios_print_nodisplay( f, " SdfAtomsDT Output Hydrogen Isotopes to SDfile as Atoms D and T\n"); #endif #if ( BUILD_WITH_AMI == 1 ) inchi_ios_print_nodisplay( f, " AMIOutStd Write output to stdout (in AMI mode)\n"); inchi_ios_print_nodisplay( f, " AMILogStd Write log to stderr (in AMI mode)\n"); inchi_ios_print_nodisplay( f, " AMIPrbNone Suppress creation of problem files (in AMI mode)\n"); #endif inchi_ios_print_nodisplay( f, "Structure perception\n"); inchi_ios_print_nodisplay( f, " SNon Exclude stereo (default: include absolute stereo)\n"); inchi_ios_print_nodisplay( f, " NEWPSOFF Both ends of wedge point to stereocenters (default: a narrow end)\n"); inchi_ios_print_nodisplay( f, " DoNotAddH All H are explicit (default: add H according to usual valences)\n"); #ifndef USE_STDINCHI_API inchi_ios_print_nodisplay( f, "Stereo perception modifiers (non-standard InChI)\n"); inchi_ios_print_nodisplay( f, " SRel Relative stereo\n"); inchi_ios_print_nodisplay( f, " SRac Racemic stereo\n"); inchi_ios_print_nodisplay( f, " SUCF Use Chiral Flag: On means Absolute stereo, Off - Relative\n"); inchi_ios_print_nodisplay( f, "Customizing InChI creation (non-standard InChI)\n"); inchi_ios_print_nodisplay( f, " SUU Always include omitted unknown/undefined stereo\n"); inchi_ios_print_nodisplay( f, " SLUUD Make labels for unknown and undefined stereo different\n"); inchi_ios_print_nodisplay( f, " RecMet Include reconnected metals results\n"); inchi_ios_print_nodisplay( f, " FixedH Include Fixed H layer\n"); inchi_ios_print_nodisplay( f, " KET Account for keto-enol tautomerism (experimental)\n"); inchi_ios_print_nodisplay( f, " 15T Account for 1,5-tautomerism (experimental)\n"); #endif inchi_ios_print_nodisplay( f, "Generation\n"); inchi_ios_print_nodisplay( f, " Wnumber Set time-out per structure in seconds; W0 means unlimited\n"); inchi_ios_print_nodisplay( f, " WarnOnEmptyStructure Warn and produce empty %s for empty structure\n", INCHI_NAME); inchi_ios_print_nodisplay( f, " Key Generate InChIKey\n"); inchi_ios_print_nodisplay( f, " XHash1 Generate hash extension (to 256 bits) for 1st block of InChIKey\n"); inchi_ios_print_nodisplay( f, " XHash2 Generate hash extension (to 256 bits) for 2nd block of InChIKey\n"); #ifdef BUILD_WITH_ENG_OPTIONS #if 0 inchi_ios_print_nodisplay( f, "Engineering options (for testing only)\n"); inchi_ios_print_nodisplay( f, " NoADP Disable Aggressive Deprotonation\n"); #if ( FIX_ADJ_RAD == 1 ) inchi_ios_print_nodisplay( f, " FixRad Fix Adjacent Radicals\n"); #endif inchi_ios_print_nodisplay( f, " SPXYZOFF Do not include Phosphines Stereochemistry\n"); inchi_ios_print_nodisplay( f, " SAsXYZOFF Do not include Arsines Stereochemistry\n"); inchi_ios_print_nodisplay( f, " FBOFF Do not fix bug leading to missing or undefined sp3 parity\n" ); inchi_ios_print_nodisplay( f, " FB2OFF Do not fix bugs found after v.1.02b release\n" ); inchi_ios_print_nodisplay( f, " FNUDOFF Do not fix non-uniform drawing issues\n" ); #endif #endif #endif /* #if ( bRELEASE_VERSION == 1 ) */ } #define fprintf2 inchi_fprintf #ifndef TARGET_API_LIB /************************************************************************************/ int OpenFiles( FILE **inp_file, FILE **output_file, FILE **log_file, FILE **prb_file, INPUT_PARMS *ip ) { /* -- Files -- ip->path[0] => Input ip->path[1] => Output (INChI) ip->path[2] => Log ip->path[3] => Problem structures ip->path[4] => Errors file (ACD Labs) */ /* logfile -- open as early as possible */ if ( !ip->path[2] || !ip->path[2][0] ) { fprintf2( stderr, "%s version %s%s%s\n", INCHI_NAME, INCHI_VERSION, TARGET_ID_STRING, bRELEASE_VERSION? "":""); /* (Pre-release, for evaluation purposes only)" ); */ fprintf2( stderr, "Log file not specified. Using standard error output.\n"); *log_file = stderr; } else if ( !(*log_file = fopen( ip->path[2], "w" ) ) ) { fprintf2( stderr, "%s version %s%s%s\n", INCHI_NAME, INCHI_VERSION, TARGET_ID_STRING, bRELEASE_VERSION? "":""); /* (Pre-release, for evaluation purposes only)" );*/ fprintf2( stderr, "Cannot open log file '%s'. Using standard error output.\n", ip->path[2] ); *log_file = stderr; } else { fprintf2( *log_file, "%s version %s%s%s\n", INCHI_NAME, INCHI_VERSION, TARGET_ID_STRING, bRELEASE_VERSION? "":""); /* (Pre-release, for evaluation purposes only)" );*/ fprintf2( *log_file, "Opened log file '%s'\n", ip->path[2] ); } /* input file */ if ( (ip->nInputType == INPUT_MOLFILE || ip->nInputType == INPUT_SDFILE || ip->nInputType == INPUT_CMLFILE || ip->nInputType == INPUT_INCHI || ip->nInputType == INPUT_INCHI_PLAIN ) && ip->num_paths > 0 ) { const char *fmode = NULL; #if ( defined(_MSC_VER)&&defined(_WIN32) || defined(__BORLANDC__)&&defined(__WIN32__) || defined(__GNUC__)&&defined(__MINGW32__)&&defined(_WIN32) ) /* compilers that definitely allow fopen "rb" (binary read) mode */ fmode = "rb"; if ( !ip->path[0] || !ip->path[0][0] || !(*inp_file = fopen( ip->path[0], "rb" ) ) ) { fprintf2( *log_file, "Cannot open input file '%s'. Terminating.\n", ip->path[0]? ip->path[0] : "" ); goto exit_function; } else { if ( ip->nInputType == INPUT_CMLFILE ) { int c; #ifdef CML_DEBUG printf ("cr %d lf %d ret %d\n", (int) '\r', (int) '\f', (int) '\n'); #endif /* read up to the end of the first line */ while( (c = fgetc( *inp_file )) && c != EOF && c != '\n' && c != '\r' ) ; if ( c == '\r' || c == EOF ) { /* text file contains CR; close and reopen as "text" */ fclose( *inp_file ); if ( !(*inp_file = fopen( ip->path[0], "r" ) ) ) { fprintf2( *log_file, "Cannot open input file '%s' (2nd attempt). Terminating.\n", ip->path[0] ); goto exit_function; } fprintf2( *log_file, "Opened input file '%s'\n", ip->path[0] ); fmode = "r"; } else { fclose( *inp_file ); if ( !(*inp_file = fopen( ip->path[0], "rb" ) ) ) { fprintf2( *log_file, "Cannot open input file '%s' (2nd attempt). Terminating.\n", ip->path[0] ); goto exit_function; } fprintf2( *log_file, "Opened input file '%s': no CR.\n", ip->path[0] ); fmode = "rb"; } } /* CML */ else fprintf2( *log_file, "Opened input file '%s'\n", ip->path[0] ); } #else if ( !ip->path[0] || !ip->path[0][0] || !(*inp_file = fopen( ip->path[0], "r" ) ) ) { fprintf2( *log_file, "Cannot open input file '%s'. Terminating.\n", ip->path[0]? ip->path[0] : "" ); goto exit_function; } else { fprintf2( *log_file, "Opened input file '%s'\n", ip->path[0] ); } fmode = "r"; #endif DetectInputINChIFileType( inp_file, ip, fmode ); } else if ( (ip->nInputType != INPUT_MOLFILE && ip->nInputType != INPUT_SDFILE && ip->nInputType != INPUT_CMLFILE && ip->nInputType != INPUT_INCHI /*^^^ post-1.02b */ && ip->nInputType != INPUT_INCHI_PLAIN )) { fprintf2( *log_file, "Input file type not specified. Terminating.\n"); goto exit_function; } else { fprintf2( *log_file, "Input file not specified. Using standard input.\n"); *inp_file = stdin; } /* output file */ if ( !ip->path[1] || !ip->path[1][0] ) { fprintf2( *log_file, "Output file not specified. Using standard output.\n"); *output_file = stdout; } else { if ( !(*output_file = fopen( ip->path[1], "w" ) ) ) { fprintf2( *log_file, "Cannot open output file '%s'. Terminating.\n", ip->path[1] ); goto exit_function; } else { fprintf2( *log_file, "Opened output file '%s'\n", ip->path[1] ); if ( (ip->bINChIOutputOptions & (INCHI_OUT_PLAIN_TEXT)) && *inp_file != stdin && !(ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) && !ip->bNoStructLabels && !(ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT)) { PrintFileName( "* Input_File: \"%s\"\n", *output_file, ip->path[0] ); } } } /* problem file */ if ( ip->path[3] && ip->path[3][0] ) { const char *fmode = "w"; #if ( defined(_MSC_VER)&&defined(_WIN32) || defined(__BORLANDC__)&&defined(__WIN32__) || defined(__GNUC__)&&defined(__MINGW32__)&&defined(_WIN32) ) if ( ip->nInputType != INPUT_CMLFILE ) { fmode = "wb"; } #endif if ( !(*prb_file = fopen( ip->path[3], fmode ) ) ) { fprintf2( *log_file, "Cannot open problem file '%s'. Terminating.\n", ip->path[3] ); goto exit_function; } else { fprintf2( *log_file, "Opened problem file '%s'\n", ip->path[3] ); } } return 1; /* success */ exit_function: return 0; /* failed */ } #define NUM_VERSIONS 7 #define LEN_VERSIONS 64 /*******************************************************************/ static int bMatchOnePrefix( int len, char *str, int lenPrefix[], char strPrefix[][LEN_VERSIONS], int numPrefix); /*******************************************************************/ static int bMatchOnePrefix( int len, char *str, int lenPrefix[], char strPrefix[][LEN_VERSIONS], int numPrefix) { int i; for ( i = 0; i < numPrefix; i ++ ) { if ( len >= lenPrefix[i] && !memcmp( str, strPrefix[i], lenPrefix[i] ) ) { return 1; } } return 0; } /*******************************************************************/ int DetectInputINChIFileType( FILE **inp_file, INPUT_PARMS *ip, const char *fmode ) { char szLine[256], ret = 0; static char szPlnVersion[NUM_VERSIONS][LEN_VERSIONS]; /* = "INChI:1.1Beta/";*/ static int lenPlnVersion[NUM_VERSIONS]; static char szPlnAuxVer[NUM_VERSIONS][LEN_VERSIONS]; /* = "AuxInfo:1.1Beta/";*/ static int lenPlnAuxVer[NUM_VERSIONS]; static char szXmlVersion[NUM_VERSIONS][LEN_VERSIONS]; /* = "";*/ static int lenXmlVersion[NUM_VERSIONS]; static char szXmlStruct[LEN_VERSIONS] = "nInputType == INPUT_INCHI_XML || ip->nInputType == INPUT_INCHI_PLAIN || ip->nInputType == INPUT_INCHI ) { return 1; } if ( !bInitilized ) { lenPlnVersion[0] = sprintf( szPlnVersion[0], "%s=%s/", INCHI_NAME, INCHI_VERSION ); lenPlnVersion[1] = sprintf( szPlnVersion[1], "INChI=1.12Beta/" ); lenPlnVersion[2] = sprintf( szPlnVersion[2], "INChI=1.0RC/" ); lenPlnVersion[3] = sprintf( szPlnVersion[3], "InChI=1.0RC/" ); lenPlnVersion[4] = sprintf( szPlnVersion[4], "InChI=1/" ); lenPlnVersion[5] = sprintf( szPlnVersion[5], "MoChI=1a/" ); lenPlnVersion[6] = sprintf( szPlnVersion[6], "InChI=1S/" ); lenPlnAuxVer[0] = sprintf( szPlnAuxVer[0], "AuxInfo=%s/", INCHI_VERSION ); lenPlnAuxVer[1] = sprintf( szPlnAuxVer[1], "AuxInfo=1.12Beta/" ); lenPlnAuxVer[2] = sprintf( szPlnAuxVer[2], "AuxInfo=1.0RC/" ); lenPlnAuxVer[3] = sprintf( szPlnAuxVer[3], "AuxInfo=1.0RC/" ); lenPlnAuxVer[4] = sprintf( szPlnAuxVer[4], "AuxInfo=1/" ); lenPlnAuxVer[5] = sprintf( szPlnAuxVer[5], "AuxInfo=1a/" ); lenPlnAuxVer[6] = sprintf( szPlnAuxVer[6], "AuxInfo=1/" ); lenXmlVersion[0] = sprintf( szXmlVersion[0], "<%s version=\"%s\">", INCHI_NAME, INCHI_VERSION ); lenXmlVersion[1] = sprintf( szXmlVersion[1], "" ); lenXmlVersion[2] = sprintf( szXmlVersion[2], "" ); lenXmlVersion[3] = sprintf( szXmlVersion[3], "" ); lenXmlVersion[4] = sprintf( szXmlVersion[4], "" ); lenXmlVersion[5] = sprintf( szXmlVersion[5], "" ); lenXmlVersion[6] = sprintf( szXmlVersion[6], "" ); lenXmlIdentVer[0] = sprintf( szXmlIdentVer[0], "= 2 && !bINChI_xml ) { ip->nInputType = INPUT_INCHI_PLAIN; ret = 1; } else if ( !bINChI_plain && bINChI_xml >= 3 ) { ip->nInputType = INPUT_INCHI_XML; ret = 1; } /*exit_function:*/ fclose ( *inp_file ); *inp_file = fopen( ip->path[0], fmode ); return ret; } #undef NUM_VERSIONS #undef LEN_VERSIONS #endif /* TARGET_API_LIB */