/* * 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 __INCHIMAIN_H__ #define __INCHIMAIN_H__ #define ESC_KEY 27 #define INCHI_SEGM_BUFLEN 64000 /********************************************************************/ typedef struct tagStructData { unsigned long ulStructTime; int nErrorCode; int nErrorType; int nStructReadError; char pStrErrStruct[STR_ERR_LEN]; long fPtrStart; /* or number of processed structures */ long fPtrEnd; /* or number of errors */ int bXmlStructStarted; int bUserQuit; int bUserQuitComponent; int bUserQuitComponentDisplay; int bChiralFlag; /* information related to normal or disconnected layers */ int num_taut[INCHI_NUM]; int num_non_taut[INCHI_NUM]; INCHI_MODE bTautFlags[INCHI_NUM]; /* reconnected does not have TG_FLAG_DISCONNECT_COORD_DONE flag */ INCHI_MODE bTautFlagsDone[INCHI_NUM]; /* reconnected does not have TG_FLAG_DISCONNECT_COORD_DONE flag */ int num_components[INCHI_NUM]; /* number of allocated INChI, INChI_Aux data structures */ /* debugging info */ #if ( bRELEASE_VERSION == 0 ) int bExtract; #endif } STRUCT_DATA; #ifndef COMPILE_ALL_CPP #ifdef __cplusplus extern "C" { #endif #endif int process_single_input( int argc, char *argv[ ] ); int ReadCommandLineParms(int argc, const char *argv[], INPUT_PARMS *ip, char *szSdfDataValue, unsigned long *ulDisplTime, int bReleaseVersion, INCHI_IOSTREAM *log_file); void HelpCommandLineParms(INCHI_IOSTREAM *f); int OpenFiles( FILE **inp_file, FILE **output_file, FILE **log_file, FILE **prb_file, INPUT_PARMS *ip ); #ifndef COMPILE_ANSI_ONLY int DisplayStructure( inp_ATOM *at, int num_at, int num_removed_H, int bAdd_DT_to_num_H, int nNumRemovedProtons, NUM_H nNumRemovedProtonsIsotopic[], int bIsotopic, int j /*bTautomeric*/, INChI **cur_INChI, INChI_Aux **cur_INChI_Aux, int bAbcNumbers, DRAW_PARMS *dp, INCHI_MODE nMode, char *szTitle ); void FillTableParms( SET_DRAW_PARMS *sdp, INChI **cur_INChI, INChI_Aux **cur_INChI_Aux, INCHI_MODE nMode, int bShowIsotopic, int bShowTaut ); void FillCompositeTableParms( SET_DRAW_PARMS *sdp, AT_NUMB StereoFlags, INCHI_MODE nMode, int bShowIsotopic, int bShowTaut ); #endif int PrintInputParms(INCHI_IOSTREAM *log_file, INPUT_PARMS *ip); const char *ErrMsg( int nErrorCode ); int SortAndPrintINChI(INCHI_IOSTREAM *output_file, char *pStr, int nStrLen, INCHI_IOSTREAM *log_file, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, COMP_ATOM_DATA composite_norm_data[INCHI_NUM][TAUT_NUM+1], ORIG_STRUCT *pOrigStruct, int num_components[INCHI_NUM], int num_non_taut[INCHI_NUM], int num_taut[INCHI_NUM], INCHI_MODE bTautFlags[INCHI_NUM], INCHI_MODE bTautFlagsDone[INCHI_NUM], NORM_CANON_FLAGS *pncFlags, long num_inp, PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM], int *pSortPrintINChIFlags, unsigned char save_opt_bits); void FreeAllINChIArrays(PINChI2 *pINChI[INCHI_NUM], PINChI_Aux2 *pINChI_Aux[INCHI_NUM], int num_components[2]); void FreeINChIArrays(PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, int num_components ); void SplitTime(unsigned long ulTotalTime, int *hours, int *minutes, int *seconds, int *mseconds ); int ReadTheStructure( STRUCT_DATA *sd, INPUT_PARMS *ip, INCHI_IOSTREAM *inp_file, ORIG_ATOM_DATA *orig_inp_data, int inp_index, int *out_index ); int TreatReadTheStructureErrors( STRUCT_DATA *sd, INPUT_PARMS *ip, int nLogMask, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *output_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, long *num_inp, char *pStr, int nStrLen ); int GetOneComponent(STRUCT_DATA *sd, INPUT_PARMS *ip, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *output_file, INP_ATOM_DATA *inp_cur_data, ORIG_ATOM_DATA *orig_inp_data, int i, long num_inp, char *pStr, int nStrLen ); int CreateOneComponentINChI(STRUCT_DATA *sd, INPUT_PARMS *ip, INP_ATOM_DATA *inp_cur_data, ORIG_ATOM_DATA *orig_inp_data, PINChI2 *pINChI, PINChI_Aux2 *pINChI_Aux, int iINChI, int i, long num_inp, INP_ATOM_DATA **inp_norm_data, NORM_CANON_FLAGS *pncFlags, INCHI_IOSTREAM *log_file); int TreatCreateOneComponentINChIError(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, int i, long num_inp, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *output_file, INCHI_IOSTREAM *prb_file, char *pStr, int nStrLen ); int TreatCreateINChIWarning(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, long num_inp, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *output_file, INCHI_IOSTREAM *prb_file, char *pStr, int nStrLen ); #if ( TEST_RENUMB_ATOMS == 1 || READ_INCHI_STRING == 1 ) /* { */ int CompareINChI( INChI *i1, INChI *i2, INChI_Aux *a1, INChI_Aux *a2 ); #endif void eat_keyboard_input( void ); int user_quit( const char *msg, unsigned long ulMaxTime ); int GetOneStructure(STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *output_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, long *num_inp, char *pStr, int nStrLen, STRUCT_FPTRS *struct_fptrs ); int ProcessOneStructure(STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *output_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, long num_inp, char *pStr, int nStrLen, unsigned char save_opt_bits); int CreateOneStructureINChI(STRUCT_DATA *sd, INPUT_PARMS *ip, char *szTitle, PINChI2 *pINChI2[INCHI_NUM], PINChI_Aux2 *pINChI_Aux2[INCHI_NUM], int iINChI, INCHI_IOSTREAM *inp_file, INCHI_IOSTREAM *log_file, INCHI_IOSTREAM *output_file, INCHI_IOSTREAM *prb_file, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data, COMP_ATOM_DATA composite_norm_data2[][TAUT_NUM+1], long num_inp, char *pStr, int nStrLen, NORM_CANON_FLAGS *pncFlags ); int bIsStructChiral(PINChI2 *pINChI2[INCHI_NUM], int num_components[]); int PreprocessOneStructure(STRUCT_DATA *sd, INPUT_PARMS *ip, ORIG_ATOM_DATA *orig_inp_data, ORIG_ATOM_DATA *prep_inp_data ); int FillOutOrigStruct(ORIG_ATOM_DATA *orig_inp_data, ORIG_STRUCT *pOrigStruct, STRUCT_DATA *sd); void FreeOrigStruct( ORIG_STRUCT *pOrigStruct); int ReadWriteInChI(INCHI_IOSTREAM *pInp, INCHI_IOSTREAM *pOut, INCHI_IOSTREAM *pLog, INPUT_PARMS *ip_inp, STRUCT_DATA *sd_inp, /* the following are InChI library-specific parameters */ inp_ATOM **at, int *num_at, char *szMsg, int nMsgLen, unsigned long WarningFlags[2][2]); int CompareHillFormulasNoH(const char *f1, const char *f2, int *num_H1, int *num_H2); #ifndef COMPILE_ALL_CPP #ifdef __cplusplus } #endif #endif #endif /* __INCHIMAIN_H__ */