| 1 |  | /********************************************************************** | 
| 2 | < | main.cpp - Main conversion program, command-line handling. | 
| 2 | > | atom2md.cpp - OpenBabel-based conversion program to OOPSE MD file, | 
| 3 | > | command-line handling. | 
| 4 |  |  | 
| 5 |  | Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. | 
| 6 | < | Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison | 
| 7 | < | Some portions Copyright (C) 2004-2005 by Chris Morley | 
| 6 | > | Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison | 
| 7 | > | Some portions Copyright (C) 2004-2006 by Chris Morley | 
| 8 | > | Some portions Copyright (C) 2008 by J. Daniel Gezelter | 
| 9 |  |  | 
| 10 | < | This file is part of the Open Babel project. | 
| 11 | < | For more information, see <http://openbabel.sourceforge.net/> | 
| 10 | > | This file is part of both the OOPSE and Open Babel projects. | 
| 11 | > | For more information, see <http://oopse.org> and <http://openbabel.sourceforge.net/> | 
| 12 |  |  | 
| 13 |  | This program is free software; you can redistribute it and/or modify | 
| 14 |  | it under the terms of the GNU General Public License as published by | 
| 21 |  | ***********************************************************************/ | 
| 22 |  |  | 
| 23 |  | #include "config.h" | 
| 24 | < | #if HAVE_IOSTREAM | 
| 25 | < | #include <iostream> | 
| 26 | < | #elif HAVE_IOSTREAM_H | 
| 27 | < | #include <iostream.h> | 
| 24 | > |  | 
| 25 | > | // used to set import/export for Cygwin DLLs | 
| 26 | > | #ifdef WIN32 | 
| 27 | > | #define USING_OBDLL | 
| 28 |  | #endif | 
| 27 | – | #if HAVE_FSTREAM | 
| 28 | – | #include <fstream> | 
| 29 | – | #elif HAVE_FSTREAM_H | 
| 30 | – | #include <fstream.h> | 
| 31 | – | #endif | 
| 32 | – | #if HAVE_SSTREAM | 
| 33 | – | #include <sstream> | 
| 34 | – | #elif | 
| 35 | – | #include <sstream.h> | 
| 36 | – | #endif | 
| 29 |  |  | 
| 30 | + | #include <openbabel/babelconfig.h> | 
| 31 | + |  | 
| 32 | + | #include <iostream> | 
| 33 | + | #include <fstream> | 
| 34 | + | #include <sstream> | 
| 35 | + |  | 
| 36 |  | #include <string> | 
| 37 |  | #include <map> | 
| 38 |  | #if HAVE_CONIO_H | 
| 39 |  | #include <conio.h> | 
| 40 |  | #endif | 
| 41 | + | #include <cstdlib> | 
| 42 |  |  | 
| 43 |  | #if !HAVE_STRNCASECMP | 
| 44 |  | extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); | 
| 45 |  | #endif | 
| 46 |  |  | 
| 47 | < | #include "openbabel/obconversion.hpp" | 
| 49 | < | #include "brains/Register.hpp" | 
| 47 | > | #include <openbabel/obconversion.h> | 
| 48 |  |  | 
| 49 |  | using namespace std; | 
| 50 |  | using namespace OpenBabel; | 
| 51 | < | using namespace oopse; | 
| 52 | < | void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, | 
| 53 | < | int& arg, int argc, char *argv[]); | 
| 51 | > |  | 
| 52 | > | void DoOption(const char* p, OBConversion& Conv, | 
| 53 | > | OBConversion::Option_type typ, int& arg, int argc, | 
| 54 | > | char *argv[]); | 
| 55 |  | void usage(); | 
| 56 |  | void help(); | 
| 57 |  |  | 
| 60 |  |  | 
| 61 |  | int main(int argc,char *argv[]) | 
| 62 |  | { | 
| 64 | – | registerOBFormats(); | 
| 63 |  | OBConversion Conv(&cin, &cout); //default input and output are console | 
| 64 |  |  | 
| 67 | – | //  string GenOptions; | 
| 65 |  | OBFormat* pInFormat = NULL; | 
| 66 |  | OBFormat* pOutFormat = NULL; | 
| 67 |  | vector<string> FileList, OutputFileList; | 
| 68 |  | string OutputFileName; | 
| 72 | – | //  obMessageLevel filterLevel = obWarning; // 2 out of 5 | 
| 69 |  |  | 
| 70 |  | // Parse commandline | 
| 71 |  | bool gotInType = false, gotOutType = false; | 
| 72 | < | bool UseSavedOptions = false; | 
| 72 | > | bool SplitOrBatch=false; | 
| 73 |  |  | 
| 74 |  | char *oext; | 
| 75 |  | char *iext; | 
| 78 |  |  | 
| 79 |  | //Save name of program without its path (and .exe) | 
| 80 |  | string pn(argv[0]); | 
| 81 | < | unsigned int pos; | 
| 81 | > | string::size_type pos; | 
| 82 |  | #ifdef _WIN32 | 
| 83 |  | pos = pn.find(".exe"); | 
| 84 |  | if(pos!=string::npos) | 
| 90 |  | else | 
| 91 |  | program_name=argv[0]+pos+1; | 
| 92 |  |  | 
| 93 | < | const char* p; | 
| 94 | < | int arg; | 
| 95 | < | for (arg = 1; arg < argc; arg++) | 
| 96 | < | { | 
| 97 | < | if (argv[arg]) | 
| 98 | < | { | 
| 99 | < | if (argv[arg][0] == '-') | 
| 100 | < | { | 
| 101 | < | switch (argv[arg][1]) | 
| 102 | < | { | 
| 93 | > | const char* p; | 
| 94 | > | int arg; | 
| 95 | > | for (arg = 1; arg < argc; ++arg) | 
| 96 | > | { | 
| 97 | > | if (argv[arg]) | 
| 98 | > | { | 
| 99 | > | if (argv[arg][0] == '-') | 
| 100 | > | { | 
| 101 | > | switch (argv[arg][1]) | 
| 102 | > | { | 
| 103 |  |  | 
| 104 | < | case 'V': | 
| 105 | < | { | 
| 106 | < | cout << "Open Babel " << BABEL_VERSION << " -- " | 
| 107 | < | << __DATE__ << " -- " << __TIME__ << endl; | 
| 108 | < | exit(0); | 
| 109 | < | } | 
| 104 | > | case 'V': | 
| 105 | > | { | 
| 106 | > | cout << program_name << ": part of OOPSE " << | 
| 107 | > | OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << | 
| 108 | > | "." << OOPSE_VERSION_TINY << | 
| 109 | > | " and Open Babel " << BABEL_VERSION << " -- " | 
| 110 | > | << __DATE__ << " -- " << __TIME__ << endl; | 
| 111 | > | exit(0); | 
| 112 | > | } | 
| 113 |  |  | 
| 114 | < | case 'i': | 
| 115 | < | gotInType = true; | 
| 116 | < | iext = argv[arg] + 2; | 
| 117 | < | if(!*iext) | 
| 118 | < | iext = argv[++arg]; //space left after -i: use next argument | 
| 114 | > | case 'i': | 
| 115 | > | gotInType = true; | 
| 116 | > | iext = argv[arg] + 2; | 
| 117 | > | if(!*iext) | 
| 118 | > | iext = argv[++arg]; // space left after -i: use next | 
| 119 | > | // argument | 
| 120 |  |  | 
| 121 | < | if (strncasecmp(iext, "MIME", 4) == 0) | 
| 122 | < | { | 
| 123 | < | // get the MIME type from the next argument | 
| 124 | < | iext = argv[++arg]; | 
| 125 | < | pInFormat = Conv.FormatFromMIME(iext); | 
| 126 | < | } | 
| 127 | < | else | 
| 128 | < | { | 
| 129 | < | //The ID provided by the OBFormat class is used as the identifying file extension | 
| 130 | < | pInFormat = Conv.FindFormat(iext); | 
| 131 | < | } | 
| 132 | < | if(pInFormat==NULL) | 
| 133 | < | { | 
| 134 | < | cerr << program_name << ": cannot read input format!" << endl; | 
| 135 | < | usage(); | 
| 136 | < | } | 
| 137 | < | inputExt = iext; | 
| 138 | < | break; | 
| 121 | > | if (strncasecmp(iext, "MIME", 4) == 0) | 
| 122 | > | { | 
| 123 | > | // get the MIME type from the next argument | 
| 124 | > | iext = argv[++arg]; | 
| 125 | > | pInFormat = Conv.FormatFromMIME(iext); | 
| 126 | > | } | 
| 127 | > | else | 
| 128 | > | { | 
| 129 | > | // The ID provided by the OBFormat class is used as the | 
| 130 | > | // identifying file extension | 
| 131 | > | pInFormat = Conv.FindFormat(iext); | 
| 132 | > | } | 
| 133 | > | if(pInFormat==NULL) | 
| 134 | > | { | 
| 135 | > | cerr << program_name << ": cannot read input format!" | 
| 136 | > | << endl; | 
| 137 | > | usage(); | 
| 138 | > | } | 
| 139 | > | break; | 
| 140 | > |  | 
| 141 | > | case 'o': | 
| 142 | > | gotOutType = true; | 
| 143 | > | oext = argv[arg] + 2; | 
| 144 | > | if(!*oext) | 
| 145 | > | oext = argv[++arg]; // space left after -i: use next | 
| 146 | > | // argument | 
| 147 |  |  | 
| 148 | < | case 'o': | 
| 149 | < | gotOutType = true; | 
| 150 | < | oext = argv[arg] + 2; | 
| 151 | < | if(!*oext) | 
| 152 | < | oext = argv[++arg]; //space left after -i: use next argument | 
| 153 | < |  | 
| 154 | < | if (strncasecmp(oext, "MIME", 4) == 0) | 
| 155 | < | { | 
| 148 | < | // get the MIME type from the next argument | 
| 149 | < | oext = argv[++arg]; | 
| 150 | < | pOutFormat = Conv.FormatFromMIME(oext); | 
| 151 | < | } | 
| 152 | < | else | 
| 153 | < | pOutFormat = Conv.FindFormat(oext); | 
| 148 | > | if (strncasecmp(oext, "MIME", 4) == 0) | 
| 149 | > | { | 
| 150 | > | // get the MIME type from the next argument | 
| 151 | > | oext = argv[++arg]; | 
| 152 | > | pOutFormat = Conv.FormatFromMIME(oext); | 
| 153 | > | } | 
| 154 | > | else | 
| 155 | > | pOutFormat = Conv.FindFormat(oext); | 
| 156 |  |  | 
| 157 | < | if(pOutFormat==NULL) | 
| 158 | < | { | 
| 159 | < | cerr << program_name << ": cannot write output format!" << endl; | 
| 160 | < | usage(); | 
| 161 | < | } | 
| 162 | < | outputExt = oext; | 
| 163 | < | break; | 
| 164 | < |  | 
| 165 | < | case '?': | 
| 166 | < | case 'H': | 
| 167 | < | if(isalnum(argv[arg][2])) | 
| 168 | < | { | 
| 169 | < | if(strncasecmp(argv[arg]+2,"all",3)) | 
| 170 | < | { | 
| 171 | < | OBFormat* pFormat = Conv.FindFormat(argv[arg]+2); | 
| 172 | < | if(pFormat) | 
| 173 | < | { | 
| 174 | < | cout << argv[arg]+2 << "  " << pFormat->Description() << endl; | 
| 175 | < | if(strlen(pFormat->SpecificationURL())) | 
| 176 | < | cout << "Specification at: " << pFormat->SpecificationURL() << endl; | 
| 177 | < | } | 
| 178 | < | else | 
| 179 | < | cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl; | 
| 180 | < | } | 
| 181 | < | else | 
| 182 | < | { | 
| 183 | < | Formatpos pos; | 
| 184 | < | OBFormat* pFormat; | 
| 185 | < | const char* str=NULL; | 
| 186 | < | while(OBConversion::GetNextFormat(pos,str,pFormat)) | 
| 187 | < | { | 
| 188 | < | if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) | 
| 189 | < | continue; | 
| 190 | < | cout << str << endl; | 
| 191 | < | const char* p = strchr(pFormat->Description(),'\n'); | 
| 192 | < | cout << p+1; //second line of description | 
| 193 | < | if(strlen(pFormat->SpecificationURL())) | 
| 194 | < | cout << "Specification at: " << pFormat->SpecificationURL(); | 
| 195 | < | cout << endl << endl; | 
| 196 | < | } | 
| 197 | < | } | 
| 198 | < | } | 
| 199 | < | else | 
| 200 | < | help(); | 
| 201 | < | exit(0); | 
| 157 | > | if(pOutFormat==NULL) | 
| 158 | > | { | 
| 159 | > | cerr << program_name << ": cannot write output format!" | 
| 160 | > | << endl; | 
| 161 | > | usage(); | 
| 162 | > | } | 
| 163 | > | break; | 
| 164 | > |  | 
| 165 | > | case 'F': | 
| 166 | > | if(!Conv.SetOutFormat("fpt")) | 
| 167 | > | cout << "FingerprintFormat needs to be loaded" << endl; | 
| 168 | > | else | 
| 169 | > | { | 
| 170 | > | Conv.AddOption("F",OBConversion::OUTOPTIONS); | 
| 171 | > | Conv.Write(NULL); | 
| 172 | > | } | 
| 173 | > | return 0; | 
| 174 | > |  | 
| 175 | > | case '?': | 
| 176 | > | case 'H': | 
| 177 | > | if(isalnum(argv[arg][2])) | 
| 178 | > | { | 
| 179 | > | if(strncasecmp(argv[arg]+2,"all",3)) | 
| 180 | > | { | 
| 181 | > | OBFormat* pFormat = Conv.FindFormat(argv[arg]+2); | 
| 182 | > | if(pFormat) | 
| 183 | > | { | 
| 184 | > | cout << argv[arg]+2 << "  " << pFormat->Description() << endl; | 
| 185 | > | if(strlen(pFormat->SpecificationURL())) | 
| 186 | > | cout << "Specification at: " << pFormat->SpecificationURL() << endl; | 
| 187 | > | } | 
| 188 | > | else | 
| 189 | > | cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl; | 
| 190 | > | } | 
| 191 | > | else | 
| 192 | > | { | 
| 193 | > | Formatpos pos; | 
| 194 | > | OBFormat* pFormat; | 
| 195 | > | const char* str=NULL; | 
| 196 | > | while(OBConversion::GetNextFormat(pos,str,pFormat)) | 
| 197 | > | { | 
| 198 | > | if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) | 
| 199 | > | continue; | 
| 200 | > | cout << str << endl; | 
| 201 | > | const char* p = strchr(pFormat->Description(),'\n'); | 
| 202 | > | cout << p+1; //second line of description | 
| 203 | > | if(strlen(pFormat->SpecificationURL())) | 
| 204 | > | cout << "Specification at: " << pFormat->SpecificationURL(); | 
| 205 | > | cout << endl << endl; | 
| 206 | > | } | 
| 207 | > | } | 
| 208 | > | } | 
| 209 | > | else | 
| 210 | > | help(); | 
| 211 | > | exit(0); | 
| 212 |  |  | 
| 213 | + | case '-': //long option --name text | 
| 214 | + | { | 
| 215 | + | //Do nothing if name is empty | 
| 216 | + | //Option's text is the next arg provided it doesn't start with - | 
| 217 | + | char* nam = argv[arg]+2; | 
| 218 | + | if(*nam != '\0') | 
| 219 | + | { | 
| 220 | + | string txt; | 
| 221 | + | int i; | 
| 222 | + | for(i=0; i<Conv.GetOptionParams(nam, OBConversion::GENOPTIONS) | 
| 223 | + | && arg<argc-1 && argv[arg+1];++i) //removed  && *argv[arg+1]!='-' | 
| 224 | + | { | 
| 225 | + | if(!txt.empty()) txt+=' '; | 
| 226 | + | txt += argv[++arg]; | 
| 227 | + | } | 
| 228 | + | if(*nam=='-') | 
| 229 | + | { | 
| 230 | + | // Is a API directive, e.g.---errorlevel | 
| 231 | + | //Send to the pseudoformat "obapi" (without any leading -) | 
| 232 | + | OBConversion apiConv; | 
| 233 | + | OBFormat* pAPI= OBConversion::FindFormat("obapi"); | 
| 234 | + | if(pAPI) | 
| 235 | + | { | 
| 236 | + | apiConv.SetOutFormat(pAPI); | 
| 237 | + | apiConv.AddOption(nam+1, OBConversion::GENOPTIONS, txt.c_str()); | 
| 238 | + | apiConv.Write(NULL, &std::cout); | 
| 239 | + | } | 
| 240 | + | } | 
| 241 | + | else | 
| 242 | + | // Is a long option name, e.g --addtotitle | 
| 243 | + | Conv.AddOption(nam,OBConversion::GENOPTIONS,txt.c_str()); | 
| 244 | + | } | 
| 245 | + | } | 
| 246 | + | break; | 
| 247 |  |  | 
| 248 | < | default: //single character general option | 
| 249 | < | p = argv[arg]+1; | 
| 250 | < | DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv); | 
| 251 | < | break; | 
| 252 | < | } | 
| 253 | < | } | 
| 254 | < | else | 
| 255 | < | { | 
| 256 | < | //filenames | 
| 257 | < | if(!gotOutType) | 
| 258 | < | FileList.push_back(argv[arg]); | 
| 259 | < | else | 
| 260 | < | OutputFileName = argv[arg]; | 
| 261 | < | } | 
| 262 | < | } | 
| 263 | < | } | 
| 264 | < |  | 
| 265 | < | //user didn't specify input and output format in commandline option | 
| 266 | < | //try to parse it from program name (pdb2mdin means input format is pdb, output format is mdin) | 
| 248 | > | case 'm': //multiple output files | 
| 249 | > | SplitOrBatch=true; | 
| 250 | > | break; | 
| 251 | > |  | 
| 252 | > | case 'a': //single character input option | 
| 253 | > | p = argv[arg]+2; | 
| 254 | > | DoOption(p,Conv,OBConversion::INOPTIONS,arg,argc,argv); | 
| 255 | > | break; | 
| 256 | > |  | 
| 257 | > | case 'x': //single character output option | 
| 258 | > | p = argv[arg]+2; | 
| 259 | > | DoOption(p,Conv,OBConversion::OUTOPTIONS,arg,argc,argv); | 
| 260 | > | break; | 
| 261 | > |  | 
| 262 | > | default: //single character general option | 
| 263 | > | p = argv[arg]+1; | 
| 264 | > | DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv); | 
| 265 | > | break; | 
| 266 | > | } | 
| 267 | > | } | 
| 268 | > | else | 
| 269 | > | { | 
| 270 | > | //filenames | 
| 271 | > | if(!gotOutType) | 
| 272 | > | FileList.push_back(argv[arg]); | 
| 273 | > | else | 
| 274 | > | OutputFileName = argv[arg]; | 
| 275 | > | } | 
| 276 | > | } | 
| 277 | > | } | 
| 278 | > |  | 
| 279 | > | // user didn't specify input and output format in commandline option | 
| 280 | > | // try to parse it from program name (pdb2mdin means input format is pdb, | 
| 281 | > | // output format is mdin) | 
| 282 | > |  | 
| 283 |  | string formatName(program_name); | 
| 284 |  | pos = formatName.find_first_of("2"); | 
| 285 |  | if(pos!=string::npos) { | 
| 286 |  | if (!gotInType) | 
| 287 | < | { | 
| 287 | > | { | 
| 288 |  | string tmpExt = formatName.substr(0, pos); | 
| 289 |  | pInFormat = Conv.FindFormat(tmpExt.c_str()); | 
| 290 | < | if(pInFormat==NULL) | 
| 291 | < | { | 
| 292 | < | cerr << program_name << ": cannot read input format!" << endl; | 
| 293 | < | usage(); | 
| 294 | < | } else | 
| 295 | < | { | 
| 290 | > | if(pInFormat==NULL) | 
| 291 | > | { | 
| 292 | > | cerr << program_name << ": cannot read input format!" << endl; | 
| 293 | > | usage(); | 
| 294 | > | } else | 
| 295 | > | { | 
| 296 |  | gotInType = true; | 
| 297 |  | inputExt = tmpExt; | 
| 298 | < | } | 
| 299 | < | } | 
| 298 | > | } | 
| 299 | > | } | 
| 300 |  |  | 
| 301 |  | if (!gotOutType) | 
| 302 | < | { | 
| 302 | > | { | 
| 303 |  | string tmpExt = formatName.substr(pos+1, string::npos); | 
| 304 |  | pOutFormat = Conv.FindFormat(tmpExt.c_str()); | 
| 305 | < | if(pOutFormat==NULL) | 
| 306 | < | { | 
| 307 | < | cerr << program_name << ": cannot write output format!" << endl; | 
| 308 | < | usage(); | 
| 309 | < | }else { | 
| 310 | < | gotOutType = true; | 
| 311 | < | outputExt = tmpExt; | 
| 312 | < | } | 
| 313 | < | } | 
| 305 | > | if(pOutFormat==NULL) | 
| 306 | > | { | 
| 307 | > | cerr << program_name << ": cannot write output format!" << endl; | 
| 308 | > | usage(); | 
| 309 | > | }else { | 
| 310 | > | gotOutType = true; | 
| 311 | > | outputExt = tmpExt; | 
| 312 | > | } | 
| 313 | > | } | 
| 314 |  | } | 
| 315 | < |  | 
| 316 | < | if(FileList.empty()) | 
| 315 | > |  | 
| 316 | > | if (!gotInType) | 
| 317 |  | { | 
| 318 | < | cerr << "No input file or format spec!" <<endl; | 
| 319 | < | usage(); | 
| 318 | > | if(FileList.empty()) | 
| 319 | > | { | 
| 320 | > | cerr << "No input file or format spec!" <<endl; | 
| 321 | > | usage(); | 
| 322 | > | } | 
| 323 |  | } | 
| 324 | < |  | 
| 325 | < | if (OutputFileName.empty()) | 
| 326 | < | { | 
| 327 | < | pos = FileList.front().rfind("."); | 
| 328 | < | if(pos==string::npos) | 
| 329 | < | OutputFileName = FileList.front()+ "." + outputExt; | 
| 330 | < | else | 
| 331 | < | OutputFileName = FileList.front().substr(0, pos) + "." + outputExt; | 
| 324 | > |  | 
| 325 | > | if (!gotOutType) | 
| 326 | > | { | 
| 327 | > | pOutFormat = Conv.FormatFromExt(OutputFileName.c_str()); | 
| 328 | > | if(pOutFormat==NULL) | 
| 329 | > | { | 
| 330 | > | cerr << program_name << ": cannot write output format!" << endl; | 
| 331 | > | usage(); | 
| 332 | > | } | 
| 333 |  | } | 
| 334 |  |  | 
| 335 | < | Conv.SetInAndOutFormats(pInFormat,pOutFormat); | 
| 335 | > | Conv.SetInAndOutFormats(pInFormat, pOutFormat); | 
| 336 | > |  | 
| 337 | > | if(SplitOrBatch) | 
| 338 | > | { | 
| 339 | > | //Put * into output file name before extension (or ext.gz) | 
| 340 | > | if(OutputFileName.empty()) | 
| 341 | > | { | 
| 342 | > | OutputFileName = "*."; | 
| 343 | > | OutputFileName += oext; | 
| 344 | > | } | 
| 345 | > | else | 
| 346 | > | { | 
| 347 | > | string::size_type pos = OutputFileName.rfind(".gz"); | 
| 348 | > | if(pos==string::npos) | 
| 349 | > | pos = OutputFileName.rfind('.'); | 
| 350 | > | else | 
| 351 | > | pos = OutputFileName.rfind('.',pos-1); | 
| 352 | > | if(pos==string::npos) | 
| 353 | > | OutputFileName += '*'; | 
| 354 | > | else | 
| 355 | > | OutputFileName.insert(pos,"*"); | 
| 356 | > | } | 
| 357 | > | } | 
| 358 |  |  | 
| 271 | – |  | 
| 272 | – | // send info message to clog -- don't mess up cerr or cout for user programs | 
| 359 |  | int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList); | 
| 274 | – | if ( count == 1 ) | 
| 275 | – | clog << count << " molecule converted" << endl; | 
| 276 | – | else | 
| 277 | – | clog << count << " molecules converted" << endl; | 
| 360 |  |  | 
| 361 | + | // send info message to clog -- don't mess up cerr or cout for user programs | 
| 362 | + | //Get the last word on the first line of the description which should | 
| 363 | + | //be "molecules", "reactions", etc and remove the s if only one object converted | 
| 364 | + | std::string objectname(pOutFormat->TargetClassDescription()); | 
| 365 | + | pos = objectname.find('\n'); | 
| 366 | + | if(count==1) --pos; | 
| 367 | + | objectname.erase(pos); | 
| 368 | + | pos = objectname.rfind(' '); | 
| 369 | + | if(pos==std::string::npos) | 
| 370 | + | pos=0; | 
| 371 | + | std::clog << count << objectname.substr(pos) << " converted" << endl; | 
| 372 |  | if(OutputFileList.size()>1) | 
| 373 | < | { | 
| 374 | < | clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl; | 
| 375 | < | } | 
| 373 | > | { | 
| 374 | > | clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl; | 
| 375 | > | } | 
| 376 | > |  | 
| 377 | > | std::string messageSummary = obErrorLog.GetMessageSummary(); | 
| 378 | > | if (messageSummary.size()) | 
| 379 | > | { | 
| 380 | > | clog << messageSummary << endl; | 
| 381 | > | } | 
| 382 |  |  | 
| 383 |  | #ifdef _DEBUG | 
| 384 |  | //CM keep window open | 
| 385 |  | cout << "Press any key to finish" <<endl; | 
| 386 |  | getch(); | 
| 387 |  | #endif | 
| 289 | – |  | 
| 388 |  | return 0; | 
| 389 |  | } | 
| 390 |  |  | 
| 391 | < | void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, int& arg, int argc, char *argv[]) | 
| 391 | > | void DoOption(const char* p, OBConversion& Conv, | 
| 392 | > | OBConversion::Option_type typ, int& arg, int argc, char *argv[]) | 
| 393 |  | { | 
| 394 | < | while(p && *p) //can have multiple single char options | 
| 395 | < | { | 
| 396 | < | char ch[2]="?"; | 
| 397 | < | *ch = *p++; | 
| 398 | < | const char* txt=NULL; | 
| 399 | < | //Get the option text if needed | 
| 400 | < | int nParams = Conv.GetOptionParams(ch, typ); | 
| 401 | < | if(nParams) | 
| 402 | < | { | 
| 403 | < | if(*p) | 
| 404 | < | { | 
| 405 | < | txt = p; //use text immediately following the option letter | 
| 406 | < | p=NULL; //no more single char options | 
| 407 | < | } | 
| 408 | < | else if(arg<argc-1) | 
| 409 | < | { | 
| 410 | < | txt = argv[++arg]; //use text from next arg | 
| 411 | < | if(*txt=='-') | 
| 412 | < | { | 
| 413 | < | //...unless it is another option | 
| 414 | < | cerr << "Option -" << ch << " takes a parameter" << endl; | 
| 415 | < | exit(0); | 
| 416 | < | } | 
| 417 | < | } | 
| 418 | < | } | 
| 419 | < | Conv.AddOption(ch, typ, txt); | 
| 420 | < | } | 
| 394 | > | while(p && *p) //can have multiple single char options | 
| 395 | > | { | 
| 396 | > | char ch[2]="?"; | 
| 397 | > | *ch = *p++; | 
| 398 | > | const char* txt=NULL; | 
| 399 | > | //Get the option text if needed | 
| 400 | > | int nParams = Conv.GetOptionParams(ch, typ); | 
| 401 | > | if(nParams) | 
| 402 | > | { | 
| 403 | > | if(*p) | 
| 404 | > | { | 
| 405 | > | txt = p; //use text immediately following the option letter | 
| 406 | > | p=NULL; //no more single char options | 
| 407 | > | } | 
| 408 | > | else if(arg<argc-1) | 
| 409 | > | { | 
| 410 | > | txt = argv[++arg]; //use text from next arg | 
| 411 | > | if(*txt=='-') | 
| 412 | > | { | 
| 413 | > | //...unless it is another option | 
| 414 | > | cerr << "Option -" << ch << " takes a parameter" << endl; | 
| 415 | > | exit(0); | 
| 416 | > | } | 
| 417 | > | } | 
| 418 | > | } | 
| 419 | > | Conv.AddOption(ch, typ, txt); | 
| 420 | > | } | 
| 421 |  | } | 
| 422 |  |  | 
| 423 |  | void usage() | 
| 424 |  | { | 
| 425 | < | cout << "Open Babel " << BABEL_VERSION << " -- " << __DATE__ << " -- " | 
| 426 | < | << __TIME__ << endl; | 
| 425 | > | cout << program_name << ": part of OOPSE " << | 
| 426 | > | OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << "." << | 
| 427 | > | OOPSE_VERSION_TINY << " and OpenBabel " << BABEL_VERSION << " -- " | 
| 428 | > | << __DATE__ << " -- " << __TIME__ << endl; | 
| 429 |  | cout << "Usage: " << program_name | 
| 430 |  | << " [-i<input-type>] <name> [-o<output-type>] <name>" << endl; | 
| 431 |  | cout << "Try  -H option for more information." << endl; | 
| 441 |  |  | 
| 442 |  | void help() | 
| 443 |  | { | 
| 444 | < | cout << "Open Babel converts chemical structures from one file format to another"<< endl << endl; | 
| 444 | > | cout << program_name << " converts chemical structures from one file format to another"<< endl << endl; | 
| 445 |  | cout << "Usage: " << program_name << " <input spec> <output spec> [Options]" << endl << endl; | 
| 446 |  | cout << "Each spec can be a file whose extension decides the format." << endl; | 
| 447 |  | cout << "Optionally the format can be specified by preceding the file by" << endl; | 
| 459 |  |  | 
| 460 |  |  | 
| 461 |  | OBFormat* pDefault = OBConversion::GetDefaultFormat(); | 
| 462 | < | if(pDefault) | 
| 463 | < | cout << pDefault->TargetClassDescription();// some more options probably for OBMol | 
| 462 | > | if(pDefault) | 
| 463 | > | cout << pDefault->TargetClassDescription();// some more options probably for OBMol | 
| 464 |  |  | 
| 465 | < | OBFormat* pAPI= OBConversion::FindFormat("obapi"); | 
| 466 | < | if(pAPI) | 
| 467 | < | cout << pAPI->Description(); | 
| 468 | < |  | 
| 469 | < | cout << "The following file formats are recognized:" << endl; | 
| 465 | > | OBFormat* pAPI= OBConversion::FindFormat("obapi"); | 
| 466 | > | if(pAPI) | 
| 467 | > | cout << pAPI->Description(); | 
| 468 | > |  | 
| 469 | > | cout << "The following file formats are recognized:" << endl; | 
| 470 |  | Formatpos pos; | 
| 471 |  | OBFormat* pFormat; | 
| 472 |  | const char* str=NULL; | 
| 473 |  | while(OBConversion::GetNextFormat(pos,str,pFormat)) | 
| 474 | < | { | 
| 475 | < | if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) | 
| 476 | < | continue; | 
| 477 | < | cout << "  " << str << endl; | 
| 478 | < | } | 
| 474 | > | { | 
| 475 | > | if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) | 
| 476 | > | continue; | 
| 477 | > | cout << "  " << str << endl; | 
| 478 | > | } | 
| 479 |  | cout << "\nSee further specific info and options using -H<format-type>, e.g. -Hpdb" << endl; | 
| 480 |  | } | 
| 481 |  |  |