| 1 |
tim |
747 |
/********************************************************************** |
| 2 |
|
|
main.cpp - Main conversion program, command-line handling. |
| 3 |
|
|
|
| 4 |
|
|
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
| 5 |
|
|
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
| 6 |
|
|
Some portions Copyright (C) 2004-2005 by Chris Morley |
| 7 |
|
|
|
| 8 |
|
|
This file is part of the Open Babel project. |
| 9 |
|
|
For more information, see <http://openbabel.sourceforge.net/> |
| 10 |
|
|
|
| 11 |
|
|
This program is free software; you can redistribute it and/or modify |
| 12 |
|
|
it under the terms of the GNU General Public License as published by |
| 13 |
|
|
the Free Software Foundation version 2 of the License. |
| 14 |
|
|
|
| 15 |
|
|
This program is distributed in the hope that it will be useful, |
| 16 |
|
|
but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 17 |
|
|
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 18 |
|
|
GNU General Public License for more details. |
| 19 |
|
|
***********************************************************************/ |
| 20 |
|
|
|
| 21 |
|
|
#include "openbabel/babelconfig.hpp" |
| 22 |
|
|
#if HAVE_IOSTREAM |
| 23 |
|
|
#include <iostream> |
| 24 |
|
|
#elif HAVE_IOSTREAM_H |
| 25 |
|
|
#include <iostream.h> |
| 26 |
|
|
#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 |
| 37 |
|
|
|
| 38 |
|
|
#include <string> |
| 39 |
|
|
#include <map> |
| 40 |
|
|
#if HAVE_CONIO_H |
| 41 |
|
|
#include <conio.h> |
| 42 |
|
|
#endif |
| 43 |
|
|
|
| 44 |
|
|
#if !HAVE_STRNCASECMP |
| 45 |
|
|
extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); |
| 46 |
|
|
#endif |
| 47 |
|
|
|
| 48 |
|
|
#include "openbabel/obconversion.hpp" |
| 49 |
|
|
#include "brains/Register.hpp" |
| 50 |
|
|
|
| 51 |
|
|
using namespace std; |
| 52 |
|
|
using namespace OpenBabel; |
| 53 |
|
|
using namespace oopse; |
| 54 |
|
|
void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, |
| 55 |
|
|
int& arg, int argc, char *argv[]); |
| 56 |
|
|
void usage(); |
| 57 |
|
|
void help(); |
| 58 |
|
|
|
| 59 |
|
|
// There isn't a great way to do this -- we need to save argv[0] for usage() |
| 60 |
|
|
static char *program_name; |
| 61 |
|
|
|
| 62 |
|
|
int main(int argc,char *argv[]) |
| 63 |
|
|
{ |
| 64 |
|
|
registerOBFormats(); |
| 65 |
|
|
OBConversion Conv(&cin, &cout); //default input and output are console |
| 66 |
|
|
|
| 67 |
|
|
// string GenOptions; |
| 68 |
|
|
OBFormat* pInFormat = NULL; |
| 69 |
|
|
OBFormat* pOutFormat = NULL; |
| 70 |
|
|
vector<string> FileList, OutputFileList; |
| 71 |
|
|
string OutputFileName; |
| 72 |
|
|
// obMessageLevel filterLevel = obWarning; // 2 out of 5 |
| 73 |
|
|
|
| 74 |
|
|
// Parse commandline |
| 75 |
|
|
bool gotInType = false, gotOutType = false; |
| 76 |
|
|
bool UseSavedOptions = false; |
| 77 |
|
|
bool SplitOrBatch=false; |
| 78 |
|
|
|
| 79 |
|
|
char *oext; |
| 80 |
|
|
char *iext; |
| 81 |
|
|
|
| 82 |
|
|
//Save name of program without its path (and .exe) |
| 83 |
|
|
string pn(argv[0]); |
| 84 |
|
|
unsigned int pos; |
| 85 |
|
|
#ifdef _WIN32 |
| 86 |
|
|
pos = pn.find(".exe"); |
| 87 |
|
|
if(pos!=string::npos) |
| 88 |
|
|
argv[0][pos]='\0'; |
| 89 |
|
|
#endif |
| 90 |
|
|
pos = pn.find_last_of("/\\"); |
| 91 |
|
|
if(pos==string::npos) |
| 92 |
|
|
program_name=argv[0]; |
| 93 |
|
|
else |
| 94 |
|
|
program_name=argv[0]+pos+1; |
| 95 |
|
|
|
| 96 |
|
|
const char* p; |
| 97 |
|
|
int arg; |
| 98 |
|
|
for (arg = 1; arg < argc; arg++) |
| 99 |
|
|
{ |
| 100 |
|
|
if (argv[arg]) |
| 101 |
|
|
{ |
| 102 |
|
|
if (argv[arg][0] == '-') |
| 103 |
|
|
{ |
| 104 |
|
|
switch (argv[arg][1]) |
| 105 |
|
|
{ |
| 106 |
|
|
|
| 107 |
|
|
case 'V': |
| 108 |
|
|
{ |
| 109 |
|
|
cout << "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 |
| 119 |
|
|
|
| 120 |
|
|
if (strncasecmp(iext, "MIME", 4) == 0) |
| 121 |
|
|
{ |
| 122 |
|
|
// get the MIME type from the next argument |
| 123 |
|
|
iext = argv[++arg]; |
| 124 |
|
|
pInFormat = Conv.FormatFromMIME(iext); |
| 125 |
|
|
} |
| 126 |
|
|
else |
| 127 |
|
|
{ |
| 128 |
|
|
//The ID provided by the OBFormat class is used as the identifying file extension |
| 129 |
|
|
pInFormat = Conv.FindFormat(iext); |
| 130 |
|
|
} |
| 131 |
|
|
if(pInFormat==NULL) |
| 132 |
|
|
{ |
| 133 |
|
|
cerr << program_name << ": cannot read input format!" << endl; |
| 134 |
|
|
usage(); |
| 135 |
|
|
} |
| 136 |
|
|
break; |
| 137 |
|
|
|
| 138 |
|
|
case 'o': |
| 139 |
|
|
gotOutType = true; |
| 140 |
|
|
oext = argv[arg] + 2; |
| 141 |
|
|
if(!*oext) |
| 142 |
|
|
oext = argv[++arg]; //space left after -i: use next argument |
| 143 |
|
|
|
| 144 |
|
|
if (strncasecmp(oext, "MIME", 4) == 0) |
| 145 |
|
|
{ |
| 146 |
|
|
// get the MIME type from the next argument |
| 147 |
|
|
oext = argv[++arg]; |
| 148 |
|
|
pOutFormat = Conv.FormatFromMIME(oext); |
| 149 |
|
|
} |
| 150 |
|
|
else |
| 151 |
|
|
pOutFormat = Conv.FindFormat(oext); |
| 152 |
|
|
|
| 153 |
|
|
if(pOutFormat==NULL) |
| 154 |
|
|
{ |
| 155 |
|
|
cerr << program_name << ": cannot write output format!" << endl; |
| 156 |
|
|
usage(); |
| 157 |
|
|
} |
| 158 |
|
|
break; |
| 159 |
|
|
|
| 160 |
|
|
case 'F': |
| 161 |
|
|
if(!Conv.SetOutFormat("fpt")) |
| 162 |
|
|
cout << "FingerprintFormat needs to be loaded" << endl; |
| 163 |
|
|
else |
| 164 |
|
|
{ |
| 165 |
|
|
Conv.AddOption("F",OBConversion::OUTOPTIONS); |
| 166 |
|
|
Conv.Write(NULL); |
| 167 |
|
|
} |
| 168 |
|
|
return 0; |
| 169 |
|
|
|
| 170 |
|
|
case '?': |
| 171 |
|
|
case 'H': |
| 172 |
|
|
if(isalnum(argv[arg][2])) |
| 173 |
|
|
{ |
| 174 |
|
|
if(strncasecmp(argv[arg]+2,"all",3)) |
| 175 |
|
|
{ |
| 176 |
|
|
OBFormat* pFormat = Conv.FindFormat(argv[arg]+2); |
| 177 |
|
|
if(pFormat) |
| 178 |
|
|
{ |
| 179 |
|
|
cout << argv[arg]+2 << " " << pFormat->Description() << endl; |
| 180 |
|
|
if(strlen(pFormat->SpecificationURL())) |
| 181 |
|
|
cout << "Specification at: " << pFormat->SpecificationURL() << endl; |
| 182 |
|
|
} |
| 183 |
|
|
else |
| 184 |
|
|
cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl; |
| 185 |
|
|
} |
| 186 |
|
|
else |
| 187 |
|
|
{ |
| 188 |
|
|
Formatpos pos; |
| 189 |
|
|
OBFormat* pFormat; |
| 190 |
|
|
const char* str=NULL; |
| 191 |
|
|
while(OBConversion::GetNextFormat(pos,str,pFormat)) |
| 192 |
|
|
{ |
| 193 |
|
|
if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) |
| 194 |
|
|
continue; |
| 195 |
|
|
cout << str << endl; |
| 196 |
|
|
const char* p = strchr(pFormat->Description(),'\n'); |
| 197 |
|
|
cout << p+1; //second line of description |
| 198 |
|
|
if(strlen(pFormat->SpecificationURL())) |
| 199 |
|
|
cout << "Specification at: " << pFormat->SpecificationURL(); |
| 200 |
|
|
cout << endl << endl; |
| 201 |
|
|
} |
| 202 |
|
|
} |
| 203 |
|
|
} |
| 204 |
|
|
else |
| 205 |
|
|
help(); |
| 206 |
|
|
exit(0); |
| 207 |
|
|
|
| 208 |
|
|
case '-': //long option --name text |
| 209 |
|
|
{ |
| 210 |
|
|
//Do nothing if name is empty |
| 211 |
|
|
//Option's text is the next arg provided it doesn't start with - |
| 212 |
|
|
char* nam = argv[arg]+2; |
| 213 |
|
|
if(*nam != '\0') |
| 214 |
|
|
{ |
| 215 |
|
|
const char* txt=NULL; |
| 216 |
|
|
if(Conv.GetOptionParams(nam, OBConversion::OUTOPTIONS) |
| 217 |
|
|
&& arg<argc-1 && argv[arg+1] && *argv[arg+1]!='-') |
| 218 |
|
|
txt = argv[++arg]; |
| 219 |
|
|
if(*nam=='-') |
| 220 |
|
|
{ |
| 221 |
|
|
// Is a API directive, e.g.---errorlevel |
| 222 |
|
|
//Send to the pseudoformat "obapi" (without any leading -) |
| 223 |
|
|
OBConversion apiConv; |
| 224 |
|
|
OBFormat* pAPI= OBConversion::FindFormat("obapi"); |
| 225 |
|
|
if(pAPI) |
| 226 |
|
|
{ |
| 227 |
|
|
apiConv.SetOutFormat(pAPI); |
| 228 |
|
|
apiConv.AddOption(nam+1, OBConversion::OUTOPTIONS, txt); |
| 229 |
|
|
apiConv.Write(NULL); |
| 230 |
|
|
} |
| 231 |
|
|
} |
| 232 |
|
|
else |
| 233 |
|
|
// Is a long option name, e.g --addtotitle |
| 234 |
|
|
Conv.AddOption(nam,OBConversion::GENOPTIONS,txt); |
| 235 |
|
|
} |
| 236 |
|
|
} |
| 237 |
|
|
break; |
| 238 |
|
|
|
| 239 |
|
|
case 'm': //multiple output files |
| 240 |
|
|
SplitOrBatch=true; |
| 241 |
|
|
break; |
| 242 |
|
|
|
| 243 |
|
|
case 'a': //single character input option |
| 244 |
|
|
p = argv[arg]+2; |
| 245 |
|
|
DoOption(p,Conv,OBConversion::INOPTIONS,arg,argc,argv); |
| 246 |
|
|
break; |
| 247 |
|
|
|
| 248 |
|
|
case 'x': //single character output option |
| 249 |
|
|
p = argv[arg]+2; |
| 250 |
|
|
DoOption(p,Conv,OBConversion::OUTOPTIONS,arg,argc,argv); |
| 251 |
|
|
break; |
| 252 |
|
|
|
| 253 |
|
|
default: //single character general option |
| 254 |
|
|
p = argv[arg]+1; |
| 255 |
|
|
DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv); |
| 256 |
|
|
break; |
| 257 |
|
|
} |
| 258 |
|
|
} |
| 259 |
|
|
else |
| 260 |
|
|
{ |
| 261 |
|
|
//filenames |
| 262 |
|
|
if(!gotOutType) |
| 263 |
|
|
FileList.push_back(argv[arg]); |
| 264 |
|
|
else |
| 265 |
|
|
OutputFileName = argv[arg]; |
| 266 |
|
|
} |
| 267 |
|
|
} |
| 268 |
|
|
} |
| 269 |
|
|
|
| 270 |
|
|
if(!gotOutType) //the last file is the output |
| 271 |
|
|
{ |
| 272 |
|
|
if(FileList.empty()) |
| 273 |
|
|
{ |
| 274 |
|
|
cerr << "No output file or format spec!" << endl; |
| 275 |
|
|
usage(); |
| 276 |
|
|
} |
| 277 |
|
|
OutputFileName = FileList.back(); |
| 278 |
|
|
FileList.pop_back(); |
| 279 |
|
|
} |
| 280 |
|
|
|
| 281 |
|
|
#ifdef _WIN32 |
| 282 |
|
|
//Expand wildcards in input filenames and add to FileList |
| 283 |
|
|
vector<string> tempFileList(FileList); |
| 284 |
|
|
FileList.clear(); |
| 285 |
|
|
vector<string>::iterator itr; |
| 286 |
|
|
for(itr=tempFileList.begin();itr!=tempFileList.end();itr++) |
| 287 |
|
|
DLHandler::findFiles (FileList, *itr); |
| 288 |
|
|
#endif |
| 289 |
|
|
|
| 290 |
|
|
// Conv.SetGeneralOptions(GenOptions.c_str()); |
| 291 |
|
|
|
| 292 |
|
|
if (!gotInType) |
| 293 |
|
|
{ |
| 294 |
|
|
if(FileList.empty()) |
| 295 |
|
|
{ |
| 296 |
|
|
cerr << "No input file or format spec!" <<endl; |
| 297 |
|
|
usage(); |
| 298 |
|
|
} |
| 299 |
|
|
} |
| 300 |
|
|
|
| 301 |
|
|
if (!gotOutType) |
| 302 |
|
|
{ |
| 303 |
|
|
pOutFormat = Conv.FormatFromExt(OutputFileName.c_str()); |
| 304 |
|
|
if(pOutFormat==NULL) |
| 305 |
|
|
{ |
| 306 |
|
|
cerr << program_name << ": cannot write output format!" << endl; |
| 307 |
|
|
usage(); |
| 308 |
|
|
} |
| 309 |
|
|
} |
| 310 |
|
|
|
| 311 |
|
|
Conv.SetInAndOutFormats(pInFormat,pOutFormat); |
| 312 |
|
|
|
| 313 |
|
|
if(SplitOrBatch) |
| 314 |
|
|
{ |
| 315 |
|
|
//Put * into output file name before extension (or ext.gz) |
| 316 |
|
|
if(OutputFileName.empty()) |
| 317 |
|
|
{ |
| 318 |
|
|
OutputFileName = "*."; |
| 319 |
|
|
OutputFileName += oext; |
| 320 |
|
|
} |
| 321 |
|
|
else |
| 322 |
|
|
{ |
| 323 |
|
|
unsigned int pos = OutputFileName.rfind(".gz"); |
| 324 |
|
|
if(pos==string::npos) |
| 325 |
|
|
pos = OutputFileName.rfind('.'); |
| 326 |
|
|
else |
| 327 |
|
|
pos = OutputFileName.rfind('.',pos-1); |
| 328 |
|
|
if(pos==string::npos) |
| 329 |
|
|
OutputFileName += '*'; |
| 330 |
|
|
else |
| 331 |
|
|
OutputFileName.insert(pos,"*"); |
| 332 |
|
|
} |
| 333 |
|
|
} |
| 334 |
|
|
|
| 335 |
|
|
// send info message to clog -- don't mess up cerr or cout for user programs |
| 336 |
|
|
int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList); |
| 337 |
|
|
if ( count == 1 ) |
| 338 |
|
|
clog << count << " molecule converted" << endl; |
| 339 |
|
|
else |
| 340 |
|
|
clog << count << " molecules converted" << endl; |
| 341 |
|
|
|
| 342 |
|
|
if(OutputFileList.size()>1) |
| 343 |
|
|
{ |
| 344 |
|
|
clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl; |
| 345 |
|
|
} |
| 346 |
|
|
|
| 347 |
|
|
#ifdef _DEBUG |
| 348 |
|
|
//CM keep window open |
| 349 |
|
|
cout << "Press any key to finish" <<endl; |
| 350 |
|
|
getch(); |
| 351 |
|
|
#endif |
| 352 |
|
|
|
| 353 |
|
|
return 0; |
| 354 |
|
|
}; |
| 355 |
|
|
|
| 356 |
|
|
void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, int& arg, int argc, char *argv[]) |
| 357 |
|
|
{ |
| 358 |
|
|
while(p && *p) //can have multiple single char options |
| 359 |
|
|
{ |
| 360 |
|
|
char ch[2]="?"; |
| 361 |
|
|
*ch = *p++; |
| 362 |
|
|
const char* txt=NULL; |
| 363 |
|
|
//Get the option text if needed |
| 364 |
|
|
int nParams = Conv.GetOptionParams(ch, typ); |
| 365 |
|
|
if(nParams) |
| 366 |
|
|
{ |
| 367 |
|
|
if(*p) |
| 368 |
|
|
{ |
| 369 |
|
|
txt = p; //use text immediately following the option letter |
| 370 |
|
|
p=NULL; //no more single char options |
| 371 |
|
|
} |
| 372 |
|
|
else if(arg<argc-1) |
| 373 |
|
|
{ |
| 374 |
|
|
txt = argv[++arg]; //use text from next arg |
| 375 |
|
|
if(*txt=='-') |
| 376 |
|
|
{ |
| 377 |
|
|
//...unless it is another option |
| 378 |
|
|
cerr << "Option -" << ch << " takes a parameter" << endl; |
| 379 |
|
|
exit(0); |
| 380 |
|
|
} |
| 381 |
|
|
} |
| 382 |
|
|
} |
| 383 |
|
|
Conv.AddOption(ch, typ, txt); |
| 384 |
|
|
} |
| 385 |
|
|
} |
| 386 |
|
|
|
| 387 |
|
|
void usage() |
| 388 |
|
|
{ |
| 389 |
|
|
cout << "Open Babel " << BABEL_VERSION << " -- " << __DATE__ << " -- " |
| 390 |
|
|
<< __TIME__ << endl; |
| 391 |
|
|
cout << "Usage: " << program_name |
| 392 |
|
|
<< " [-i<input-type>] <name> [-o<output-type>] <name>" << endl; |
| 393 |
|
|
cout << "Try -H option for more information." << endl; |
| 394 |
|
|
/* |
| 395 |
|
|
#ifdef _DEBUG |
| 396 |
|
|
//CM keep window open |
| 397 |
|
|
cout << "Press any key to finish" <<endl; |
| 398 |
|
|
getch(); |
| 399 |
|
|
#endif |
| 400 |
|
|
*/ |
| 401 |
|
|
exit (0); |
| 402 |
|
|
} |
| 403 |
|
|
|
| 404 |
|
|
void help() |
| 405 |
|
|
{ |
| 406 |
|
|
cout << "Open Babel converts chemical structures from one file format to another"<< endl << endl; |
| 407 |
|
|
cout << "Usage: " << program_name << " <input spec> <output spec> [Options]" << endl << endl; |
| 408 |
|
|
cout << "Each spec can be a file whose extension decides the format." << endl; |
| 409 |
|
|
cout << "Optionally the format can be specified by preceding the file by" << endl; |
| 410 |
|
|
cout << "-i<format-type> e.g. -icml, for input and -o<format-type> for output" << endl << endl; |
| 411 |
|
|
cout << "See below for available format-types, which are the same as the " << endl; |
| 412 |
|
|
cout << "file extensions and are case independent." << endl; |
| 413 |
|
|
cout << "If no input or output file is given stdin or stdout are used instead." << endl << endl; |
| 414 |
|
|
cout << "More than one input file can be specified and their names can contain" <<endl; |
| 415 |
|
|
cout << "wildcard chars (* and ?).The molecules are aggregated in the output file.\n" << endl; |
| 416 |
|
|
cout << OBConversion::Description(); // Conversion options |
| 417 |
|
|
cout << " -H Outputs this help text" << endl; |
| 418 |
|
|
cout << " -Hxxx (xxx is file format ID e.g. -Hcml) gives format info" <<endl; |
| 419 |
|
|
cout << " -Hall Outputs details of all formats" <<endl; |
| 420 |
|
|
cout << " -V Outputs version number" <<endl; |
| 421 |
|
|
cout << " -F Outputs the available fingerprint types" <<endl; |
| 422 |
|
|
cout << " -m Produces multiple output files, to allow:" <<endl; |
| 423 |
|
|
cout << " Splitting: e.g. " << program_name << " infile.mol new.smi -m" <<endl; |
| 424 |
|
|
cout << " puts each molecule into new1.smi new2.smi etc" <<endl; |
| 425 |
|
|
cout << " Batch conversion: e.g. " << program_name << " *.mol -osmi -m" <<endl; |
| 426 |
|
|
cout << " converts each input file to a .smi file" << endl; |
| 427 |
|
|
#ifdef _WIN32 |
| 428 |
|
|
cout << " In Windows these can also be done using the forms" <<endl; |
| 429 |
|
|
cout << " " << program_name << " infile.mol new*.smi and " << program_name << " *.mol *.smi respectively.\n" <<endl; |
| 430 |
|
|
#endif |
| 431 |
|
|
|
| 432 |
|
|
OBFormat* pDefault = OBConversion::GetDefaultFormat(); |
| 433 |
|
|
if(pDefault) |
| 434 |
|
|
cout << pDefault->TargetClassDescription();// some more options probably for OBMol |
| 435 |
|
|
|
| 436 |
|
|
OBFormat* pAPI= OBConversion::FindFormat("obapi"); |
| 437 |
|
|
if(pAPI) |
| 438 |
|
|
cout << pAPI->Description(); |
| 439 |
|
|
|
| 440 |
|
|
cout << "The following file formats are recognized:" << endl; |
| 441 |
|
|
Formatpos pos; |
| 442 |
|
|
OBFormat* pFormat; |
| 443 |
|
|
const char* str=NULL; |
| 444 |
|
|
while(OBConversion::GetNextFormat(pos,str,pFormat)) |
| 445 |
|
|
{ |
| 446 |
|
|
if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) |
| 447 |
|
|
continue; |
| 448 |
|
|
cout << " " << str << endl; |
| 449 |
|
|
} |
| 450 |
|
|
cout << "\nSee further specific info and options using -H<format-type>, e.g. -Hcml" << endl; |
| 451 |
|
|
} |
| 452 |
|
|
|
| 453 |
|
|
/* OpenBabel man page*/ |
| 454 |
|
|
/** \page babel a converter for chemistry and molecular modeling data files |
| 455 |
|
|
* |
| 456 |
|
|
* \n |
| 457 |
|
|
* \par SYNOPSIS |
| 458 |
|
|
* |
| 459 |
|
|
* \b babel [-H<help-options>] [-V] [-m] [-d] [-h] [-p] [-s<SMARTS-pattern>] [-v<SMARTS-pattern>] [-f<#> -l<#>] [-c] [-x<format-options>] [-i<input-type>] \<infile\> [-o<output-type>] \<outfile\> |
| 460 |
|
|
* |
| 461 |
|
|
* \par DESCRIPTION |
| 462 |
|
|
* |
| 463 |
|
|
* Open Babel is a program designed to interconvert a number of |
| 464 |
|
|
* file formats currently used in molecular modeling software. \n\n |
| 465 |
|
|
* |
| 466 |
|
|
* Note that Open Babel can also be used as a library to interconvert |
| 467 |
|
|
* many file formats and to provide standard chemistry software routines. |
| 468 |
|
|
* See the Open Babel web pages (http://openbabel.sourceforge.net) for more |
| 469 |
|
|
* information. |
| 470 |
|
|
* |
| 471 |
|
|
* \par OPTIONS |
| 472 |
|
|
* |
| 473 |
|
|
* If only input and ouput files are given, Open Babel will guess |
| 474 |
|
|
* the file type from the filename extension. \n\n |
| 475 |
|
|
* |
| 476 |
|
|
* \b -V : |
| 477 |
|
|
* Output version number and exit \n\n |
| 478 |
|
|
* \b -H : |
| 479 |
|
|
* Output usage information \n\n |
| 480 |
|
|
* \b -H\<format-ID\> : |
| 481 |
|
|
* Output formatting information and options for format specified\n\n |
| 482 |
|
|
* \b -Hall : |
| 483 |
|
|
* Output formatting information and options for all formats\n\n |
| 484 |
|
|
* \b -i : |
| 485 |
|
|
* Specifies input format, see below for the available formats \n\n |
| 486 |
|
|
* \b -o : |
| 487 |
|
|
* Specifies output format, see below for the available formats \n\n |
| 488 |
|
|
* \b -m : |
| 489 |
|
|
* Produce multiple output files, to allow:\n |
| 490 |
|
|
* * Splitting one input file - put each molecule into consecutively numbered output files \n |
| 491 |
|
|
* * Batch conversion - convert each of multiple input files into a specified output format \n |
| 492 |
|
|
* See examples below \n\n |
| 493 |
|
|
* \b -d : |
| 494 |
|
|
* Delete Hydrogens \n\n |
| 495 |
|
|
* \b -h : |
| 496 |
|
|
* Add Hydrogens \n\n |
| 497 |
|
|
* \b -p : |
| 498 |
|
|
* Add Hydrogens appropriate for pH (use transforms in phmodel.txt) \n\n |
| 499 |
|
|
* \b -t : |
| 500 |
|
|
* All input files describe a single molecule \n\n |
| 501 |
|
|
* \b -f\<#\> : |
| 502 |
|
|
* For multiple entries input, start import at molecule # \n\n |
| 503 |
|
|
* \b -l\<#\> : |
| 504 |
|
|
* For multiple entries input, stop import at molecule # \n\n |
| 505 |
|
|
* \b -c : |
| 506 |
|
|
* Center atomic coordinates at (0,0,0) \n\n |
| 507 |
|
|
* \b -s\<SMARTS\> : |
| 508 |
|
|
* Convert only molecules matching the SMARTS pattern specified \n\n |
| 509 |
|
|
* \b -v\<SMARTS\> : |
| 510 |
|
|
* Convert only molecules \b NOT matching SMARTS pattern specified \n\n |
| 511 |
|
|
* |
| 512 |
|
|
* \par FILE FORMATS |
| 513 |
|
|
* |
| 514 |
|
|
* The following formats are currently supported by Open Babel: |
| 515 |
|
|
* \n alc -- Alchemy format |
| 516 |
|
|
* \n bgf -- BGF format |
| 517 |
|
|
* \n box -- Dock 3.5 Box format |
| 518 |
|
|
* \n bs -- Ball and Stick format |
| 519 |
|
|
* \n c3d1 -- Chem3D Cartesian 1 format |
| 520 |
|
|
* \n c3d2 -- Chem3D Cartesian2 format |
| 521 |
|
|
* \n caccrt -- Cacao format |
| 522 |
|
|
* \n cache -- CAChe format [Writeonly] |
| 523 |
|
|
* \n cacint -- CacaoInternal format [Writeonly] |
| 524 |
|
|
* \n car -- MSI Biosym/Insight II CAR format [Readonly] |
| 525 |
|
|
* \n ccc -- CCC format [Readonly] |
| 526 |
|
|
* \n cht -- ChemTool format [Writeonly] |
| 527 |
|
|
* \n cml -- Chemical Markup Language |
| 528 |
|
|
* \n crk2d -- Chemical Resource Kit diagram format (2D) |
| 529 |
|
|
* \n crk3d -- Chemical Resource Kit 3D format |
| 530 |
|
|
* \n csr -- CSR format [Writeonly] |
| 531 |
|
|
* \n cssr -- CSD CSSR format [Writeonly] |
| 532 |
|
|
* \n ct -- ChemDraw Connection Table format |
| 533 |
|
|
* \n dmol -- DMol3 coordinates format |
| 534 |
|
|
* \n ent -- Protein Data Bank format |
| 535 |
|
|
* \n feat -- Feature format |
| 536 |
|
|
* \n fh -- Fenske-Hall Z-Matrix format [Writeonly] |
| 537 |
|
|
* \n fix -- FIX format [Writeonly] |
| 538 |
|
|
* \n g03 -- Gaussian98/03 Cartesian [Writeonly] |
| 539 |
|
|
* \n g98 -- Gaussian98/03 Cartesian [Writeonly] |
| 540 |
|
|
* \n gam -- GAMESS Output |
| 541 |
|
|
* \n gamout -- GAMESS Output |
| 542 |
|
|
* \n gau -- Gaussian98/03 Cartesian [Writeonly] |
| 543 |
|
|
* \n gpr -- Ghemical format |
| 544 |
|
|
* \n gr96 -- GROMOS96 format [Writeonly] |
| 545 |
|
|
* \n hin -- HyperChem Input format |
| 546 |
|
|
* \n ins -- ShelX format [Readonly] |
| 547 |
|
|
* \n jout -- Jaguar output format |
| 548 |
|
|
* \n mdl -- MDL MOL format |
| 549 |
|
|
* \n mm1gp -- Ghemical format |
| 550 |
|
|
* \n mm3 -- MM3 format [Writeonly] |
| 551 |
|
|
* \n mmd -- MacroMod format |
| 552 |
|
|
* \n mmod -- MacroMod format |
| 553 |
|
|
* \n mol -- MDL MOL format |
| 554 |
|
|
* \n mol2 -- Sybyl Mol2 format |
| 555 |
|
|
* \n mopcrt -- MOPAC Cartesian format |
| 556 |
|
|
* \n mopout -- MOPAC Output format [Readonly] |
| 557 |
|
|
* \n mpqc -- MPQC format [Readonly] |
| 558 |
|
|
* \n nwo -- NWChem format |
| 559 |
|
|
* \n pdb -- Protein Data Bank format |
| 560 |
|
|
* \n pov -- POV-Ray input format [Writeonly] |
| 561 |
|
|
* \n pqs -- Parallel Quantum Solutions format |
| 562 |
|
|
* \n prep -- Amber Prep format [Readonly] |
| 563 |
|
|
* \n qcout -- QChem output format |
| 564 |
|
|
* \n qm1gp -- Ghemical format |
| 565 |
|
|
* \n report -- Report format [Writeonly] |
| 566 |
|
|
* \n res -- ShelX format [Readonly] |
| 567 |
|
|
* \n rxn -- MDL RXN format |
| 568 |
|
|
* \n sd -- MDL MOL format |
| 569 |
|
|
* \n sdf -- MDL MOL format |
| 570 |
|
|
* \n smi -- SMILES format |
| 571 |
|
|
* \n tmol -- TurboMole Coordinate format |
| 572 |
|
|
* \n txyz -- Tinker format [Writeonly] |
| 573 |
|
|
* \n unixyz -- UniChem XYZ format |
| 574 |
|
|
* \n vmol -- ViewMol format |
| 575 |
|
|
* \n xed -- XED format [Writeonly] |
| 576 |
|
|
* \n xyz -- XYZ cartesian coordinates format |
| 577 |
|
|
* \n zin -- ZINDO input format [Writeonly] |
| 578 |
|
|
* |
| 579 |
|
|
* \par FORMAT OPTIONS |
| 580 |
|
|
* Individual file formats may have additional formatting options. \n |
| 581 |
|
|
* Input format options are preceded by 'a', e.g. -as \n |
| 582 |
|
|
* Output format options are preceded by 'x', e.g. -xn \n |
| 583 |
|
|
* For further specific information and options, use -H<format-type> \n |
| 584 |
|
|
* e.g., -Hcml |
| 585 |
|
|
* |
| 586 |
|
|
* \par EXAMPLES |
| 587 |
|
|
* - Standard conversion \n |
| 588 |
|
|
* babel -ixyz ethanol.xyz -opdb ethanol.pdb \n |
| 589 |
|
|
* - Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT \n |
| 590 |
|
|
* babel -ismi -omol2 \n |
| 591 |
|
|
* - Split a multi-molecule file into new1.smi, new2.smi, etc. \n |
| 592 |
|
|
* babel infile.mol new.smi -m \n |
| 593 |
|
|
* |
| 594 |
|
|
* \par AUTHORS |
| 595 |
|
|
* |
| 596 |
|
|
* Open Babel is currently maintained by \b Geoff \b Hutchison, \b Chris \b Morley and \b Michael \b Banck. |
| 597 |
|
|
* |
| 598 |
|
|
* For more contributors to Open Babel, see http://openbabel.sourceforge.net/THANKS.shtml |
| 599 |
|
|
* |
| 600 |
|
|
* \par COPYRIGHT |
| 601 |
|
|
* Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
| 602 |
|
|
* Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison \n \n |
| 603 |
|
|
* This program is free software; you can redistribute it and/or modify |
| 604 |
|
|
* it under the terms of the GNU General Public License as published by |
| 605 |
|
|
* the Free Software Foundation version 2 of the License.\n \n |
| 606 |
|
|
* This program is distributed in the hope that it will be useful, |
| 607 |
|
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 608 |
|
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 609 |
|
|
* GNU General Public License for more details. |
| 610 |
|
|
* |
| 611 |
|
|
* \par SEE ALSO |
| 612 |
|
|
* The web pages for Open Babel can be found at http://openbabel.sourceforge.net/ |
| 613 |
|
|
**/ |
