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Comparing trunk/src/applications/atom2md/atom2md.cpp (file contents):
Revision 1209 by gezelter, Wed Aug 2 19:40:39 2006 UTC vs.
Revision 1210 by gezelter, Wed Jan 23 03:45:33 2008 UTC

# Line 3 | Line 3 | Copyright (C) 1998-2001 by OpenEye Scientific Software
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 OOPSE and Open Babel projects.
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
# Line 20 | Line 21 | GNU General Public License for more details.
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
28 – #if HAVE_FSTREAM
29 –        #include <fstream>
30 – #elif HAVE_FSTREAM_H
31 –        #include <fstream.h>
32 – #endif
33 – #if HAVE_SSTREAM
34 –        #include <sstream>
35 – #elif
36 –        #include <sstream.h>
37 – #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"
50 < #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  
# Line 62 | Line 60 | int main(int argc,char *argv[])
60  
61   int main(int argc,char *argv[])
62   {
65 –  registerOBFormats();  
63    OBConversion Conv(&cin, &cout); //default input and output are console
64 <  
68 <  //  string GenOptions;
64 >
65    OBFormat* pInFormat = NULL;
66    OBFormat* pOutFormat = NULL;
67    vector<string> FileList, OutputFileList;
68    string OutputFileName;
69 <  //  obMessageLevel filterLevel = obWarning; // 2 out of 5
74 <  
69 >
70    // Parse commandline
71    bool gotInType = false, gotOutType = false;
72 <  bool UseSavedOptions = false;
73 <  
72 >  bool SplitOrBatch=false;
73 >
74    char *oext;
75    char *iext;
76    string inputExt;
77    string outputExt;
78 <  
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)
# Line 94 | Line 89 | int main(int argc,char *argv[])
89      program_name=argv[0];
90    else
91      program_name=argv[0]+pos+1;
92 <  
92 >
93    const char* p;
94    int arg;
95 <  for (arg = 1; arg < argc; arg++)
95 >  for (arg = 1; arg < argc; ++arg)
96      {
97        if (argv[arg])
98          {
# Line 105 | Line 100 | int main(int argc,char *argv[])
100              {
101                switch (argv[arg][1])
102                  {
103 <                  
103 >
104                  case 'V':
105                    {
106 <                    cout << "atom2md: part of OOPSE " <<
107 <                      OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << "." <<
108 <                      OOPSE_VERSION_TINY << " and Open Babel " << BABEL_VERSION << " -- "
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 <                  
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 <                  
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
# Line 129 | Line 126 | int main(int argc,char *argv[])
126                      }
127                    else
128                      {
129 <                      //The ID provided by the OBFormat class is used as the identifying file extension
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!" << endl;
135 >                      cerr << program_name << ": cannot read input format!"
136 >                           << endl;
137                        usage();
138                      }
140 –                  inputExt = iext;
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 argument
146 <                  
145 >                    oext = argv[++arg]; // space left after -i: use next
146 >                                        // argument
147 >                                        
148                    if (strncasecmp(oext, "MIME", 4) == 0)
149                      {
150                        // get the MIME type from the next argument
# Line 154 | Line 153 | int main(int argc,char *argv[])
153                      }
154                    else
155                      pOutFormat = Conv.FindFormat(oext);
156 <                  
156 >
157                    if(pOutFormat==NULL)
158                      {
159 <                      cerr << program_name << ": cannot write output format!" << endl;
159 >                      cerr << program_name << ": cannot write output format!"
160 >                           << endl;
161                        usage();
162                      }
163 <                  outputExt = oext;
164 <                  break;                                
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]))
# Line 199 | Line 208 | int main(int argc,char *argv[])
208                      }
209                    else
210                      help();
211 <                  exit(0);                                      
212 <                  
213 <                  
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 >                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);
# Line 219 | Line 276 | int main(int argc,char *argv[])
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, output format is mdin)
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) {
# Line 238 | Line 297 | int main(int argc,char *argv[])
297              inputExt = tmpExt;
298            }
299        }
300 <    
300 >
301      if (!gotOutType)
302        {
303          string tmpExt = formatName.substr(pos+1, string::npos);
# Line 254 | Line 313 | int main(int argc,char *argv[])
313        }
314    }
315    
316 <  if(FileList.empty())
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())
325 >  if (!gotOutType)
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;            
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 <  
338 <  // send info message to clog -- don't mess up cerr or cout for user programs
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 >
359    int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList);
277 –  if ( count == 1 )
278 –    clog << count << " molecule converted" << endl;
279 –  else
280 –    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      }
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;
# Line 293 | Line 389 | int main(int argc,char *argv[])
389    return 0;
390   }
391  
392 < void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, int& arg, int argc, char *argv[])
392 > void DoOption(const char* p, OBConversion& Conv,
393 >              OBConversion::Option_type typ, int& arg, int argc, char *argv[])
394   {
395    while(p && *p) //can have multiple single char options
396 +  {
397 +    char ch[2]="?";
398 +    *ch = *p++;
399 +    const char* txt=NULL;                              
400 +    //Get the option text if needed
401 +    int nParams = Conv.GetOptionParams(ch, typ);
402 +    if(nParams)
403      {
404 <      char ch[2]="?";
405 <      *ch = *p++;
406 <      const char* txt=NULL;                            
407 <      //Get the option text if needed
408 <      int nParams = Conv.GetOptionParams(ch, typ);
409 <      if(nParams)
404 >      if(*p)
405 >      {
406 >        txt = p; //use text immediately following the option letter
407 >        p=NULL; //no more single char options
408 >      }
409 >      else if(arg<argc-1)
410 >      {
411 >        txt = argv[++arg]; //use text from next arg
412 >        if(*txt=='-')
413          {
414 <          if(*p)
415 <            {
416 <              txt = p; //use text immediately following the option letter
310 <              p=NULL; //no more single char options
311 <            }
312 <          else if(arg<argc-1)
313 <            {
314 <              txt = argv[++arg]; //use text from next arg
315 <              if(*txt=='-')
316 <                {
317 <                  //...unless it is another option
318 <                  cerr << "Option -" << ch << " takes a parameter" << endl;
319 <                  exit(0);
320 <                }
321 <            }
414 >          //...unless it is another option
415 >          cerr << "Option -" << ch << " takes a parameter" << endl;
416 >          exit(0);
417          }
418 <      Conv.AddOption(ch, typ, txt);
418 >      }
419      }
420 +    Conv.AddOption(ch, typ, txt);
421 +  }
422   }
423  
424   void usage()
425   {
426 <  cout << "atom2md: part of OOPSE " <<
426 >  cout << program_name << ": part of OOPSE " <<
427      OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << "." <<
428 <    OOPSE_VERSION_TINY << " and Open Babel " << BABEL_VERSION << " -- "
428 >    OOPSE_VERSION_TINY << " and OpenBabel " << BABEL_VERSION << " -- "
429         << __DATE__ << " -- " << __TIME__ << endl;
430    cout << "Usage: " << program_name
431         << " [-i<input-type>] <name> [-o<output-type>] <name>" << endl;
# Line 345 | Line 442 | void help()
442  
443   void help()
444   {
445 <  cout << "Open Babel converts chemical structures from one file format to another"<< endl << endl;
445 >  cout << program_name << " converts chemical structures from one file format to another"<< endl << endl;
446    cout << "Usage: " << program_name << " <input spec> <output spec> [Options]" << endl << endl;
447    cout << "Each spec can be a file whose extension decides the format." << endl;
448    cout << "Optionally the format can be specified by preceding the file by" << endl;
# Line 377 | Line 474 | void help()
474    while(OBConversion::GetNextFormat(pos,str,pFormat))
475      {
476        if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE))
477 <        continue;
477 >        continue;
478        cout << "  " << str << endl;
479      }
480    cout << "\nSee further specific info and options using -H<format-type>, e.g. -Hpdb" << endl;

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