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Comparing trunk/src/applications/atom2md/atom2md.cpp (file contents):
Revision 1210 by gezelter, Wed Jan 23 03:45:33 2008 UTC vs.
Revision 1399 by gezelter, Thu Dec 24 05:45:30 2009 UTC

# Line 1 | Line 1
1   /**********************************************************************
2 < atom2md.cpp - OpenBabel-based conversion program to OOPSE MD file,
2 > atom2md.cpp - OpenBabel-based conversion program to OpenMD file,
3                command-line handling.
4  
5   Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
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
8 > Some portions Copyright (C) 2008-2009 by J. Daniel Gezelter
9  
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/>
10 > This file is part of both the OpenMD and Open Babel projects.
11 > For more information, see <http://openmd.net> 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
# Line 38 | Line 38 | GNU General Public License for more details.
38   #if HAVE_CONIO_H
39          #include <conio.h>
40   #endif
41 – #include <cstdlib>
41  
42   #if !HAVE_STRNCASECMP
43   extern "C" int strncasecmp(const char *s1, const char *s2, size_t n);
44   #endif
45  
46   #include <openbabel/obconversion.h>
47 + #include <openbabel/plugin.h>
48 + #include <cstdlib>
49 + #include <cstring>
50  
51   using namespace std;
52   using namespace OpenBabel;
53  
54 < void DoOption(const char* p, OBConversion& Conv,
55 <              OBConversion::Option_type typ, int& arg, int argc,
54 <              char *argv[]);
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  
# Line 71 | Line 72 | int main(int argc,char *argv[])
72    bool gotInType = false, gotOutType = false;
73    bool SplitOrBatch=false;
74  
75 <  char *oext;
76 <  char *iext;
75 >  char *oext = NULL;
76 >  char *iext = NULL;
77 >
78 >  // for use with command name to type conversion
79    string inputExt;
80    string outputExt;
81  
# Line 103 | Line 106 | int main(int argc,char *argv[])
106  
107                  case 'V':
108                    {
109 <                    cout << program_name << ": part of OOPSE " <<
110 <                      OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR <<
111 <                      "." << OOPSE_VERSION_TINY <<
109 >                    cout << program_name << ": part of OpenMD " <<
110 >                      OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR <<
111 >                      "." << OPENMD_VERSION_TINY <<
112                        " and Open Babel " << BABEL_VERSION << " -- "
113                           << __DATE__ << " -- " << __TIME__ << endl;
114                      exit(0);
# Line 115 | Line 118 | int main(int argc,char *argv[])
118                    gotInType = true;
119                    iext = argv[arg] + 2;
120                    if(!*iext)
121 <                    iext = argv[++arg]; // space left after -i: use next
119 <                                        // argument
121 >                    iext = argv[++arg]; //space left after -i: use next argument
122  
123                    if (strncasecmp(iext, "MIME", 4) == 0)
124                      {
# Line 126 | Line 128 | int main(int argc,char *argv[])
128                      }
129                    else
130                      {
131 <                      // The ID provided by the OBFormat class is used as the
130 <                      // identifying file extension
131 >                      //The ID provided by the OBFormat class is used as the identifying file extension
132                        pInFormat = Conv.FindFormat(iext);
133                      }
134                    if(pInFormat==NULL)
135                      {
136 <                      cerr << program_name << ": cannot read input format!"
136 <                           << endl;
136 >                      cerr << program_name << ": cannot read input format!" << endl;
137                        usage();
138                      }
139                    break;
# Line 142 | Line 142 | int main(int argc,char *argv[])
142                    gotOutType = true;
143                    oext = argv[arg] + 2;
144                    if(!*oext)
145 <                    oext = argv[++arg]; // space left after -i: use next
146 <                                        // argument
145 >                    oext = argv[++arg]; //space left after -i: use next argument
146                                          
147                    if (strncasecmp(oext, "MIME", 4) == 0)
148                      {
# Line 156 | Line 155 | int main(int argc,char *argv[])
155  
156                    if(pOutFormat==NULL)
157                      {
158 <                      cerr << program_name << ": cannot write output format!"
160 <                           << endl;
158 >                      cerr << program_name << ": cannot write output format!" << endl;
159                        usage();
160                      }
161                    break;
162 <                  
163 <                case 'F':
162 >
163 >                /*case 'F':
164                    if(!Conv.SetOutFormat("fpt"))
165                      cout << "FingerprintFormat needs to be loaded" << endl;
166                    else
# Line 171 | Line 169 | int main(int argc,char *argv[])
169                        Conv.Write(NULL);
170                      }
171                    return 0;
172 <                  
172 >                  */
173 >                case 'L': //display a list of plugin type or classes
174 >                  {
175 >                    const char* param=NULL;
176 >                    if(argc>arg+1)
177 >                      param = argv[arg+2];
178 >                    OBPlugin::List(argv[arg+1], param);
179 >                    return 0;
180 >                  }
181                  case '?':
182                  case 'H':
183 <                  if(isalnum(argv[arg][2]))
183 >                  if(isalnum(argv[arg][2]) || arg==argc-2)
184                      {
185                        if(strncasecmp(argv[arg]+2,"all",3))
186                          {
187 <                          OBFormat* pFormat = Conv.FindFormat(argv[arg]+2);
187 >                          const char* pID= (arg==argc-2) ? argv[arg+1] : argv[arg]+2;
188 >                          OBFormat* pFormat = Conv.FindFormat(pID);
189                            if(pFormat)
190                              {
191 <                              cout << argv[arg]+2 << "  " << pFormat->Description() << endl;
191 >                              cout << pID << "  " << pFormat->Description() << endl;
192 >                              if(pFormat->Flags() & NOTWRITABLE)
193 >                                cout << " This format is Read-only" << endl;
194 >                              if(pFormat->Flags() & NOTREADABLE)
195 >                                cout << " This format is Write-only" << endl;
196 >
197                                if(strlen(pFormat->SpecificationURL()))
198                                  cout << "Specification at: " << pFormat->SpecificationURL() << endl;
199                              }
200                            else
201 <                            cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl;
201 >                            cout << "Format type: " << pID << " was not recognized" <<endl;
202                          }
203                        else
204                          {
205 <                          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 <                            }
205 >                          OBPlugin::List("formats","verbose");
206                          }
207                      }
208                    else
209                      help();
210 <                  exit(0);
210 >                  return 0;
211                                          
212                  case '-': //long option --name text
213                    {
# Line 277 | Line 276 | int main(int argc,char *argv[])
276      }
277    
278    // user didn't specify input and output format in commandline option
279 <  // try to parse it from program name (pdb2mdin means input format is pdb,
280 <  // output format is mdin)
279 >  // try to parse it from program name (pdb2md means input format is pdb,
280 >  // output format is md)
281  
282    string formatName(program_name);
283    pos = formatName.find_first_of("2");
# Line 311 | Line 310 | int main(int argc,char *argv[])
310            outputExt = tmpExt;
311          }
312        }
313 <  }
313 >  }
314 >
315 >  if(!gotOutType) //the last file is the output
316 >    {
317 >      if(FileList.empty())
318 >        {
319 >          cerr << "No output file or format spec!" << endl;
320 >          usage();
321 >        }
322 >      OutputFileName = FileList.back();
323 >      FileList.pop_back();
324 >    }
325 >
326 > #ifdef _WIN32
327 >  //Expand wildcards in input filenames and add to FileList
328 >  vector<string> tempFileList(FileList);
329 >  FileList.clear();
330 >  vector<string>::iterator itr;
331 >  for(itr=tempFileList.begin();itr!=tempFileList.end();++itr)
332 >    DLHandler::findFiles (FileList, *itr);
333 > #endif
334    
335    if (!gotInType)
336      {
# Line 321 | Line 340 | int main(int argc,char *argv[])
340            usage();
341          }
342      }
343 <  
344 <  if (!gotOutType)
343 >
344 >  if (!gotOutType)
345      {
346        pOutFormat = Conv.FormatFromExt(OutputFileName.c_str());
347        if(pOutFormat==NULL)
# Line 332 | Line 351 | int main(int argc,char *argv[])
351          }
352      }
353    
354 <  Conv.SetInAndOutFormats(pInFormat, pOutFormat);
355 <  
354 >    if(!Conv.SetInFormat(pInFormat))
355 >    {
356 >      cerr << "Invalid input format" << endl;
357 >      usage();
358 >    }
359 >    if(!Conv.SetOutFormat(pOutFormat))
360 >    {
361 >      cerr << "Invalid output format" << endl;
362 >      usage();
363 >    }
364 >
365    if(SplitOrBatch)
366      {
367        //Put * into output file name before extension (or ext.gz)
368        if(OutputFileName.empty())
369          {
370            OutputFileName = "*.";
371 <          OutputFileName += oext;
371 >          if (oext != NULL)
372 >            OutputFileName += oext;
373          }
374        else
375          {
# Line 357 | Line 386 | int main(int argc,char *argv[])
386      }
387  
388    int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList);
389 <  
390 <  // send info message to clog -- don't mess up cerr or cout for user programs
391 <  //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;
389 >
390 >  Conv.ReportNumberConverted(count);
391 >
392    if(OutputFileList.size()>1)
393      {
394        clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl;
395      }
396 <  
396 >
397    std::string messageSummary = obErrorLog.GetMessageSummary();
398    if (messageSummary.size())
399      {
400        clog << messageSummary << endl;
401      }
402 <  
402 >
403   #ifdef _DEBUG
404    //CM keep window open
405    cout << "Press any key to finish" <<endl;
# Line 423 | Line 443 | void usage()
443  
444   void usage()
445   {
446 <  cout << program_name << ": part of OOPSE " <<
447 <    OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << "." <<
448 <    OOPSE_VERSION_TINY << " and OpenBabel " << BABEL_VERSION << " -- "
446 >  cout << program_name << ": part of OpenMD " <<
447 >    OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << "." <<
448 >    OPENMD_VERSION_TINY << " and OpenBabel " << BABEL_VERSION << " -- "
449         << __DATE__ << " -- " << __TIME__ << endl;
450    cout << "Usage: " << program_name
451         << " [-i<input-type>] <name> [-o<output-type>] <name>" << endl;
452    cout << "Try  -H option for more information." << endl;
453 < /*  
453 >
454   #ifdef _DEBUG
455    //CM keep window open
456    cout << "Press any key to finish" <<endl;
457    getch();
458   #endif
439 – */  
459    exit (0);
460   }
461  

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