applications/atom2md/atom2md.cpp

/**********************************************************************
atom2md.cpp - OpenBabel-based conversion program to OOPSE MD file, 
              command-line handling.

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
Some portions Copyright (C) 2004-2006 by Chris Morley
Some portions Copyright (C) 2008 by J. Daniel Gezelter

This file is part of both the OOPSE and Open Babel projects.
For more information, see <http://oopse.org> and <http://openbabel.sourceforge.net/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#include "config.h"

// used to set import/export for Cygwin DLLs
#ifdef WIN32
#define USING_OBDLL
#endif

#include <openbabel/babelconfig.h>

#include <iostream>
#include <fstream>
#include <sstream>

#include <string>
#include <map>
#if HAVE_CONIO_H
        #include <conio.h>
#endif
#include <cstdlib>

#if !HAVE_STRNCASECMP
extern "C" int strncasecmp(const char *s1, const char *s2, size_t n);
#endif

#include <openbabel/obconversion.h>

using namespace std;
using namespace OpenBabel;

void DoOption(const char* p, OBConversion& Conv, 
              OBConversion::Option_type typ, int& arg, int argc, 
              char *argv[]); 
void usage();
void help();

// There isn't a great way to do this -- we need to save argv[0] for usage()
static char *program_name;

int main(int argc,char *argv[])
{
  OBConversion Conv(&cin, &cout); //default input and output are console 

  OBFormat* pInFormat = NULL;
  OBFormat* pOutFormat = NULL;
  vector<string> FileList, OutputFileList;
  string OutputFileName;

  // Parse commandline
  bool gotInType = false, gotOutType = false;
  bool SplitOrBatch=false;

  char *oext;
  char *iext;
  string inputExt;
  string outputExt;

  //Save name of program without its path (and .exe)
  string pn(argv[0]);
  string::size_type pos;
#ifdef _WIN32
  pos = pn.find(".exe");
  if(pos!=string::npos)
    argv[0][pos]='\0';
#endif
  pos = pn.find_last_of("/\\");
  if(pos==string::npos)
    program_name=argv[0];
  else
    program_name=argv[0]+pos+1;

  const char* p;
  int arg;
  for (arg = 1; arg < argc; ++arg)
    {
      if (argv[arg])
        {
          if (argv[arg][0] == '-')
            {
              switch (argv[arg][1])
                {

                case 'V':
                  {
                    cout << program_name << ": part of OOPSE " << 
                      OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << 
                      "." << OOPSE_VERSION_TINY << 
                      " and Open Babel " << BABEL_VERSION << " -- " 
                         << __DATE__ << " -- " << __TIME__ << endl;
                    exit(0);
                  }

                case 'i':
                  gotInType = true;
                  iext = argv[arg] + 2;
                  if(!*iext)
                    iext = argv[++arg]; // space left after -i: use next 
                                        // argument

                  if (strncasecmp(iext, "MIME", 4) == 0)
                    {
                      // get the MIME type from the next argument
                      iext = argv[++arg];
                      pInFormat = Conv.FormatFromMIME(iext);
                    }
                  else
                    {
                      // The ID provided by the OBFormat class is used as the 
                      // identifying file extension
                      pInFormat = Conv.FindFormat(iext);
                    }
                  if(pInFormat==NULL)
                    {
                      cerr << program_name << ": cannot read input format!" 
                           << endl;
                      usage();
                    }
                  break;
                  
                case 'o':
                  gotOutType = true;
                  oext = argv[arg] + 2;
                  if(!*oext)
                    oext = argv[++arg]; // space left after -i: use next 
                                        // argument
                                        
                  if (strncasecmp(oext, "MIME", 4) == 0)
                    {
                      // get the MIME type from the next argument
                      oext = argv[++arg];
                      pOutFormat = Conv.FormatFromMIME(oext);
                    }
                  else
                    pOutFormat = Conv.FindFormat(oext);

                  if(pOutFormat==NULL)
                    {
                      cerr << program_name << ": cannot write output format!" 
                           << endl;
                      usage();
                    }
                  break;
                  
                case 'F':
                  if(!Conv.SetOutFormat("fpt"))
                    cout << "FingerprintFormat needs to be loaded" << endl;
                  else
                    {
                      Conv.AddOption("F",OBConversion::OUTOPTIONS);
                      Conv.Write(NULL);
                    }
                  return 0;
                  
                case '?':
                case 'H':
                  if(isalnum(argv[arg][2]))
                    {
                      if(strncasecmp(argv[arg]+2,"all",3))
                        {
                          OBFormat* pFormat = Conv.FindFormat(argv[arg]+2);
                          if(pFormat)
                            {
                              cout << argv[arg]+2 << "  " << pFormat->Description() << endl;
                              if(strlen(pFormat->SpecificationURL()))
                                cout << "Specification at: " << pFormat->SpecificationURL() << endl;
                            }
                          else
                            cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl;
                        }
                      else
                        {
                          Formatpos pos;
                          OBFormat* pFormat;
                          const char* str=NULL;
                          while(OBConversion::GetNextFormat(pos,str,pFormat))
                            {
                              if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE))
                                continue;
                              cout << str << endl;
                              const char* p = strchr(pFormat->Description(),'\n');
                              cout << p+1; //second line of description
                              if(strlen(pFormat->SpecificationURL()))
                                cout << "Specification at: " << pFormat->SpecificationURL();
                              cout << endl << endl;
                            }
                        }
                    }
                  else
                    help();
                  exit(0);
                                        
                case '-': //long option --name text
                  {
                    //Do nothing if name is empty
                    //Option's text is the next arg provided it doesn't start with -
                    char* nam = argv[arg]+2;
                    if(*nam != '\0')
                      {
                        string txt;
                        int i;
                        for(i=0; i<Conv.GetOptionParams(nam, OBConversion::GENOPTIONS)
                              && arg<argc-1 && argv[arg+1];++i) //removed  && *argv[arg+1]!='-'
                          {
                            if(!txt.empty()) txt+=' ';
                            txt += argv[++arg];
                          }
                        if(*nam=='-')
                          {
                            // Is a API directive, e.g.---errorlevel
                            //Send to the pseudoformat "obapi" (without any leading -)
                            OBConversion apiConv;
                            OBFormat* pAPI= OBConversion::FindFormat("obapi");
                            if(pAPI)
                              {
                                apiConv.SetOutFormat(pAPI);
                                apiConv.AddOption(nam+1, OBConversion::GENOPTIONS, txt.c_str());
                                apiConv.Write(NULL, &std::cout);
                              }
                          }
                        else
                          // Is a long option name, e.g --addtotitle
                          Conv.AddOption(nam,OBConversion::GENOPTIONS,txt.c_str());
                      }
                  }
                  break;
                                        
                case 'm': //multiple output files
                  SplitOrBatch=true;
                  break;
                                        
                case 'a': //single character input option
                  p = argv[arg]+2;
                  DoOption(p,Conv,OBConversion::INOPTIONS,arg,argc,argv);
                  break;

                case 'x': //single character output option
                  p = argv[arg]+2;
                  DoOption(p,Conv,OBConversion::OUTOPTIONS,arg,argc,argv);
                  break;
                                        
                default: //single character general option
                  p = argv[arg]+1;
                  DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv);
                  break;
                }
            }
          else 
            {
              //filenames
              if(!gotOutType)
                FileList.push_back(argv[arg]);
              else
                OutputFileName = argv[arg];
            }
        }
    }
  
  // user didn't specify input and output format in commandline option
  // try to parse it from program name (pdb2mdin means input format is pdb, 
  // output format is mdin)

  string formatName(program_name);
  pos = formatName.find_first_of("2");
  if(pos!=string::npos) {
    if (!gotInType)
      {
        string tmpExt = formatName.substr(0, pos);
        pInFormat = Conv.FindFormat(tmpExt.c_str());
        if(pInFormat==NULL)
          {
            cerr << program_name << ": cannot read input format!" << endl;
            usage();
          } else 
          {
            gotInType = true;
            inputExt = tmpExt;
          }
      }

    if (!gotOutType)
      {
        string tmpExt = formatName.substr(pos+1, string::npos);
        pOutFormat = Conv.FindFormat(tmpExt.c_str());
        if(pOutFormat==NULL)
          {
            cerr << program_name << ": cannot write output format!" << endl;
            usage();
          }else {
          gotOutType = true;
          outputExt = tmpExt;
        }
      }
  }
  
  if (!gotInType)
    {
      if(FileList.empty())
        {
          cerr << "No input file or format spec!" <<endl;
          usage();
        }
    }
  
  if (!gotOutType) 
    {
      pOutFormat = Conv.FormatFromExt(OutputFileName.c_str());
      if(pOutFormat==NULL)
        {
          cerr << program_name << ": cannot write output format!" << endl;
          usage();
        }
    }
  
  Conv.SetInAndOutFormats(pInFormat, pOutFormat);
  
  if(SplitOrBatch)
    {
      //Put * into output file name before extension (or ext.gz)
      if(OutputFileName.empty())
        {
          OutputFileName = "*.";
          OutputFileName += oext;
        }
      else
        {
          string::size_type pos = OutputFileName.rfind(".gz");
          if(pos==string::npos)
            pos = OutputFileName.rfind('.');
          else
            pos = OutputFileName.rfind('.',pos-1);
          if(pos==string::npos)
            OutputFileName += '*';
          else
            OutputFileName.insert(pos,"*");
        }
    }

  int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList);
  
  // send info message to clog -- don't mess up cerr or cout for user programs
  //Get the last word on the first line of the description which should
  //be "molecules", "reactions", etc and remove the s if only one object converted 
  std::string objectname(pOutFormat->TargetClassDescription());
  pos = objectname.find('\n');
  if(count==1) --pos;
  objectname.erase(pos);
  pos = objectname.rfind(' ');
  if(pos==std::string::npos)
    pos=0;
  std::clog << count << objectname.substr(pos) << " converted" << endl;
  if(OutputFileList.size()>1)
    {
      clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl;
    }
  
  std::string messageSummary = obErrorLog.GetMessageSummary();
  if (messageSummary.size())
    {
      clog << messageSummary << endl;
    }
  
#ifdef _DEBUG
  //CM keep window open
  cout << "Press any key to finish" <<endl;
  getch();
#endif
  
  return 0;
}

void DoOption(const char* p, OBConversion& Conv,
              OBConversion::Option_type typ, int& arg, int argc, char *argv[]) 
{
  while(p && *p) //can have multiple single char options
  {
    char ch[2]="?";
    *ch = *p++;
    const char* txt=NULL;                               
    //Get the option text if needed
    int nParams = Conv.GetOptionParams(ch, typ);
    if(nParams)
    {
      if(*p)
      {
        txt = p; //use text immediately following the option letter
        p=NULL; //no more single char options
      }
      else if(arg<argc-1)
      {
        txt = argv[++arg]; //use text from next arg
        if(*txt=='-')
        {
          //...unless it is another option
          cerr << "Option -" << ch << " takes a parameter" << endl;
          exit(0);
        }
      }
    }
    Conv.AddOption(ch, typ, txt);
  }
}

void usage()
{
  cout << program_name << ": part of OOPSE " << 
    OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << "." << 
    OOPSE_VERSION_TINY << " and OpenBabel " << BABEL_VERSION << " -- " 
       << __DATE__ << " -- " << __TIME__ << endl;
  cout << "Usage: " << program_name
       << " [-i<input-type>] <name> [-o<output-type>] <name>" << endl;
  cout << "Try  -H option for more information." << endl;
/*  
#ifdef _DEBUG
  //CM keep window open
  cout << "Press any key to finish" <<endl;
  getch();
#endif
*/  
  exit (0);
}

void help()
{
  cout << program_name << " converts chemical structures from one file format to another"<< endl << endl;
  cout << "Usage: " << program_name << " <input spec> <output spec> [Options]" << endl << endl;
  cout << "Each spec can be a file whose extension decides the format." << endl;
  cout << "Optionally the format can be specified by preceding the file by" << endl;
  cout << "-i<format-type> e.g. -ipdb, for input and -o<format-type> for output" << endl << endl;
  cout << "See below for available format-types, which are the same as the " << endl;
  cout << "file extensions and are case independent." << endl; 
  cout << "If no input or output file is given stdin or stdout are used instead." << endl << endl; 
  cout << "More than one input file can be specified and their names can contain" <<endl;
  cout << "wildcard chars (* and ?).The molecules are aggregated in the output file.\n" << endl;
  cout << OBConversion::Description(); // Conversion options
  cout << "  -H Outputs this help text" << endl;
  cout << "  -Hxxx (xxx is file format ID e.g. -Hpdb) gives format info" <<endl; 
  cout << "  -Hall Outputs details of all formats" <<endl; 
  cout << "  -V Outputs version number" <<endl; 

  
  OBFormat* pDefault = OBConversion::GetDefaultFormat();
  if(pDefault)
    cout << pDefault->TargetClassDescription();// some more options probably for OBMol
  
  OBFormat* pAPI= OBConversion::FindFormat("obapi");
  if(pAPI)
    cout << pAPI->Description();
  
  cout << "The following file formats are recognized:" << endl;
  Formatpos pos;
  OBFormat* pFormat;
  const char* str=NULL;
  while(OBConversion::GetNextFormat(pos,str,pFormat))
    {
      if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE))
        continue;
      cout << "  " << str << endl;
    }
  cout << "\nSee further specific info and options using -H<format-type>, e.g. -Hpdb" << endl;
}

Revision:	1210
Committed:	Wed Jan 23 03:45:33 2008 UTC (17 years, 9 months ago) by gezelter
File size:	16289 byte(s)
Log Message:	Removed older version of openbabel from our code. We now have a configure check to see if openbabel is installed and then we link to the stuff we need. Conversion to OOPSE's md format is handled by only one application (atom2md), so most of the work went on there. ElementsTable still needs some work to function in parallel.
#	User	Rev	Content
1	gezelter	1020	/**********************************************************************
2	gezelter	1021	atom2md.cpp - OpenBabel-based conversion program to OOPSE MD file,
3			command-line handling.
4	gezelter	1020
5			Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
6	gezelter	1210	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	gezelter	1020
10	gezelter	1210	This file is part of both the OOPSE and Open Babel projects.
11	gezelter	1021	For more information, see <http://oopse.org> and <http://openbabel.sourceforge.net/>
12	gezelter	1020
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
15			the Free Software Foundation version 2 of the License.
16
17			This program is distributed in the hope that it will be useful,
18			but WITHOUT ANY WARRANTY; without even the implied warranty of
19			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
20			GNU General Public License for more details.
21			***********************************************************************/
22
23			#include "config.h"
24	gezelter	1210
25			// used to set import/export for Cygwin DLLs
26			#ifdef WIN32
27			#define USING_OBDLL
28	gezelter	1020	#endif
29
30	gezelter	1210	#include <openbabel/babelconfig.h>
31
32			#include <iostream>
33			#include <fstream>
34			#include <sstream>
35
36	gezelter	1020	#include <string>
37			#include <map>
38			#if HAVE_CONIO_H
39			#include <conio.h>
40			#endif
41	gezelter	1210	#include <cstdlib>
42	gezelter	1020
43			#if !HAVE_STRNCASECMP
44			extern "C" int strncasecmp(const char s1, const char s2, size_t n);
45			#endif
46
47	gezelter	1210	#include <openbabel/obconversion.h>
48	gezelter	1020
49			using namespace std;
50			using namespace OpenBabel;
51	gezelter	1210
52			void DoOption(const char* p, OBConversion& Conv,
53			OBConversion::Option_type typ, int& arg, int argc,
54			char *argv[]);
55	gezelter	1020	void usage();
56			void help();
57
58			// There isn't a great way to do this -- we need to save argv[0] for usage()
59			static char *program_name;
60
61			int main(int argc,char *argv[])
62			{
63			OBConversion Conv(&cin, &cout); //default input and output are console
64	gezelter	1210
65	gezelter	1020	OBFormat* pInFormat = NULL;
66			OBFormat* pOutFormat = NULL;
67			vector<string> FileList, OutputFileList;
68			string OutputFileName;
69	gezelter	1210
70	gezelter	1020	// Parse commandline
71			bool gotInType = false, gotOutType = false;
72	gezelter	1210	bool SplitOrBatch=false;
73
74	gezelter	1020	char *oext;
75			char *iext;
76			string inputExt;
77			string outputExt;
78	gezelter	1210
79	gezelter	1020	//Save name of program without its path (and .exe)
80			string pn(argv[0]);
81	gezelter	1210	string::size_type pos;
82	gezelter	1020	#ifdef _WIN32
83			pos = pn.find(".exe");
84			if(pos!=string::npos)
85			argv[0][pos]='\0';
86			#endif
87			pos = pn.find_last_of("/\\");
88			if(pos==string::npos)
89			program_name=argv[0];
90			else
91			program_name=argv[0]+pos+1;
92	gezelter	1210
93	gezelter	1021	const char* p;
94			int arg;
95	gezelter	1210	for (arg = 1; arg < argc; ++arg)
96	gezelter	1021	{
97			if (argv[arg])
98			{
99			if (argv[arg][0] == '-')
100			{
101			switch (argv[arg][1])
102			{
103	gezelter	1210
104	gezelter	1021	case 'V':
105			{
106	gezelter	1210	cout << program_name << ": part of OOPSE " <<
107			OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR <<
108			"." << OOPSE_VERSION_TINY <<
109			" and Open Babel " << BABEL_VERSION << " -- "
110	gezelter	1021	<< __DATE__ << " -- " << __TIME__ << endl;
111			exit(0);
112			}
113	gezelter	1210
114	gezelter	1021	case 'i':
115			gotInType = true;
116			iext = argv[arg] + 2;
117			if(!*iext)
118	gezelter	1210	iext = argv[++arg]; // space left after -i: use next
119			// argument
120
121	gezelter	1021	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	gezelter	1210	// The ID provided by the OBFormat class is used as the
130			// identifying file extension
131	gezelter	1021	pInFormat = Conv.FindFormat(iext);
132			}
133			if(pInFormat==NULL)
134			{
135	gezelter	1210	cerr << program_name << ": cannot read input format!"
136			<< endl;
137	gezelter	1021	usage();
138			}
139			break;
140
141			case 'o':
142			gotOutType = true;
143			oext = argv[arg] + 2;
144			if(!*oext)
145	gezelter	1210	oext = argv[++arg]; // space left after -i: use next
146			// argument
147
148	gezelter	1021	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	gezelter	1210
157	gezelter	1021	if(pOutFormat==NULL)
158			{
159	gezelter	1210	cerr << program_name << ": cannot write output format!"
160			<< endl;
161	gezelter	1021	usage();
162			}
163	gezelter	1210	break;
164	gezelter	1021
165	gezelter	1210	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	gezelter	1021	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	gezelter	1210	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	gezelter	1021	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	gezelter	1210	// 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	gezelter	1020	string formatName(program_name);
284			pos = formatName.find_first_of("2");
285			if(pos!=string::npos) {
286			if (!gotInType)
287	gezelter	1021	{
288	gezelter	1020	string tmpExt = formatName.substr(0, pos);
289			pInFormat = Conv.FindFormat(tmpExt.c_str());
290	gezelter	1021	if(pInFormat==NULL)
291			{
292			cerr << program_name << ": cannot read input format!" << endl;
293			usage();
294			} else
295			{
296	gezelter	1020	gotInType = true;
297			inputExt = tmpExt;
298	gezelter	1021	}
299			}
300	gezelter	1210
301	gezelter	1020	if (!gotOutType)
302	gezelter	1021	{
303	gezelter	1020	string tmpExt = formatName.substr(pos+1, string::npos);
304			pOutFormat = Conv.FindFormat(tmpExt.c_str());
305	gezelter	1021	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	gezelter	1020	}
315	gezelter	1021
316	gezelter	1210	if (!gotInType)
317	gezelter	1020	{
318	gezelter	1210	if(FileList.empty())
319			{
320			cerr << "No input file or format spec!" <<endl;
321			usage();
322			}
323	gezelter	1020	}
324	gezelter	1021
325	gezelter	1210	if (!gotOutType)
326	gezelter	1021	{
327	gezelter	1210	pOutFormat = Conv.FormatFromExt(OutputFileName.c_str());
328			if(pOutFormat==NULL)
329			{
330			cerr << program_name << ": cannot write output format!" << endl;
331			usage();
332			}
333	gezelter	1020	}
334
335	gezelter	1210	Conv.SetInAndOutFormats(pInFormat, pOutFormat);
336	gezelter	1021
337	gezelter	1210	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);
360	gezelter	1021
361	gezelter	1020	// send info message to clog -- don't mess up cerr or cout for user programs
362	gezelter	1210	//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	gezelter	1020	if(OutputFileList.size()>1)
373	gezelter	1021	{
374			clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl;
375			}
376
377	gezelter	1210	std::string messageSummary = obErrorLog.GetMessageSummary();
378			if (messageSummary.size())
379			{
380			clog << messageSummary << endl;
381			}
382
383	gezelter	1020	#ifdef _DEBUG
384			//CM keep window open
385			cout << "Press any key to finish" <<endl;
386			getch();
387			#endif
388
389			return 0;
390			}
391
392	gezelter	1210	void DoOption(const char* p, OBConversion& Conv,
393			OBConversion::Option_type typ, int& arg, int argc, char *argv[])
394	gezelter	1020	{
395	gezelter	1021	while(p && *p) //can have multiple single char options
396	gezelter	1210	{
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	gezelter	1021	{
404	gezelter	1210	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	gezelter	1021	{
414	gezelter	1210	//...unless it is another option
415			cerr << "Option -" << ch << " takes a parameter" << endl;
416			exit(0);
417	gezelter	1021	}
418	gezelter	1210	}
419	gezelter	1021	}
420	gezelter	1210	Conv.AddOption(ch, typ, txt);
421			}
422	gezelter	1020	}
423
424			void usage()
425			{
426	gezelter	1210	cout << program_name << ": part of OOPSE " <<
427	gezelter	1021	OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << "." <<
428	gezelter	1210	OOPSE_VERSION_TINY << " and OpenBabel " << BABEL_VERSION << " -- "
429	gezelter	1021	<< __DATE__ << " -- " << __TIME__ << endl;
430	gezelter	1020	cout << "Usage: " << program_name
431			<< " [-i<input-type>] <name> [-o<output-type>] <name>" << endl;
432			cout << "Try -H option for more information." << endl;
433			/*
434			#ifdef _DEBUG
435			//CM keep window open
436			cout << "Press any key to finish" <<endl;
437			getch();
438			#endif
439			*/
440			exit (0);
441			}
442
443			void help()
444			{
445	gezelter	1210	cout << program_name << " converts chemical structures from one file format to another"<< endl << endl;
446	gezelter	1020	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;
449			cout << "-i<format-type> e.g. -ipdb, for input and -o<format-type> for output" << endl << endl;
450			cout << "See below for available format-types, which are the same as the " << endl;
451			cout << "file extensions and are case independent." << endl;
452			cout << "If no input or output file is given stdin or stdout are used instead." << endl << endl;
453			cout << "More than one input file can be specified and their names can contain" <<endl;
454			cout << "wildcard chars (* and ?).The molecules are aggregated in the output file.\n" << endl;
455			cout << OBConversion::Description(); // Conversion options
456			cout << " -H Outputs this help text" << endl;
457			cout << " -Hxxx (xxx is file format ID e.g. -Hpdb) gives format info" <<endl;
458			cout << " -Hall Outputs details of all formats" <<endl;
459			cout << " -V Outputs version number" <<endl;
460
461
462			OBFormat* pDefault = OBConversion::GetDefaultFormat();
463	gezelter	1021	if(pDefault)
464			cout << pDefault->TargetClassDescription();// some more options probably for OBMol
465	gezelter	1020
466	gezelter	1021	OBFormat* pAPI= OBConversion::FindFormat("obapi");
467			if(pAPI)
468			cout << pAPI->Description();
469
470			cout << "The following file formats are recognized:" << endl;
471	gezelter	1020	Formatpos pos;
472			OBFormat* pFormat;
473			const char* str=NULL;
474			while(OBConversion::GetNextFormat(pos,str,pFormat))
475	gezelter	1021	{
476			if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE))
477	gezelter	1210	continue;
478	gezelter	1021	cout << " " << str << endl;
479			}
480	gezelter	1020	cout << "\nSee further specific info and options using -H<format-type>, e.g. -Hpdb" << endl;
481			}
482