applications/atom2md/atom2md.cpp

/**********************************************************************
main.cpp - Main conversion program, command-line handling.

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
Some portions Copyright (C) 2004-2005 by Chris Morley

This file is part of the Open Babel project.
For more information, see <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"
#if HAVE_IOSTREAM
        #include <iostream>
#elif HAVE_IOSTREAM_H
        #include <iostream.h>
#endif
#if HAVE_FSTREAM
        #include <fstream>
#elif HAVE_FSTREAM_H
        #include <fstream.h>
#endif
#if HAVE_SSTREAM
        #include <sstream>
#elif
        #include <sstream.h>
#endif

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

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

#include "openbabel/obconversion.hpp"
#include "brains/Register.hpp"

using namespace std;
using namespace OpenBabel;
using namespace oopse;
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[])
{
  registerOBFormats();  
  OBConversion Conv(&cin, &cout); //default input and output are console 

//  string GenOptions;
  OBFormat* pInFormat = NULL;
  OBFormat* pOutFormat = NULL;
  vector<string> FileList, OutputFileList;
  string OutputFileName;
//  obMessageLevel filterLevel = obWarning; // 2 out of 5

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

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

  //Save name of program without its path (and .exe)
  string pn(argv[0]);
  unsigned int 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 << "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();
                                        }
                                inputExt = iext;
                                        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();
                                        }
                                outputExt = oext;
                                        break;                          
                                
                                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);                                        
                                        
                                        
                                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(FileList.empty())
    {
        cerr << "No input file or format spec!" <<endl;
        usage();
    }

   if (OutputFileName.empty())
   {
        pos = FileList.front().rfind(".");
        if(pos==string::npos)
            OutputFileName = FileList.front()+ "." + outputExt;
        else
            OutputFileName = FileList.front().substr(0, pos) + "." + outputExt;            
    }
  
  Conv.SetInAndOutFormats(pInFormat,pOutFormat);


  // send info message to clog -- don't mess up cerr or cout for user programs
  int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList);
  if ( count == 1 )
    clog << count << " molecule converted" << endl;
  else
    clog << count << " molecules converted" << endl;
  
  if(OutputFileList.size()>1)
  {
    clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<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 << "Open Babel " << 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 << "Open Babel 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:	1020
Committed:	Wed Aug 2 18:06:18 2006 UTC (19 years, 3 months ago) by gezelter
File size:	10530 byte(s)
Log Message:	Changing atom2mdin into atom2md to reflect new unified file format
#	User	Rev	Content
1	gezelter	1020	/**********************************************************************
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 "config.h"
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
78			char *oext;
79			char *iext;
80			string inputExt;
81			string outputExt;
82
83			//Save name of program without its path (and .exe)
84			string pn(argv[0]);
85			unsigned int pos;
86			#ifdef _WIN32
87			pos = pn.find(".exe");
88			if(pos!=string::npos)
89			argv[0][pos]='\0';
90			#endif
91			pos = pn.find_last_of("/\\");
92			if(pos==string::npos)
93			program_name=argv[0];
94			else
95			program_name=argv[0]+pos+1;
96
97			const char* p;
98			int arg;
99			for (arg = 1; arg < argc; arg++)
100			{
101			if (argv[arg])
102			{
103			if (argv[arg][0] == '-')
104			{
105			switch (argv[arg][1])
106			{
107
108			case 'V':
109			{
110			cout << "Open Babel " << BABEL_VERSION << " -- "
111			<< __DATE__ << " -- " << __TIME__ << endl;
112			exit(0);
113			}
114
115			case 'i':
116			gotInType = true;
117			iext = argv[arg] + 2;
118			if(!*iext)
119			iext = argv[++arg]; //space left after -i: use next 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;
139
140			case 'o':
141			gotOutType = true;
142			oext = argv[arg] + 2;
143			if(!*oext)
144			oext = argv[++arg]; //space left after -i: use next argument
145
146			if (strncasecmp(oext, "MIME", 4) == 0)
147			{
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);
154
155			if(pOutFormat==NULL)
156			{
157			cerr << program_name << ": cannot write output format!" << endl;
158			usage();
159			}
160			outputExt = oext;
161			break;
162
163			case '?':
164			case 'H':
165			if(isalnum(argv[arg][2]))
166			{
167			if(strncasecmp(argv[arg]+2,"all",3))
168			{
169			OBFormat* pFormat = Conv.FindFormat(argv[arg]+2);
170			if(pFormat)
171			{
172			cout << argv[arg]+2 << " " << pFormat->Description() << endl;
173			if(strlen(pFormat->SpecificationURL()))
174			cout << "Specification at: " << pFormat->SpecificationURL() << endl;
175			}
176			else
177			cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl;
178			}
179			else
180			{
181			Formatpos pos;
182			OBFormat* pFormat;
183			const char* str=NULL;
184			while(OBConversion::GetNextFormat(pos,str,pFormat))
185			{
186			if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE))
187			continue;
188			cout << str << endl;
189			const char* p = strchr(pFormat->Description(),'\n');
190			cout << p+1; //second line of description
191			if(strlen(pFormat->SpecificationURL()))
192			cout << "Specification at: " << pFormat->SpecificationURL();
193			cout << endl << endl;
194			}
195			}
196			}
197			else
198			help();
199			exit(0);
200
201
202			default: //single character general option
203			p = argv[arg]+1;
204			DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv);
205			break;
206			}
207			}
208			else
209			{
210			//filenames
211			if(!gotOutType)
212			FileList.push_back(argv[arg]);
213			else
214			OutputFileName = argv[arg];
215			}
216			}
217			}
218
219			//user didn't specify input and output format in commandline option
220			//try to parse it from program name (pdb2mdin means input format is pdb, output format is mdin)
221			string formatName(program_name);
222			pos = formatName.find_first_of("2");
223			if(pos!=string::npos) {
224			if (!gotInType)
225			{
226			string tmpExt = formatName.substr(0, pos);
227			pInFormat = Conv.FindFormat(tmpExt.c_str());
228			if(pInFormat==NULL)
229			{
230			cerr << program_name << ": cannot read input format!" << endl;
231			usage();
232			} else
233			{
234			gotInType = true;
235			inputExt = tmpExt;
236			}
237			}
238
239			if (!gotOutType)
240			{
241			string tmpExt = formatName.substr(pos+1, string::npos);
242			pOutFormat = Conv.FindFormat(tmpExt.c_str());
243			if(pOutFormat==NULL)
244			{
245			cerr << program_name << ": cannot write output format!" << endl;
246			usage();
247			}else {
248			gotOutType = true;
249			outputExt = tmpExt;
250			}
251			}
252			}
253
254			if(FileList.empty())
255			{
256			cerr << "No input file or format spec!" <<endl;
257			usage();
258			}
259
260			if (OutputFileName.empty())
261			{
262			pos = FileList.front().rfind(".");
263			if(pos==string::npos)
264			OutputFileName = FileList.front()+ "." + outputExt;
265			else
266			OutputFileName = FileList.front().substr(0, pos) + "." + outputExt;
267			}
268
269			Conv.SetInAndOutFormats(pInFormat,pOutFormat);
270
271
272			// send info message to clog -- don't mess up cerr or cout for user programs
273			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;
278
279			if(OutputFileList.size()>1)
280			{
281			clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl;
282			}
283
284			#ifdef _DEBUG
285			//CM keep window open
286			cout << "Press any key to finish" <<endl;
287			getch();
288			#endif
289
290			return 0;
291			}
292
293			void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, int& arg, int argc, char *argv[])
294			{
295			while(p && *p) //can have multiple single char options
296			{
297			char ch[2]="?";
298			ch = p++;
299			const char* txt=NULL;
300			//Get the option text if needed
301			int nParams = Conv.GetOptionParams(ch, typ);
302			if(nParams)
303			{
304			if(*p)
305			{
306			txt = p; //use text immediately following the option letter
307			p=NULL; //no more single char options
308			}
309			else if(arg<argc-1)
310			{
311			txt = argv[++arg]; //use text from next arg
312			if(*txt=='-')
313			{
314			//...unless it is another option
315			cerr << "Option -" << ch << " takes a parameter" << endl;
316			exit(0);
317			}
318			}
319			}
320			Conv.AddOption(ch, typ, txt);
321			}
322			}
323
324			void usage()
325			{
326			cout << "Open Babel " << BABEL_VERSION << " -- " << __DATE__ << " -- "
327			<< __TIME__ << endl;
328			cout << "Usage: " << program_name
329			<< " [-i<input-type>] <name> [-o<output-type>] <name>" << endl;
330			cout << "Try -H option for more information." << endl;
331			/*
332			#ifdef _DEBUG
333			//CM keep window open
334			cout << "Press any key to finish" <<endl;
335			getch();
336			#endif
337			*/
338			exit (0);
339			}
340
341			void help()
342			{
343			cout << "Open Babel converts chemical structures from one file format to another"<< endl << endl;
344			cout << "Usage: " << program_name << " <input spec> <output spec> [Options]" << endl << endl;
345			cout << "Each spec can be a file whose extension decides the format." << endl;
346			cout << "Optionally the format can be specified by preceding the file by" << endl;
347			cout << "-i<format-type> e.g. -ipdb, for input and -o<format-type> for output" << endl << endl;
348			cout << "See below for available format-types, which are the same as the " << endl;
349			cout << "file extensions and are case independent." << endl;
350			cout << "If no input or output file is given stdin or stdout are used instead." << endl << endl;
351			cout << "More than one input file can be specified and their names can contain" <<endl;
352			cout << "wildcard chars (* and ?).The molecules are aggregated in the output file.\n" << endl;
353			cout << OBConversion::Description(); // Conversion options
354			cout << " -H Outputs this help text" << endl;
355			cout << " -Hxxx (xxx is file format ID e.g. -Hpdb) gives format info" <<endl;
356			cout << " -Hall Outputs details of all formats" <<endl;
357			cout << " -V Outputs version number" <<endl;
358
359
360			OBFormat* pDefault = OBConversion::GetDefaultFormat();
361			if(pDefault)
362			cout << pDefault->TargetClassDescription();// some more options probably for OBMol
363
364			OBFormat* pAPI= OBConversion::FindFormat("obapi");
365			if(pAPI)
366			cout << pAPI->Description();
367
368			cout << "The following file formats are recognized:" << endl;
369			Formatpos pos;
370			OBFormat* pFormat;
371			const char* str=NULL;
372			while(OBConversion::GetNextFormat(pos,str,pFormat))
373			{
374			if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE))
375			continue;
376			cout << " " << str << endl;
377			}
378			cout << "\nSee further specific info and options using -H<format-type>, e.g. -Hpdb" << endl;
379			}
380