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/********************************************************************** |
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main.cpp - Main conversion program, command-line handling. |
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|
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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Some portions Copyright (C) 2004-2005 by Chris Morley |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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#include "openbabel/babelconfig.hpp" |
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#if HAVE_IOSTREAM |
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#include <iostream> |
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#elif HAVE_IOSTREAM_H |
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#include <iostream.h> |
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#endif |
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#if HAVE_FSTREAM |
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#include <fstream> |
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#elif HAVE_FSTREAM_H |
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#include <fstream.h> |
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#endif |
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#if HAVE_SSTREAM |
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#include <sstream> |
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#elif |
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#include <sstream.h> |
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#endif |
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|
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#include <string> |
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#include <map> |
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#if HAVE_CONIO_H |
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#include <conio.h> |
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#endif |
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|
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#if !HAVE_STRNCASECMP |
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extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); |
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#endif |
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|
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#include "openbabel/obconversion.hpp" |
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#include "brains/Register.hpp" |
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|
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using namespace std; |
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using namespace OpenBabel; |
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using namespace oopse; |
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void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, |
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int& arg, int argc, char *argv[]); |
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void usage(); |
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void help(); |
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|
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// There isn't a great way to do this -- we need to save argv[0] for usage() |
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static char *program_name; |
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|
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int main(int argc,char *argv[]) |
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{ |
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registerOBFormats(); |
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OBConversion Conv(&cin, &cout); //default input and output are console |
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|
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// string GenOptions; |
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OBFormat* pInFormat = NULL; |
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OBFormat* pOutFormat = NULL; |
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vector<string> FileList, OutputFileList; |
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string OutputFileName; |
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// obMessageLevel filterLevel = obWarning; // 2 out of 5 |
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|
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// Parse commandline |
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bool gotInType = false, gotOutType = false; |
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bool UseSavedOptions = false; |
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bool SplitOrBatch=false; |
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|
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char *oext; |
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char *iext; |
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|
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//Save name of program without its path (and .exe) |
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string pn(argv[0]); |
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unsigned int pos; |
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#ifdef _WIN32 |
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pos = pn.find(".exe"); |
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if(pos!=string::npos) |
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argv[0][pos]='\0'; |
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#endif |
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pos = pn.find_last_of("/\\"); |
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if(pos==string::npos) |
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program_name=argv[0]; |
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else |
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program_name=argv[0]+pos+1; |
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|
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const char* p; |
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int arg; |
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for (arg = 1; arg < argc; arg++) |
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{ |
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if (argv[arg]) |
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{ |
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if (argv[arg][0] == '-') |
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{ |
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switch (argv[arg][1]) |
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{ |
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|
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case 'V': |
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{ |
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cout << "Open Babel " << BABEL_VERSION << " -- " |
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<< __DATE__ << " -- " << __TIME__ << endl; |
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exit(0); |
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} |
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|
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case 'i': |
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gotInType = true; |
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iext = argv[arg] + 2; |
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if(!*iext) |
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iext = argv[++arg]; //space left after -i: use next argument |
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|
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if (strncasecmp(iext, "MIME", 4) == 0) |
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{ |
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// get the MIME type from the next argument |
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iext = argv[++arg]; |
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pInFormat = Conv.FormatFromMIME(iext); |
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} |
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else |
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{ |
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//The ID provided by the OBFormat class is used as the identifying file extension |
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pInFormat = Conv.FindFormat(iext); |
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} |
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if(pInFormat==NULL) |
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{ |
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cerr << program_name << ": cannot read input format!" << endl; |
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usage(); |
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} |
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break; |
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|
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case 'o': |
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gotOutType = true; |
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oext = argv[arg] + 2; |
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if(!*oext) |
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oext = argv[++arg]; //space left after -i: use next argument |
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|
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if (strncasecmp(oext, "MIME", 4) == 0) |
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{ |
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// get the MIME type from the next argument |
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oext = argv[++arg]; |
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pOutFormat = Conv.FormatFromMIME(oext); |
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} |
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else |
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pOutFormat = Conv.FindFormat(oext); |
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|
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if(pOutFormat==NULL) |
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{ |
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cerr << program_name << ": cannot write output format!" << endl; |
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usage(); |
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} |
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break; |
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|
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case 'F': |
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if(!Conv.SetOutFormat("fpt")) |
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cout << "FingerprintFormat needs to be loaded" << endl; |
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else |
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{ |
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Conv.AddOption("F",OBConversion::OUTOPTIONS); |
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Conv.Write(NULL); |
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} |
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return 0; |
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|
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case '?': |
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case 'H': |
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if(isalnum(argv[arg][2])) |
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{ |
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if(strncasecmp(argv[arg]+2,"all",3)) |
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{ |
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OBFormat* pFormat = Conv.FindFormat(argv[arg]+2); |
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if(pFormat) |
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{ |
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cout << argv[arg]+2 << " " << pFormat->Description() << endl; |
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if(strlen(pFormat->SpecificationURL())) |
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cout << "Specification at: " << pFormat->SpecificationURL() << endl; |
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} |
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else |
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cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl; |
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} |
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else |
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{ |
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Formatpos pos; |
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OBFormat* pFormat; |
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const char* str=NULL; |
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while(OBConversion::GetNextFormat(pos,str,pFormat)) |
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{ |
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if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) |
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continue; |
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cout << str << endl; |
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const char* p = strchr(pFormat->Description(),'\n'); |
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cout << p+1; //second line of description |
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if(strlen(pFormat->SpecificationURL())) |
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cout << "Specification at: " << pFormat->SpecificationURL(); |
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cout << endl << endl; |
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} |
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} |
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} |
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else |
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help(); |
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exit(0); |
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|
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case '-': //long option --name text |
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{ |
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//Do nothing if name is empty |
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//Option's text is the next arg provided it doesn't start with - |
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char* nam = argv[arg]+2; |
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if(*nam != '\0') |
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{ |
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const char* txt=NULL; |
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if(Conv.GetOptionParams(nam, OBConversion::OUTOPTIONS) |
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&& arg<argc-1 && argv[arg+1] && *argv[arg+1]!='-') |
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txt = argv[++arg]; |
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if(*nam=='-') |
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{ |
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// Is a API directive, e.g.---errorlevel |
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//Send to the pseudoformat "obapi" (without any leading -) |
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OBConversion apiConv; |
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OBFormat* pAPI= OBConversion::FindFormat("obapi"); |
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if(pAPI) |
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{ |
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apiConv.SetOutFormat(pAPI); |
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apiConv.AddOption(nam+1, OBConversion::OUTOPTIONS, txt); |
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apiConv.Write(NULL); |
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} |
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} |
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else |
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// Is a long option name, e.g --addtotitle |
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Conv.AddOption(nam,OBConversion::GENOPTIONS,txt); |
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} |
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} |
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break; |
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|
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case 'm': //multiple output files |
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SplitOrBatch=true; |
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break; |
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|
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case 'a': //single character input option |
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p = argv[arg]+2; |
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DoOption(p,Conv,OBConversion::INOPTIONS,arg,argc,argv); |
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break; |
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|
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case 'x': //single character output option |
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p = argv[arg]+2; |
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DoOption(p,Conv,OBConversion::OUTOPTIONS,arg,argc,argv); |
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break; |
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|
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default: //single character general option |
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p = argv[arg]+1; |
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DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv); |
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break; |
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} |
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} |
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else |
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{ |
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//filenames |
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if(!gotOutType) |
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FileList.push_back(argv[arg]); |
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else |
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OutputFileName = argv[arg]; |
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} |
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} |
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} |
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|
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if(!gotOutType) //the last file is the output |
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{ |
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if(FileList.empty()) |
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{ |
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cerr << "No output file or format spec!" << endl; |
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usage(); |
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} |
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OutputFileName = FileList.back(); |
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FileList.pop_back(); |
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} |
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|
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#ifdef _WIN32 |
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//Expand wildcards in input filenames and add to FileList |
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vector<string> tempFileList(FileList); |
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FileList.clear(); |
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vector<string>::iterator itr; |
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for(itr=tempFileList.begin();itr!=tempFileList.end();itr++) |
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DLHandler::findFiles (FileList, *itr); |
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#endif |
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|
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// Conv.SetGeneralOptions(GenOptions.c_str()); |
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|
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if (!gotInType) |
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{ |
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if(FileList.empty()) |
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{ |
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cerr << "No input file or format spec!" <<endl; |
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usage(); |
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} |
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} |
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|
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if (!gotOutType) |
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{ |
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pOutFormat = Conv.FormatFromExt(OutputFileName.c_str()); |
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if(pOutFormat==NULL) |
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{ |
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cerr << program_name << ": cannot write output format!" << endl; |
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usage(); |
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} |
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} |
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|
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Conv.SetInAndOutFormats(pInFormat,pOutFormat); |
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|
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if(SplitOrBatch) |
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{ |
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//Put * into output file name before extension (or ext.gz) |
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if(OutputFileName.empty()) |
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{ |
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OutputFileName = "*."; |
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OutputFileName += oext; |
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} |
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else |
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{ |
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unsigned int pos = OutputFileName.rfind(".gz"); |
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if(pos==string::npos) |
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pos = OutputFileName.rfind('.'); |
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else |
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pos = OutputFileName.rfind('.',pos-1); |
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if(pos==string::npos) |
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OutputFileName += '*'; |
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else |
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OutputFileName.insert(pos,"*"); |
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} |
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} |
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|
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// send info message to clog -- don't mess up cerr or cout for user programs |
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int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList); |
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if ( count == 1 ) |
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clog << count << " molecule converted" << endl; |
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else |
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clog << count << " molecules converted" << endl; |
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|
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if(OutputFileList.size()>1) |
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{ |
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clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl; |
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} |
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|
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#ifdef _DEBUG |
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//CM keep window open |
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cout << "Press any key to finish" <<endl; |
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getch(); |
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#endif |
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|
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return 0; |
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}; |
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|
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void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, int& arg, int argc, char *argv[]) |
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{ |
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while(p && *p) //can have multiple single char options |
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{ |
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char ch[2]="?"; |
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*ch = *p++; |
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const char* txt=NULL; |
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//Get the option text if needed |
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int nParams = Conv.GetOptionParams(ch, typ); |
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if(nParams) |
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{ |
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if(*p) |
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{ |
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txt = p; //use text immediately following the option letter |
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p=NULL; //no more single char options |
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} |
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else if(arg<argc-1) |
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{ |
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txt = argv[++arg]; //use text from next arg |
| 375 |
if(*txt=='-') |
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{ |
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//...unless it is another option |
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cerr << "Option -" << ch << " takes a parameter" << endl; |
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exit(0); |
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} |
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} |
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} |
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Conv.AddOption(ch, typ, txt); |
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} |
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} |
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|
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void usage() |
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{ |
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cout << "Open Babel " << BABEL_VERSION << " -- " << __DATE__ << " -- " |
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<< __TIME__ << endl; |
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cout << "Usage: " << program_name |
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<< " [-i<input-type>] <name> [-o<output-type>] <name>" << endl; |
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cout << "Try -H option for more information." << endl; |
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/* |
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#ifdef _DEBUG |
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//CM keep window open |
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cout << "Press any key to finish" <<endl; |
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getch(); |
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#endif |
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*/ |
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exit (0); |
| 402 |
} |
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|
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void help() |
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{ |
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cout << "Open Babel converts chemical structures from one file format to another"<< endl << endl; |
| 407 |
cout << "Usage: " << program_name << " <input spec> <output spec> [Options]" << endl << endl; |
| 408 |
cout << "Each spec can be a file whose extension decides the format." << endl; |
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cout << "Optionally the format can be specified by preceding the file by" << endl; |
| 410 |
cout << "-i<format-type> e.g. -icml, for input and -o<format-type> for output" << endl << endl; |
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cout << "See below for available format-types, which are the same as the " << endl; |
| 412 |
cout << "file extensions and are case independent." << endl; |
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cout << "If no input or output file is given stdin or stdout are used instead." << endl << endl; |
| 414 |
cout << "More than one input file can be specified and their names can contain" <<endl; |
| 415 |
cout << "wildcard chars (* and ?).The molecules are aggregated in the output file.\n" << endl; |
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cout << OBConversion::Description(); // Conversion options |
| 417 |
cout << " -H Outputs this help text" << endl; |
| 418 |
cout << " -Hxxx (xxx is file format ID e.g. -Hcml) gives format info" <<endl; |
| 419 |
cout << " -Hall Outputs details of all formats" <<endl; |
| 420 |
cout << " -V Outputs version number" <<endl; |
| 421 |
cout << " -F Outputs the available fingerprint types" <<endl; |
| 422 |
cout << " -m Produces multiple output files, to allow:" <<endl; |
| 423 |
cout << " Splitting: e.g. " << program_name << " infile.mol new.smi -m" <<endl; |
| 424 |
cout << " puts each molecule into new1.smi new2.smi etc" <<endl; |
| 425 |
cout << " Batch conversion: e.g. " << program_name << " *.mol -osmi -m" <<endl; |
| 426 |
cout << " converts each input file to a .smi file" << endl; |
| 427 |
#ifdef _WIN32 |
| 428 |
cout << " In Windows these can also be done using the forms" <<endl; |
| 429 |
cout << " " << program_name << " infile.mol new*.smi and " << program_name << " *.mol *.smi respectively.\n" <<endl; |
| 430 |
#endif |
| 431 |
|
| 432 |
OBFormat* pDefault = OBConversion::GetDefaultFormat(); |
| 433 |
if(pDefault) |
| 434 |
cout << pDefault->TargetClassDescription();// some more options probably for OBMol |
| 435 |
|
| 436 |
OBFormat* pAPI= OBConversion::FindFormat("obapi"); |
| 437 |
if(pAPI) |
| 438 |
cout << pAPI->Description(); |
| 439 |
|
| 440 |
cout << "The following file formats are recognized:" << endl; |
| 441 |
Formatpos pos; |
| 442 |
OBFormat* pFormat; |
| 443 |
const char* str=NULL; |
| 444 |
while(OBConversion::GetNextFormat(pos,str,pFormat)) |
| 445 |
{ |
| 446 |
if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) |
| 447 |
continue; |
| 448 |
cout << " " << str << endl; |
| 449 |
} |
| 450 |
cout << "\nSee further specific info and options using -H<format-type>, e.g. -Hcml" << endl; |
| 451 |
} |
| 452 |
|
| 453 |
/* OpenBabel man page*/ |
| 454 |
/** \page babel a converter for chemistry and molecular modeling data files |
| 455 |
* |
| 456 |
* \n |
| 457 |
* \par SYNOPSIS |
| 458 |
* |
| 459 |
* \b babel [-H<help-options>] [-V] [-m] [-d] [-h] [-p] [-s<SMARTS-pattern>] [-v<SMARTS-pattern>] [-f<#> -l<#>] [-c] [-x<format-options>] [-i<input-type>] \<infile\> [-o<output-type>] \<outfile\> |
| 460 |
* |
| 461 |
* \par DESCRIPTION |
| 462 |
* |
| 463 |
* Open Babel is a program designed to interconvert a number of |
| 464 |
* file formats currently used in molecular modeling software. \n\n |
| 465 |
* |
| 466 |
* Note that Open Babel can also be used as a library to interconvert |
| 467 |
* many file formats and to provide standard chemistry software routines. |
| 468 |
* See the Open Babel web pages (http://openbabel.sourceforge.net) for more |
| 469 |
* information. |
| 470 |
* |
| 471 |
* \par OPTIONS |
| 472 |
* |
| 473 |
* If only input and ouput files are given, Open Babel will guess |
| 474 |
* the file type from the filename extension. \n\n |
| 475 |
* |
| 476 |
* \b -V : |
| 477 |
* Output version number and exit \n\n |
| 478 |
* \b -H : |
| 479 |
* Output usage information \n\n |
| 480 |
* \b -H\<format-ID\> : |
| 481 |
* Output formatting information and options for format specified\n\n |
| 482 |
* \b -Hall : |
| 483 |
* Output formatting information and options for all formats\n\n |
| 484 |
* \b -i : |
| 485 |
* Specifies input format, see below for the available formats \n\n |
| 486 |
* \b -o : |
| 487 |
* Specifies output format, see below for the available formats \n\n |
| 488 |
* \b -m : |
| 489 |
* Produce multiple output files, to allow:\n |
| 490 |
* * Splitting one input file - put each molecule into consecutively numbered output files \n |
| 491 |
* * Batch conversion - convert each of multiple input files into a specified output format \n |
| 492 |
* See examples below \n\n |
| 493 |
* \b -d : |
| 494 |
* Delete Hydrogens \n\n |
| 495 |
* \b -h : |
| 496 |
* Add Hydrogens \n\n |
| 497 |
* \b -p : |
| 498 |
* Add Hydrogens appropriate for pH (use transforms in phmodel.txt) \n\n |
| 499 |
* \b -t : |
| 500 |
* All input files describe a single molecule \n\n |
| 501 |
* \b -f\<#\> : |
| 502 |
* For multiple entries input, start import at molecule # \n\n |
| 503 |
* \b -l\<#\> : |
| 504 |
* For multiple entries input, stop import at molecule # \n\n |
| 505 |
* \b -c : |
| 506 |
* Center atomic coordinates at (0,0,0) \n\n |
| 507 |
* \b -s\<SMARTS\> : |
| 508 |
* Convert only molecules matching the SMARTS pattern specified \n\n |
| 509 |
* \b -v\<SMARTS\> : |
| 510 |
* Convert only molecules \b NOT matching SMARTS pattern specified \n\n |
| 511 |
* |
| 512 |
* \par FILE FORMATS |
| 513 |
* |
| 514 |
* The following formats are currently supported by Open Babel: |
| 515 |
* \n alc -- Alchemy format |
| 516 |
* \n bgf -- BGF format |
| 517 |
* \n box -- Dock 3.5 Box format |
| 518 |
* \n bs -- Ball and Stick format |
| 519 |
* \n c3d1 -- Chem3D Cartesian 1 format |
| 520 |
* \n c3d2 -- Chem3D Cartesian2 format |
| 521 |
* \n caccrt -- Cacao format |
| 522 |
* \n cache -- CAChe format [Writeonly] |
| 523 |
* \n cacint -- CacaoInternal format [Writeonly] |
| 524 |
* \n car -- MSI Biosym/Insight II CAR format [Readonly] |
| 525 |
* \n ccc -- CCC format [Readonly] |
| 526 |
* \n cht -- ChemTool format [Writeonly] |
| 527 |
* \n cml -- Chemical Markup Language |
| 528 |
* \n crk2d -- Chemical Resource Kit diagram format (2D) |
| 529 |
* \n crk3d -- Chemical Resource Kit 3D format |
| 530 |
* \n csr -- CSR format [Writeonly] |
| 531 |
* \n cssr -- CSD CSSR format [Writeonly] |
| 532 |
* \n ct -- ChemDraw Connection Table format |
| 533 |
* \n dmol -- DMol3 coordinates format |
| 534 |
* \n ent -- Protein Data Bank format |
| 535 |
* \n feat -- Feature format |
| 536 |
* \n fh -- Fenske-Hall Z-Matrix format [Writeonly] |
| 537 |
* \n fix -- FIX format [Writeonly] |
| 538 |
* \n g03 -- Gaussian98/03 Cartesian [Writeonly] |
| 539 |
* \n g98 -- Gaussian98/03 Cartesian [Writeonly] |
| 540 |
* \n gam -- GAMESS Output |
| 541 |
* \n gamout -- GAMESS Output |
| 542 |
* \n gau -- Gaussian98/03 Cartesian [Writeonly] |
| 543 |
* \n gpr -- Ghemical format |
| 544 |
* \n gr96 -- GROMOS96 format [Writeonly] |
| 545 |
* \n hin -- HyperChem Input format |
| 546 |
* \n ins -- ShelX format [Readonly] |
| 547 |
* \n jout -- Jaguar output format |
| 548 |
* \n mdl -- MDL MOL format |
| 549 |
* \n mm1gp -- Ghemical format |
| 550 |
* \n mm3 -- MM3 format [Writeonly] |
| 551 |
* \n mmd -- MacroMod format |
| 552 |
* \n mmod -- MacroMod format |
| 553 |
* \n mol -- MDL MOL format |
| 554 |
* \n mol2 -- Sybyl Mol2 format |
| 555 |
* \n mopcrt -- MOPAC Cartesian format |
| 556 |
* \n mopout -- MOPAC Output format [Readonly] |
| 557 |
* \n mpqc -- MPQC format [Readonly] |
| 558 |
* \n nwo -- NWChem format |
| 559 |
* \n pdb -- Protein Data Bank format |
| 560 |
* \n pov -- POV-Ray input format [Writeonly] |
| 561 |
* \n pqs -- Parallel Quantum Solutions format |
| 562 |
* \n prep -- Amber Prep format [Readonly] |
| 563 |
* \n qcout -- QChem output format |
| 564 |
* \n qm1gp -- Ghemical format |
| 565 |
* \n report -- Report format [Writeonly] |
| 566 |
* \n res -- ShelX format [Readonly] |
| 567 |
* \n rxn -- MDL RXN format |
| 568 |
* \n sd -- MDL MOL format |
| 569 |
* \n sdf -- MDL MOL format |
| 570 |
* \n smi -- SMILES format |
| 571 |
* \n tmol -- TurboMole Coordinate format |
| 572 |
* \n txyz -- Tinker format [Writeonly] |
| 573 |
* \n unixyz -- UniChem XYZ format |
| 574 |
* \n vmol -- ViewMol format |
| 575 |
* \n xed -- XED format [Writeonly] |
| 576 |
* \n xyz -- XYZ cartesian coordinates format |
| 577 |
* \n zin -- ZINDO input format [Writeonly] |
| 578 |
* |
| 579 |
* \par FORMAT OPTIONS |
| 580 |
* Individual file formats may have additional formatting options. \n |
| 581 |
* Input format options are preceded by 'a', e.g. -as \n |
| 582 |
* Output format options are preceded by 'x', e.g. -xn \n |
| 583 |
* For further specific information and options, use -H<format-type> \n |
| 584 |
* e.g., -Hcml |
| 585 |
* |
| 586 |
* \par EXAMPLES |
| 587 |
* - Standard conversion \n |
| 588 |
* babel -ixyz ethanol.xyz -opdb ethanol.pdb \n |
| 589 |
* - Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT \n |
| 590 |
* babel -ismi -omol2 \n |
| 591 |
* - Split a multi-molecule file into new1.smi, new2.smi, etc. \n |
| 592 |
* babel infile.mol new.smi -m \n |
| 593 |
* |
| 594 |
* \par AUTHORS |
| 595 |
* |
| 596 |
* Open Babel is currently maintained by \b Geoff \b Hutchison, \b Chris \b Morley and \b Michael \b Banck. |
| 597 |
* |
| 598 |
* For more contributors to Open Babel, see http://openbabel.sourceforge.net/THANKS.shtml |
| 599 |
* |
| 600 |
* \par COPYRIGHT |
| 601 |
* Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
| 602 |
* Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison \n \n |
| 603 |
* This program is free software; you can redistribute it and/or modify |
| 604 |
* it under the terms of the GNU General Public License as published by |
| 605 |
* the Free Software Foundation version 2 of the License.\n \n |
| 606 |
* This program is distributed in the hope that it will be useful, |
| 607 |
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 608 |
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 609 |
* GNU General Public License for more details. |
| 610 |
* |
| 611 |
* \par SEE ALSO |
| 612 |
* The web pages for Open Babel can be found at http://openbabel.sourceforge.net/ |
| 613 |
**/ |
