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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 |
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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); |
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} |
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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; |
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cout << "Usage: " << program_name << " <input spec> <output spec> [Options]" << endl << endl; |
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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; |
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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; |
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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; |
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cout << "More than one input file can be specified and their names can contain" <<endl; |
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cout << "wildcard chars (* and ?).The molecules are aggregated in the output file.\n" << endl; |
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cout << OBConversion::Description(); // Conversion options |
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cout << " -H Outputs this help text" << endl; |
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cout << " -Hxxx (xxx is file format ID e.g. -Hcml) gives format info" <<endl; |
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cout << " -Hall Outputs details of all formats" <<endl; |
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cout << " -V Outputs version number" <<endl; |
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cout << " -F Outputs the available fingerprint types" <<endl; |
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cout << " -m Produces multiple output files, to allow:" <<endl; |
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cout << " Splitting: e.g. " << program_name << " infile.mol new.smi -m" <<endl; |
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cout << " puts each molecule into new1.smi new2.smi etc" <<endl; |
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cout << " Batch conversion: e.g. " << program_name << " *.mol -osmi -m" <<endl; |
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cout << " converts each input file to a .smi file" << endl; |
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#ifdef _WIN32 |
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cout << " In Windows these can also be done using the forms" <<endl; |
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cout << " " << program_name << " infile.mol new*.smi and " << program_name << " *.mol *.smi respectively.\n" <<endl; |
430 |
#endif |
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|
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OBFormat* pDefault = OBConversion::GetDefaultFormat(); |
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if(pDefault) |
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cout << pDefault->TargetClassDescription();// some more options probably for OBMol |
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|
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OBFormat* pAPI= OBConversion::FindFormat("obapi"); |
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if(pAPI) |
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cout << pAPI->Description(); |
439 |
|
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cout << "The following file formats are recognized:" << endl; |
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Formatpos pos; |
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OBFormat* pFormat; |
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const char* str=NULL; |
444 |
while(OBConversion::GetNextFormat(pos,str,pFormat)) |
445 |
{ |
446 |
if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) |
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continue; |
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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 |
**/ |