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/********************************************************************** |
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atom2md.cpp - OpenBabel-based conversion program to OOPSE MD file, |
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atom2md.cpp - OpenBabel-based conversion program to OpenMD file, |
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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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Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison |
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Some portions Copyright (C) 2004-2006 by Chris Morley |
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Some portions Copyright (C) 2008-2009 by J. Daniel Gezelter |
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|
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This file is part of the OOPSE and Open Babel projects. |
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For more information, see <http://oopse.org> and <http://openbabel.sourceforge.net/> |
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This file is part of both the OpenMD and Open Babel projects. |
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For more information, see <http://openmd.net> and <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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***********************************************************************/ |
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#include "config.h" |
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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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> |
|
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// used to set import/export for Cygwin DLLs |
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#ifdef WIN32 |
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#define USING_OBDLL |
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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 <openbabel/babelconfig.h> |
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|
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#include <iostream> |
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#include <fstream> |
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#include <sstream> |
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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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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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#include <openbabel/obconversion.h> |
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#include <openbabel/plugin.h> |
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#include <cstdlib> |
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#include <cstring> |
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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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|
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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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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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|
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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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|
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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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|
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char *oext; |
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char *iext; |
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bool SplitOrBatch=false; |
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|
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char *oext = NULL; |
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char *iext = NULL; |
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|
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// for use with command name to type conversion |
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string inputExt; |
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string outputExt; |
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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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string::size_type 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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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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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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{ |
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switch (argv[arg][1]) |
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{ |
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|
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|
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case 'V': |
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{ |
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cout << "atom2md: part of OOPSE " << |
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OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << "." << |
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OOPSE_VERSION_TINY << " and Open Babel " << BABEL_VERSION << " -- " |
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cout << program_name << ": part of OpenMD " << |
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OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << |
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"." << OPENMD_VERSION_TINY << |
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" and 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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> |
|
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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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cerr << program_name << ": cannot read input format!" << endl; |
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usage(); |
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} |
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inputExt = iext; |
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break; |
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|
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case 'o': |
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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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> |
|
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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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} |
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else |
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pOutFormat = Conv.FindFormat(oext); |
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|
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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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outputExt = oext; |
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break; |
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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 'L': //display a list of plugin type or classes |
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{ |
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> |
const char* param=NULL; |
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> |
if(argc>arg+1) |
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> |
param = argv[arg+2]; |
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OBPlugin::List(argv[arg+1], param); |
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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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> |
if(isalnum(argv[arg][2]) || arg==argc-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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> |
const char* pID= (arg==argc-2) ? argv[arg+1] : argv[arg]+2; |
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> |
OBFormat* pFormat = Conv.FindFormat(pID); |
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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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> |
cout << pID << " " << pFormat->Description() << endl; |
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> |
if(pFormat->Flags() & NOTWRITABLE) |
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cout << " This format is Read-only" << endl; |
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> |
if(pFormat->Flags() & NOTREADABLE) |
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> |
cout << " This format is Write-only" << endl; |
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> |
|
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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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> |
cout << "Format type: " << pID << " 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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> |
OBPlugin::List("formats","verbose"); |
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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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|
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> |
return 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; |
| 217 |
> |
if(*nam != '\0') |
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> |
{ |
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> |
string txt; |
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> |
int i; |
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> |
for(i=0; i<Conv.GetOptionParams(nam, OBConversion::GENOPTIONS) |
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> |
&& arg<argc-1 && argv[arg+1];++i) //removed && *argv[arg+1]!='-' |
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> |
{ |
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> |
if(!txt.empty()) txt+=' '; |
| 225 |
> |
txt += argv[++arg]; |
| 226 |
> |
} |
| 227 |
> |
if(*nam=='-') |
| 228 |
> |
{ |
| 229 |
> |
// Is a API directive, e.g.---errorlevel |
| 230 |
> |
//Send to the pseudoformat "obapi" (without any leading -) |
| 231 |
> |
OBConversion apiConv; |
| 232 |
> |
OBFormat* pAPI= OBConversion::FindFormat("obapi"); |
| 233 |
> |
if(pAPI) |
| 234 |
> |
{ |
| 235 |
> |
apiConv.SetOutFormat(pAPI); |
| 236 |
> |
apiConv.AddOption(nam+1, OBConversion::GENOPTIONS, txt.c_str()); |
| 237 |
> |
apiConv.Write(NULL, &std::cout); |
| 238 |
> |
} |
| 239 |
> |
} |
| 240 |
> |
else |
| 241 |
> |
// Is a long option name, e.g --addtotitle |
| 242 |
> |
Conv.AddOption(nam,OBConversion::GENOPTIONS,txt.c_str()); |
| 243 |
> |
} |
| 244 |
> |
} |
| 245 |
> |
break; |
| 246 |
> |
|
| 247 |
> |
case 'm': //multiple output files |
| 248 |
> |
SplitOrBatch=true; |
| 249 |
> |
break; |
| 250 |
> |
|
| 251 |
> |
case 'a': //single character input option |
| 252 |
> |
p = argv[arg]+2; |
| 253 |
> |
DoOption(p,Conv,OBConversion::INOPTIONS,arg,argc,argv); |
| 254 |
> |
break; |
| 255 |
> |
|
| 256 |
> |
case 'x': //single character output option |
| 257 |
> |
p = argv[arg]+2; |
| 258 |
> |
DoOption(p,Conv,OBConversion::OUTOPTIONS,arg,argc,argv); |
| 259 |
> |
break; |
| 260 |
> |
|
| 261 |
|
default: //single character general option |
| 262 |
|
p = argv[arg]+1; |
| 263 |
|
DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv); |
| 275 |
|
} |
| 276 |
|
} |
| 277 |
|
|
| 278 |
< |
//user didn't specify input and output format in commandline option |
| 279 |
< |
//try to parse it from program name (pdb2mdin means input format is pdb, output format is mdin) |
| 278 |
> |
// user didn't specify input and output format in commandline option |
| 279 |
> |
// try to parse it from program name (pdb2md means input format is pdb, |
| 280 |
> |
// output format is md) |
| 281 |
> |
|
| 282 |
|
string formatName(program_name); |
| 283 |
|
pos = formatName.find_first_of("2"); |
| 284 |
|
if(pos!=string::npos) { |
| 296 |
|
inputExt = tmpExt; |
| 297 |
|
} |
| 298 |
|
} |
| 299 |
< |
|
| 299 |
> |
|
| 300 |
|
if (!gotOutType) |
| 301 |
|
{ |
| 302 |
|
string tmpExt = formatName.substr(pos+1, string::npos); |
| 310 |
|
outputExt = tmpExt; |
| 311 |
|
} |
| 312 |
|
} |
| 313 |
< |
} |
| 313 |
> |
} |
| 314 |
> |
|
| 315 |
> |
if(!gotOutType) //the last file is the output |
| 316 |
> |
{ |
| 317 |
> |
if(FileList.empty()) |
| 318 |
> |
{ |
| 319 |
> |
cerr << "No output file or format spec!" << endl; |
| 320 |
> |
usage(); |
| 321 |
> |
} |
| 322 |
> |
OutputFileName = FileList.back(); |
| 323 |
> |
FileList.pop_back(); |
| 324 |
> |
} |
| 325 |
> |
|
| 326 |
> |
#ifdef _WIN32 |
| 327 |
> |
//Expand wildcards in input filenames and add to FileList |
| 328 |
> |
vector<string> tempFileList(FileList); |
| 329 |
> |
FileList.clear(); |
| 330 |
> |
vector<string>::iterator itr; |
| 331 |
> |
for(itr=tempFileList.begin();itr!=tempFileList.end();++itr) |
| 332 |
> |
DLHandler::findFiles (FileList, *itr); |
| 333 |
> |
#endif |
| 334 |
|
|
| 335 |
< |
if(FileList.empty()) |
| 335 |
> |
if (!gotInType) |
| 336 |
|
{ |
| 337 |
< |
cerr << "No input file or format spec!" <<endl; |
| 338 |
< |
usage(); |
| 337 |
> |
if(FileList.empty()) |
| 338 |
> |
{ |
| 339 |
> |
cerr << "No input file or format spec!" <<endl; |
| 340 |
> |
usage(); |
| 341 |
> |
} |
| 342 |
|
} |
| 343 |
+ |
|
| 344 |
+ |
if (!gotOutType) |
| 345 |
+ |
{ |
| 346 |
+ |
pOutFormat = Conv.FormatFromExt(OutputFileName.c_str()); |
| 347 |
+ |
if(pOutFormat==NULL) |
| 348 |
+ |
{ |
| 349 |
+ |
cerr << program_name << ": cannot write output format!" << endl; |
| 350 |
+ |
usage(); |
| 351 |
+ |
} |
| 352 |
+ |
} |
| 353 |
|
|
| 354 |
< |
if (OutputFileName.empty()) |
| 354 |
> |
if(!Conv.SetInFormat(pInFormat)) |
| 355 |
|
{ |
| 356 |
< |
pos = FileList.front().rfind("."); |
| 357 |
< |
if(pos==string::npos) |
| 358 |
< |
OutputFileName = FileList.front()+ "." + outputExt; |
| 356 |
> |
cerr << "Invalid input format" << endl; |
| 357 |
> |
usage(); |
| 358 |
> |
} |
| 359 |
> |
if(!Conv.SetOutFormat(pOutFormat)) |
| 360 |
> |
{ |
| 361 |
> |
cerr << "Invalid output format" << endl; |
| 362 |
> |
usage(); |
| 363 |
> |
} |
| 364 |
> |
|
| 365 |
> |
if(SplitOrBatch) |
| 366 |
> |
{ |
| 367 |
> |
//Put * into output file name before extension (or ext.gz) |
| 368 |
> |
if(OutputFileName.empty()) |
| 369 |
> |
{ |
| 370 |
> |
OutputFileName = "*."; |
| 371 |
> |
if (oext != NULL) |
| 372 |
> |
OutputFileName += oext; |
| 373 |
> |
} |
| 374 |
|
else |
| 375 |
< |
OutputFileName = FileList.front().substr(0, pos) + "." + outputExt; |
| 375 |
> |
{ |
| 376 |
> |
string::size_type pos = OutputFileName.rfind(".gz"); |
| 377 |
> |
if(pos==string::npos) |
| 378 |
> |
pos = OutputFileName.rfind('.'); |
| 379 |
> |
else |
| 380 |
> |
pos = OutputFileName.rfind('.',pos-1); |
| 381 |
> |
if(pos==string::npos) |
| 382 |
> |
OutputFileName += '*'; |
| 383 |
> |
else |
| 384 |
> |
OutputFileName.insert(pos,"*"); |
| 385 |
> |
} |
| 386 |
|
} |
| 387 |
< |
|
| 272 |
< |
Conv.SetInAndOutFormats(pInFormat,pOutFormat); |
| 273 |
< |
|
| 274 |
< |
|
| 275 |
< |
// send info message to clog -- don't mess up cerr or cout for user programs |
| 387 |
> |
|
| 388 |
|
int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList); |
| 389 |
< |
if ( count == 1 ) |
| 390 |
< |
clog << count << " molecule converted" << endl; |
| 391 |
< |
else |
| 280 |
< |
clog << count << " molecules converted" << endl; |
| 281 |
< |
|
| 389 |
> |
|
| 390 |
> |
Conv.ReportNumberConverted(count); |
| 391 |
> |
|
| 392 |
|
if(OutputFileList.size()>1) |
| 393 |
|
{ |
| 394 |
|
clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl; |
| 395 |
|
} |
| 396 |
< |
|
| 396 |
> |
|
| 397 |
> |
std::string messageSummary = obErrorLog.GetMessageSummary(); |
| 398 |
> |
if (messageSummary.size()) |
| 399 |
> |
{ |
| 400 |
> |
clog << messageSummary << endl; |
| 401 |
> |
} |
| 402 |
> |
|
| 403 |
|
#ifdef _DEBUG |
| 404 |
|
//CM keep window open |
| 405 |
|
cout << "Press any key to finish" <<endl; |
| 409 |
|
return 0; |
| 410 |
|
} |
| 411 |
|
|
| 412 |
< |
void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, int& arg, int argc, char *argv[]) |
| 412 |
> |
void DoOption(const char* p, OBConversion& Conv, |
| 413 |
> |
OBConversion::Option_type typ, int& arg, int argc, char *argv[]) |
| 414 |
|
{ |
| 415 |
|
while(p && *p) //can have multiple single char options |
| 416 |
+ |
{ |
| 417 |
+ |
char ch[2]="?"; |
| 418 |
+ |
*ch = *p++; |
| 419 |
+ |
const char* txt=NULL; |
| 420 |
+ |
//Get the option text if needed |
| 421 |
+ |
int nParams = Conv.GetOptionParams(ch, typ); |
| 422 |
+ |
if(nParams) |
| 423 |
|
{ |
| 424 |
< |
char ch[2]="?"; |
| 425 |
< |
*ch = *p++; |
| 426 |
< |
const char* txt=NULL; |
| 427 |
< |
//Get the option text if needed |
| 428 |
< |
int nParams = Conv.GetOptionParams(ch, typ); |
| 429 |
< |
if(nParams) |
| 424 |
> |
if(*p) |
| 425 |
> |
{ |
| 426 |
> |
txt = p; //use text immediately following the option letter |
| 427 |
> |
p=NULL; //no more single char options |
| 428 |
> |
} |
| 429 |
> |
else if(arg<argc-1) |
| 430 |
> |
{ |
| 431 |
> |
txt = argv[++arg]; //use text from next arg |
| 432 |
> |
if(*txt=='-') |
| 433 |
|
{ |
| 434 |
< |
if(*p) |
| 435 |
< |
{ |
| 436 |
< |
txt = p; //use text immediately following the option letter |
| 310 |
< |
p=NULL; //no more single char options |
| 311 |
< |
} |
| 312 |
< |
else if(arg<argc-1) |
| 313 |
< |
{ |
| 314 |
< |
txt = argv[++arg]; //use text from next arg |
| 315 |
< |
if(*txt=='-') |
| 316 |
< |
{ |
| 317 |
< |
//...unless it is another option |
| 318 |
< |
cerr << "Option -" << ch << " takes a parameter" << endl; |
| 319 |
< |
exit(0); |
| 320 |
< |
} |
| 321 |
< |
} |
| 434 |
> |
//...unless it is another option |
| 435 |
> |
cerr << "Option -" << ch << " takes a parameter" << endl; |
| 436 |
> |
exit(0); |
| 437 |
|
} |
| 438 |
< |
Conv.AddOption(ch, typ, txt); |
| 438 |
> |
} |
| 439 |
|
} |
| 440 |
+ |
Conv.AddOption(ch, typ, txt); |
| 441 |
+ |
} |
| 442 |
|
} |
| 443 |
|
|
| 444 |
|
void usage() |
| 445 |
|
{ |
| 446 |
< |
cout << "atom2md: part of OOPSE " << |
| 447 |
< |
OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << "." << |
| 448 |
< |
OOPSE_VERSION_TINY << " and Open Babel " << BABEL_VERSION << " -- " |
| 446 |
> |
cout << program_name << ": part of OpenMD " << |
| 447 |
> |
OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << "." << |
| 448 |
> |
OPENMD_VERSION_TINY << " and OpenBabel " << BABEL_VERSION << " -- " |
| 449 |
|
<< __DATE__ << " -- " << __TIME__ << endl; |
| 450 |
|
cout << "Usage: " << program_name |
| 451 |
|
<< " [-i<input-type>] <name> [-o<output-type>] <name>" << endl; |
| 452 |
|
cout << "Try -H option for more information." << endl; |
| 453 |
< |
/* |
| 453 |
> |
|
| 454 |
|
#ifdef _DEBUG |
| 455 |
|
//CM keep window open |
| 456 |
|
cout << "Press any key to finish" <<endl; |
| 457 |
|
getch(); |
| 458 |
|
#endif |
| 342 |
– |
*/ |
| 459 |
|
exit (0); |
| 460 |
|
} |
| 461 |
|
|
| 462 |
|
void help() |
| 463 |
|
{ |
| 464 |
< |
cout << "Open Babel converts chemical structures from one file format to another"<< endl << endl; |
| 464 |
> |
cout << program_name << " converts chemical structures from one file format to another"<< endl << endl; |
| 465 |
|
cout << "Usage: " << program_name << " <input spec> <output spec> [Options]" << endl << endl; |
| 466 |
|
cout << "Each spec can be a file whose extension decides the format." << endl; |
| 467 |
|
cout << "Optionally the format can be specified by preceding the file by" << endl; |
| 493 |
|
while(OBConversion::GetNextFormat(pos,str,pFormat)) |
| 494 |
|
{ |
| 495 |
|
if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) |
| 496 |
< |
continue; |
| 496 |
> |
continue; |
| 497 |
|
cout << " " << str << endl; |
| 498 |
|
} |
| 499 |
|
cout << "\nSee further specific info and options using -H<format-type>, e.g. -Hpdb" << endl; |
