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/********************************************************************** |
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atom2md.cpp - OpenBabel-based conversion program to OOPSE MD 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) 2001-2006 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 by J. Daniel Gezelter |
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|
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This file is part of both 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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|
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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 "config.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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|
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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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#include <conio.h> |
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#endif |
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#include <cstdlib> |
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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.h> |
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|
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using namespace std; |
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using namespace OpenBabel; |
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|
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void DoOption(const char* p, OBConversion& Conv, |
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OBConversion::Option_type typ, int& arg, int argc, |
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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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OBConversion Conv(&cin, &cout); //default input and output are console |
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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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|
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// Parse commandline |
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bool gotInType = false, gotOutType = 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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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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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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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 << program_name << ": part of OOPSE " << |
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OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << |
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"." << OOPSE_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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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 |
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// 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 |
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// 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!" |
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<< 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 |
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// 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!" |
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<< 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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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+=' '; |
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txt += argv[++arg]; |
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} |
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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::GENOPTIONS, txt.c_str()); |
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apiConv.Write(NULL, &std::cout); |
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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.c_str()); |
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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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// user didn't specify input and output format in commandline option |
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// try to parse it from program name (pdb2mdin means input format is pdb, |
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// output format is mdin) |
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|
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string formatName(program_name); |
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pos = formatName.find_first_of("2"); |
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if(pos!=string::npos) { |
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if (!gotInType) |
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{ |
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string tmpExt = formatName.substr(0, pos); |
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pInFormat = Conv.FindFormat(tmpExt.c_str()); |
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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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} else |
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{ |
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gotInType = true; |
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inputExt = tmpExt; |
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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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string tmpExt = formatName.substr(pos+1, string::npos); |
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pOutFormat = Conv.FindFormat(tmpExt.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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}else { |
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gotOutType = true; |
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outputExt = tmpExt; |
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} |
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} |
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} |
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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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string::size_type 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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int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList); |
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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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//Get the last word on the first line of the description which should |
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//be "molecules", "reactions", etc and remove the s if only one object converted |
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std::string objectname(pOutFormat->TargetClassDescription()); |
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pos = objectname.find('\n'); |
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if(count==1) --pos; |
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objectname.erase(pos); |
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pos = objectname.rfind(' '); |
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if(pos==std::string::npos) |
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pos=0; |
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std::clog << count << objectname.substr(pos) << " converted" << endl; |
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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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std::string messageSummary = obErrorLog.GetMessageSummary(); |
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if (messageSummary.size()) |
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{ |
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clog << messageSummary << 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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return 0; |
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} |
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|
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void DoOption(const char* p, OBConversion& Conv, |
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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 << program_name << ": part of OOPSE " << |
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OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << "." << |
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OOPSE_VERSION_TINY << " and OpenBabel " << BABEL_VERSION << " -- " |
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<< __DATE__ << " -- " << __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 << program_name << " 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. -ipdb, for input and -o<format-type> for output" << endl << endl; |
| 449 |
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. -Hpdb) 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; |
| 459 |
|
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|
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OBFormat* pDefault = OBConversion::GetDefaultFormat(); |
| 462 |
if(pDefault) |
| 463 |
cout << pDefault->TargetClassDescription();// some more options probably for OBMol |
| 464 |
|
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OBFormat* pAPI= OBConversion::FindFormat("obapi"); |
| 466 |
if(pAPI) |
| 467 |
cout << pAPI->Description(); |
| 468 |
|
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cout << "The following file formats are recognized:" << endl; |
| 470 |
Formatpos pos; |
| 471 |
OBFormat* pFormat; |
| 472 |
const char* str=NULL; |
| 473 |
while(OBConversion::GetNextFormat(pos,str,pFormat)) |
| 474 |
{ |
| 475 |
if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) |
| 476 |
continue; |
| 477 |
cout << " " << str << endl; |
| 478 |
} |
| 479 |
cout << "\nSee further specific info and options using -H<format-type>, e.g. -Hpdb" << endl; |
| 480 |
} |
| 481 |
|
