mirror of
https://github.com/openbabel/openbabel.git
synced 2026-08-10 04:58:04 -05:00
Geoffrey Hutchison
2b8127c377
* */Makefile.in: Regenerate UNIX build files. * src/plugin.cpp: Make sure to #include <iterator> to solve GCC compile problem. * src/descriptor.cpp: Change _isnan to IsNan, as discussed on the list to solve GCC compile problem. * scripts/*: Updated to compile. May have removed functionality because of plugin changes. * tools/obminimize.cpp, tools/obgen.cpp, tools/obenergy.cpp: Switch to OBPlugin::List().
135 lines
3.7 KiB
C++
135 lines
3.7 KiB
C++
/**********************************************************************
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obgen.cpp - test program for SMILES 3D coordinate generation
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- using systematic rotor search
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Copyright (C) 2006 Tim Vandermeersch
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Some portions Copyright (C) 2006 Geoffrey R. Hutchison
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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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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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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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// 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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#include <openbabel/babelconfig.h>
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#include <openbabel/base.h>
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#include <openbabel/mol.h>
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#include <openbabel/obconversion.h>
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#include <openbabel/forcefield.h>
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#include <unistd.h>
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using namespace std;
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using namespace OpenBabel;
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// PROTOTYPES /////////////////////////////////////////////////////////////////
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///////////////////////////////////////////////////////////////////////////////
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//! \brief Generate rough 3D coordinates for SMILES (or other 0D files).
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//
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int main(int argc,char **argv)
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{
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char *program_name= argv[0];
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int c;
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string basename, filename = "", option, option2, ff = "";
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if (argc < 2) {
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cout << "Usage: obgen <filename> [options]" << endl;
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cout << endl;
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cout << "options: description:" << endl;
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cout << endl;
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cout << " -ff select a forcefield" << endl;
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cout << endl;
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OBPlugin::List("forcefields", "verbose");
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exit(-1);
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} else {
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basename = filename = argv[1];
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size_t extPos = filename.rfind('.');
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if (extPos!= string::npos) {
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basename = filename.substr(0, extPos);
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}
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for (int i = 2; i < argc; i++) {
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option = argv[i];
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if ((option == "-ff") && (argc > (i+1)))
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ff = argv[i+1];
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}
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}
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// Find Input filetype
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OBConversion conv;
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OBFormat *format_in = conv.FormatFromExt(filename.c_str());
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OBFormat *format_out = conv.FindFormat("pdb");
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if (!format_in || !format_out || !conv.SetInAndOutFormats(format_in, format_out)) {
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cerr << program_name << ": cannot read input/output format!" << endl;
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exit (-1);
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}
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ifstream ifs;
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ofstream ofs;
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// Read the file
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ifs.open(filename.c_str());
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if (!ifs) {
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cerr << program_name << ": cannot read input file!" << endl;
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exit (-1);
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}
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OBMol mol;
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for (c=1;;c++) {
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mol.Clear();
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if (!conv.Read(&mol, &ifs))
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break;
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if (mol.Empty())
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break;
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OBForceField* pFF = OBForceField::FindForceField(ff);
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if (!pFF) {
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cerr << program_name << ": could not find forcefield '" << ff << "'." <<endl;
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exit (-1);
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}
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mol.AddHydrogens(false, true); // hydrogens must be added before Setup(mol) is called
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pFF->SetLogFile(&cerr);
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pFF->SetLogLevel(OBFF_LOGLVL_LOW);
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if (!pFF->Setup(mol)) {
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cerr << program_name << ": could not setup force field." << endl;
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exit (-1);
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}
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pFF->GenerateCoordinates();
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pFF->SystematicRotorSearch();
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pFF->UpdateCoordinates(mol);
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//pFF->ValidateGradients();
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pFF->SetLogLevel(OBFF_LOGLVL_HIGH);
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pFF->Energy();
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//char FileOut[32];
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//sprintf(FileOut, "%s_obgen.pdb", basename.c_str());
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//ofs.open(FileOut);
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//conv.Write(&mol, &ofs);
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//ofs.close();
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conv.Write(&mol, &cout);
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} // end for loop
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return(1);
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}
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