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/**********************************************************************
obgen.cpp - test program for SMILES 3D coordinate generation
- using systematic rotor search
Copyright (C) 2006 Tim Vandermeersch
Some portions Copyright (C) 2006 Geoffrey R. Hutchison
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
// used to set import/export for Cygwin DLLs
#ifdef WIN32
#define USING_OBDLL
#endif
#include <openbabel/babelconfig.h>
#include <openbabel/base.h>
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/forcefield.h>
#include <openbabel/builder.h>
using namespace std;
using namespace OpenBabel;
// PROTOTYPES /////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////
//! \brief Generate rough 3D coordinates for SMILES (or other 0D files).
//
int main(int argc,char **argv)
{
char *program_name= argv[0];
int c;
string basename, filename = "", option, option2, ff = "MMFF94";
if (argc < 2) {
cout << "Usage: obgen <filename> [options]" << endl;
cout << endl;
cout << "options: description:" << endl;
cout << endl;
cout << " -ff select a forcefield" << endl;
cout << endl;
OBPlugin::List("forcefields", "verbose");
exit(-1);
} else {
basename = filename = argv[1];
size_t extPos = filename.rfind('.');
if (extPos!= string::npos) {
basename = filename.substr(0, extPos);
}
for (int i = 2; i < argc; i++) {
option = argv[i];
if ((option == "-ff") && (argc > (i+1)))
ff = argv[i+1];
}
}
// Find Input filetype
OBConversion conv;
OBFormat *format_in = conv.FormatFromExt(filename.c_str());
OBFormat *format_out = conv.FindFormat("sdf");
if (!format_in || !format_out || !conv.SetInAndOutFormats(format_in, format_out)) {
cerr << program_name << ": cannot read input/output format!" << endl;
exit (-1);
}
ifstream ifs;
ofstream ofs;
// Read the file
ifs.open(filename.c_str());
if (!ifs) {
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
for (c=1;;c++) {
mol.Clear();
if (!conv.Read(&mol, &ifs))
break;
if (mol.Empty())
break;
OBForceField* pFF = OBForceField::FindForceField(ff);
if (!pFF) {
cerr << program_name << ": could not find forcefield '" << ff << "'." <<endl;
exit (-1);
}
//mol.AddHydrogens(false, true); // hydrogens must be added before Setup(mol) is called
pFF->SetLogFile(&cerr);
pFF->SetLogLevel(OBFF_LOGLVL_LOW);
//pFF->GenerateCoordinates();
OBBuilder builder;
builder.Build(mol);
mol.AddHydrogens(false, true); // hydrogens must be added before Setup(mol) is called
if (!pFF->Setup(mol)) {
cerr << program_name << ": could not setup force field." << endl;
exit (-1);
}
pFF->SteepestDescent(500, 1.0e-4);
pFF->WeightedRotorSearch(250, 50);
pFF->SteepestDescent(500, 1.0e-6);
pFF->UpdateCoordinates(mol);
//pFF->ValidateGradients();
//pFF->SetLogLevel(OBFF_LOGLVL_HIGH);
//pFF->Energy();
//char FileOut[32];
//sprintf(FileOut, "%s_obgen.pdb", basename.c_str());
//ofs.open(FileOut);
//conv.Write(&mol, &ofs);
//ofs.close();
conv.Write(&mol, &cout);
} // end for loop
return(1);
}
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