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/**********************************************************************
obgen.cpp - test program for SMILES 3D coordinate generation
- using distance geometry
Copyright (C) 2006 Tim Vandermeersch
Some portions Copyright (C) 2006-2012 Geoffrey R. Hutchison
This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>
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/distgeom.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 = "";
if (argc < 2) {
cout << "Usage: obdistgen <filename>" << endl;
cout << endl;
exit(-1);
} else {
basename = filename = argv[1];
size_t extPos = filename.rfind('.');
if (extPos!= string::npos) {
basename = filename.substr(0, extPos);
}
}
// 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;
OBForceField* pFF = OBForceField::FindForceField("mmff94");
for (c=1;;c++) {
mol.Clear();
if (!conv.Read(&mol, &ifs))
break;
if (mol.Empty())
break;
// hydrogens must be added before Setup(mol) is called
// to ensure stereochemistry
mol.AddHydrogens();
OBDistanceGeometry dg;
dg.Setup(mol);
for (unsigned int i = 1; i < 2; ++i) {
// cout << i << endl;
dg.AddConformer();
}
dg.GetConformers(mol);
// cout << " Conformers: " << mol.NumConformers() << endl;
// Check the energies
pFF->Setup(mol);
// load through all the conformers
unsigned int minConf = 0;
double e, minE = 1.0e10;
for (unsigned int n = 0; n < mol.NumConformers();++n)
{
mol.SetConformer(n);
pFF->SetCoordinates(mol);
e = pFF->Energy(false);
// cout << " Conformer: " << n << " " << e << endl;
if (e < minE) {
minE = e;
minConf = n;
}
}
mol.SetConformer(minConf);
conv.Write(&mol, &cout);
} // end for loop
return(0);
}
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