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/**********************************************************************
obenergy.cpp - calculate the energy for a molecule
Copyright (C) 2006 Tim Vandermeersch
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>
#ifndef _MSC_VER
#include <unistd.h>
#endif
using namespace std;
using namespace OpenBabel;
int main(int argc,char **argv)
{
char *program_name= argv[0];
int c;
int verbose = 0;
bool hydrogens = false;
string basename, filename = "", option, option2, ff = "";
OBConversion conv;
if (argc < 2) {
cout << "Usage: obenergy [options] <filename>" << endl;
cout << endl;
cout << "options: description:" << endl;
cout << endl;
cout << " -v verbose: print out indivual energy interactions" << endl;
cout << endl;
cout << " -h add hydrogens before calculating energy" << endl;
cout << endl;
cout << " -ff ffid select a forcefield" << endl;
cout << endl;
cout << " available forcefields:" << endl;
cout << endl;
OBPlugin::List("forcefields", "verbose");
exit(-1);
} else {
int ifile = 1;
for (int i = 1; i < argc; i++) {
option = argv[i];
if (option == "-v") {
verbose = 1;
ifile++;
break;
}
if (option == "-h") {
hydrogens = true;
ifile++;
}
if ((option == "-ff") && (argc > (i+1))) {
ff = argv[i+1];
ifile += 2;
}
}
basename = filename = argv[ifile];
size_t extPos = filename.rfind('.');
if (extPos!= string::npos) {
basename = filename.substr(0, extPos);
}
}
// Find Input filetype
OBFormat *format_in = conv.FormatFromExt(filename.c_str());
if (!format_in || !conv.SetInFormat(format_in)) {
cerr << program_name << ": cannot read input 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);
}
OBForceField* pFF = OBForceField::FindForceField(ff);
if (!pFF) {
cerr << program_name << ": could not find forcefield '" << ff << "'." <<endl;
exit (-1);
}
pFF->SetLogFile(&cout);
if (verbose)
pFF->SetLogLevel(OBFF_LOGLVL_HIGH);
else
pFF->SetLogLevel(OBFF_LOGLVL_MEDIUM);
OBMol mol;
double energy;
for (c=1;;c++) {
mol.Clear();
if (!conv.Read(&mol, &ifs))
break;
if (mol.Empty())
break;
if (hydrogens)
mol.AddHydrogens();
if (!pFF->Setup(mol)) {
cerr << program_name << ": could not setup force field." << endl;
exit (-1);
}
energy = pFF->Energy(false);
if (!isfinite(energy)) {
cerr << " Title: " << mol.GetTitle() << endl;
FOR_ATOMS_OF_MOL(atom, mol) {
cerr << " x: " << atom->x() << " y: " << atom->y() << " z: " << atom->z() << endl;
}
}
} // end for loop
return(1);
}
/* obenergy man page*/
/** \page calculate the energy for a molecule
*
* \n
* \par SYNOPSIS
*
* \b obenergy [options] \<filename\>
*
* \par DESCRIPTION
*
* The obenergy tool can be used to calculate the energy for molecules
* inside (multi-)molecule files (e.g., MOL2, etc.)
*
* \par OPTIONS
*
* If no filename is given, obenergy will give all options including the
* available forcefields.
*
* \b -v:
* Verbose: print out all individual energy interactions \n\n
* \b -ff \<forcefield\>:
* Select the forcefield \n\n
*
* \par EXAMPLES
* - View the possible options, including available forcefields:
* obenergy
* - Calculate the energy for the molecule(s) in file test.mol2:
* obenergy test.mol2
* - Calculate the energy for the molecule(s) in file test.mol2 using the Ghemical forcefield:
* obenergy -ff Ghemical test.mol2
* - Calculate the energy for the molecule(s) in file test.mol2 and print out all individual energy interactions:
* obenergy -v test.mol2
*
* \par AUTHORS
*
* The obenergy program was contributed by \b Tim \b Vandermeersch.
*
* Open Babel is currently maintained by \b Geoff \b Hutchison, \b Chris \b Morley and \b Michael \b Banck.
*
* For more contributors to Open Babel, see http://openbabel.org/THANKS.shtml
*
* \par COPYRIGHT
* Copyright (C) 2007 by Tim Vandermeersch. \n \n
* 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.\n \n
* 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.
*
* \par SEE ALSO
* The web pages for Open Babel can be found at: http://openbabel.org/ \n
* The web pages for Open Babel Molecular Mechanics can be found at:
* http://openbabel.org/wiki/Molecular_mechanics \n
**/
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