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// $Id$
//
// Copyright (C) 2004 Rational Discovery LLC
// All Rights Reserved
//
#include <iostream>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/utils.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/ForceFieldHelpers/UFF/AtomTyper.h>
#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
#include <ForceField/ForceField.h>
using namespace RDKit;
void runMol(ROMol *mol, int checkEvery = 10, bool verbose = true) {
ForceFields::ForceField *field;
std::cout << MolToMolBlock(*mol) << "$$$$" << std::endl;
try {
field = UFF::constructForceField(*mol, 2.5);
} catch (...) {
field = 0;
}
if (field) {
field->initialize();
int needMore = 1;
int nPasses = 0;
while (needMore) {
#if 1
needMore = field->minimize(checkEvery);
if (verbose) std::cerr << "\t" << ++nPasses << std::endl;
#else
needMore = field->minimize(1);
std::cout << MolToMolBlock(mol) << "$$$$" << std::endl;
#endif
}
std::cout << MolToMolBlock(*mol) << "$$$$" << std::endl;
delete field;
} else {
std::cerr << "failed";
}
}
void runMolFile(std::string fileName, int checkEvery = 10) {
RWMol *mol = MolFileToMol(fileName, false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
ROMol *mol2 = MolOps::addHs(*mol, false, true);
runMol(mol2, checkEvery);
delete mol;
delete mol2;
}
void runSDFile(std::string fileName, int checkEvery = 10) {
SDMolSupplier suppl(fileName, false);
RWMol *mol;
mol = (RWMol *)suppl.next();
while (mol) {
std::string name;
mol->getProp(common_properties::_Name, name);
std::cerr << "Mol: " << name << std::endl;
try {
MolOps::sanitizeMol(*mol);
} catch (...) {
std::cerr << " sanitization failed" << std::endl;
delete mol;
mol = 0;
}
if (mol) {
ROMol *mol2 = MolOps::addHs(*mol, false, true);
delete mol;
runMol(mol2, checkEvery, false);
delete mol2;
}
mol = (RWMol *)suppl.next();
}
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main(int argc, char *argv[]) {
PRECONDITION(argc > 1, "bad arguments");
std::string fileName = argv[1];
int checkEvery = 10;
std::cerr << ">" << fileName << " " << fileName.find(".sdf") << std::endl;
if (fileName.find(".sdf") == std::string::npos) {
runMolFile(fileName, checkEvery);
} else {
runSDFile(fileName, checkEvery);
}
std::cerr << "done" << std::endl;
}
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