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rdkit/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp
Ricardo Rodriguez 7b7a8a4e17 Refactor iostreams includes (#8846) 
* refactor iostreams includes

* restore ostream to MonomerInfo.cpp
2025-10-08 16:08:01 +02:00

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//
// Copyright (C) 2004-2021 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/test.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/ForceFieldHelpers/FFConvenience.h>
#include <GraphMol/ForceFieldHelpers/UFF/AtomTyper.h>
#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
#include <GraphMol/ForceFieldHelpers/UFF/UFF.h>
#include <ForceField/ForceField.h>
#include <GraphMol/DistGeomHelpers/Embedder.h>
using namespace RDKit;
void testUFFTyper1() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test UFF atom labels." << std::endl;
ROMol *mol;
std::string key;
mol = SmilesToMol("[SiH3]CC(=O)NC");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key == "Si3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key == "C_3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key == "C_R");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(3));
TEST_ASSERT(key == "O_R");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(4));
TEST_ASSERT(key == "N_R");
delete mol;
mol = SmilesToMol("CC(=O)C");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key == "C_3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key == "C_2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key == "O_2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(3));
TEST_ASSERT(key == "C_3");
delete mol;
mol = SmilesToMol("C(=O)S");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key == "C_2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key == "O_2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key == "S_3+2");
delete mol;
mol = SmilesToMol("SCS(=O)S(=O)(=O)O");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key == "S_3+2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key == "C_3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key == "S_3+4");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(4));
TEST_ASSERT(key == "S_3+6");
delete mol;
mol = SmilesToMol("PCP(O)CP(=O)(=O)");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key == "P_3+3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key == "C_3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key == "P_3+3");
// FIX: I am not 100% convinced that this should be SP2
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(5));
TEST_ASSERT(key == "P_3+5");
delete mol;
mol = SmilesToMol("C(F)(Cl)(Br)I");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key == "C_3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key == "F_");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key == "Cl");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(3));
TEST_ASSERT(key == "Br");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(4));
TEST_ASSERT(key == "I_");
delete mol;
mol = SmilesToMol("[Li].[Na].[K].[Rb].[Cs]");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key == "Li");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key == "Na");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key == "K_");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(3));
TEST_ASSERT(key == "Rb");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(4));
TEST_ASSERT(key == "Cs");
delete mol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testUFFTyper2() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test UFF atom typer." << std::endl;
ROMol *mol, *mol2;
std::string key;
mol = SmilesToMol("[SiH3]CC(=O)NC");
TEST_ASSERT(mol);
UFF::AtomicParamVect types;
bool foundAll;
boost::tie(types, foundAll) = UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size() == mol->getNumAtoms());
for (UFF::AtomicParamVect::const_iterator it = types.begin();
it != types.end(); it++) {
TEST_ASSERT((*it));
}
mol2 = MolOps::addHs(*mol);
delete mol;
boost::tie(types, foundAll) = UFF::getAtomTypes(*mol2);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size() == mol2->getNumAtoms());
for (UFF::AtomicParamVect::const_iterator it = types.begin();
it != types.end(); it++) {
TEST_ASSERT((*it));
}
delete mol2;
// connected with sf.net bug 2094445
mol = SmilesToMol("[SiH2]=C");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key == "Si3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key == "C_2");
delete mol;
mol = SmilesToMol("[AlH]=C");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key == "Al3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key == "C_2");
delete mol;
mol = SmilesToMol("[Mg]=C");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key == "Mg3+2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key == "C_2");
delete mol;
mol = SmilesToMol("[SiH3][Si]([SiH3])=C");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key == "Si3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key == "Si3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key == "Si3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(3));
TEST_ASSERT(key == "C_2");
delete mol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testUFFBuilder1() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing UFF builder tools." << std::endl;
ROMol *mol, *mol2;
std::string key;
UFF::AtomicParamVect types;
bool foundAll;
ForceFields::ForceField *field;
boost::shared_array<std::uint8_t> nbrMat;
mol = SmilesToMol("CC(O)C");
auto *conf = new Conformer(mol->getNumAtoms());
int cid = static_cast<int>(mol->addConformer(conf, true));
TEST_ASSERT(mol);
boost::tie(types, foundAll) = UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size() == mol->getNumAtoms());
field = new ForceFields::ForceField();
// add the atomic positions:
for (unsigned int i = 0; i < mol->getNumAtoms(); ++i) {
field->positions().push_back(&((conf->getAtomPos(i))));
}
UFF::Tools::addBonds(*mol, types, field);
TEST_ASSERT(field->contribs().size() == 3);
nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
// the neighbor matrix is an upper triangular matrix
// position indices are as follows:
// 0 1 2 3
// 4 5 6
// 7 8
// 9
TEST_ASSERT(UFF::Tools::twoBitCellPos(mol->getNumAtoms(), 1, 1) == 4);
TEST_ASSERT(UFF::Tools::twoBitCellPos(mol->getNumAtoms(), 2, 1) == 5);
TEST_ASSERT(UFF::Tools::twoBitCellPos(mol->getNumAtoms(), 1, 2) == 5);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat, 0) == UFF::Tools::RELATION_1_X);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat, 1) == UFF::Tools::RELATION_1_2);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat, 2) == UFF::Tools::RELATION_1_3);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat, 3) == UFF::Tools::RELATION_1_3);
UFF::Tools::addAngles(*mol, types, field);
TEST_ASSERT(field->contribs().size() == 6);
// there are no non-bonded terms here:
UFF::Tools::addNonbonded(*mol, cid, types, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 6);
// and no torsions either, until we add Hs:
UFF::Tools::addTorsions(*mol, types, field);
TEST_ASSERT(field->contribs().size() == 6);
delete mol;
delete field;
mol = SmilesToMol("CCOC");
auto *conf2 = new Conformer(mol->getNumAtoms());
cid = static_cast<int>(mol->addConformer(conf2, true));
TEST_ASSERT(mol);
boost::tie(types, foundAll) = UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size() == mol->getNumAtoms());
field = new ForceFields::ForceField();
// add the atomic positions:
for (unsigned int i = 0; i < mol->getNumAtoms(); ++i) {
field->positions().push_back(&(conf2->getAtomPos(i)));
}
UFF::Tools::addBonds(*mol, types, field);
TEST_ASSERT(field->contribs().size() == 3);
nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat, 0) == UFF::Tools::RELATION_1_X);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat, 1) == UFF::Tools::RELATION_1_2);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat, 2) == UFF::Tools::RELATION_1_3);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat, 3) == UFF::Tools::RELATION_1_X);
UFF::Tools::addAngles(*mol, types, field);
TEST_ASSERT(field->contribs().size() == 5);
UFF::Tools::addNonbonded(*mol, cid, types, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 6);
UFF::Tools::addTorsions(*mol, types, field);
TEST_ASSERT(field->contribs().size() == 7);
delete mol;
delete field;
mol = SmilesToMol("CO");
auto *conf3 = new Conformer(mol->getNumAtoms());
cid = static_cast<int>(mol->addConformer(conf3, true));
TEST_ASSERT(mol);
boost::tie(types, foundAll) = UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size() == mol->getNumAtoms());
field = new ForceFields::ForceField();
// add the atomic positions:
for (unsigned int i = 0; i < mol->getNumAtoms(); ++i) {
field->positions().push_back(&(conf3->getAtomPos(i)));
}
UFF::Tools::addBonds(*mol, types, field);
TEST_ASSERT(field->contribs().size() == 1);
nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat, 0) == UFF::Tools::RELATION_1_X);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat, 1) == UFF::Tools::RELATION_1_2);
UFF::Tools::addAngles(*mol, types, field);
TEST_ASSERT(field->contribs().size() == 1);
UFF::Tools::addNonbonded(*mol, cid, types, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 1);
UFF::Tools::addTorsions(*mol, types, field);
TEST_ASSERT(field->contribs().size() == 1);
mol2 = MolOps::addHs(*mol);
TEST_ASSERT(mol2->getNumAtoms() == 6);
delete field;
boost::tie(types, foundAll) = UFF::getAtomTypes(*mol2);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size() == mol2->getNumAtoms());
auto *conf4 = new Conformer(mol2->getNumAtoms());
cid = static_cast<int>(mol2->addConformer(conf4, true));
field = new ForceFields::ForceField();
// add the atomic positions:
for (unsigned int i = 0; i < mol2->getNumAtoms(); ++i) {
field->positions().push_back(&(conf4->getAtomPos(i)));
}
UFF::Tools::addBonds(*mol2, types, field);
TEST_ASSERT(field->contribs().size() == 5);
nbrMat = UFF::Tools::buildNeighborMatrix(*mol2);
UFF::Tools::addAngles(*mol2, types, field);
TEST_ASSERT(field->contribs().size() == 12);
UFF::Tools::addNonbonded(*mol2, cid, types, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 15);
UFF::Tools::addTorsions(*mol2, types, field);
TEST_ASSERT(field->contribs().size() == 18);
delete mol2;
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testUFFBuilder2() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing UFF builder+minimization." << std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
{
RWMol *mol = MolFileToMol(pathName + "/small1.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
ForceFields::ForceField *field;
field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
// std::cout << MolToMolBlock(mol);
delete mol;
delete field;
}
{ // make sure the confId argument works
RWMol *mol = MolFileToMol(pathName + "/small1.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
auto *newConf = new Conformer(mol->getConformer());
newConf->setId(111);
mol->addConformer(newConf, false);
RDGeom::Point3D p0 = mol->getConformer().getAtomPos(0);
RDGeom::Point3D p1 = mol->getConformer().getAtomPos(1);
ForceFields::ForceField *field;
field = UFF::constructForceField(*mol, 100, 111);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
// std::cout << MolToMolBlock(mol);
RDGeom::Point3D np0 = mol->getConformer().getAtomPos(0);
RDGeom::Point3D np1 = mol->getConformer().getAtomPos(1);
TEST_ASSERT(feq(p0.z, np0.z));
TEST_ASSERT(feq(p1.x, np1.x));
TEST_ASSERT(feq(p1.y, np1.y));
TEST_ASSERT(feq(p1.z, np1.z));
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName + "/small2.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
ForceFields::ForceField *field;
field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize(150);
TEST_ASSERT(!needMore);
// std::cout << MolToMolBlock(mol);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName + "/benzene.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
ForceFields::ForceField *field;
field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
// std::cout << MolToMolBlock(mol);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName + "/toluene.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
ForceFields::ForceField *field;
field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
// std::cout << MolToMolBlock(mol);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName + "/complex1.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
ForceFields::ForceField *field;
field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
// std::cout << MolToMolBlock(mol);
delete mol;
delete field;
}
{ // test the convenience function
RWMol *mol = MolFileToMol(pathName + "/small1.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
UFF::AtomicParamVect types;
bool foundAll;
boost::shared_array<std::uint8_t> nbrMat;
boost::tie(types, foundAll) = UFF::getAtomTypes(*mol);
ForceFields::ForceField *field;
field = new ForceFields::ForceField();
// add the atomic positions:
for (unsigned int i = 0; i < mol->getNumAtoms(); ++i) {
field->positions().push_back(&((mol->getConformer().getAtomPos(i))));
}
UFF::Tools::addBonds(*mol, types, field);
nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
UFF::Tools::addAngles(*mol, types, field);
UFF::Tools::addTorsions(*mol, types, field);
// std::cout << field->contribs().size() << std::endl;
UFF::Tools::addNonbonded(*mol, 0, types, field, nbrMat);
delete field;
field = UFF::constructForceField(*mol);
field->initialize();
field->minimize();
delete field;
auto *mol2 = new RWMol(*mol);
field = UFF::constructForceField(*mol2);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
delete field;
needMore = UFF::UFFOptimizeMolecule(*mol2).first;
TEST_ASSERT(!needMore);
for (unsigned int i = 0; i < mol->getNumAtoms(); ++i) {
const RDGeom::Point3D p1 = mol->getConformer().getAtomPos(i);
const RDGeom::Point3D p2 = mol2->getConformer().getAtomPos(i);
TEST_ASSERT(feq(p1.x, p2.x));
TEST_ASSERT(feq(p1.y, p2.y));
TEST_ASSERT(feq(p1.z, p2.z));
}
delete mol;
delete mol2;
}
{ // test the convenience function for all confs
RWMol *mol = MolFileToMol(pathName + "/complex1.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
auto *mol2 = new RWMol(*mol);
auto *newConf = new Conformer(mol->getConformer());
newConf->setId(111);
mol->addConformer(newConf, false);
ForceFields::ForceField *field;
field = UFF::constructForceField(*mol, 100, 111);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
delete field;
// the first conf is the same as above,
// but we add a second that's already minimized
newConf = new Conformer(mol->getConformer(111));
newConf->setId(112);
mol2->addConformer(newConf, false);
std::vector<std::pair<int, double>> res;
UFF::UFFOptimizeMoleculeConfs(*mol2, res);
TEST_ASSERT(res.size() == 2);
TEST_ASSERT(!res[0].first);
TEST_ASSERT(!res[1].first);
// we expect the energy to go down at least a little bit.
TEST_ASSERT(res[1].second < res[0].second);
for (unsigned int i = 0; i < mol->getNumAtoms(); ++i) {
const RDGeom::Point3D p1 = mol->getConformer(111).getAtomPos(i);
const RDGeom::Point3D p2 = mol2->getConformer(0).getAtomPos(i);
TEST_ASSERT(feq(p1.x, p2.x));
TEST_ASSERT(feq(p1.y, p2.y));
TEST_ASSERT(feq(p1.z, p2.z));
}
delete mol;
delete mol2;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
#ifdef RDK_TEST_MULTITHREADED
void testUFFBatch() {}
#else
void testUFFBatch() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Testing bulk UFF (regression to check that things run)."
<< std::endl;
ROMol *mol;
std::string key;
ForceFields::ForceField *field;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
SDMolSupplier suppl(pathName + "/bulk.sdf", false);
int count = 0;
mol = suppl.next();
while (mol && !suppl.atEnd()) {
count++;
MolOps::sanitizeMol(*(RWMol *)mol);
std::string origMolBlock = MolToMolBlock(*mol);
BOOST_LOG(rdErrorLog) << "Mol:" << count << std::endl;
try {
field = UFF::constructForceField(*mol);
} catch (...) {
field = nullptr;
}
if (field) {
field->initialize();
int failed = field->minimize(500);
if (failed) {
BOOST_LOG(rdErrorLog)
<< " not converged (code=" << failed << ")" << std::endl;
std::cout << origMolBlock << "$$$$" << std::endl;
std::cout << MolToMolBlock(*mol) << "$$$$" << std::endl;
}
delete field;
}
delete mol;
mol = suppl.next();
}
delete mol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
#endif
void testUFFBuilderSpecialCases() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing UFF special cases." << std::endl;
RWMol *mol;
std::string key;
int needMore;
RDGeom::Point3D v1, v2;
ForceFields::ForceField *field;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
// ----------
// Trigonal bipyramid
// ----------
mol = MolFileToMol(pathName + "/tbp.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
const Conformer &conf = mol->getConformer();
field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize(200, 1e-8, 1e-4);
TEST_ASSERT(!needMore);
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(1));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(2));
TEST_ASSERT(feq(v1.dotProduct(v2), -1.0, 1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
TEST_ASSERT(feq(v1.dotProduct(v2), 0.0, 1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
TEST_ASSERT(feq(v1.dotProduct(v2), 0.0, 1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2), 0.0, 1e-3));
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(2));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
TEST_ASSERT(feq(v1.dotProduct(v2), 0.0, 1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
TEST_ASSERT(feq(v1.dotProduct(v2), 0.0, 1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2), 0.0, 1e-3));
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
TEST_ASSERT(feq(v1.dotProduct(v2), -0.5, 1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2), -0.5, 1e-3));
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2), -0.5, 1e-3));
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue239() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing Issue239." << std::endl;
RWMol *mol;
int needMore;
(void)needMore; // add test later
ForceFields::ForceField *field;
double e1, e2;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
mol = MolFileToMol(pathName + "/Issue239.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize(200, 1e-6, 1e-3);
e1 = field->calcEnergy();
needMore = field->minimize(200, 1e-6, 1e-3);
e2 = field->calcEnergy();
TEST_ASSERT(feq(e2, e1, 0.1));
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testCalcEnergyPassedCoords() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing calcEnergy with passed coords."
<< std::endl;
RWMol *mol;
ForceFields::ForceField *field;
double e1, e2, e3;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";
mol = MolFileToMol(pathName + "/Issue239.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
auto *savedPos = new double[3 * field->numPoints()];
size_t i = 0;
for (const auto pptr : field->positions()) {
for (size_t j = 0; j < 3; ++j) {
savedPos[i++] = (*pptr)[j];
}
}
e1 = field->calcEnergy();
field->minimize(10000, 1.0e-6, 1.0e-3);
e2 = field->calcEnergy();
TEST_ASSERT(e2 < e1);
e3 = field->calcEnergy(savedPos);
TEST_ASSERT(feq(e3, e1, 0.01));
delete[] savedPos;
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testCalcGrad() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing calcGrad." << std::endl;
RWMol *mol;
ForceFields::ForceField *field;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";
mol = MolFileToMol(pathName + "/Issue239.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
size_t l = 3 * field->numPoints();
auto *savedPos = new double[l];
auto *grad1 = new double[l];
auto *grad2 = new double[l];
size_t i = 0;
for (const auto pptr : field->positions()) {
for (size_t j = 0; j < 3; ++j) {
savedPos[i++] = (*pptr)[j];
}
}
TEST_ASSERT(i == l);
std::memset(grad1, 0, l * sizeof(double));
field->calcGrad(grad1);
for (i = 0; i < l; ++i) {
TEST_ASSERT(!feq(grad1[i], 0.0, 0.001));
}
field->minimize(10000, 1.0e-6, 1.0e-3);
std::memset(grad2, 0, l * sizeof(double));
field->calcGrad(grad2);
for (i = 0; i < l; ++i) {
TEST_ASSERT(feq(grad2[i], 0.0, 0.001));
}
field->initialize();
std::memset(grad2, 0, l * sizeof(double));
field->calcGrad(savedPos, grad2);
for (i = 0; i < l; ++i) {
TEST_ASSERT(feq(grad1[i], grad2[i], 0.001));
}
delete[] savedPos;
delete[] grad1;
delete[] grad2;
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testSFIssue1653802() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing SFIssue1653802." << std::endl;
RWMol *mol;
int needMore;
ForceFields::ForceField *field;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
mol = MolFileToMol(pathName + "/cyclobutadiene.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
UFF::AtomicParamVect types;
bool foundAll;
boost::shared_array<std::uint8_t> nbrMat;
boost::tie(types, foundAll) = UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size() == mol->getNumAtoms());
field = new ForceFields::ForceField();
// add the atomic positions:
for (unsigned int i = 0; i < mol->getNumAtoms(); ++i) {
field->positions().push_back(&((mol->getConformer().getAtomPos(i))));
}
UFF::Tools::addBonds(*mol, types, field);
TEST_ASSERT(field->contribs().size() == 8);
nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
UFF::Tools::addAngles(*mol, types, field);
TEST_ASSERT(field->contribs().size() == 20);
UFF::Tools::addTorsions(*mol, types, field);
// std::cout << field->contribs().size() << std::endl;
TEST_ASSERT(field->contribs().size() == 36);
UFF::Tools::addNonbonded(*mol, 0, types, field, nbrMat);
delete field;
field = UFF::constructForceField(*mol);
field->initialize();
needMore = field->minimize(200, 1e-6, 1e-3);
TEST_ASSERT(!needMore);
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testSFIssue2378119() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing SFIssue2378119." << std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
{
RWMol *mol = MolFileToMol(pathName + "/Issue2378119.mol");
TEST_ASSERT(mol);
ForceFields::ForceField *field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1 > 0.0 && e1 < 1e12);
int needMore = field->minimize(200, 1e-6, 1e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2 < e1);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName + "/Issue2378119.2.mol");
TEST_ASSERT(mol);
ForceFields::ForceField *field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1 == 0.0);
int needMore = field->minimize(200, 1e-6, 1e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2 == e1);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName + "/Issue2378119.2.mol");
TEST_ASSERT(mol);
ForceFields::ForceField *field =
UFF::constructForceField(*mol, 100.0, -1, false);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1 > 0.0 && e1 < 1e12);
int needMore = field->minimize(200, 1e-6, 1e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2 < e1);
delete mol;
delete field;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMissingParams() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing handling missing parameters."
<< std::endl;
{
UFF::AtomicParamVect types;
bool foundAll;
ROMol *mol = SmilesToMol("[Cu](C)(C)(C)(C)C");
TEST_ASSERT(mol);
ROMol *mol2 = MolOps::addHs(*mol);
delete mol;
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol2) >= 0);
boost::tie(types, foundAll) = UFF::getAtomTypes(*mol2);
TEST_ASSERT(!foundAll);
TEST_ASSERT(types.size() == mol2->getNumAtoms());
TEST_ASSERT(!types[0]);
// make sure we can optimize anyway:
ForceFields::ForceField *field = UFF::constructForceField(*mol2, types);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
int needMore = field->minimize();
TEST_ASSERT(needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2 < e1);
// std::cerr<<" DE: "<<e1<<" -> "<<e2<<std::endl;
delete mol2;
delete field;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testSFIssue3009337() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing SFIssue3009337." << std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
{
RWMol *mol = MolFileToMol(pathName + "/Issue3009337.mol", true, false);
TEST_ASSERT(mol);
ForceFields::ForceField *field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1 > 0.0 && e1 < 1e12);
int needMore = field->minimize(200, 1e-6, 1e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2 < e1);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName + "/Issue3009337.2.mol", true, false);
TEST_ASSERT(mol);
ForceFields::ForceField *field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1 > 0.0 && e1 < 1e12);
int needMore = field->minimize(200, 1e-6, 1e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2 < e1);
delete mol;
delete field;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGitHubIssue62() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing GitHubIssue62." << std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
{
double energyValues[] = {
38.687, 174.698, 337.986, 115.248, 2.482, 1.918, 10.165, 99.492,
41.016, 267.236, 15.747, 203.398, 206.852, 20.044, 218.879, 79.614};
SmilesMolSupplier smiSupplier(pathName + "/Issue62.smi");
SDWriter *sdfWriter = new SDWriter(pathName + "/Issue62.sdf");
for (unsigned int i = 0; i < smiSupplier.length(); ++i) {
auto *tmp = smiSupplier[i];
ROMol *mol = MolOps::addHs(*tmp);
delete tmp;
TEST_ASSERT(mol);
std::string molName = "";
if (mol->hasProp(common_properties::_Name)) {
mol->getProp(common_properties::_Name, molName);
}
DGeomHelpers::EmbedMolecule(*mol);
ForceFields::ForceField *field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize(200, 1.e-6, 1.e-3);
TEST_ASSERT(!needMore);
sdfWriter->write(*mol);
double e = field->calcEnergy();
BOOST_LOG(rdErrorLog) << molName << " " << e << std::endl;
TEST_ASSERT(fabs(e - energyValues[i]) < 1.);
delete field;
delete mol;
}
sdfWriter->close();
delete sdfWriter;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
}
void testUFFParamGetters() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test UFF force-field parameter getters."
<< std::endl;
{
ROMol *mol = SmilesToMol("c1ccccc1CCNN");
TEST_ASSERT(mol);
ROMol *molH = MolOps::addHs(*mol);
delete mol;
TEST_ASSERT(molH);
ForceFields::UFF::UFFBond uffBondStretchParams;
TEST_ASSERT(
UFF::getUFFBondStretchParams(*molH, 6, 7, uffBondStretchParams));
TEST_ASSERT(((int)std::round(uffBondStretchParams.kb * 1000) == 699592) &&
((int)std::round(uffBondStretchParams.r0 * 1000) == 1514));
TEST_ASSERT(
!UFF::getUFFBondStretchParams(*molH, 0, 7, uffBondStretchParams));
ForceFields::UFF::UFFAngle uffAngleBendParams;
TEST_ASSERT(UFF::getUFFAngleBendParams(*molH, 6, 7, 8, uffAngleBendParams));
TEST_ASSERT(((int)std::round(uffAngleBendParams.ka * 1000) == 303297) &&
((int)std::round(uffAngleBendParams.theta0 * 1000) == 109470));
TEST_ASSERT(
!UFF::getUFFAngleBendParams(*molH, 0, 7, 8, uffAngleBendParams));
ForceFields::UFF::UFFTor uffTorsionParams;
TEST_ASSERT(UFF::getUFFTorsionParams(*molH, 6, 7, 8, 9, uffTorsionParams));
TEST_ASSERT(((int)std::round(uffTorsionParams.V * 1000) == 976));
TEST_ASSERT(!UFF::getUFFTorsionParams(*molH, 0, 7, 8, 9, uffTorsionParams));
ForceFields::UFF::UFFInv uffInversionParams;
TEST_ASSERT(
UFF::getUFFInversionParams(*molH, 6, 5, 4, 0, uffInversionParams));
TEST_ASSERT(((int)std::round(uffInversionParams.K * 1000) == 2000));
TEST_ASSERT(
!UFF::getUFFInversionParams(*molH, 6, 5, 4, 1, uffInversionParams));
ForceFields::UFF::UFFVdW uffVdWParams;
TEST_ASSERT(UFF::getUFFVdWParams(*molH, 0, 9, uffVdWParams));
TEST_ASSERT(((int)std::round(uffVdWParams.x_ij * 1000) == 3754) &&
((int)std::round(uffVdWParams.D_ij * 1000) == 85));
delete molH;
}
}
#ifdef RDK_TEST_MULTITHREADED
namespace {
void runblock_uff(const std::vector<ROMol *> &mols,
const std::vector<double> &energies, unsigned int count,
unsigned int idx) {
for (unsigned int rep = 0; rep < 200; ++rep) {
for (unsigned int i = 0; i < mols.size(); ++i) {
if (i % count != idx) {
continue;
}
ROMol *mol = mols[i];
ForceFields::ForceField *field = nullptr;
if (!(rep % 100)) {
BOOST_LOG(rdErrorLog) << "Rep: " << rep << " Mol:" << i << std::endl;
}
try {
field = UFF::constructForceField(*mol);
} catch (...) {
field = nullptr;
}
TEST_ASSERT(field);
field->initialize();
int failed = field->minimize(500);
TEST_ASSERT(!failed);
double eng = field->calcEnergy();
TEST_ASSERT(feq(eng, energies[i]));
delete field;
}
}
}
} // namespace
#include <thread>
#include <future>
void testUFFMultiThread() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test UFF multithreading" << std::endl;
// ForceFields::ForceField *field;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
SDMolSupplier suppl(pathName + "/bulk.sdf");
std::vector<ROMol *> mols;
while (!suppl.atEnd() && mols.size() < 100) {
ROMol *mol = nullptr;
try {
mol = suppl.next();
} catch (...) {
continue;
}
if (!mol) {
continue;
}
mols.push_back(mol);
}
std::cerr << "generating reference data" << std::endl;
std::vector<double> energies(mols.size(), 0.0);
for (unsigned int i = 0; i < mols.size(); ++i) {
ROMol mol(*mols[i]);
ForceFields::ForceField *field = nullptr;
try {
field = UFF::constructForceField(mol);
} catch (...) {
field = nullptr;
}
TEST_ASSERT(field);
field->initialize();
int failed = field->minimize(500);
TEST_ASSERT(!failed);
energies[i] = field->calcEnergy();
delete field;
}
std::vector<std::future<void>> tg;
std::cerr << "processing" << std::endl;
unsigned int count = 4;
for (unsigned int i = 0; i < count; ++i) {
std::cerr << " launch :" << i << std::endl;
std::cerr.flush();
tg.emplace_back(
std::async(std::launch::async, runblock_uff, mols, energies, count, i));
}
for (auto &fut : tg) {
fut.get();
}
for (auto *mol : mols) {
delete mol;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testUFFMultiThread2() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test UFF multithreading2" << std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
SDMolSupplier suppl(pathName + "/bulk.sdf");
ROMol *m = suppl[4];
TEST_ASSERT(m);
auto *om = new ROMol(*m);
for (unsigned int i = 0; i < 200; ++i) {
m->addConformer(new Conformer(m->getConformer()), true);
}
std::vector<std::pair<int, double>> res;
UFF::UFFOptimizeMolecule(*om);
UFF::UFFOptimizeMoleculeConfs(*m, res, 0);
for (unsigned int i = 1; i < res.size(); ++i) {
TEST_ASSERT(!res[i].first);
TEST_ASSERT(feq(res[i].second, res[0].second, .00001));
}
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
RDGeom::Point3D p0 = om->getConformer().getAtomPos(i);
RDGeom::Point3D np0 = m->getConformer().getAtomPos(i);
TEST_ASSERT(feq(p0.x, np0.x));
TEST_ASSERT(feq(p0.y, np0.y));
TEST_ASSERT(feq(p0.z, np0.z));
np0 =
m->getConformer(11).getAtomPos(i); // pick some random other conformer
TEST_ASSERT(feq(p0.x, np0.x));
TEST_ASSERT(feq(p0.y, np0.y));
TEST_ASSERT(feq(p0.z, np0.z));
}
delete m;
delete om;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testUFFMultiThread3() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test UFF multithreading3" << std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
SDMolSupplier suppl(pathName + "/bulk.sdf");
ROMol *m = suppl[4];
TEST_ASSERT(m);
auto *om = new ROMol(*m);
for (unsigned int i = 0; i < 200; ++i) {
m->addConformer(new Conformer(m->getConformer()), true);
}
std::vector<std::pair<int, double>> res;
ForceFields::ForceField *omField = UFF::constructForceField(*om);
TEST_ASSERT(omField);
omField->initialize();
ForceFields::ForceField *mField = UFF::constructForceField(*m);
TEST_ASSERT(mField);
mField->initialize();
ForceFieldsHelper::OptimizeMolecule(*omField);
ForceFieldsHelper::OptimizeMoleculeConfs(*m, *mField, res, 0);
for (unsigned int i = 1; i < res.size(); ++i) {
TEST_ASSERT(!res[i].first);
TEST_ASSERT(feq(res[i].second, res[0].second, .00001));
}
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
RDGeom::Point3D p0 = om->getConformer().getAtomPos(i);
RDGeom::Point3D np0 = m->getConformer().getAtomPos(i);
TEST_ASSERT(feq(p0.x, np0.x));
TEST_ASSERT(feq(p0.y, np0.y));
TEST_ASSERT(feq(p0.z, np0.z));
np0 =
m->getConformer(11).getAtomPos(i); // pick some random other conformer
TEST_ASSERT(feq(p0.x, np0.x));
TEST_ASSERT(feq(p0.y, np0.y));
TEST_ASSERT(feq(p0.z, np0.z));
}
delete m;
delete om;
delete mField;
delete omField;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
#endif
void testGitHubIssue613() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Github Issue 613: UFF Atom type not "
"properly assigned to lanthanides."
<< std::endl;
{
ROMol *mol =
SmilesToMol("[Eu+3]123456.[Cl]1.[Cl]2.[Cl]3.[Cl]4.[Cl]5.[Cl]6");
TEST_ASSERT(mol);
mol->getAtomWithIdx(0)->setHybridization(Atom::SP3D2);
UFF::AtomicParamVect types;
bool foundAll;
boost::tie(types, foundAll) = UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size() == mol->getNumAtoms());
auto params = ForceFields::UFF::ParamCollection::getParams();
const ForceFields::UFF::AtomicParams *ap = (*params)("Eu6+3");
TEST_ASSERT(ap);
TEST_ASSERT(ap->r1 == types[0]->r1);
TEST_ASSERT(ap->theta0 == types[0]->theta0);
delete mol;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testSquarePlanar() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test square planar complexes" << std::endl;
auto mol = R"CTAB(
Mrv2102 09072117482D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 4 0 0 0
M V30 BEGIN ATOM
M V30 1 Cl -8.4583 1.2083 0 0
M V30 2 Pt -6.9183 1.2083 0 0
M V30 3 F -5.3783 1.2083 0 0 CHG=-1
M V30 4 Cl -6.9183 2.7483 0 0
M V30 5 F -6.9183 -0.3317 0 0 CHG=-1
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 9 3 2
M V30 3 1 2 4
M V30 4 9 5 2
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
TEST_ASSERT(mol);
// explicit hybridization:
mol->getAtomWithIdx(1)->setHybridization(Atom::HybridizationType::SP2D);
std::unique_ptr<ForceFields::ForceField> field{
UFF::constructForceField(*mol)};
TEST_ASSERT(field);
field->initialize();
auto e1 = field->calcEnergy();
auto needMore = field->minimize(200, 1e-6, 1e-3);
auto e2 = field->calcEnergy();
TEST_ASSERT(e2 < e1);
TEST_ASSERT(!needMore);
// make sure it's still square planar
auto conf = mol->getConformer();
for (unsigned int i = 0; i < mol->getNumAtoms(); ++i) {
TEST_ASSERT(feq(conf.getAtomPos(i).z, 0.0));
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testOctahedral() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test octahedral complexes" << std::endl;
auto mol = R"CTAB(
Mrv2102 09082104493D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 7 6 0 0 0
M V30 BEGIN ATOM
M V30 1 F 1.9744 4.203 5.9405 0
M V30 2 U 0.2018 4.3631 7.0863 0
M V30 3 F 1.3377 4.551 8.8617 0
M V30 4 F 0.2351 6.4527 6.7888 0
M V30 5 F 0.1927 2.2693 7.3707 0
M V30 6 F -1.5636 4.5586 8.2312 0
M V30 7 F -0.977 4.1505 5.3427 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 4
M V30 3 1 5 2
M V30 4 1 3 2
M V30 5 1 2 6
M V30 6 1 2 7
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->getHybridization() ==
Atom::HybridizationType::SP3D2);
std::unique_ptr<ForceFields::ForceField> field{
UFF::constructForceField(*mol)};
TEST_ASSERT(field);
field->initialize();
auto e1 = field->calcEnergy();
auto needMore = field->minimize(200, 1e-6, 1e-3);
auto e2 = field->calcEnergy();
TEST_ASSERT(e2 < e1);
TEST_ASSERT(!needMore);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main() {
RDLog::InitLogs();
// we get a ton of warnings here about missing Hs... disable them
boost::logging::disable_logs("rdApp.warning");
testUFFTyper1();
testUFFTyper2();
testUFFBuilder1();
testUFFBuilder2();
testUFFBatch();
testUFFBuilderSpecialCases();
testIssue239();
testCalcEnergyPassedCoords();
testCalcGrad();
testSFIssue1653802();
testSFIssue2378119();
testUFFParamGetters();
testMissingParams();
testSFIssue3009337();
#ifdef RDK_TEST_MULTITHREADED
testUFFMultiThread();
testUFFMultiThread2();
testUFFMultiThread3();
#endif
testGitHubIssue62();
testGitHubIssue613();
testSquarePlanar();
testOctahedral();
}
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