pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-03 21:44:30 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
7488840ac4e8e6fc5d001a0af6c4be34b1b48e06
rdkit/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp
Brian Kelley 7488840ac4 Fix/urange check (#1506) 
* Fixes atom documentation

* Fixes #1461

This is a complicated one.  Basically URANGE_CHECK when
used on unsigned integers has a problem when the size of
the range it’s checking is 0.  The standard operations is
to check

URANGE(num, size-1)

Which (for unsigned integers) obviously rolls over.

This fixes all usage cases to be

URANGE(num+1, size)

And fixes the bugs found.  (addBond and the mmff tests)

* Fixes #1461 - Updates URANGE_CHECK to be 0<=x<hi
2017-09-11 21:17:33 +02:00

936 lines
30 KiB
C++
Raw Blame History

// $Id$
//
// Copyright (C) 2004-2010 Greg Landrum and Rational Discovery LLC
//
// @@ 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 <iostream>
#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/ForceFieldHelpers/MMFF/AtomTyper.h>
#include <GraphMol/ForceFieldHelpers/MMFF/Builder.h>
#include <GraphMol/ForceFieldHelpers/MMFF/MMFF.h>
#include <ForceField/ForceField.h>
#include <ForceField/MMFF/Params.h>
#include <GraphMol/DistGeomHelpers/Embedder.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <boost/math/special_functions/round.hpp>
using namespace RDKit;
void testMMFFTyper1() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test MMFF atom types." << std::endl;
{
boost::uint8_t type;
ROMol *mol = SmilesToMol("[SiH3]CC(=O)NC");
TEST_ASSERT(mol);
MMFF::MMFFMolProperties mmffMolProperties(*mol);
TEST_ASSERT(mmffMolProperties.isValid());
type = mmffMolProperties.getMMFFAtomType(0);
TEST_ASSERT(type == 19);
type = mmffMolProperties.getMMFFAtomType(1);
TEST_ASSERT(type == 1);
type = mmffMolProperties.getMMFFAtomType(2);
TEST_ASSERT(type == 3);
type = mmffMolProperties.getMMFFAtomType(3);
TEST_ASSERT(type == 7);
type = mmffMolProperties.getMMFFAtomType(4);
TEST_ASSERT(type == 10);
delete mol;
}
{
boost::uint8_t type;
ROMol *mol = SmilesToMol("CC(=O)C");
TEST_ASSERT(mol);
MMFF::MMFFMolProperties mmffMolProperties(*mol);
TEST_ASSERT(mmffMolProperties.isValid());
type = mmffMolProperties.getMMFFAtomType(0);
TEST_ASSERT(type == 1);
type = mmffMolProperties.getMMFFAtomType(1);
TEST_ASSERT(type == 3);
type = mmffMolProperties.getMMFFAtomType(2);
TEST_ASSERT(type == 7);
type = mmffMolProperties.getMMFFAtomType(3);
TEST_ASSERT(type == 1);
delete mol;
}
{
boost::uint8_t type;
ROMol *mol = SmilesToMol("C(=O)S");
TEST_ASSERT(mol);
MMFF::MMFFMolProperties mmffMolProperties(*mol);
TEST_ASSERT(mmffMolProperties.isValid());
type = mmffMolProperties.getMMFFAtomType(0);
TEST_ASSERT(type == 3);
type = mmffMolProperties.getMMFFAtomType(1);
TEST_ASSERT(type == 7);
type = mmffMolProperties.getMMFFAtomType(2);
TEST_ASSERT(type == 15);
delete mol;
}
{
boost::uint8_t type;
ROMol *mol = SmilesToMol("SCS(=O)S(=O)(=O)O");
TEST_ASSERT(mol);
MMFF::MMFFMolProperties mmffMolProperties(*mol);
TEST_ASSERT(mmffMolProperties.isValid());
type = mmffMolProperties.getMMFFAtomType(0);
TEST_ASSERT(type == 15);
type = mmffMolProperties.getMMFFAtomType(1);
TEST_ASSERT(type == 1);
type = mmffMolProperties.getMMFFAtomType(2);
TEST_ASSERT(type == 17);
type = mmffMolProperties.getMMFFAtomType(4);
TEST_ASSERT(type == 18);
delete mol;
}
{
boost::uint8_t type;
ROMol *mol = SmilesToMol("PCP(O)CP(=O)(=O)");
TEST_ASSERT(mol);
MMFF::MMFFMolProperties mmffMolProperties(*mol);
TEST_ASSERT(mmffMolProperties.isValid());
type = mmffMolProperties.getMMFFAtomType(0);
TEST_ASSERT(type == 26);
type = mmffMolProperties.getMMFFAtomType(1);
TEST_ASSERT(type == 1);
type = mmffMolProperties.getMMFFAtomType(2);
TEST_ASSERT(type == 26);
type = mmffMolProperties.getMMFFAtomType(5);
TEST_ASSERT(type == 26);
delete mol;
}
{
boost::uint8_t type;
ROMol *mol = SmilesToMol("C(F)(Cl)(Br)I");
TEST_ASSERT(mol);
MMFF::MMFFMolProperties mmffMolProperties(*mol);
TEST_ASSERT(mmffMolProperties.isValid());
type = mmffMolProperties.getMMFFAtomType(0);
TEST_ASSERT(type == 1);
type = mmffMolProperties.getMMFFAtomType(1);
TEST_ASSERT(type == 11);
type = mmffMolProperties.getMMFFAtomType(2);
TEST_ASSERT(type == 12);
type = mmffMolProperties.getMMFFAtomType(3);
TEST_ASSERT(type == 13);
type = mmffMolProperties.getMMFFAtomType(4);
TEST_ASSERT(type == 14);
delete mol;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMMFFBuilder1() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing MMFF builder tools." << std::endl;
ROMol *mol, *mol2;
ForceFields::ForceField *field;
boost::shared_array<boost::uint8_t> nbrMat;
mol = SmilesToMol("CC(O)C");
Conformer *conf = new Conformer(mol->getNumAtoms());
int cid = static_cast<int>(mol->addConformer(conf, true));
TEST_ASSERT(mol);
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
field = new ForceFields::ForceField();
// add the atomic positions:
for (unsigned int i = 0; i < mol->getNumAtoms(); ++i) {
field->positions().push_back(&(conf->getAtomPos(i)));
}
MMFF::Tools::addBonds(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 3);
nbrMat = MMFF::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(MMFF::Tools::twoBitCellPos(mol->getNumAtoms(), 1, 1) == 4);
TEST_ASSERT(MMFF::Tools::twoBitCellPos(mol->getNumAtoms(), 2, 1) == 5);
TEST_ASSERT(MMFF::Tools::twoBitCellPos(mol->getNumAtoms(), 1, 2) == 5);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 0) ==
MMFF::Tools::RELATION_1_X);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 1) ==
MMFF::Tools::RELATION_1_2);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 2) ==
MMFF::Tools::RELATION_1_3);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 3) ==
MMFF::Tools::RELATION_1_3);
MMFF::Tools::addAngles(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 6);
// there are no non-bonded terms here:
MMFF::Tools::addVdW(*mol, cid, mmffMolProperties, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 6);
// and no torsions either, until we add Hs:
MMFF::Tools::addTorsions(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 6);
delete mol;
delete field;
delete mmffMolProperties;
mol = SmilesToMol("CCOC");
Conformer *conf2 = new Conformer(mol->getNumAtoms());
cid = static_cast<int>(mol->addConformer(conf2, true));
TEST_ASSERT(mol);
mmffMolProperties = new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
field = new ForceFields::ForceField();
// add the atomic positions:
for (unsigned int i = 0; i < mol->getNumAtoms(); ++i) {
field->positions().push_back(&(conf2->getAtomPos(i)));
}
MMFF::Tools::addBonds(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 3);
nbrMat = MMFF::Tools::buildNeighborMatrix(*mol);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 0) ==
MMFF::Tools::RELATION_1_X);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 1) ==
MMFF::Tools::RELATION_1_2);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 2) ==
MMFF::Tools::RELATION_1_3);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 3) ==
MMFF::Tools::RELATION_1_4);
MMFF::Tools::addAngles(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 5);
MMFF::Tools::addVdW(*mol, cid, mmffMolProperties, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 6);
MMFF::Tools::addTorsions(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 7);
delete mol;
delete field;
delete mmffMolProperties;
mol = SmilesToMol("CO");
Conformer *conf3 = new Conformer(mol->getNumAtoms());
cid = static_cast<int>(mol->addConformer(conf3, true));
TEST_ASSERT(mol);
mmffMolProperties = new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
field = new ForceFields::ForceField();
// add the atomic positions:
for (unsigned int i = 0; i < mol->getNumAtoms(); ++i) {
field->positions().push_back(&(conf3->getAtomPos(i)));
}
MMFF::Tools::addBonds(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 1);
nbrMat = MMFF::Tools::buildNeighborMatrix(*mol);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 0) ==
MMFF::Tools::RELATION_1_X);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 1) ==
MMFF::Tools::RELATION_1_2);
MMFF::Tools::addAngles(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 1);
MMFF::Tools::addVdW(*mol, cid, mmffMolProperties, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 1);
MMFF::Tools::addTorsions(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 1);
mol2 = MolOps::addHs(*mol);
TEST_ASSERT(mol2->getNumAtoms() == 6);
Conformer *conf4 = new Conformer(mol2->getNumAtoms());
cid = static_cast<int>(mol2->addConformer(conf4, true));
delete field;
delete mmffMolProperties;
mmffMolProperties = new MMFF::MMFFMolProperties(*mol2);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
field = new ForceFields::ForceField();
// add the atomic positions:
for (unsigned int i = 0; i < mol2->getNumAtoms(); ++i) {
field->positions().push_back(&(conf4->getAtomPos(i)));
}
MMFF::Tools::addBonds(*mol2, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 5);
nbrMat = MMFF::Tools::buildNeighborMatrix(*mol2);
MMFF::Tools::addAngles(*mol2, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 12);
MMFF::Tools::addVdW(*mol2, cid, mmffMolProperties, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 15);
MMFF::Tools::addTorsions(*mol2, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 18);
delete mol2;
delete mol;
delete field;
delete mmffMolProperties;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMMFFBuilder2() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing MMFF builder+minimization."
<< std::endl;
RWMol *mol;
int needMore;
ForceFields::ForceField *field;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";
mol = MolFileToMol(pathName + "/small1.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize();
TEST_ASSERT(!needMore);
// std::cout << MolToMolBlock(mol);
delete mol;
delete field;
mol = MolFileToMol(pathName + "/small2.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize(100);
TEST_ASSERT(!needMore);
// std::cout << MolToMolBlock(mol);
delete mol;
delete field;
mol = MolFileToMol(pathName + "/benzene.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize();
TEST_ASSERT(!needMore);
// std::cout << MolToMolBlock(mol);
delete mol;
delete field;
mol = MolFileToMol(pathName + "/toluene.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize();
TEST_ASSERT(!needMore);
// std::cout << MolToMolBlock(mol);
delete mol;
delete field;
mol = MolFileToMol(pathName + "/complex1.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize();
TEST_ASSERT(!needMore);
// std::cout << MolToMolBlock(mol);
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMMFFBatch() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Testing bulk MMFF (regression to check that things run)."
<< std::endl;
ROMol *mol;
ForceFields::ForceField *field;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";
SDMolSupplier suppl(pathName + "/bulk.sdf");
int count = 0;
mol = suppl.next();
while (mol && (!(suppl.atEnd()))) {
++count;
std::string origMolBlock = MolToMolBlock(*mol);
BOOST_LOG(rdErrorLog) << "Mol:" << count << std::endl;
try {
field = MMFF::constructForceField(*mol);
} catch (...) {
field = 0;
}
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();
}
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/MMFF/test_data";
mol = MolFileToMol(pathName + "/Issue239.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize(200, 1.0e-6, 1.0e-3);
e1 = field->calcEnergy();
needMore = field->minimize(200, 1.0e-6, 1.0e-3);
e2 = field->calcEnergy();
TEST_ASSERT(feq(e2, e1, 0.1));
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue242() {
// FIX: Changes to the forcefield (connected to Issue 408) have
// made it so that this particular problem no longer manifests
// in this molecule/embedding. A new test case is needed.
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing Issue242." << std::endl;
RWMol *mol, *mol2;
int needMore;
(void)needMore; // add test later
ForceFields::ForceField *field = 0, *field2 = 0;
std::string mb1, mb2;
double e1, e2;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";
mol = MolFileToMol(pathName + "/Issue242-2.mol");
TEST_ASSERT(mol);
mol2 = MolFileToMol(pathName + "/Issue242-2.mol");
TEST_ASSERT(mol2);
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol2, 30, 2370) >= 0);
mb1 = MolToMolBlock(*mol);
mb2 = MolToMolBlock(*mol2);
// std::cout << mb1 << "------\n";
// std::cout << mb2 << "------\n";
field = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
field2 = MMFF::constructForceField(*mol2);
TEST_ASSERT(field2);
field2->initialize();
e1 = field->calcEnergy();
e2 = field2->calcEnergy();
BOOST_LOG(rdInfoLog) << "E1: " << e1 << std::endl;
BOOST_LOG(rdInfoLog) << "E2: " << e2 << std::endl;
// TEST_ASSERT(feq(e2,e1,0.1));
needMore = field->minimize(200, 1.0e-4);
needMore = field2->minimize(200, 1.0e-4);
e1 = field->calcEnergy();
e2 = field2->calcEnergy();
BOOST_LOG(rdInfoLog) << "E1: " << e1 << std::endl;
BOOST_LOG(rdInfoLog) << "E2: " << e2 << std::endl;
TEST_ASSERT(feq(e2, e1, 0.1));
delete mol;
delete mol2;
delete field;
delete field2;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGithub308() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Testing github 308: crash during MMFF parameterization ."
<< std::endl;
ROMol *mol = SmilesToMol("FF");
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol) >= 0);
int needMore;
ForceFields::ForceField *field = 0;
TEST_ASSERT(mol);
MMFF::MMFFMolProperties mmffMolProperties(*mol);
TEST_ASSERT(mmffMolProperties.isValid());
field = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize(200, 1.0e-6, 1.0e-3);
TEST_ASSERT(!needMore);
}
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/MMFF/test_data";
mol = MolFileToMol(pathName + "/cyclobutadiene.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
boost::shared_array<boost::uint8_t> nbrMat;
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))));
}
MMFF::Tools::addBonds(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 8);
nbrMat = MMFF::Tools::buildNeighborMatrix(*mol);
MMFF::Tools::addAngles(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 20);
MMFF::Tools::addTorsions(*mol, mmffMolProperties, field);
// std::cout << field->contribs().size() << std::endl;
TEST_ASSERT(field->contribs().size() == 36);
MMFF::Tools::addVdW(*mol, 0, mmffMolProperties, field, nbrMat);
delete field;
field = MMFF::constructForceField(*mol);
field->initialize();
needMore = field->minimize(200, 1.0e-6, 1.0e-3);
TEST_ASSERT(!needMore);
delete mol;
delete field;
delete mmffMolProperties;
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/MMFF/test_data";
{
RWMol *mol = MolFileToMol(pathName + "/Issue2378119.mol");
TEST_ASSERT(mol);
ForceFields::ForceField *field = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1 > 0.0 && e1 < 1.0e12);
int needMore = field->minimize(200, 1.0e-6, 1.0e-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 = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1 == 0.0);
int needMore = field->minimize(200, 1.0e-6, 1.0e-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 =
MMFF::constructForceField(*mol, 100.0, -1, false);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1 > 0.0 && e1 < 1.0e12);
int needMore = field->minimize(200, 1.0e-6, 1.0e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2 < e1);
delete mol;
delete field;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGithub162() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing github 162: Incorrect SMILES after "
"MMFF parameterization ." << std::endl;
{
ROMol *mol = SmilesToMol("C1=CNC=C1");
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(2)->getNumExplicitHs() == 1);
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
TEST_ASSERT(mol->getAtomWithIdx(2)->getNumExplicitHs() == 1);
delete mol;
delete mmffMolProperties;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMMFFParamGetters() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test MMFF force-field parameter getters."
<< std::endl;
{
ROMol *mol = SmilesToMol("c1ccccc1CCNN");
TEST_ASSERT(mol);
ROMol *molH = MolOps::addHs(*mol);
TEST_ASSERT(molH);
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(*molH);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
unsigned int bondType;
ForceFields::MMFF::MMFFBond mmffBondStretchParams[2];
TEST_ASSERT(mmffMolProperties->getMMFFBondStretchParams(
*molH, 6, 7, bondType, mmffBondStretchParams[0]));
TEST_ASSERT(
(bondType == 0) &&
((int)boost::math::round(mmffBondStretchParams[0].r0 * 1000) == 1508) &&
((int)boost::math::round(mmffBondStretchParams[0].kb * 1000) == 4258));
TEST_ASSERT(!(mmffMolProperties->getMMFFBondStretchParams(
*molH, 0, 7, bondType, mmffBondStretchParams[0])));
unsigned int angleType;
ForceFields::MMFF::MMFFAngle mmffAngleBendParams;
TEST_ASSERT(mmffMolProperties->getMMFFAngleBendParams(
*molH, 6, 7, 8, angleType, mmffAngleBendParams));
TEST_ASSERT(
(angleType == 0) &&
((int)boost::math::round(mmffAngleBendParams.theta0 * 1000) ==
108290) &&
((int)boost::math::round(mmffAngleBendParams.ka * 1000) == 777));
TEST_ASSERT(!(mmffMolProperties->getMMFFAngleBendParams(
*molH, 0, 7, 8, angleType, mmffAngleBendParams)));
unsigned int stretchBendType;
ForceFields::MMFF::MMFFStbn mmffStretchBendParams;
TEST_ASSERT(mmffMolProperties->getMMFFStretchBendParams(
*molH, 6, 7, 8, stretchBendType, mmffStretchBendParams,
mmffBondStretchParams, mmffAngleBendParams));
TEST_ASSERT(
(stretchBendType == 0) &&
((int)boost::math::round(mmffStretchBendParams.kbaIJK * 1000) == 136) &&
((int)boost::math::round(mmffStretchBendParams.kbaKJI * 1000) == 282) &&
((int)boost::math::round(mmffAngleBendParams.theta0 * 1000) ==
108290) &&
((int)boost::math::round(mmffAngleBendParams.ka * 1000) == 777) &&
((int)boost::math::round(mmffBondStretchParams[0].r0 * 1000) == 1508) &&
((int)boost::math::round(mmffBondStretchParams[0].kb * 1000) == 4258) &&
((int)boost::math::round(mmffBondStretchParams[1].r0 * 1000) == 1451) &&
((int)boost::math::round(mmffBondStretchParams[1].kb * 1000) == 5084));
TEST_ASSERT(!(mmffMolProperties->getMMFFStretchBendParams(
*molH, 0, 7, 8, stretchBendType, mmffStretchBendParams,
mmffBondStretchParams, mmffAngleBendParams)));
unsigned int torType;
ForceFields::MMFF::MMFFTor mmffTorsionParams;
TEST_ASSERT(mmffMolProperties->getMMFFTorsionParams(
*molH, 6, 7, 8, 9, torType, mmffTorsionParams));
TEST_ASSERT(
(torType == 0) &&
((int)boost::math::round(mmffTorsionParams.V1 * 1000) == 0) &&
((int)boost::math::round(mmffTorsionParams.V2 * 1000) == -300) &&
((int)boost::math::round(mmffTorsionParams.V3 * 1000) == 500));
TEST_ASSERT(!(mmffMolProperties->getMMFFTorsionParams(
*molH, 0, 7, 8, 9, torType, mmffTorsionParams)));
ForceFields::MMFF::MMFFOop mmffOopBendParams;
TEST_ASSERT(mmffMolProperties->getMMFFOopBendParams(*molH, 6, 5, 4, 0,
mmffOopBendParams));
TEST_ASSERT(((int)boost::math::round(mmffOopBendParams.koop * 1000) == 40));
TEST_ASSERT(!(mmffMolProperties->getMMFFOopBendParams(*molH, 6, 5, 4, 1,
mmffOopBendParams)));
ForceFields::MMFF::MMFFVdWRijstarEps mmffVdWParams;
RWMol *patt = SmartsToMol("NN[H]");
MatchVectType matchVect;
TEST_ASSERT(SubstructMatch(*molH, (ROMol &)*patt, matchVect));
unsigned int nIdx = matchVect[0].second;
unsigned int hIdx = matchVect[2].second;
TEST_ASSERT(mmffMolProperties->getMMFFVdWParams(nIdx, hIdx, mmffVdWParams));
TEST_ASSERT(
((int)boost::math::round(mmffVdWParams.R_ij_starUnscaled * 1000) ==
3321) &&
((int)boost::math::round(mmffVdWParams.epsilonUnscaled * 1000) == 34) &&
((int)boost::math::round(mmffVdWParams.R_ij_star * 1000) == 2657) &&
((int)boost::math::round(mmffVdWParams.epsilon * 1000) == 17));
}
}
#ifdef RDK_TEST_MULTITHREADED
namespace {
void runblock_mmff(const std::vector<ROMol *> &mols,
const std::vector<double> &energies, unsigned int count,
unsigned int idx) {
for (unsigned int rep = 0; rep < 500; ++rep) {
for (unsigned int i = 0; i < mols.size(); ++i) {
if (i % count != idx) continue;
ROMol *mol = mols[i];
ForceFields::ForceField *field = 0;
if (!(rep % 100)) {
BOOST_LOG(rdErrorLog) << "Rep: " << rep << " Mol:" << i << std::endl;
}
try {
field = MMFF::constructForceField(*mol);
} catch (...) {
field = 0;
}
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;
}
}
}
}
#include <boost/thread.hpp>
void testMMFFMultiThread() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test MMFF multithreading" << std::endl;
// ForceFields::ForceField *field;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";
SDMolSupplier suppl(pathName + "/bulk.sdf");
std::vector<ROMol *> mols;
while (!suppl.atEnd() && mols.size() < 100) {
ROMol *mol = 0;
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 = 0;
try {
field = MMFF::constructForceField(mol);
} catch (...) {
field = 0;
}
TEST_ASSERT(field);
field->initialize();
int failed = field->minimize(500);
TEST_ASSERT(!failed);
energies[i] = field->calcEnergy();
delete field;
}
boost::thread_group 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.add_thread(new boost::thread(runblock_mmff, mols, energies, count, i));
}
tg.join_all();
BOOST_FOREACH (ROMol *mol, mols) { delete mol; }
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMMFFMultiThread2() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test MMFF 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);
ROMol *om = new ROMol(*m);
for (unsigned int i = 0; i < 1000; ++i) {
m->addConformer(new Conformer(m->getConformer()), true);
}
std::vector<std::pair<int, double> > res;
MMFF::MMFFOptimizeMolecule(*om);
MMFF::MMFFOptimizeMoleculeConfs(*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;
}
#endif
void testGithub224() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Testing github 224: crash during MMFF parameterization ."
<< std::endl;
{
ROMol *mol = SmilesToMol("[1*]C");
TEST_ASSERT(mol);
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(!mmffMolProperties->isValid());
delete mol;
delete mmffMolProperties;
}
{
ROMol *mol = SmilesToMol("[1*]c1ccc(S(=O)(=O)Nc2ccc([2*])cc2)cc1");
TEST_ASSERT(mol);
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(!mmffMolProperties->isValid());
delete mol;
delete mmffMolProperties;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main() {
RDLog::InitLogs();
#if 1
testMMFFTyper1();
testMMFFBuilder1();
testMMFFBuilder2();
testIssue239();
testIssue242();
testGithub308();
testSFIssue1653802();
testSFIssue2378119();
testMMFFBatch();
testMMFFParamGetters();
#ifdef RDK_TEST_MULTITHREADED
testMMFFMultiThread();
testMMFFMultiThread2();
#endif
testGithub162();
#endif
testGithub224();
}
Reference in New Issue View Git Blame Copy Permalink