ForceFields::ForceField *constructForceField(
const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions,
const VECT_CHIRALSET &csets, double weightChiral, double weightFourthDim,
std::map<std::pair<int, int>, double> *extraWeights, double basinSizeTol) {
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
ForceFields::ForceField *field =
new ForceFields::ForceField(positions[0]->dimension());
for (unsigned int i = 0; i < N; i++) {
field->positions().push_back(positions[i]);
}
for (unsigned int i = 1; i < N; i++) {
for (unsigned int j = 0; j < i; j++) {
double w = 1.0;
double l = mmat.getLowerBound(i, j);
double u = mmat.getUpperBound(i, j);
bool includeIt = false;
if (extraWeights) {
std::map<std::pair<int, int>, double>::const_iterator mapIt;
mapIt = extraWeights->find(std::make_pair(i, j));
if (mapIt != extraWeights->end()) {
w = mapIt->second;
includeIt = true;
}
}
if (u - l <= basinSizeTol) {
includeIt = true;
}
if (includeIt) {
DistViolationContrib *contrib =
new DistViolationContrib(field, i, j, u, l, w);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
}
// now add chiral constraints
if (weightChiral > 1.e-8) {
for (VECT_CHIRALSET::const_iterator csi = csets.begin(); csi != csets.end();
csi++) {
ChiralViolationContrib *contrib =
new ChiralViolationContrib(field, csi->get(), weightChiral);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
// finally the contribution from the fourth dimension if we need to
if ((field->dimension() == 4) && (weightFourthDim > 1.e-8)) {
for (unsigned int i = 1; i < N; i++) {
FourthDimContrib *contrib =
new FourthDimContrib(field, i, weightFourthDim);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
return field;
} // constructForceField
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<boost::uint8_t> nbrMat;
boost::tie(types,foundAll)=UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size()==mol->getNumAtoms());
field=new ForceFields::ForceField();
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 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();
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;
}
ForceFields::ForceField *construct3DImproperForceField(
const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
const std::vector<std::vector<int> > &improperAtoms,
const std::vector<int> &atomNums) {
(void)atomNums;
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
ForceFields::ForceField *field =
new ForceFields::ForceField(positions[0]->dimension());
for (unsigned int i = 0; i < N; ++i) {
field->positions().push_back(positions[i]);
}
// improper torsions / out-of-plane bend / inversion
double oobForceScalingFactor = 10.0;
for (unsigned int t = 0; t < improperAtoms.size(); ++t) {
std::vector<int> n(4);
for (unsigned int i = 0; i < 3; ++i) {
n[1] = 1;
switch (i) {
case 0:
n[0] = 0;
n[2] = 2;
n[3] = 3;
break;
case 1:
n[0] = 0;
n[2] = 3;
n[3] = 2;
break;
case 2:
n[0] = 2;
n[2] = 3;
n[3] = 0;
break;
}
ForceFields::UFF::InversionContrib *contrib =
new ForceFields::UFF::InversionContrib(
field, improperAtoms[t][n[0]], improperAtoms[t][n[1]],
improperAtoms[t][n[2]], improperAtoms[t][n[3]],
improperAtoms[t][4], improperAtoms[t][5], oobForceScalingFactor);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
return field;
} // construct3DImproperForceField
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<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);
boost::tie(types,foundAll)=UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size()==mol->getNumAtoms());
field=new ForceFields::ForceField();
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_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");
Conformer *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();
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");
Conformer *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();
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());
field=new ForceFields::ForceField();
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 testTorsionAngleM6() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << " Test CrystalFF torsional term." << std::endl;
ForceFields::ForceField ff;
Point3D p1, p2, p3, p4;
RDGeom::PointPtrVect &ps = ff.positions();
ps.push_back(&p1);
ps.push_back(&p2);
ps.push_back(&p3);
ps.push_back(&p4);
ForceFields::CrystalFF::TorsionAngleContribM6 *contrib;
// ------- ------- ------- ------- ------- ------- -------
// Basic SP3 - SP3
// ------- ------- ------- ------- ------- ------- -------
// [!#1:1][CX4H2:2]!@[CX4H2:3][!#1:4] 1 0.0 1 0.0 1 4.0 1 0.0 1 0.0 1 0.0
std::vector<int> signs(6, 1);
std::vector<double> v(6, 0.0);
v[2] = 4.0;
contrib = new ForceFields::CrystalFF::TorsionAngleContribM6(&ff, 0, 1, 2, 3,
v, signs);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = 0;
p1.y = 1.5;
p1.z = 0;
p2.x = 0.0;
p2.y = 0.0;
p2.z = 0.0;
p3.x = 1.5;
p3.y = 0.0;
p3.z = 0.0;
p4.x = 1.5;
p4.y = 0.0;
p4.z = 1.5;
ff.initialize();
ff.minimize(10, 1e-8, 1e-8);
double cosPhi = ForceFields::MMFF::Utils::calcTorsionCosPhi(
*(RDGeom::Point3D *)ff.positions()[0],
*(RDGeom::Point3D *)ff.positions()[1],
*(RDGeom::Point3D *)ff.positions()[2],
*(RDGeom::Point3D *)ff.positions()[3]);
TEST_ASSERT(RDKit::feq(cosPhi, 0.5, 1e-4));
// ------- ------- ------- ------- ------- ------- -------
// Basic SP2 - SP2
// ------- ------- ------- ------- ------- ------- -------
signs[1] = -1;
v[2] = 0.0;
v[1] = 7.0;
ff.contribs().pop_back();
contrib = new ForceFields::CrystalFF::TorsionAngleContribM6(&ff, 0, 1, 2, 3,
v, signs);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = 0;
p1.y = 1.5;
p1.z = 0.1;
p2.x = 0.0;
p2.y = 0.0;
p2.z = 0.0;
p3.x = 1.5;
p3.y = 0.0;
p3.z = 0.0;
p4.x = 1.5;
p4.y = 0.2;
p4.z = 1.5;
ff.initialize();
ff.minimize(10, 1e-8, 1e-8);
cosPhi = ForceFields::MMFF::Utils::calcTorsionCosPhi(
*(RDGeom::Point3D *)ff.positions()[0],
*(RDGeom::Point3D *)ff.positions()[1],
*(RDGeom::Point3D *)ff.positions()[2],
*(RDGeom::Point3D *)ff.positions()[3]);
TEST_ASSERT(RDKit::feq(cosPhi, 1.0, 1e-4));
}
ForceFields::ForceField *constructPlain3DForceField(
const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
const std::vector<std::pair<int, int> > &bonds,
const std::vector<std::vector<int> > &angles,
const std::vector<std::vector<int> > &expTorsionAtoms,
const std::vector<std::pair<std::vector<int>, std::vector<double> > > &
expTorsionAngles,
const std::vector<int> &atomNums) {
(void)atomNums;
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
CHECK_INVARIANT(expTorsionAtoms.size() == expTorsionAngles.size(), "");
ForceFields::ForceField *field =
new ForceFields::ForceField(positions[0]->dimension());
for (unsigned int i = 0; i < N; ++i) {
field->positions().push_back(positions[i]);
}
// keep track which atoms are 1,2- or 1,3-restrained
boost::dynamic_bitset<> atomPairs(N * N);
// torsion constraints
for (unsigned int t = 0; t < expTorsionAtoms.size(); ++t) {
int i = expTorsionAtoms[t][0];
int j = expTorsionAtoms[t][1];
int k = expTorsionAtoms[t][2];
int l = expTorsionAtoms[t][3];
if (i < j)
atomPairs[i * N + j] = 1;
else
atomPairs[j * N + i] = 1;
// expTorsionAngles[t][0] = (signs, V's)
ForceFields::CrystalFF::TorsionAngleContribM6 *contrib =
new ForceFields::CrystalFF::TorsionAngleContribM6(
field, i, j, k, l, expTorsionAngles[t].second,
expTorsionAngles[t].first);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
} // torsion constraints
double fdist = 100.0; // force constant
// 1,2 distance constraints
std::vector<std::pair<int, int> >::const_iterator bi;
for (bi = bonds.begin(); bi != bonds.end(); ++bi) {
unsigned int i = bi->first;
unsigned int j = bi->second;
if (i < j)
atomPairs[i * N + j] = 1;
else
atomPairs[j * N + i] = 1;
double d = ((*positions[i]) - (*positions[j])).length();
double l = d - 0.01;
double u = d + 0.01;
ForceFields::UFF::DistanceConstraintContrib *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, j, l, u,
fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
// 1,3 distance constraints
for (unsigned int a = 1; a < angles.size(); ++a) {
unsigned int i = angles[a][0];
unsigned int j = angles[a][2];
if (i < j)
atomPairs[i * N + j] = 1;
else
atomPairs[j * N + i] = 1;
double d = ((*positions[i]) - (*positions[j])).length();
double l = d - 0.01;
double u = d + 0.01;
ForceFields::UFF::DistanceConstraintContrib *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, j, l, u,
fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
// minimum distance for all other atom pairs
fdist = 10.0;
for (unsigned int i = 1; i < N; ++i) {
for (unsigned int j = 0; j < i; ++j) {
if (!atomPairs[j * N + i]) {
double l = mmat.getLowerBound(i, j);
double u = mmat.getUpperBound(i, j);
ForceFields::UFF::DistanceConstraintContrib *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, j, l, u,
fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
}
return field;
} // constructPlain3DForceField
ForceFields::ForceField *construct3DForceField(
const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
const std::vector<std::pair<int, int> > &bonds,
const std::vector<std::vector<int> > &angles,
const std::vector<std::vector<int> > &expTorsionAtoms,
const std::vector<std::pair<std::vector<int>, std::vector<double> > > &
expTorsionAngles,
const std::vector<std::vector<int> > &improperAtoms,
const std::vector<int> &atomNums) {
(void)atomNums;
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
CHECK_INVARIANT(expTorsionAtoms.size() == expTorsionAngles.size(), "");
ForceFields::ForceField *field =
new ForceFields::ForceField(positions[0]->dimension());
for (unsigned int i = 0; i < N; ++i) {
field->positions().push_back(positions[i]);
}
// keep track which atoms are 1,2- or 1,3-restrained
boost::dynamic_bitset<> atomPairs(N * N);
// torsion constraints
for (unsigned int t = 0; t < expTorsionAtoms.size(); ++t) {
int i = expTorsionAtoms[t][0];
int j = expTorsionAtoms[t][1];
int k = expTorsionAtoms[t][2];
int l = expTorsionAtoms[t][3];
if (i < j)
atomPairs[i * N + j] = 1;
else
atomPairs[j * N + i] = 1;
// expTorsionAngles[t][0] = (signs, V's)
ForceFields::CrystalFF::TorsionAngleContribM6 *contrib =
new ForceFields::CrystalFF::TorsionAngleContribM6(
field, i, j, k, l, expTorsionAngles[t].second,
expTorsionAngles[t].first);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
} // torsion constraints
// improper torsions / out-of-plane bend / inversion
double oobForceScalingFactor = 10.0;
for (unsigned int t = 0; t < improperAtoms.size(); ++t) {
std::vector<int> n(4);
for (unsigned int i = 0; i < 3; ++i) {
n[1] = 1;
switch (i) {
case 0:
n[0] = 0;
n[2] = 2;
n[3] = 3;
break;
case 1:
n[0] = 0;
n[2] = 3;
n[3] = 2;
break;
case 2:
n[0] = 2;
n[2] = 3;
n[3] = 0;
break;
}
ForceFields::UFF::InversionContrib *contrib =
new ForceFields::UFF::InversionContrib(
field, improperAtoms[t][n[0]], improperAtoms[t][n[1]],
improperAtoms[t][n[2]], improperAtoms[t][n[3]],
improperAtoms[t][4], improperAtoms[t][5], oobForceScalingFactor);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
double fdist = 100.0; // force constant
// 1,2 distance constraints
std::vector<std::pair<int, int> >::const_iterator bi;
for (bi = bonds.begin(); bi != bonds.end(); ++bi) {
unsigned int i = bi->first;
unsigned int j = bi->second;
if (i < j)
atomPairs[i * N + j] = 1;
else
atomPairs[j * N + i] = 1;
double d = ((*positions[i]) - (*positions[j])).length();
double l = d - 0.01;
double u = d + 0.01;
ForceFields::UFF::DistanceConstraintContrib *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, j, l, u,
fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
// 1,3 distance constraints
for (unsigned int a = 0; a < angles.size(); ++a) {
unsigned int i = angles[a][0];
unsigned int j = angles[a][1];
unsigned int k = angles[a][2];
if (i < j)
atomPairs[i * N + j] = 1;
else
atomPairs[j * N + i] = 1;
// check for triple bonds
if (angles[a][3]) {
ForceFields::UFF::AngleConstraintContrib *contrib =
new ForceFields::UFF::AngleConstraintContrib(field, i, j, k, 179.0,
180.0, fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
} else {
double d = ((*positions[i]) - (*positions[k])).length();
double l = d - 0.01;
double u = d + 0.01;
ForceFields::UFF::DistanceConstraintContrib *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, k, l, u,
fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
// minimum distance for all other atom pairs
fdist = 10.0;
for (unsigned int i = 1; i < N; ++i) {
for (unsigned int j = 0; j < i; ++j) {
if (!atomPairs[j * N + i]) {
double l = mmat.getLowerBound(i, j);
double u = mmat.getUpperBound(i, j);
ForceFields::UFF::DistanceConstraintContrib *contrib =
new ForceFields::UFF::DistanceConstraintContrib(field, i, j, l, u,
fdist);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
}
return field;
} // construct3DForceField
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();
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();
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();
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);
delete field;
delete mmffMolProperties;
mmffMolProperties = new MMFF::MMFFMolProperties(*mol2);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
field = new ForceFields::ForceField();
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;
}