// ------------------------------------------------------------------------
//
//
//
// ------------------------------------------------------------------------
void addNonbonded(const ROMol &mol,int confId,const AtomicParamVect ¶ms,
ForceFields::ForceField *field,boost::shared_array<boost::uint8_t> neighborMatrix,
double vdwThresh,bool ignoreInterfragInteractions){
PRECONDITION(mol.getNumAtoms()==params.size(),"bad parameters");
PRECONDITION(field,"bad forcefield");
INT_VECT fragMapping;
if(ignoreInterfragInteractions){
std::vector<ROMOL_SPTR> molFrags=MolOps::getMolFrags(mol,true,&fragMapping);
}
unsigned int nAtoms=mol.getNumAtoms();
const Conformer &conf = mol.getConformer(confId);
for(unsigned int i=0;i<nAtoms;i++){
if(!params[i]) continue;
for(unsigned int j=i+1;j<nAtoms;j++){
if(!params[j] || (ignoreInterfragInteractions && fragMapping[i]!=fragMapping[j])){
continue;
}
if(getTwoBitCell(neighborMatrix,i*nAtoms+j)>=RELATION_1_4){
double dist=(conf.getAtomPos(i) - conf.getAtomPos(j)).length();
if(dist <
vdwThresh*Utils::calcNonbondedMinimum(params[i],params[j])){
vdWContrib *contrib;
contrib = new vdWContrib(field,i,j,params[i],params[j]);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
}
}
}
// ------------------------------------------------------------------------
//
//
//
// ------------------------------------------------------------------------
void addEle(const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties,
ForceFields::ForceField *field,
boost::shared_array<boost::uint8_t> neighborMatrix,
double nonBondedThresh, bool ignoreInterfragInteractions) {
PRECONDITION(field, "bad ForceField");
PRECONDITION(mmffMolProperties, "bad MMFFMolProperties");
PRECONDITION(mmffMolProperties->isValid(),
"missing atom types - invalid force-field");
std::ostream &oStream = mmffMolProperties->getMMFFOStream();
INT_VECT fragMapping;
if (ignoreInterfragInteractions) {
std::vector<ROMOL_SPTR> molFrags =
MolOps::getMolFrags(mol, true, &fragMapping);
}
unsigned int nAtoms = mol.getNumAtoms();
double totalEleEnergy = 0.0;
if (mmffMolProperties->getMMFFVerbosity()) {
if (mmffMolProperties->getMMFFVerbosity() == MMFF_VERBOSITY_HIGH) {
oStream << "\n"
"E L E C T R O S T A T I C\n\n"
"------ATOMS------ ATOM TYPES\n"
" I J I J DISTANCE ENERGY\n"
"--------------------------------------------------"
<< std::endl;
}
}
const Conformer &conf = mol.getConformer(confId);
double dielConst = mmffMolProperties->getMMFFDielectricConstant();
boost::uint8_t dielModel = mmffMolProperties->getMMFFDielectricModel();
for (unsigned int i = 0; i < nAtoms; ++i) {
for (unsigned int j = i + 1; j < nAtoms; ++j) {
if (ignoreInterfragInteractions && (fragMapping[i] != fragMapping[j])) {
continue;
}
boost::uint8_t cell = getTwoBitCell(neighborMatrix, twoBitCellPos(nAtoms, i, j));
bool is1_4 = (cell == RELATION_1_4);
if (cell >= RELATION_1_4) {
if (isDoubleZero(mmffMolProperties->getMMFFPartialCharge(i))
|| isDoubleZero(mmffMolProperties->getMMFFPartialCharge(j)))
continue;
double dist = (conf.getAtomPos(i) - conf.getAtomPos(j)).length();
if (dist > nonBondedThresh) {
continue;
}
double chargeTerm = mmffMolProperties->getMMFFPartialCharge(i) *
mmffMolProperties->getMMFFPartialCharge(j) /
dielConst;
EleContrib *contrib = new EleContrib(
field, i, j, chargeTerm, dielModel, is1_4);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
if (mmffMolProperties->getMMFFVerbosity()) {
const unsigned int iAtomType = mmffMolProperties->getMMFFAtomType(i);
const unsigned int jAtomType = mmffMolProperties->getMMFFAtomType(j);
const Atom *iAtom = mol.getAtomWithIdx(i);
const Atom *jAtom = mol.getAtomWithIdx(j);
const double eleEnergy = MMFF::Utils::calcEleEnergy(
i, j, dist, chargeTerm, dielModel, is1_4);
if (mmffMolProperties->getMMFFVerbosity() == MMFF_VERBOSITY_HIGH) {
oStream << std::left << std::setw(2) << iAtom->getSymbol() << " #"
<< std::setw(5) << i + 1 << std::setw(2)
<< jAtom->getSymbol() << " #" << std::setw(5) << j + 1
<< std::right << std::setw(5) << iAtomType << std::setw(5)
<< jAtomType << " " << std::fixed << std::setprecision(3)
<< std::setw(9) << dist << std::setw(10) << eleEnergy
<< std::endl;
}
totalEleEnergy += eleEnergy;
}
}
}
}
if (mmffMolProperties->getMMFFVerbosity()) {
if (mmffMolProperties->getMMFFVerbosity() == MMFF_VERBOSITY_HIGH) {
oStream << std::endl;
}
oStream << "TOTAL ELECTROSTATIC ENERGY =" << std::right << std::setw(16)
<< std::fixed << std::setprecision(4) << totalEleEnergy
<< std::endl;
}
}
// ------------------------------------------------------------------------
//
//
//
// ------------------------------------------------------------------------
void addVdW(const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties,
ForceFields::ForceField *field,
boost::shared_array<boost::uint8_t> neighborMatrix,
double nonBondedThresh, bool ignoreInterfragInteractions) {
PRECONDITION(field, "bad ForceField");
PRECONDITION(mmffMolProperties, "bad MMFFMolProperties");
PRECONDITION(mmffMolProperties->isValid(),
"missing atom types - invalid force-field");
std::ostream &oStream = mmffMolProperties->getMMFFOStream();
INT_VECT fragMapping;
if (ignoreInterfragInteractions) {
std::vector<ROMOL_SPTR> molFrags =
MolOps::getMolFrags(mol, true, &fragMapping);
}
unsigned int nAtoms = mol.getNumAtoms();
double totalVdWEnergy = 0.0;
if (mmffMolProperties->getMMFFVerbosity()) {
if (mmffMolProperties->getMMFFVerbosity() == MMFF_VERBOSITY_HIGH) {
oStream << "\n"
"V A N D E R W A A L S\n\n"
"------ATOMS------ ATOM TYPES "
" WELL\n"
" I J I J DISTANCE ENERGY R* "
" DEPTH\n"
"-------------------------------------------------------------"
"-------" << std::endl;
}
}
const Conformer &conf = mol.getConformer(confId);
for (unsigned int i = 0; i < nAtoms; ++i) {
for (unsigned int j = i + 1; j < nAtoms; ++j) {
if (ignoreInterfragInteractions && (fragMapping[i] != fragMapping[j])) {
continue;
}
if (getTwoBitCell(neighborMatrix, twoBitCellPos(nAtoms, i, j)) >= RELATION_1_4) {
double dist = (conf.getAtomPos(i) - conf.getAtomPos(j)).length();
if (dist > nonBondedThresh) {
continue;
}
MMFFVdWRijstarEps mmffVdWConstants;
if (mmffMolProperties->getMMFFVdWParams(i, j, mmffVdWConstants)) {
VdWContrib *contrib = new VdWContrib(field, i, j, &mmffVdWConstants);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
if (mmffMolProperties->getMMFFVerbosity()) {
const Atom *iAtom = mol.getAtomWithIdx(i);
const Atom *jAtom = mol.getAtomWithIdx(j);
const double vdWEnergy = MMFF::Utils::calcVdWEnergy(
dist, mmffVdWConstants.R_ij_star, mmffVdWConstants.epsilon);
if (mmffMolProperties->getMMFFVerbosity() == MMFF_VERBOSITY_HIGH) {
unsigned int iAtomType = mmffMolProperties->getMMFFAtomType(i);
unsigned int jAtomType = mmffMolProperties->getMMFFAtomType(j);
oStream << std::left << std::setw(2) << iAtom->getSymbol() << " #"
<< std::setw(5) << i + 1 << std::setw(2)
<< jAtom->getSymbol() << " #" << std::setw(5) << j + 1
<< std::right << std::setw(5) << iAtomType << std::setw(5)
<< jAtomType << " " << std::fixed << std::setprecision(3)
<< std::setw(9) << dist << std::setw(10) << vdWEnergy
<< std::setw(9) << mmffVdWConstants.R_ij_star << std::setw(9)
<< mmffVdWConstants.epsilon << std::endl;
}
totalVdWEnergy += vdWEnergy;
}
}
}
}
}
if (mmffMolProperties->getMMFFVerbosity()) {
if (mmffMolProperties->getMMFFVerbosity() == MMFF_VERBOSITY_HIGH) {
oStream << std::endl;
}
oStream << "TOTAL VAN DER WAALS ENERGY =" << std::right << std::setw(16)
<< std::fixed << std::setprecision(4) << totalVdWEnergy
<< std::endl;
}
}
// ------------------------------------------------------------------------
//
// the two-bit matrix returned by this contains:
// 0: if atoms i and j are directly connected
// 1: if atoms i and j are connected via an atom
// 2: if atoms i and j are in a 1,4 relationship
// 3: otherwise
//
// NOTE: the caller is responsible for calling delete []
// on the result
//
// ------------------------------------------------------------------------
boost::shared_array<boost::uint8_t> buildNeighborMatrix(const ROMol &mol) {
const boost::uint8_t RELATION_1_X_INIT = RELATION_1_X
| (RELATION_1_X << 2) | (RELATION_1_X << 4) | (RELATION_1_X << 6);
unsigned int nAtoms = mol.getNumAtoms();
unsigned nTwoBitCells = (nAtoms * (nAtoms + 1) - 1) / 8 + 1;
boost::shared_array<boost::uint8_t> res(new boost::uint8_t[nTwoBitCells]);
std::memset(res.get(), RELATION_1_X_INIT, nTwoBitCells);
for (ROMol::ConstBondIterator bondi = mol.beginBonds(); bondi != mol.endBonds(); ++bondi) {
setTwoBitCell(res, twoBitCellPos(nAtoms, (*bondi)->getBeginAtomIdx(),
(*bondi)->getEndAtomIdx()), RELATION_1_2);
unsigned int bondiBeginAtomIdx = (*bondi)->getBeginAtomIdx();
unsigned int bondiEndAtomIdx = (*bondi)->getEndAtomIdx();
for (ROMol::ConstBondIterator bondj = bondi; ++bondj != mol.endBonds();) {
int idx1 = -1;
int idx3 = -1;
unsigned int bondjBeginAtomIdx = (*bondj)->getBeginAtomIdx();
unsigned int bondjEndAtomIdx = (*bondj)->getEndAtomIdx();
if (bondiBeginAtomIdx == bondjBeginAtomIdx) {
idx1 = bondiEndAtomIdx;
idx3 = bondjEndAtomIdx;
} else if (bondiBeginAtomIdx == bondjEndAtomIdx) {
idx1 = bondiEndAtomIdx;
idx3 = bondjBeginAtomIdx;
} else if (bondiEndAtomIdx == bondjBeginAtomIdx) {
idx1 = bondiBeginAtomIdx;
idx3 = bondjEndAtomIdx;
} else if (bondiEndAtomIdx == bondjEndAtomIdx) {
idx1 = bondiBeginAtomIdx;
idx3 = bondjBeginAtomIdx;
} else {
// check if atoms i and j are in a 1,4-relationship
if ((mol.getBondBetweenAtoms(bondiBeginAtomIdx,
bondjBeginAtomIdx)) &&
(getTwoBitCell(res, twoBitCellPos(nAtoms, bondiEndAtomIdx,
bondjEndAtomIdx)) == RELATION_1_X)) {
setTwoBitCell(
res, twoBitCellPos(nAtoms, bondiEndAtomIdx, bondjEndAtomIdx),
RELATION_1_4);
} else if ((mol.getBondBetweenAtoms(bondiBeginAtomIdx,
bondjEndAtomIdx)) &&
(getTwoBitCell(res, twoBitCellPos(nAtoms, bondiEndAtomIdx,
bondjBeginAtomIdx)) ==
RELATION_1_X)) {
setTwoBitCell(
res, twoBitCellPos(nAtoms, bondiEndAtomIdx, bondjBeginAtomIdx),
RELATION_1_4);
} else if ((mol.getBondBetweenAtoms(bondiEndAtomIdx,
bondjBeginAtomIdx)) &&
(getTwoBitCell(res, twoBitCellPos(nAtoms, bondiBeginAtomIdx,
bondjEndAtomIdx)) ==
RELATION_1_X)) {
setTwoBitCell(
res, twoBitCellPos(nAtoms, bondiBeginAtomIdx, bondjEndAtomIdx),
RELATION_1_4);
} else if ((mol.getBondBetweenAtoms(bondiEndAtomIdx,
bondjEndAtomIdx)) &&
(getTwoBitCell(res, twoBitCellPos(nAtoms, bondiBeginAtomIdx,
bondjBeginAtomIdx)) ==
RELATION_1_X)) {
setTwoBitCell(
res, twoBitCellPos(nAtoms, bondiBeginAtomIdx, bondjBeginAtomIdx),
RELATION_1_4);
}
}
if (idx1 > -1) {
setTwoBitCell(res, twoBitCellPos(nAtoms, idx1, idx3), RELATION_1_3);
}
}
}
return res;
}