void TorsionAngleContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
RDGeom::Point3D iPoint(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D jPoint(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D kPoint(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D lPoint(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
double *g[4] = {&(grad[3 * d_at1Idx]), &(grad[3 * d_at2Idx]),
&(grad[3 * d_at3Idx]), &(grad[3 * d_at4Idx])};
RDGeom::Point3D r[4] = {iPoint - jPoint, kPoint - jPoint, jPoint - kPoint,
lPoint - kPoint};
RDGeom::Point3D t[2] = {r[0].crossProduct(r[1]), r[2].crossProduct(r[3])};
double d[2] = {t[0].length(), t[1].length()};
if (isDoubleZero(d[0]) || isDoubleZero(d[1])) {
return;
}
t[0] /= d[0];
t[1] /= d[1];
double cosPhi = t[0].dotProduct(t[1]);
clipToOne(cosPhi);
double sinPhiSq = 1.0 - cosPhi * cosPhi;
double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
double sin2Phi = 2.0 * sinPhi * cosPhi;
double sin3Phi = 3.0 * sinPhi - 4.0 * sinPhi * sinPhiSq;
// dE/dPhi is independent of cartesians:
double dE_dPhi =
0.5 * (-(d_V1)*sinPhi + 2.0 * d_V2 * sin2Phi - 3.0 * d_V3 * sin3Phi);
#if 0
if(dE_dPhi!=dE_dPhi){
std::cout << "\tNaN in Torsion("<<d_at1Idx<<","<<d_at2Idx<<","<<d_at3Idx<<","<<d_at4Idx<<")"<< std::endl;
std::cout << "sin: " << sinPhi << std::endl;
std::cout << "cos: " << cosPhi << std::endl;
}
#endif
// FIX: use a tolerance here
// this is hacky, but it's per the
// recommendation from Niketic and Rasmussen:
double sinTerm =
-dE_dPhi * (isDoubleZero(sinPhi) ? (1.0 / cosPhi) : (1.0 / sinPhi));
Utils::calcTorsionGrad(r, t, d, g, sinTerm, cosPhi);
}
void InversionContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
RDGeom::Point3D p1(pos[3 * d_at1Idx],
pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D p2(pos[3 * d_at2Idx],
pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D p3(pos[3 * d_at3Idx],
pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D p4(pos[3 * d_at4Idx],
pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
double *g1 = &(grad[3 * d_at1Idx]);
double *g2 = &(grad[3 * d_at2Idx]);
double *g3 = &(grad[3 * d_at3Idx]);
double *g4 = &(grad[3 * d_at4Idx]);
RDGeom::Point3D rJI = p1 - p2;
RDGeom::Point3D rJK = p3 - p2;
RDGeom::Point3D rJL = p4 - p2;
double dJI = rJI.length();
double dJK = rJK.length();
double dJL = rJL.length();
if (isDoubleZero(dJI) || isDoubleZero(dJK) || isDoubleZero(dJL)) {
return;
}
rJI /= dJI;
rJK /= dJK;
rJL /= dJL;
RDGeom::Point3D n = (-rJI).crossProduct(rJK);
n /= n.length();
double cosY = n.dotProduct(rJL);
double sinYSq = 1.0 - cosY * cosY;
double sinY = std::max(((sinYSq > 0.0) ? sqrt(sinYSq) : 0.0), 1.0e-8);
double cosTheta = rJI.dotProduct(rJK);
double sinThetaSq = std::max(1.0 - cosTheta * cosTheta, 1.0e-8);
double sinTheta = std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);
// sin(2 * W) = 2 * sin(W) * cos(W) = 2 * cos(Y) * sin(Y)
double dE_dW = -d_forceConstant
* (d_C1 * cosY - 4.0 * d_C2 * cosY * sinY);
RDGeom::Point3D t1 = rJL.crossProduct(rJK);
RDGeom::Point3D t2 = rJI.crossProduct(rJL);
RDGeom::Point3D t3 = rJK.crossProduct(rJI);
double term1 = sinY * sinTheta;
double term2 = cosY / (sinY * sinThetaSq);
double tg1[3] = { (t1.x / term1 - (rJI.x - rJK.x * cosTheta) * term2) / dJI,
(t1.y / term1 - (rJI.y - rJK.y * cosTheta) * term2) / dJI,
(t1.z / term1 - (rJI.z - rJK.z * cosTheta) * term2) / dJI };
double tg3[3] = { (t2.x / term1 - (rJK.x - rJI.x * cosTheta) * term2) / dJK,
(t2.y / term1 - (rJK.y - rJI.y * cosTheta) * term2) / dJK,
(t2.z / term1 - (rJK.z - rJI.z * cosTheta) * term2) / dJK };
double tg4[3] = { (t3.x / term1 - rJL.x * cosY / sinY) / dJL,
(t3.y / term1 - rJL.y * cosY / sinY) / dJL,
(t3.z / term1 - rJL.z * cosY / sinY) / dJL };
for (unsigned int i = 0; i < 3; ++i) {
g1[i] += dE_dW * tg1[i];
g2[i] += -dE_dW * (tg1[i] + tg3[i] + tg4[i]);
g3[i] += dE_dW * tg3[i];
g4[i] += dE_dW * tg4[i];
}
}
void OopBendContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
RDGeom::Point3D iPoint(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D jPoint(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D kPoint(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D lPoint(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
double *g1 = &(grad[3 * d_at1Idx]);
double *g2 = &(grad[3 * d_at2Idx]);
double *g3 = &(grad[3 * d_at3Idx]);
double *g4 = &(grad[3 * d_at4Idx]);
RDGeom::Point3D rJI = iPoint - jPoint;
RDGeom::Point3D rJK = kPoint - jPoint;
RDGeom::Point3D rJL = lPoint - jPoint;
double dJI = rJI.length();
double dJK = rJK.length();
double dJL = rJL.length();
if (isDoubleZero(dJI) || isDoubleZero(dJK) || isDoubleZero(dJL)) {
return;
}
rJI /= dJI;
rJK /= dJK;
rJL /= dJL;
RDGeom::Point3D n = (-rJI).crossProduct(rJK);
n /= n.length();
double const c2 = MDYNE_A_TO_KCAL_MOL * DEG2RAD * DEG2RAD;
double sinChi = rJL.dotProduct(n);
clipToOne(sinChi);
double cosChiSq = 1.0 - sinChi * sinChi;
double cosChi = std::max(((cosChiSq > 0.0) ? sqrt(cosChiSq) : 0.0), 1.0e-8);
double chi = RAD2DEG * asin(sinChi);
double cosTheta = rJI.dotProduct(rJK);
clipToOne(cosTheta);
double sinThetaSq = std::max(1.0 - cosTheta * cosTheta, 1.0e-8);
double sinTheta =
std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);
double dE_dChi = RAD2DEG * c2 * d_koop * chi;
RDGeom::Point3D t1 = rJL.crossProduct(rJK);
RDGeom::Point3D t2 = rJI.crossProduct(rJL);
RDGeom::Point3D t3 = rJK.crossProduct(rJI);
double term1 = cosChi * sinTheta;
double term2 = sinChi / (cosChi * sinThetaSq);
double tg1[3] = {(t1.x / term1 - (rJI.x - rJK.x * cosTheta) * term2) / dJI,
(t1.y / term1 - (rJI.y - rJK.y * cosTheta) * term2) / dJI,
(t1.z / term1 - (rJI.z - rJK.z * cosTheta) * term2) / dJI};
double tg3[3] = {(t2.x / term1 - (rJK.x - rJI.x * cosTheta) * term2) / dJK,
(t2.y / term1 - (rJK.y - rJI.y * cosTheta) * term2) / dJK,
(t2.z / term1 - (rJK.z - rJI.z * cosTheta) * term2) / dJK};
double tg4[3] = {(t3.x / term1 - rJL.x * sinChi / cosChi) / dJL,
(t3.y / term1 - rJL.y * sinChi / cosChi) / dJL,
(t3.z / term1 - rJL.z * sinChi / cosChi) / dJL};
for (unsigned int i = 0; i < 3; ++i) {
g1[i] += dE_dChi * tg1[i];
g2[i] += -dE_dChi * (tg1[i] + tg3[i] + tg4[i]);
g3[i] += dE_dChi * tg3[i];
g4[i] += dE_dChi * tg4[i];
}
}
// ------------------------------------------------------------------------
//
//
//
// ------------------------------------------------------------------------
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 addStretchBend(const ROMol &mol, MMFFMolProperties *mmffMolProperties,
ForceFields::ForceField *field) {
PRECONDITION(field, "bad ForceField");
PRECONDITION(mmffMolProperties, "bad MMFFMolProperties");
PRECONDITION(mmffMolProperties->isValid(),
"missing atom types - invalid force-field");
std::ostream &oStream = mmffMolProperties->getMMFFOStream();
unsigned int idx[3];
MMFFPropCollection *mmffProp = MMFFPropCollection::getMMFFProp();
std::pair<bool, const MMFFStbn *> mmffStbnParams;
ROMol::ADJ_ITER nbr1Idx;
ROMol::ADJ_ITER end1Nbrs;
ROMol::ADJ_ITER nbr2Idx;
ROMol::ADJ_ITER end2Nbrs;
unsigned int nAtoms = mol.getNumAtoms();
double totalStretchBendEnergy = 0.0;
RDGeom::PointPtrVect points;
if (mmffMolProperties->getMMFFVerbosity()) {
if (mmffMolProperties->getMMFFVerbosity() == MMFF_VERBOSITY_HIGH) {
oStream << "\n"
"S T R E T C H B E N D I N G\n\n"
"-----------ATOMS----------- ATOM TYPES FF VALENCE "
" DELTA DELTA DELTA F CON\n"
" I J K I J K CLASS ANGLE "
" ANGLE R(I,J) R(J,K) ENERGY I-J (J-K)\n"
"-------------------------------------------------------------"
"-----------------------------------------------------"
<< std::endl;
}
points = field->positions();
}
for (idx[1] = 0; idx[1] < nAtoms; ++idx[1]) {
const Atom *jAtom = mol.getAtomWithIdx(idx[1]);
if (jAtom->getDegree() == 1) {
continue;
}
unsigned int jAtomType = mmffMolProperties->getMMFFAtomType(idx[1]);
const MMFFProp *mmffPropParamsCentralAtom = (*mmffProp)(jAtomType);
if (mmffPropParamsCentralAtom->linh) {
continue;
}
boost::tie(nbr1Idx, end1Nbrs) = mol.getAtomNeighbors(jAtom);
unsigned int i = 0;
for (; nbr1Idx != end1Nbrs; ++nbr1Idx) {
const Atom *iAtom = mol[*nbr1Idx].get();
boost::tie(nbr2Idx, end2Nbrs) = mol.getAtomNeighbors(jAtom);
unsigned int j = 0;
for (; nbr2Idx != end2Nbrs; ++nbr2Idx) {
const Atom *kAtom = mol[*nbr2Idx].get();
if (j < (i + 1)) {
++j;
continue;
}
idx[0] = iAtom->getIdx();
idx[2] = kAtom->getIdx();
unsigned int stretchBendType;
MMFFStbn mmffStbnParams;
MMFFBond mmffBondParams[2];
MMFFAngle mmffAngleParams;
if (mmffMolProperties->getMMFFStretchBendParams(
mol, idx[0], idx[1], idx[2], stretchBendType, mmffStbnParams,
mmffBondParams, mmffAngleParams)) {
StretchBendContrib *contrib = new StretchBendContrib(
field, idx[0], idx[1], idx[2], &mmffStbnParams, &mmffAngleParams,
&mmffBondParams[0], &mmffBondParams[1]);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
if (mmffMolProperties->getMMFFVerbosity()) {
unsigned int iAtomType = mmffMolProperties->getMMFFAtomType(idx[0]);
unsigned int jAtomType = mmffMolProperties->getMMFFAtomType(idx[1]);
unsigned int kAtomType = mmffMolProperties->getMMFFAtomType(idx[2]);
const double dist1 = field->distance(idx[0], idx[1]);
const double dist2 = field->distance(idx[1], idx[2]);
const RDGeom::Point3D p1((*(points[idx[0]]))[0],
(*(points[idx[0]]))[1],
(*(points[idx[0]]))[2]);
const RDGeom::Point3D p2((*(points[idx[1]]))[0],
(*(points[idx[1]]))[1],
(*(points[idx[1]]))[2]);
const RDGeom::Point3D p3((*(points[idx[2]]))[0],
(*(points[idx[2]]))[1],
(*(points[idx[2]]))[2]);
const double cosTheta =
MMFF::Utils::calcCosTheta(p1, p2, p3, dist1, dist2);
const double theta = RAD2DEG * acos(cosTheta);
const std::pair<double, double> forceConstants =
MMFF::Utils::calcStbnForceConstants(&mmffStbnParams);
const std::pair<double, double> stretchBendEnergies =
MMFF::Utils::calcStretchBendEnergy(
dist1 - mmffBondParams[0].r0, dist2 - mmffBondParams[1].r0,
theta - mmffAngleParams.theta0, forceConstants);
if (mmffMolProperties->getMMFFVerbosity() == MMFF_VERBOSITY_HIGH) {
if (!isDoubleZero(forceConstants.first)) {
oStream << std::left << std::setw(2) << iAtom->getSymbol()
<< " #" << std::setw(5) << idx[0] + 1 << std::setw(2)
<< jAtom->getSymbol() << " #" << std::setw(5)
<< idx[1] + 1 << std::setw(2) << kAtom->getSymbol()
<< " #" << std::setw(5) << idx[2] + 1 << std::right
<< std::setw(5) << iAtomType << std::setw(5)
<< jAtomType << std::setw(5) << kAtomType
<< std::setw(6) << stretchBendType << " " << std::fixed
<< std::setprecision(3) << std::setw(10) << theta
<< std::setw(10) << theta - mmffAngleParams.theta0
<< std::setw(10) << dist1 - mmffBondParams[0].r0
<< std::setw(10) << dist2 - mmffBondParams[1].r0
<< std::setw(10) << stretchBendEnergies.first
<< std::setw(10) << mmffStbnParams.kbaIJK << std::endl;
}
if (!isDoubleZero(forceConstants.second)) {
oStream << std::left << std::setw(2) << kAtom->getSymbol()
<< " #" << std::setw(5) << idx[2] + 1 << std::setw(2)
<< jAtom->getSymbol() << " #" << std::setw(5)
<< idx[1] + 1 << std::setw(2) << iAtom->getSymbol()
<< " #" << std::setw(5) << idx[0] + 1 << std::right
<< std::setw(5) << kAtomType << std::setw(5)
<< jAtomType << std::setw(5) << iAtomType
<< std::setw(6) << stretchBendType << " " << std::fixed
<< std::setprecision(3) << std::setw(10) << theta
<< std::setw(10) << theta - mmffAngleParams.theta0
<< std::setw(10) << dist1 - mmffBondParams[0].r0
<< std::setw(10) << dist2 - mmffBondParams[1].r0
<< std::setw(10) << stretchBendEnergies.second
<< std::setw(10) << mmffStbnParams.kbaKJI << std::endl;
}
}
totalStretchBendEnergy +=
(stretchBendEnergies.first + stretchBendEnergies.second);
}
}
++j;
}
++i;
}
}
if (mmffMolProperties->getMMFFVerbosity()) {
if (mmffMolProperties->getMMFFVerbosity() == MMFF_VERBOSITY_HIGH) {
oStream << std::endl;
}
oStream << "TOTAL STRETCH-BEND ENERGY =" << std::right << std::setw(16)
<< std::fixed << std::setprecision(4) << totalStretchBendEnergy
<< std::endl;
}
}
void TorsionConstraintContrib::getGrad(double *pos, double *grad) const
{
PRECONDITION(dp_forceField,"no owner");
PRECONDITION(pos,"bad vector");
PRECONDITION(grad,"bad vector");
RDGeom::Point3D p1(pos[3 * d_at1Idx],
pos[3 * d_at1Idx + 1], pos[3 * d_at1Idx + 2]);
RDGeom::Point3D p2(pos[3 * d_at2Idx],
pos[3 * d_at2Idx + 1], pos[3 * d_at2Idx + 2]);
RDGeom::Point3D p3(pos[3 * d_at3Idx],
pos[3 * d_at3Idx + 1], pos[3 * d_at3Idx + 2]);
RDGeom::Point3D p4(pos[3 * d_at4Idx],
pos[3 * d_at4Idx + 1], pos[3 * d_at4Idx + 2]);
double *g[4] = {
&(grad[3 * d_at1Idx]),
&(grad[3 * d_at2Idx]),
&(grad[3 * d_at3Idx]),
&(grad[3 * d_at4Idx])
};
RDGeom::Point3D r[4] = {
p1 - p2,
p3 - p2,
p2 - p3,
p4 - p3
};
RDGeom::Point3D t[2] = {
r[0].crossProduct(r[1]),
r[2].crossProduct(r[3])
};
double d[2] = {
t[0].length(),
t[1].length()
};
if (isDoubleZero(d[0]) || isDoubleZero(d[1])) {
return;
}
t[0] /= d[0];
t[1] /= d[1];
double cosPhi = t[0].dotProduct(t[1]);
double sinPhiSq = 1.0 - cosPhi * cosPhi;
double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
// dE/dPhi is independent of cartesians:
RDGeom::Point3D n123 = (-r[0]).crossProduct(r[1]);
double n123SqLength = n123.lengthSq();
RDGeom::Point3D n234 = r[1].crossProduct(r[3]);
double n234SqLength = n234.lengthSq();
RDGeom::Point3D m = n123.crossProduct(r[1]);
// we want a signed dihedral, that's why we use atan2 instead of acos
double dihedral = RAD2DEG * (-atan2(m.dotProduct(n234) / sqrt(n234SqLength * m.lengthSq()),
n123.dotProduct(n234) / sqrt(n123SqLength * n234SqLength)));
//double dihedral = RAD2DEG * acos(cosPhi);
double ave = 0.5 * (d_minDihedralDeg + d_maxDihedralDeg);
dihedral += 360.0 * boost::math::round((ave - dihedral) / 360.0);
double dihedralTerm = 0.0;
if (dihedral < d_minDihedralDeg) {
dihedralTerm = dihedral - d_minDihedralDeg;
}
else if (dihedral > d_maxDihedralDeg) {
dihedralTerm = dihedral - d_maxDihedralDeg;
}
double dE_dPhi = DEG2RAD * d_forceConstant * dihedralTerm;
// FIX: use a tolerance here
// this is hacky, but it's per the
// recommendation from Niketic and Rasmussen:
double sinTerm = -dE_dPhi * (isDoubleZero(sinPhi)
? (1.0 / cosPhi) : (1.0 / sinPhi));
Utils::calcTorsionGrad(r, t, d, g, sinTerm, cosPhi);
}
void TorsionAngleContrib::getGrad(double *pos, double *grad) const
{
PRECONDITION(dp_forceField,"no owner");
PRECONDITION(pos,"bad vector");
PRECONDITION(grad,"bad vector");
RDGeom::Point3D iPoint(pos[3 * this->d_at1Idx],
pos[3 * this->d_at1Idx + 1], pos[3 * this->d_at1Idx + 2]);
RDGeom::Point3D jPoint(pos[3 * this->d_at2Idx],
pos[3 * this->d_at2Idx + 1], pos[3 * this->d_at2Idx + 2]);
RDGeom::Point3D kPoint(pos[3 * this->d_at3Idx],
pos[3 * this->d_at3Idx + 1], pos[3 * this->d_at3Idx + 2]);
RDGeom::Point3D lPoint(pos[3 * this->d_at4Idx],
pos[3 * this->d_at4Idx + 1], pos[3 * this->d_at4Idx + 2]);
double *g1 = &(grad[3 * this->d_at1Idx]);
double *g2 = &(grad[3 * this->d_at2Idx]);
double *g3 = &(grad[3 * this->d_at3Idx]);
double *g4 = &(grad[3 * this->d_at4Idx]);
RDGeom::Point3D r1 = iPoint - jPoint;
RDGeom::Point3D r2 = kPoint - jPoint;
RDGeom::Point3D r3 = jPoint - kPoint;
RDGeom::Point3D r4 = lPoint - kPoint;
RDGeom::Point3D t1 = r1.crossProduct(r2);
RDGeom::Point3D t2 = r3.crossProduct(r4);
double d1 = t1.length();
t1 /= d1;
double d2 = t2.length();
t2 /= d2;
if (isDoubleZero(d1) || isDoubleZero(d2)) {
return;
}
double cosPhi = t1.dotProduct(t2);
double sinPhiSq = 1.0 - cosPhi * cosPhi;
double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
double sin2Phi = 2.0 * sinPhi * cosPhi;
double sin3Phi = 3.0 * sinPhi - 4.0 * sinPhi * sinPhiSq;
// dE/dPhi is independent of cartesians:
double dE_dPhi = 0.5 * (-(this->d_V1) * sinPhi + 2.0
* this->d_V2 * sin2Phi - 3.0 * this->d_V3 * sin3Phi);
#if 0
if(dE_dPhi!=dE_dPhi){
std::cout << "\tNaN in Torsion("<<this->d_at1Idx<<","<<this->d_at2Idx<<","<<this->d_at3Idx<<","<<this->d_at4Idx<<")"<< std::endl;
std::cout << "sin: " << sinPhi << std::endl;
std::cout << "cos: " << cosPhi << std::endl;
}
#endif
// -------
// dTheta/dx is trickier:
double dCos_dT1 = 1.0 / d1 * (t2.x - cosPhi * t1.x);
double dCos_dT2 = 1.0 / d1 * (t2.y - cosPhi * t1.y);
double dCos_dT3 = 1.0 / d1 * (t2.z - cosPhi * t1.z);
double dCos_dT4 = 1.0 / d2 * (t1.x - cosPhi * t2.x);
double dCos_dT5 = 1.0 / d2 * (t1.y - cosPhi * t2.y);
double dCos_dT6 = 1.0 / d2 * (t1.z - cosPhi * t2.z);
// FIX: use a tolerance here
// this is hacky, but it's per the
// recommendation from Niketic and Rasmussen:
double sinTerm = -dE_dPhi * (isDoubleZero(sinPhi)
? (1.0 / cosPhi) : (1.0 / sinPhi));
g1[0] += sinTerm * (dCos_dT3 * r2.y - dCos_dT2 * r2.z);
g1[1] += sinTerm * (dCos_dT1 * r2.z - dCos_dT3 * r2.x);
g1[2] += sinTerm * (dCos_dT2 * r2.x - dCos_dT1 * r2.y);
g2[0] += sinTerm * (dCos_dT2 * (r2.z - r1.z)
+ dCos_dT3 * (r1.y - r2.y) + dCos_dT5 * (-1.0 * r4.z) + dCos_dT6 * (r4.y));
g2[1] += sinTerm * (dCos_dT1 * (r1.z - r2.z)
+ dCos_dT3 * (r2.x - r1.x) + dCos_dT4 * (r4.z) + dCos_dT6 * (-1.0 * r4.x));
g2[2] += sinTerm * (dCos_dT1 * (r2.y - r1.y)
+ dCos_dT2 * (r1.x - r2.x) + dCos_dT4 * (-1.0 * r4.y) + dCos_dT5 * (r4.x));
g3[0] += sinTerm * (dCos_dT2 * (r1.z) + dCos_dT3 * (-1.0 * r1.y) +
dCos_dT5 * (r4.z - r3.z) + dCos_dT6 * (r3.y - r4.y));
g3[1] += sinTerm * (dCos_dT1 * (-1.0 * r1.z) + dCos_dT3 * (r1.x) +
dCos_dT4 * (r3.z - r4.z) + dCos_dT6 * (r4.x - r3.x));
g3[2] += sinTerm * (dCos_dT1 * (r1.y) + dCos_dT2 * (-1.0 * r1.x) +
dCos_dT4 * (r4.y - r3.y) + dCos_dT5 * (r3.x - r4.x));
g4[0] += sinTerm * (dCos_dT5 * r3.z - dCos_dT6 * r3.y);
g4[1] += sinTerm * (dCos_dT6 * r3.x - dCos_dT4 * r3.z);
g4[2] += sinTerm * (dCos_dT4 * r3.y - dCos_dT5 * r3.x);
}
