double getAngleRad(Conformer &conf,
unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId) {
RDGeom::POINT3D_VECT &pos = conf.getPositions();
RANGE_CHECK(0, iAtomId, pos.size() - 1);
RANGE_CHECK(0, jAtomId, pos.size() - 1);
RANGE_CHECK(0, kAtomId, pos.size() - 1);
RDGeom::Point3D rJI = pos[iAtomId] - pos[jAtomId];
double rJISqLength = rJI.lengthSq();
if(rJISqLength <= 1.e-16) throw ValueErrorException("atoms i and j have identical 3D coordinates");
RDGeom::Point3D rJK = pos[kAtomId] - pos[jAtomId];
double rJKSqLength = rJK.lengthSq();
if(rJKSqLength <= 1.e-16) throw ValueErrorException("atoms j and k have identical 3D coordinates");
return rJI.angleTo(rJK);
}
void setAngleRad(Conformer &conf, unsigned int iAtomId, unsigned int jAtomId,
unsigned int kAtomId, double value) {
RDGeom::POINT3D_VECT &pos = conf.getPositions();
URANGE_CHECK(iAtomId, pos.size());
URANGE_CHECK(jAtomId, pos.size());
URANGE_CHECK(kAtomId, pos.size());
ROMol &mol = conf.getOwningMol();
Bond *bondJI = mol.getBondBetweenAtoms(jAtomId, iAtomId);
if (!bondJI) throw ValueErrorException("atoms i and j must be bonded");
Bond *bondJK = mol.getBondBetweenAtoms(jAtomId, kAtomId);
if (!bondJK) throw ValueErrorException("atoms j and k must be bonded");
if (queryIsBondInRing(bondJI) && queryIsBondInRing(bondJK))
throw ValueErrorException(
"bonds (i,j) and (j,k) must not both belong to a ring");
RDGeom::Point3D rJI = pos[iAtomId] - pos[jAtomId];
double rJISqLength = rJI.lengthSq();
if (rJISqLength <= 1.e-16)
throw ValueErrorException("atoms i and j have identical 3D coordinates");
RDGeom::Point3D rJK = pos[kAtomId] - pos[jAtomId];
double rJKSqLength = rJK.lengthSq();
if (rJKSqLength <= 1.e-16)
throw ValueErrorException("atoms j and k have identical 3D coordinates");
// we only need to rotate by delta with respect to the current angle value
value -= rJI.angleTo(rJK);
RDGeom::Point3D &rotAxisBegin = pos[jAtomId];
// our rotation axis is the normal to the plane of atoms i, j, k
RDGeom::Point3D rotAxisEnd = rJI.crossProduct(rJK) + pos[jAtomId];
RDGeom::Point3D rotAxis = rotAxisEnd - rotAxisBegin;
rotAxis.normalize();
// get all atoms bonded to j and loop through them
std::list<unsigned int> alist;
_toBeMovedIdxList(mol, jAtomId, kAtomId, alist);
for (std::list<unsigned int>::iterator it = alist.begin(); it != alist.end();
++it) {
// translate atom so that it coincides with the origin of rotation
pos[*it] -= rotAxisBegin;
// rotate around our rotation axis
RDGeom::Transform3D rotByAngle;
rotByAngle.SetRotation(value, rotAxis);
rotByAngle.TransformPoint(pos[*it]);
// translate atom back
pos[*it] += rotAxisBegin;
}
}
double getDihedralRad(const Conformer &conf, unsigned int iAtomId,
unsigned int jAtomId, unsigned int kAtomId,
unsigned int lAtomId) {
const RDGeom::POINT3D_VECT &pos = conf.getPositions();
URANGE_CHECK(iAtomId, pos.size());
URANGE_CHECK(jAtomId, pos.size());
URANGE_CHECK(kAtomId, pos.size());
URANGE_CHECK(lAtomId, pos.size());
RDGeom::Point3D rIJ = pos[jAtomId] - pos[iAtomId];
double rIJSqLength = rIJ.lengthSq();
if (rIJSqLength <= 1.e-16)
throw ValueErrorException("atoms i and j have identical 3D coordinates");
RDGeom::Point3D rJK = pos[kAtomId] - pos[jAtomId];
double rJKSqLength = rJK.lengthSq();
if (rJKSqLength <= 1.e-16)
throw ValueErrorException("atoms j and k have identical 3D coordinates");
RDGeom::Point3D rKL = pos[lAtomId] - pos[kAtomId];
double rKLSqLength = rKL.lengthSq();
if (rKLSqLength <= 1.e-16)
throw ValueErrorException("atoms k and l have identical 3D coordinates");
RDGeom::Point3D nIJK = rIJ.crossProduct(rJK);
double nIJKSqLength = nIJK.lengthSq();
RDGeom::Point3D nJKL = rJK.crossProduct(rKL);
double nJKLSqLength = nJKL.lengthSq();
RDGeom::Point3D m = nIJK.crossProduct(rJK);
// we want a signed dihedral, that's why we use atan2 instead of acos
return -atan2(m.dotProduct(nJKL) / sqrt(nJKLSqLength * m.lengthSq()),
nIJK.dotProduct(nJKL) / sqrt(nIJKSqLength * nJKLSqLength));
}
void setDihedralRad(Conformer &conf, unsigned int iAtomId, unsigned int jAtomId,
unsigned int kAtomId, unsigned int lAtomId, double value) {
RDGeom::POINT3D_VECT &pos = conf.getPositions();
URANGE_CHECK(iAtomId, pos.size());
URANGE_CHECK(jAtomId, pos.size());
URANGE_CHECK(kAtomId, pos.size());
URANGE_CHECK(lAtomId, pos.size());
ROMol &mol = conf.getOwningMol();
Bond *bondIJ = mol.getBondBetweenAtoms(iAtomId, jAtomId);
if (!bondIJ) throw ValueErrorException("atoms i and j must be bonded");
Bond *bondJK = mol.getBondBetweenAtoms(jAtomId, kAtomId);
if (!bondJK) throw ValueErrorException("atoms j and k must be bonded");
Bond *bondKL = mol.getBondBetweenAtoms(kAtomId, lAtomId);
if (!bondKL) throw ValueErrorException("atoms k and l must be bonded");
if (queryIsBondInRing(bondJK))
throw ValueErrorException("bond (j,k) must not belong to a ring");
RDGeom::Point3D rIJ = pos[jAtomId] - pos[iAtomId];
double rIJSqLength = rIJ.lengthSq();
if (rIJSqLength <= 1.e-16)
throw ValueErrorException("atoms i and j have identical 3D coordinates");
RDGeom::Point3D rJK = pos[kAtomId] - pos[jAtomId];
double rJKSqLength = rJK.lengthSq();
if (rJKSqLength <= 1.e-16)
throw ValueErrorException("atoms j and k have identical 3D coordinates");
RDGeom::Point3D rKL = pos[lAtomId] - pos[kAtomId];
double rKLSqLength = rKL.lengthSq();
if (rKLSqLength <= 1.e-16)
throw ValueErrorException("atoms k and l have identical 3D coordinates");
RDGeom::Point3D nIJK = rIJ.crossProduct(rJK);
double nIJKSqLength = nIJK.lengthSq();
RDGeom::Point3D nJKL = rJK.crossProduct(rKL);
double nJKLSqLength = nJKL.lengthSq();
RDGeom::Point3D m = nIJK.crossProduct(rJK);
// we only need to rotate by delta with respect to the current dihedral value
value -= -atan2(m.dotProduct(nJKL) / sqrt(nJKLSqLength * m.lengthSq()),
nIJK.dotProduct(nJKL) / sqrt(nIJKSqLength * nJKLSqLength));
// our rotation axis is the (j,k) bond
RDGeom::Point3D &rotAxisBegin = pos[jAtomId];
RDGeom::Point3D &rotAxisEnd = pos[kAtomId];
RDGeom::Point3D rotAxis = rotAxisEnd - rotAxisBegin;
rotAxis.normalize();
// get all atoms bonded to k and loop through them
std::list<unsigned int> alist;
_toBeMovedIdxList(mol, jAtomId, kAtomId, alist);
for (std::list<unsigned int>::iterator it = alist.begin(); it != alist.end();
++it) {
// translate atom so that it coincides with the origin of rotation
pos[*it] -= rotAxisBegin;
// rotate around our rotation axis
RDGeom::Transform3D rotByAngle;
rotByAngle.SetRotation(value, rotAxis);
rotByAngle.TransformPoint(pos[*it]);
// translate atom back
pos[*it] += rotAxisBegin;
}
}
double TorsionConstraintContrib::getEnergy(double *pos) const
{
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "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]);
RDGeom::Point3D r1 = p1 - p2;
RDGeom::Point3D r2 = p3 - p2;
RDGeom::Point3D r3 = p2 - p3;
RDGeom::Point3D r4 = p4 - p3;
RDGeom::Point3D t1 = r1.crossProduct(r2);
RDGeom::Point3D t2 = r3.crossProduct(r4);
double d1 = std::max(t1.length(), 0.0);
double d2 = std::max(t2.length(), 0.0);
t1 /= d1;
t2 /= d2;
double cosPhi = t1.dotProduct(t2);
RDGeom::Point3D n123 = (-r1).crossProduct(r2);
double n123SqLength = n123.lengthSq();
RDGeom::Point3D n234 = r2.crossProduct(r4);
double n234SqLength = n234.lengthSq();
RDGeom::Point3D m = n123.crossProduct(r2);
// 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 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 const c = 0.5 * DEG2RAD * DEG2RAD;
double res = c * d_forceConstant * dihedralTerm * dihedralTerm;
return res;
}
TorsionConstraintContrib::TorsionConstraintContrib(ForceField *owner,
unsigned int idx1, unsigned int idx2, unsigned int idx3,
unsigned int idx4, bool relative, double minDihedralDeg,
double maxDihedralDeg, double forceConst)
{
PRECONDITION(owner,"bad owner");
const RDGeom::PointPtrVect &pos = owner->positions();
RANGE_CHECK(0, idx1, pos.size() - 1);
RANGE_CHECK(0, idx2, pos.size() - 1);
RANGE_CHECK(0, idx3, pos.size() - 1);
RANGE_CHECK(0, idx4, pos.size() - 1);
PRECONDITION((!(maxDihedralDeg < minDihedralDeg))
&& ((maxDihedralDeg - minDihedralDeg) < 360.0), "bad bounds");
double dihedral = 0.0;
if (relative) {
RDGeom::Point3D p1 = *((RDGeom::Point3D *)pos[idx1]);
RDGeom::Point3D p2 = *((RDGeom::Point3D *)pos[idx2]);
RDGeom::Point3D p3 = *((RDGeom::Point3D *)pos[idx3]);
RDGeom::Point3D p4 = *((RDGeom::Point3D *)pos[idx4]);
RDGeom::Point3D r12 = p2 - p1;
RDGeom::Point3D r23 = p3 - p2;
RDGeom::Point3D r34 = p4 - p3;
RDGeom::Point3D n123 = r12.crossProduct(r23);
double nIJKSqLength = n123.lengthSq();
RDGeom::Point3D n234 = r23.crossProduct(r34);
double nJKLSqLength = n234.lengthSq();
RDGeom::Point3D m = n123.crossProduct(r23);
// we want a signed dihedral, that's why we use atan2 instead of acos
dihedral = RAD2DEG
* (-atan2(m.dotProduct(n234) / sqrt(nJKLSqLength * m.lengthSq()),
n123.dotProduct(n234) / sqrt(nIJKSqLength * nJKLSqLength)));
}
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
d_at4Idx = idx4;
minDihedralDeg += dihedral;
maxDihedralDeg += dihedral;
_pretreatDihedrals(minDihedralDeg, maxDihedralDeg);
d_minDihedralDeg = minDihedralDeg;
d_maxDihedralDeg = maxDihedralDeg;
d_forceConstant = forceConst;
}
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);
}
double AlignPoints(const RDGeom::Point3DConstPtrVect &refPoints,
const RDGeom::Point3DConstPtrVect &probePoints,
RDGeom::Transform3D &trans, const DoubleVector *weights,
bool reflect, unsigned int maxIterations) {
unsigned int npt = refPoints.size();
PRECONDITION(npt == probePoints.size(), "Mismatch in number of points");
trans.setToIdentity();
const DoubleVector *wts;
double wtsSum;
bool ownWts;
if (weights) {
PRECONDITION(npt == weights->size(), "Mismatch in number of points");
wts = weights;
wtsSum = _sumOfWeights(*wts);
ownWts = false;
} else {
wts = new DoubleVector(npt, 1.0);
wtsSum = static_cast<double>(npt);
ownWts = true;
}
RDGeom::Point3D rptSum = _weightedSumOfPoints(refPoints, *wts);
RDGeom::Point3D pptSum = _weightedSumOfPoints(probePoints, *wts);
double rptSumLenSq = _weightedSumOfLenSq(refPoints, *wts);
double pptSumLenSq = _weightedSumOfLenSq(probePoints, *wts);
double covMat[3][3];
// compute the co-variance matrix
_computeCovarianceMat(refPoints, probePoints, *wts, covMat);
if (ownWts) {
delete wts;
wts = 0;
}
if (reflect) {
rptSum *= -1.0;
reflectCovMat(covMat);
}
// convert the covariance matrix to a 4x4 matrix that needs to be diagonalized
double quad[4][4];
_covertCovMatToQuad(covMat, rptSum, pptSum, wtsSum, quad);
// get the eigenVecs and eigenVals for the matrix
double eigenVecs[4][4], eigenVals[4];
jacobi(quad, eigenVals, eigenVecs, maxIterations);
// get the quaternion
double quater[4];
quater[0] = eigenVecs[0][0];
quater[1] = eigenVecs[1][0];
quater[2] = eigenVecs[2][0];
quater[3] = eigenVecs[3][0];
trans.SetRotationFromQuaternion(quater);
if (reflect) {
// put the flip in the rotation matrix
trans.Reflect();
}
// compute the SSR value
double ssr = eigenVals[0] - (pptSum.lengthSq() + rptSum.lengthSq()) / wtsSum +
rptSumLenSq + pptSumLenSq;
if ((ssr < 0.0) && (fabs(ssr) < TOLERANCE)) {
ssr = 0.0;
}
if (reflect) {
rptSum *= -1.0;
}
// set the translation
trans.TransformPoint(pptSum);
RDGeom::Point3D move = rptSum;
move -= pptSum;
move /= wtsSum;
trans.SetTranslation(move);
return ssr;
}