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, "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;
_pretreatAngles(minDihedralDeg, maxDihedralDeg);
d_minDihedralDeg = minDihedralDeg;
d_maxDihedralDeg = maxDihedralDeg;
d_forceConstant = forceConst;
}
AngleConstraintContrib::AngleConstraintContrib(ForceField *owner,
unsigned int idx1, unsigned int idx2, unsigned int idx3,
double minAngleDeg, double maxAngleDeg, double forceConst)
{
PRECONDITION(owner,"bad owner");
RANGE_CHECK(0, idx1, owner->positions().size() - 1);
RANGE_CHECK(0, idx2, owner->positions().size() - 1);
RANGE_CHECK(0, idx3, owner->positions().size() - 1);
PRECONDITION(maxAngleDeg >= minAngleDeg, "allowedDeltaDeg must be >= 0.0");
_pretreatAngles(minAngleDeg, maxAngleDeg);
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
d_minAngleDeg = minAngleDeg;
d_maxAngleDeg = maxAngleDeg;
d_forceConstant = forceConst;
}
TorsionConstraintContrib::TorsionConstraintContrib(ForceField *owner,
unsigned int idx1, unsigned int idx2, unsigned int idx3,
unsigned int idx4, double minDihedralDeg, double maxDihedralDeg,
double forceConst)
{
PRECONDITION(owner,"bad owner");
RANGE_CHECK(0, idx1, owner->positions().size() - 1);
RANGE_CHECK(0, idx2, owner->positions().size() - 1);
RANGE_CHECK(0, idx3, owner->positions().size() - 1);
RANGE_CHECK(0, idx4, owner->positions().size() - 1);
_pretreatAngles(minDihedralDeg, maxDihedralDeg);
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
d_at4Idx = idx4;
d_minDihedralDeg = minDihedralDeg;
d_maxDihedralDeg = maxDihedralDeg;
d_forceConstant = forceConst;
}
AngleConstraintContrib::AngleConstraintContrib(ForceField *owner,
unsigned int idx1, unsigned int idx2, unsigned int idx3,
bool relative, double minAngleDeg, double maxAngleDeg,
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);
PRECONDITION(maxAngleDeg >= minAngleDeg, "allowedDeltaDeg must be >= 0.0");
double angle = 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]);
double dist1 = (p1 - p2).length();
double dist2 = (p3 - p2).length();
RDGeom::Point3D p12 = (p1 - p2) / dist1;
RDGeom::Point3D p32 = (p3 - p2) / dist2;
double cosTheta = p12.dotProduct(p32);
clipToOne(cosTheta);
angle = RAD2DEG * acos(cosTheta);
}
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
minAngleDeg += angle;
maxAngleDeg += angle;
_pretreatAngles(minAngleDeg, maxAngleDeg);
d_minAngleDeg = minAngleDeg;
d_maxAngleDeg = maxAngleDeg;
d_forceConstant = forceConst;
}
