void TrialMol::SetBasis(const uint p1, const uint p2)
{
using namespace geom;
//W is unit vec of p1->p2
XYZ wVec = axes->MinImage(tCoords.Difference(p2, p1), box);
wVec.Normalize();
XYZ uVec;
//check to make sure our W isn't in line with the standard X Axis
if (wVec.x < 0.8) {
//V will be W x the standard X unit vec
uVec = XYZ(1.0, 0.0, 0.0);
}
else {
//V will be W x the standard Y unit vec
uVec = XYZ(0.0, 1.0, 0.0);
}
XYZ vVec = Cross(wVec, uVec);
vVec.Normalize();
//U is unit vec perpendicular to both V and W
uVec = Cross(vVec, wVec);
growthToWorld.BasisRotation(uVec, vVec, wVec);
worldToGrowth = growthToWorld.Inverse();
basisPoint = tCoords.Get(p1);
}
void TrialMol::SetBasis(const uint p1, const uint p2, const uint p3)
{
using namespace geom;
//W is unit vec of p1->p2
XYZ wVec = axes->MinImage(tCoords.Difference(p2, p1), box);
wVec.Normalize();
//U will be unit projection of p2->p3 onto plane normal to W
XYZ uVec = axes->MinImage(tCoords.Difference(p3, p2), box);
//V is unit vec perpendicular to both W and U
XYZ vVec = Cross(wVec, uVec);
vVec.Normalize();
//Finish X'
uVec = Cross(vVec, wVec);
growthToWorld.BasisRotation(uVec, vVec, wVec);
worldToGrowth = growthToWorld.Inverse();
basisPoint = tCoords.Get(p1);
}