void VRMolecule::rotateBond(int a, int b, float f) {
if (atoms.count(a) == 0) return;
if (atoms.count(b) == 0) return;
VRAtom* A = atoms[a];
VRAtom* B = atoms[b];
uint now = VRGlobals::CURRENT_FRAME + rand();
A->recFlag = now;
Vec3d p1 = Vec3d( A->getTransformation()[3] );
Vec3d p2 = Vec3d( B->getTransformation()[3] );
Vec3d dir = p2-p1;
Quaterniond q(dir, f);
Matrix4d R;
R.setRotate(q);
Matrix4d T;
T[3] = B->getTransformation()[3];
Matrix4d _T;
T.inverse(_T);
T.mult(R);
T.mult(_T);
//cout << "ROTATE bound " << a << "-" << b << " around " << dir << " with " << f << endl;
B->propagateTransformation(T, now);
updateGeo();
}
void VRAtom::computePositions() {
computeGeo();
string g = geo;
if (AtomicStructures.count(geo) == 0) { cout << "Error: " << geo << " is invalid!\n"; return; }
vector<Matrix4d> structure = AtomicStructures[geo];
for (auto& b : bonds) {
if (b.first >= (int)structure.size()) break;
if (b.second.extra) continue;
Matrix4d T = transformation;
Matrix4d S = structure[b.first];
VRAtom* a = b.second.atom2;
if (a == 0) { // duplets
float r = 0.5*b.second.atom1->getParams().radius;
S[3] *= r; S[3][3] = 1;
T.mult(S);
T.mult(Pnt3d(1,0,0)*r, b.second.p1);
T.mult(Pnt3d(-1,-0,0)*r, b.second.p2);
continue;
}
if (a->ID <= ID) continue;
T.mult(S);
a->transformation = T;
}
}
// called from VRTransform::apply_constraints
void VRConstraint::apply(VRTransformPtr obj, VRObjectPtr parent, bool force) {
if (!active || obj->getPhysics()->isPhysicalized()) return;
auto now = VRGlobals::CURRENT_FRAME;
if (apply_time_stamp == now && !force) return;
apply_time_stamp = now;
if (local) parent = obj->getParent(true);
if (auto r = Referential.lock()) parent = r;
Matrix4d J;
if (parent) J = parent->getMatrixTo(obj);
else J = obj->getWorldMatrix();
J.mult(refMatrixB);
J.multLeft(refMatrixAI);
for (int i=0; i<3; i++) { // translation
if (min[i] > max[i]) continue; // free
if (min[i] > J[3][i]) J[3][i] = min[i]; // lower bound
if (max[i] < J[3][i]) J[3][i] = max[i]; // upper bound
}
Vec3d angles = VRTransform::computeEulerAngles(J);
auto sign = [](float a) {
return a<0?-1:1;
};
// TODO: this is not correct, for example [180, 20, 180], corresponds to [0, 160, 0], and not [0, 20, 0] !!
// this tries to fix it somewhat, but its not clean!
if ( abs(angles[0]) > Pi*0.5 && abs(angles[2]) > Pi*0.5) {
angles[0] -= sign(angles[0])*Pi;
angles[2] -= sign(angles[2])*Pi;
angles[1] = Pi - angles[1];
}
Vec3d angleDiff;
for (int i=3; i<6; i++) { // rotation
if (min[i] > max[i]) continue; // free
float a = angles[i-3];
float d1 = min[i]-a; while(d1 > Pi) d1 -= 2*Pi; while(d1 < -Pi) d1 += 2*Pi;
float d2 = max[i]-a; while(d2 > Pi) d2 -= 2*Pi; while(d2 < -Pi) d2 += 2*Pi;
if (d1 > 0 && abs(d1) <= abs(d2)) angleDiff[i-3] = d1; // lower bound
if (d2 < 0 && abs(d2) <= abs(d1)) angleDiff[i-3] = d2; // upper bound
}
VRTransform::applyEulerAngles(J, angles + angleDiff);
J.multLeft(refMatrixA);
J.mult(refMatrixBI);
obj->setMatrixTo(J, parent);
}
void VRMolecule::substitute(int a, VRMoleculePtr m, int b) {
if (atoms.count(a) == 0) return;
if (m->atoms.count(b) == 0) return;
Matrix4d am = atoms[a]->getTransformation();
Matrix4d bm = m->atoms[b]->getTransformation();
map<int, VRBond> bondsA = atoms[a]->getBonds();
map<int, VRBond> bondsB = m->atoms[b]->getBonds();
if (bondsA.count(0) == 0) return;
if (bondsB.count(0) == 0) return;
VRAtom* A = bondsA[0].atom2;
VRAtom* B = bondsB[0].atom2;
int Ai = A->getID();
int Bi = B->getID();
remAtom(a);
m->remAtom(b);
if (atoms.count(Ai) == 0) { cout << "AA\n"; return; }
if (m->atoms.count(Bi) == 0) { cout << "BB\n"; return; }
// copy atoms
for (auto at : m->atoms) {
int ID = getID();
at.second->setID(ID);
atoms[ID] = at.second;
}
m->set(m->getDefinition());
// attach molecules
A->append(B, 1, true);
// transform new atoms
uint now = VRGlobals::CURRENT_FRAME + rand();
A->recFlag = now;
bm.invert();
Matrix4d Bm = B->getTransformation();
bm.mult(Bm);
bm.setTranslate(Vec3d(0,0,0));
am.mult(bm);
MatrixLookAt( bm, Vec3d(0,0,0), Vec3d(0,0,1), Vec3d(0,-1,0) );
bm.mult(am);
bm[3] = am[3];
B->propagateTransformation(bm, now);
updateGeo();
}
void VRAtom::propagateTransformation(Matrix4d& T, uint flag, bool self) {
if (flag == recFlag) return;
recFlag = flag;
if (self) {
Matrix4d m = T;
m.mult(transformation);
transformation = m;
}
for (auto& b : bonds) {
if (b.second.atom2 == 0) { // duplet
T.mult(b.second.p1, b.second.p1);
T.mult(b.second.p2, b.second.p2);
}
else b.second.atom2->propagateTransformation(T, flag);
}
}
vruiMatrix *SGVruiMatrix::preTranslated(double x, double y, double z, vruiMatrix *matrix)
{
Matrix4d translate;
translate.setIdentity();
translate.setTranslate(x, y, z);
SGVruiMatrix *osgVruiMatrix = dynamic_cast<SGVruiMatrix *>(matrix);
translate.mult(osgVruiMatrix->matrix);
this->matrix = translate;
return this;
}
void VRMolecule::setLocalOrigin(int ID) {
if (atoms.count(ID) == 0) return;
uint now = VRGlobals::CURRENT_FRAME + rand();
Matrix4d m = atoms[ID]->getTransformation();
m.invert();
Matrix4d im;
MatrixLookAt( im, Vec3d(0,0,0), Vec3d(0,0,1), Vec3d(0,1,0) );
im.mult(m);
atoms[ID]->propagateTransformation(im, now);
}
void frustum::computeProfile() {
profile.clear();
Matrix4d m = trans.asMatrix();
m.invert();
for (auto d : directions) {
Vec3d p;
m.mult(d,p);
profile.addPoint( Vec2d(p[0], p[1]) );
}
if (!profile.isCCW()) profile.reverseOrder();
}
