void PeptideBuilder::setOmega_(Residue& resold, Residue& resnew, const Angle& omega)
{
PDBAtom* pcarbon = getAtomByName_(resold, "C");
PDBAtom* pnitrogen_n = getAtomByName_(resnew, "N");
Vector3 C_NN_axis =(pnitrogen_n->getPosition() - pcarbon->getPosition()).normalize();
// At this point, omega has been fixed to 180 degrees
Matrix4x4 mat;
mat.setRotation(Angle(omega-Angle(Constants::PI)), C_NN_axis);
TransformationProcessor omegatrans(mat);
// translate to 0|0|0 (needed for the rotation)
Vector3 toOrigin = pnitrogen_n->getPosition();
TranslationProcessor translation;
translation.setTranslation(((float)(-1.))*toOrigin);
resnew.apply(translation);
// rotate
resnew.apply(omegatrans);
// translate back to the correct position
translation.setTranslation(toOrigin);
resnew.apply(translation);
return;
}
void PeptideCapProcessor::optimizeCapPosition(Chain& chain, bool start)
{
Vector3 translation;
Atom* axis = NULL;
Residue* cap = NULL;
std::vector<Atom*> a;
std::vector<Atom*> b;
Size nr = chain.countResidues();
// cap at the beginning of a peptide
if (start)
{
// put ACE-C to the center
for (AtomIterator it = chain.getResidue(1)->beginAtom(); +it; ++it)
{
if (it->getName() == "N")
{
translation = it->getPosition();
}
b.push_back(&*it);
}
cap = chain.getResidue(0);
for (AtomIterator it = cap->beginAtom(); +it; ++it)
{
a.push_back(&*it);
if (it->getName() == "C")
{
axis = &*it;
}
}
}
//cap at the end of a peptide
else
{
for (AtomIterator it = chain.getResidue(nr-2)->beginAtom(); +it; ++it)
{
if (it->getName() == "C")
{
translation = it->getPosition();
}
b.push_back(&*it);
}
cap = chain.getResidue(nr-1);
for (AtomIterator it = cap->beginAtom(); +it; ++it)
{
a.push_back(&*it);
if (it->getName() == "N")
{
axis = &*it;
}
}
}
//translate the anchor to origin
TranslationProcessor tlp;
tlp.setTranslation(translation*-1.0);
chain.apply(tlp);
//try all torsions
float largest_distance = 0.0;
float tmp_distance = 0.0;
float torsion = 0.0;
float step = 2.0;
TransformationProcessor tfp;
Matrix4x4 m;
m.setRotation( Angle(step, false), axis->getPosition());
tfp.setTransformation(m);
for (Position r = step; r <= 360; r+=step)
{
cap->apply(tfp);
tmp_distance = computeDistance(a,b);
if (largest_distance < tmp_distance)
{
largest_distance = tmp_distance;
torsion = r;
}
}
//apply best rotation angle
m.setRotation( Angle(torsion, false), axis->getPosition());
tfp.setTransformation(m);
cap->apply(tfp);
//now translate the protein back
tlp.setTranslation(translation);
chain.apply(tlp);
}
void EditMode::addStructure_()
{
QAction* action = dynamic_cast<QAction*>(sender());
if (action == 0) return;
String name = ascii(action->text());
scene_->deselect();
if (!fragment_db_)
{
fragment_db_ = new FragmentDB("fragments/Editing-Fragments.db");
}
list<AtomContainer*> containers = scene_->getContainers();
if (containers.size() == 0) return;
Residue* residue = fragment_db_->getResidueCopy(name);
if (residue == 0)
{
residue = fragment_db_->getResidueCopy(name + "-Skeleton");
if (residue == 0) return;
}
Vector3 p;
Size nr = 0;
AtomIterator ait = residue->beginAtom();
for (;+ait; ++ait)
{
p += ait->getPosition();
nr++;
}
if (nr == 0)
{
BALLVIEW_DEBUG
delete residue;
return;
}
p /= (float) nr;
QPoint pos = scene_->mapFromGlobal(mouse_pos_new_);
Matrix4x4 m;
Vector3 x = scene_->mapViewportTo3D(pos.x(), pos.y());
TransformationProcessor tf;
Vector3 vv = scene_->getStage()->getCamera().getViewVector();
float l = vv.getLength();
if (!Maths::isZero(l)) vv /= l;
Vector3 axis = Vector3(1,0,0) % vv;
if (axis.getSquareLength() != 0)
{
Angle a = vv.getAngle(Vector3(1,0,0));
m.setRotation(a, axis);
tf.setTransformation(m);
residue->apply(tf);
}
m.setTranslation(x - p);
tf.setTransformation(m);
residue->apply(tf);
AtomContainer* s = *containers.begin();
if (RTTI::isKindOf<System>(*s))
{
System* system = (System*) s;
Molecule* mol = system->getMolecule(0);
if (mol == 0)
{
mol = new Molecule();
system->insert(*mol);
}
s = mol;
}
s->insert(*residue);
scene_->getMainControl()->deselectCompositeRecursive(s, true);
scene_->getMainControl()->selectCompositeRecursive(residue, true);
scene_->getMainControl()->update(*s);
scene_->notify(new NewSelectionMessage);
// setMode(MOVE__MODE);
}
void PeptideBuilder::transform_
(const Angle& phi, const Angle& psi, Residue& resold, Residue& resnew)
{
Matrix4x4 psimat; // rotation matrix
Matrix4x4 phimat; // "
Vector3 psiaxis; // rotation axis for the torsion angles
Vector3 phiaxis;
TranslationProcessor translation;
PDBAtom* pcarbon = getAtomByName_(resold, "C");
PDBAtom* pcarbona = getAtomByName_(resold, "CA");
PDBAtom* pnitrogen_n = getAtomByName_(resnew, "N");
PDBAtom* pcarbona_n = getAtomByName_(resnew, "CA");
PDBAtom* pcarbon_n = getAtomByName_(resnew, "C");
PDBAtom* pnitrogen = getAtomByName_(resold, "N");
Angle currentpsi;
Angle currentphi;
Vector3 v_pn = pnitrogen->getPosition();
Vector3 v_pca = pcarbona->getPosition();
Vector3 v_pc = pcarbon->getPosition();
Vector3 v_pn_n = pnitrogen_n->getPosition();
Vector3 v_pca_n = pcarbona_n->getPosition();
Vector3 v_pc_n = pcarbon_n->getPosition();
currentpsi = getTorsionAngle( v_pn.x, v_pn.y, v_pn.z,
v_pca.x, v_pca.y, v_pca.z,
v_pc.x, v_pc.y, v_pc.z,
v_pn_n.x, v_pn_n.y, v_pn_n.z);
psiaxis = ( pcarbon->getPosition() - pcarbona->getPosition()).normalize();
psimat.rotate((float)-1. * currentpsi, psiaxis);
TransformationProcessor psitrans(psimat);
//translate to 0|0|0 (needed for the rotation)
Vector3 toOrigin = pcarbon->getPosition();
translation.setTranslation(((float)(-1.))*toOrigin);
resnew.apply(translation);
//rotate
resnew.apply(psitrans);
psimat.rotate(psi, psiaxis);
psitrans.setTransformation(psimat);
resnew.apply(psitrans);
//translate back
translation.setTranslation(toOrigin);
resnew.apply(translation);
v_pn = pnitrogen->getPosition();
v_pca = pcarbona->getPosition();
v_pc = pcarbon->getPosition();
v_pn_n = pnitrogen_n->getPosition();
v_pca_n = pcarbona_n->getPosition();
v_pc_n = pcarbon_n->getPosition();
currentphi = getTorsionAngle( v_pc.x, v_pc.y, v_pc.z,
v_pn_n.x, v_pn_n.y, v_pn_n.z,
v_pca_n.x, v_pca_n.y, v_pca_n.z,
v_pc_n.x, v_pc_n.y, v_pc_n.z);
phiaxis = (pcarbona_n->getPosition() - pnitrogen_n->getPosition()).normalize();
phimat.rotate(phi, phiaxis);
TransformationProcessor phitrans(phimat);
// translate to 0|0|0 (needed for the rotation)
toOrigin = pcarbona_n->getPosition();
translation.setTranslation(((float)(-1.))*toOrigin);
resnew.apply(translation);
// rotate
resnew.apply(phitrans);
// translate back to the correct position
translation.setTranslation(toOrigin);
resnew.apply(translation);
return;
}
void PeptideBuilder::insert_(Residue& resnew, Residue& resold)
{
PDBAtom* pcarbon = getAtomByName_(resold, "C");
PDBAtom* pcarbona = getAtomByName_(resold, "CA");
PDBAtom* pnitrogen = getAtomByName_(resold, "N");
PDBAtom* pnitrogen_n = getAtomByName_(resnew, "N");
PDBAtom* pcarbona_n = getAtomByName_(resnew, "CA");
PDBAtom* pcarbon_n = getAtomByName_(resnew, "C");
Vector3 rot_axis; // axis for the torsion angle
// set C-N-bond
pcarbon->createBond(*pnitrogen_n)->setOrder(Bond::ORDER__SINGLE);;
// -------------- move N into 0|0|0
TranslationProcessor translation(Vector3(BOND_LENGTH_N_CA, 0., 0.));
resnew.apply(translation);
// --------------- calculate the coordinates for N
Vector3 CA_C_axis = (pcarbon->getPosition() - pcarbona->getPosition()).normalize();
Vector3 N_CA_axis = (pcarbona->getPosition() - pnitrogen->getPosition()).normalize();
Vector3 CA_N_axis = ((float)-1.) * N_CA_axis;
Vector3 newpos = (CA_N_axis - (CA_C_axis * CA_N_axis) * CA_C_axis).normalize();
Vector3 normaxis = (CA_C_axis % newpos).normalize();
Matrix4x4 mat;
mat.setRotation(Angle(-1. * 30.* Constants::PI/180.), normaxis);
newpos = mat * newpos; // rotation
newpos = newpos * BOND_LENGTH_N_C; // scaling of the bond length
newpos = newpos + pcarbon->getPosition();
// positioning of the nitrogen
translation.setTranslation(newpos);
resnew.apply(translation);
//---------------set the angle in NN to 120 degrees
Vector3 NN_C_axis = pcarbon->getPosition() - pnitrogen_n->getPosition();
Vector3 NN_NCA_axis = pcarbona_n->getPosition() - pnitrogen_n->getPosition();
CA_C_axis = pcarbon->getPosition() - pcarbona->getPosition();
// current angle for C
Angle current(acos(NN_C_axis * NN_NCA_axis /
(NN_C_axis.getLength() * NN_NCA_axis.getLength() )));
Matrix4x4 transmat;
Vector3 rotaxis;
if (current < (float)(Constants::PI - 1e-2))
{
current = Angle(120.*Constants::PI/180.) - current;
rotaxis = (NN_C_axis%NN_NCA_axis).normalize();
}
else
{
if (current > (float)(Constants::PI+1e-2))
{
// is this line really correct???
current = Angle(-120. * 120. * Constants::PI / 180.) - current;
rotaxis = (NN_C_axis % NN_NCA_axis).normalize();
}
else
{
current = Angle(-120. * Constants::PI / 180.) - current;
rotaxis = (NN_C_axis%CA_C_axis).normalize();
}
}
transmat.rotate(current, rotaxis);
TransformationProcessor transformation(transmat);
// translate to 0|0|0 (needed for the rotation)
Vector3 toOrigin = pnitrogen_n->getPosition();
translation.setTranslation(((float)(-1.))*toOrigin);
resnew.apply(translation);
// rotate in 0|0|0
resnew.apply(transformation);
// translate back to the correct position
translation.setTranslation(toOrigin);
resnew.apply(translation);
//---------------- set torsion angle to 0
Vector3 v_pca = pcarbona->getPosition();
Vector3 v_pc = pcarbon->getPosition();
Vector3 v_pn_n = pnitrogen_n->getPosition();
Vector3 v_pca_n = pcarbona_n->getPosition();
Vector3 v_pc_n = pcarbon_n->getPosition();
Vector3 v_pn =pnitrogen->getPosition();
current = getTorsionAngle( v_pca.x, v_pca.y, v_pca.z,
v_pc.x, v_pc.y, v_pc.z,
v_pn_n.x, v_pn_n.y, v_pn_n.z,
v_pca_n.x, v_pca_n.y, v_pca_n.z );
rot_axis = (pnitrogen_n->getPosition() - pcarbon->getPosition()).normalize();
transmat.getZero();/// is this necessary???
transmat.rotate(Angle(-1. * current), rot_axis);
transformation.setTransformation(transmat);
// translate to 0|0|0
toOrigin = pnitrogen_n->getPosition();
translation.setTranslation(((float)(-1.))*toOrigin);
resnew.apply(translation);
// set torsion angles
resnew.apply(transformation);
// translate back
translation.setTranslation(toOrigin);
resnew.apply(translation);
// ---------------------set the peptide bond angle omega to 180 degrees
v_pca = pcarbona->getPosition();
v_pc = pcarbon->getPosition();
v_pn_n = pnitrogen_n->getPosition();
v_pca_n = pcarbona_n->getPosition();
v_pc_n = pcarbon_n->getPosition();
current = getTorsionAngle( v_pca.x, v_pca.y, v_pca.z,
v_pc.x, v_pc.y, v_pc.z,
v_pn_n.x, v_pn_n.y, v_pn_n.z,
v_pca_n.x, v_pca_n.y, v_pca_n.z );
transmat.getZero();
transmat.rotate( Angle(Constants::PI , true),
(pnitrogen_n->getPosition() - pcarbon->getPosition()).normalize());
transformation.setTransformation(transmat);
// translate to 0|0|0 (needed for the rotation)
toOrigin = pnitrogen_n->getPosition();
translation.setTranslation(((float)(-1.))*toOrigin);
resnew.apply(translation);
//rotate in 0|0|0 about 180 degrees
resnew.apply(transformation);
//translate back
translation.setTranslation(toOrigin);
resnew.apply(translation);
//------------- angle psi
v_pca = pcarbona->getPosition();
v_pc = pcarbon->getPosition();
v_pn_n = pnitrogen_n->getPosition();
v_pca_n = pcarbona_n->getPosition();
v_pc_n = pcarbon_n->getPosition();
current = getTorsionAngle( v_pc.x, v_pc.y, v_pc.z,
v_pn_n.x, v_pn_n.y, v_pn_n.z,
v_pca_n.x, v_pca_n.y, v_pca_n.z,
v_pc_n.x, v_pc_n.y, v_pc_n.z );
rot_axis = (pcarbona_n->getPosition()-pnitrogen_n->getPosition()).normalize();
transmat.rotate(Angle(-1. * current), rot_axis);
transformation.setTransformation(transmat);
//translate to 0|0|0 (needed for the rotation)
toOrigin = pcarbona_n->getPosition();
translation.setTranslation(((float)(-1.))*toOrigin);
resnew.apply(translation);
resnew.apply(transformation);
// translate back to the correct position
translation.setTranslation(toOrigin);
resnew.apply(translation);
return;
}
