void IMGDock::saveAtomPositions()
{
original_atom_positions_.resize(scoring_function_->getNoLigandAtoms());
Size atom = 0;
for (AtomIterator it = ligand_->beginAtom(); +it; it++, atom++)
{
original_atom_positions_[atom] = it->getPosition();
}
}
void GridAnalysis::moveProbeGroup_(const Vector3& destination)
{
TMatrix4x4<float> M;
Vector3 translation_vector = destination-center_;
M.setTranslation(translation_vector);
for (AtomIterator it = probe_group_.beginAtom(); +it; it++)
{
it->setPosition(M*it->getPosition());
}
center_ = destination;
}
void IMGDock::translateLigand(Vector3& v)
{
TMatrix4x4<float> M;
M.setTranslation(v);
// transform all atoms of the ligand
for (AtomIterator it = ligand_->beginAtom(); it != ligand_->endAtom(); it++)
{
it->setPosition(M*it->getPosition());
}
}
void GridAnalysis::rotateProbeGroup_(int axis, int degree)
{
TMatrix4x4<float> M;
TAngle<float> angle(degree, false);
Vector3 axis_vector(axis == 0, axis == 1, axis == 2);
M.setRotation(angle, axis_vector);
for (AtomIterator it = probe_group_.beginAtom(); it != probe_group_.endAtom(); it++)
{
it->setPosition(M*(it->getPosition()-center_)+center_);
}
}
void IMGDock::rotateLigand(int a, int degree)
{
TMatrix4x4<float> M;
TAngle<float> angle(degree, false);
Vector3 axis(a == 0, a == 1, a == 2);
M.setRotation(angle, axis);
const Vector3& origin = scoring_function_->getLigandCenter();
for (AtomIterator it = ligand_->beginAtom(); it != ligand_->endAtom(); it++)
{
it->setPosition(M*(it->getPosition()-origin)+origin);
}
}
bool compareMolecules(Molecule& mol1, Molecule& mol2)
{
if(mol1.countAtoms()!=mol2.countAtoms())
return false;
if(mol1.countBonds()!=mol2.countBonds())
return false;
AtomIterator ai;
vector<Vector3> pos1;
vector<float> q1;
BALL_FOREACH_ATOM(mol1, ai)
{
pos1.push_back(ai->getPosition());
q1.push_back(ai->getCharge());
}
void DockingAlgorithm::mapLigandOntoReferenceLigand()
{
if (!scoring_function_)
{
Log.error()<<"Error DockingAlgorithm::mapLigandOntoReferenceLigand() : ScoringFunction not set!"<<endl;
return;
}
AtomContainer* ligand = scoring_function_->getLigand();
if (!ligand)
{
Log.error()<<"Error DockingAlgorithm::mapLigandOntoReferenceLigand() : Ligand not set!"<<endl;
return;
}
if (!reference_ligand_)
{
Log.error()<<"Error DockingAlgorithm::mapLigandOntoReferenceLigand() : Reference ligand not set!"<<endl;
return;
}
Timer timer;
timer.start();
double lower_bound = 2;
double upper_bound = 5;
double tolerance = 1;
Size no_matched_atoms = 0;
double rmsd = 0;
Matrix4x4 T = mapCompounds(*ligand, *reference_ligand_, no_matched_atoms, rmsd, upper_bound, lower_bound, tolerance);
for (AtomIterator it = ligand->beginAtom(); +it; it++)
{
it->setPosition(T*it->getPosition());
}
timer.stop();
Log.level(10)<<"superposing ligand: "<<timer.getClockTime()<<" seconds"<<endl;
}
// checking for default mode: reading AntechamberFile f(BALL_TEST_DATA_PATH(AntechamberFile_test1.ac)); TEST_EQUAL(f.isValid(), true) RESULT CHECK(AntechamberFile::read(System& system)) AntechamberFile f(BALL_TEST_DATA_PATH(AntechamberFile_test2.ac)); System S; f.read(S); f.close(); TEST_EQUAL(S.countAtoms(), 2) AtomIterator it = S.beginAtom(); TEST_EQUAL(it->getElement().getSymbol(), "H") TEST_REAL_EQUAL(it->getPosition().x, 0.0) TEST_REAL_EQUAL(it->getPosition().y, 1.0) TEST_REAL_EQUAL(it->getPosition().z, 2.0) it++; TEST_EQUAL(it->getElement().getSymbol(), "O") TEST_REAL_EQUAL(it->getPosition().x, 3.0) TEST_REAL_EQUAL(it->getPosition().y, 4.0) TEST_REAL_EQUAL(it->getPosition().z, 5.0) RESULT CHECK(AntechamberFile::read(System& system)) AntechamberFile f(BALL_TEST_DATA_PATH(AntechamberFile_test1.ac)); System S; f.read(S); f.close();
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);
}
double Polarity::updateScore()
{
score_ = 0.0;
//float val = 0.0;
//float distance;
//float R1;
//float R2;
const HashGrid3<Atom*>* hashgrid = scoring_function_->getHashGrid();
int radius = 1;
Size no_neighbor_cells = (Size)pow((double)(radius*2+1), 3); // radius of 1 cell == > 3 cells on each axis
double total_sum = 0;
AtomPairVector::const_iterator it;
for (AtomIterator it = scoring_function_->getLigand()->beginAtom(); +it; it++)
{
int no_positive_contacts = 0;
int no_negative_contacts = 0;
bool ligandatom_is_lipophilic = isLipophilic_(&*it);
if (!ligandatom_is_lipophilic)
{
continue;
}
const HashGridBox3<Atom*>* box = hashgrid->getBox(it->getPosition());
// ligand atom lies outside of grid
if (!box) continue;
Position pos_x, pos_y, pos_z;
hashgrid->getIndices(*box, pos_x, pos_y, pos_z);
// indices in HashGrid, where the search for interacting target atoms should begin ( != position of ligand atom)
int i = ((int)pos_x)-radius; if (i < 0){i = 0; }
int j0 = ((int)pos_y)-radius; if (j0 < 0){j0 = 0; }
int k0 = ((int)pos_z)-radius; if (k0 < 0){k0 = 0; }
int x_size = (int)hashgrid->getSizeX();
int y_size = (int)hashgrid->getSizeY();
int z_size = (int)hashgrid->getSizeZ();
for (; i <= pos_x+radius && i < x_size; i++)
{
for (int j = j0; j <= pos_y+radius && j < y_size; j++)
{
for (int k = k0; k <= pos_z+radius && k < z_size; k++)
{
const HashGridBox3<Atom*>* box = hashgrid->getBox(i, j, k);
if (!box->isEmpty())
{
double cell_score = 0;
for (HashGridBox3 < Atom* > ::ConstDataIterator d_it = box->beginData(); d_it != box->endData(); d_it++)
{
if (isBackboneAtom_(*d_it)) continue;
bool rec_polar = isPolar_(*d_it);
bool rec_lipophilic = 0;
if (!rec_polar) rec_lipophilic = isLipophilic_(*d_it);
if (!rec_polar && ! rec_lipophilic) continue;
double distance = ((*d_it)->getPosition()-it->getPosition()).getLength();
if (distance > (*d_it)->getElement().getVanDerWaalsRadius()+it->getElement().getVanDerWaalsRadius()+1.5) continue;
double val;
if (distance > 1) val = 1/distance;
else val = 1;
// lipophilic--lipophilic interaction; else polar rec. -- lipophilic ligand atom
if (rec_lipophilic)
{
val *= -1;
}
cell_score += val;
total_sum += val;
if (scoring_function_->storeInteractionsEnabled())
{
val = scaleScore(val);
it->addInteraction(*d_it, "pol", val);
(*d_it)->addInteraction(&*it, "pol", val);
}
}
if (cell_score < -0.1) no_positive_contacts++;
else if (cell_score > 0.1) no_negative_contacts++;
}
// if there is no neighboring receptor atom, there will be water ...
// else if(i!=pos_x||j!=pos_y||k!=pos_z)
// {
// if(ligandatom_is_lipophilic)
// {
// no_negative_contacts++;
// double scaled_atom_score = 1.0/no_neighbor_cells;
// scaleScore(scaled_atom_score);
// total_sum += scaled_atom_score;
// it->addInteraction("pol",scaled_atom_score);
// }
// }
}
}
}
score_ += (no_negative_contacts-no_positive_contacts)/((double)no_neighbor_cells);
//cout<<it->getFullName()<<" : "<<no_negative_contacts<<", "<<no_positive_contacts<<" "<<(no_negative_contacts-no_positive_contacts)/((double)no_neighbor_cells)<<endl;
}
// scaleScore();
// cout<<"polarity: total sum="<<total_sum<<endl;
// cout<<"polarity: score="<<score_<<endl;
// return score_;
return getScaledScore();
}