void calculateResidueChi2Angles
(const Chain& fragment, HashMap<const Residue*,float>& residue_angles)
{
float angle = 0; //FLOAT_VALUE_NA;
// extract all residues: iterate over all composites and
// check whether they are Residues
ResidueConstIterator it = fragment.beginResidue();
for (; +it; ++it)
{
angle = calculateResidueChi2Angles(*it);
residue_angles.insert(std::pair<const Residue*, float>(&*it, angle));
}
}
// setup the internal datastructures for the component
bool CharmmTorsion::setup()
throw(Exception::TooManyErrors)
{
if (getForceField() == 0)
{
Log.error() << "CharmmTorsion::setup: component not bound to force field" << endl;
return false;
}
// clear torsion array
torsion_.clear();
Options& options = getForceField()->options;
if (options.has(CHARMM_TORSIONS_ENABLED))
{
if (!options.getBool(CHARMM_TORSIONS_ENABLED))
{
setEnabled(false);
return true;
}
else
{
setEnabled(true);
}
}
// extract the torsion parameters from the parameter file
bool result;
CharmmFF* charmm_force_field = dynamic_cast<CharmmFF*>(force_field_);
bool has_initialized_parameters = true;
if ((charmm_force_field == 0) || !charmm_force_field->hasInitializedParameters())
{
has_initialized_parameters = false;
}
if (!has_initialized_parameters)
{
// extract the torsion parameters
result = torsion_parameters_.extractSection(getForceField()->getParameters(), "Torsions");
if (result == false)
{
Log.error() << "cannot find section Torsions" << endl;
return false;
}
// check whether the torsions are contructed from the connectivity or whether
// we read them from the ResidueTorsions section in the parameter file
if (getForceField()->getParameters().getParameterFile().hasSection("ResidueTorsions"))
{
result = residue_torsions_.extractSection(getForceField()->getParameters(), "ResidueTorsions");
if (result == false)
{
Log.error() << "CharmmTorsion::setup: cannot parse section Torsions" << endl;
return false;
}
use_residue_torsion_list_ = true;
}
}
// calculate the torsions
vector<Atom*>::const_iterator atom_it = getForceField()->getAtoms().begin();
Atom::BondIterator it1;
Atom::BondIterator it2;
Atom::BondIterator it3;
Atom* a1;
Atom* a2;
Atom* a3;
Atom* a4;
// proper torsion will be added to the torsion vector
for (; atom_it != getForceField()->getAtoms().end(); ++atom_it)
{
for (it1 = (*atom_it)->beginBond(); +it1 ; ++ it1)
{
if (it1->getType() == Bond::TYPE__HYDROGEN) continue; // Skip H-bonds!
if (*atom_it == it1->getFirstAtom())
{
// central atoms
a2 = *atom_it;
a3 = const_cast<Atom*>(it1->getSecondAtom());
for (it2 = (*atom_it)->beginBond(); +it2 ; ++it2)
{
if (it2->getType() == Bond::TYPE__HYDROGEN) continue; // Skip H-bonds!
if ((*it2).getSecondAtom() != (*it1).getSecondAtom())
{
// determine the first atom
if ((*it2).getFirstAtom() == *atom_it)
{
a1 = const_cast<Atom*>(it2->getSecondAtom());
}
else
{
a1 = const_cast<Atom*>(it2->getFirstAtom());
}
for (it3 = const_cast<Atom*>(it1->getSecondAtom())->beginBond(); +it3 ; ++it3)
{
if (it3->getType() == Bond::TYPE__HYDROGEN) continue; // Skip H-bonds!
if ((*it3).getFirstAtom() != a2 )
{
// determine the fourth atom a4
if ((*it3).getFirstAtom() == a3)
{
a4 = const_cast<Atom*>(it3->getSecondAtom());
}
else
{
a4 = const_cast<Atom*>(it3->getFirstAtom());
}
if (getForceField()->getUseSelection() == false ||
(getForceField()->getUseSelection() == true &&
(a1->isSelected() && a2->isSelected() && a3->isSelected() && a4->isSelected())))
{
// if we use ResidueTorsions (i.e. a list of torsions for each
// residue is specified in the parameter file), we have to check
// if to consider this torsion
if (use_residue_torsion_list_)
{
String atom_name_A = a1->getName();
String atom_name_B = a2->getName();
String atom_name_C = a3->getName();
String atom_name_D = a4->getName();
// the second atom is always in the residue in question
//
// now check for the other three atoms: if it is in a different residue,
// add a "+" or "-"
Residue* res = a2->getAncestor(RTTI::getDefault<Residue>());
Chain* chain = a2->getAncestor(RTTI::getDefault<Chain>());
if (res != 0 && chain != 0)
{
// check whether a1, a3, and a4 are in the same residue
// or in the previous (marked as -) or the next residue (marked as +)
ResidueIterator res_it;
if (a1->getAncestor(RTTI::getDefault<Chain>()) == chain)
{
Residue* last_res = 0;
for (res_it = chain->beginResidue(); +res_it; last_res = &*res_it, ++res_it)
{
if (&*res_it == res)
{
if (a1->getAncestor(RTTI::getDefault<Residue>()) == last_res)
{
atom_name_A = "-" + atom_name_A;
}
if (a3->getAncestor(RTTI::getDefault<Residue>()) == last_res)
{
atom_name_C = "-" + atom_name_C;
}
if (a4->getAncestor(RTTI::getDefault<Residue>()) == last_res)
{
atom_name_D = "-" + atom_name_D;
}
}
if (last_res == res)
{
if (a1->getAncestor(RTTI::getDefault<Residue>()) == &*res_it)
{
atom_name_A = "+" + atom_name_A;
}
if (a3->getAncestor(RTTI::getDefault<Residue>()) == &*res_it)
{
atom_name_C = "+" + atom_name_C;
}
if (a4->getAncestor(RTTI::getDefault<Residue>()) == &*res_it)
{
atom_name_D = "+" + atom_name_D;
}
}
}
}
}
// if we are in a CYS-S residue, all atoms that are in another CYS-S
// are prefixed by "="
if ((res != 0) && res->hasProperty(Residue::PROPERTY__HAS_SSBOND))
{
Residue* other_res = a1->getAncestor(RTTI::getDefault<Residue>());
if ((other_res != 0) && (other_res != res)
&& other_res->hasProperty(Residue::PROPERTY__HAS_SSBOND))
{
atom_name_A = "=" + atom_name_A;
}
other_res = a3->getAncestor(RTTI::getDefault<Residue>());
if ((other_res != 0) && (other_res != res)
&& other_res->hasProperty(Residue::PROPERTY__HAS_SSBOND))
{
atom_name_C = "=" + atom_name_C;
}
other_res = a4->getAncestor(RTTI::getDefault<Residue>());
if ((other_res != 0) && (other_res != res)
&& other_res->hasProperty(Residue::PROPERTY__HAS_SSBOND))
{
atom_name_D = "=" + atom_name_D;
}
}
// check whether the names are known in ResidueTorsions
if (res != 0)
{
if (!residue_torsions_.hasTorsion(res->getFullName(), atom_name_A, atom_name_B, atom_name_C, atom_name_D))
{
continue;
}
}
else
{
Log.warn() << "Cannot identify torsion for (UNKNOWN)" << " " << atom_name_A
<< "/" << atom_name_B << "/" << atom_name_C << "/" << atom_name_D << endl;
continue;
}
}
// search torsion parameters for (a1,a2,a3,a4)
Atom::Type type_a1 = a1->getType();
Atom::Type type_a2 = a2->getType();
Atom::Type type_a3 = a3->getType();
Atom::Type type_a4 = a4->getType();
CosineTorsion::Values values;
CosineTorsion::SingleData tmp;
tmp.atom1 = a1;
tmp.atom2 = a2;
tmp.atom3 = a3;
tmp.atom4 = a4;
// retrieve parameters for the torsion
bool found = false;
if (torsion_parameters_.assignParameters(values, type_a1, type_a2, type_a3, type_a4))
{
found = true;
}
else if (torsion_parameters_.assignParameters(values, Atom::ANY_TYPE, type_a2, type_a3, Atom::ANY_TYPE))
{
found = true;
}
// complain about mising parameters or store this torsion
// in the torsion_ array
if (found)
{
for (unsigned char j = 0; j < values.n; j++)
{
tmp.values = values.values[j];
torsion_.push_back(tmp);
}
}
else
{
getForceField()->error() << "CharmmTorsion::setup: cannot find torsion parameters for:"
<< force_field_->getParameters().getAtomTypes().getTypeName(type_a1) << "-"
<< force_field_->getParameters().getAtomTypes().getTypeName(type_a2) << "-"
<< force_field_->getParameters().getAtomTypes().getTypeName(type_a3) << "-"
<< force_field_->getParameters().getAtomTypes().getTypeName(type_a4) << endl;
getForceField()->getUnassignedAtoms().insert(a1);
getForceField()->getUnassignedAtoms().insert(a2);
getForceField()->getUnassignedAtoms().insert(a3);
getForceField()->getUnassignedAtoms().insert(a4);
}
}
}
}
}
}
}
}
}
return true;
}
/**********************************************
* determine the new Secondary Structure and
* replace the old one with the new one
**********************************************/
Processor::Result SecondaryStructureProcessor::operator() (Composite &composite)
{
if (!RTTI::isKindOf<Chain>(composite))
{
return Processor::CONTINUE;
}
Chain* p = RTTI::castTo<Chain>(composite);
HBondProcessor hbp;
p->apply(hbp); // find all posible HBonds
HBonds_ = hbp.getBackboneHBondPattern();
ResidueIterator ri = p->beginResidue();
if (!(+ri))
{
return Processor::CONTINUE;
}
// locate the Secondary Structures
compute_();
//----------associate new Secondary Structures (SS) for each residue -----
// - summarize equal residues in one new SS (new_ss)
// - push for each residue the new SS into new_parent
// - push all residues into residues
SecondaryStructure* ss = 0;
char last_struct = 'X';
Position resnum = 0;
vector<SecondaryStructure*> new_ss;
vector<SecondaryStructure*> new_parent;
vector<Residue*> residues;
if (summary_.size() == 0)
return Processor::CONTINUE;
for (; +ri; ++ri)
{
if (resnum >= summary_.size())
{
Log.error() << "A problem occured in " << __FILE__ << " " << __LINE__ << std::endl;
return Processor::CONTINUE;
}
// depending on the last type of secondary structure we have seen,
// we need to react differently to merge them sensibly
if (last_struct != summary_[resnum])
{
switch (last_struct)
{
case 'L': // we are in a loop
// note that we identify 'real' loops, isolated bridges and turns (-,B,T)
// and map them all to loops. Thus we need to determine here if the current
// residue also maps to a loop (we already know that the last residue was one)
switch (summary_[resnum])
{
case '-':
case 'B':
case 'T': break; // nothing to see here... please walk on...
default:
// the current residue is no loop => build a new SecondaryStructure
ss = new SecondaryStructure;
last_struct = setSecondaryStructureType_(ss, summary_[resnum]);
new_ss.push_back(ss);
}
break;
default: // in all other cases, setSecondaryStructure does the hard work
ss = new SecondaryStructure;
last_struct = setSecondaryStructureType_(ss, summary_[resnum]);
new_ss.push_back(ss);
}
}
// in all cases, ss is now the new parent of this residue
new_parent.push_back(ss);
residues.push_back(&*ri);
resnum++;
}
// ------ insert Residues to new SS ---------------
for (Position i = 0; i < residues.size(); i++)
{
new_parent[i]->insert(*residues[i]);
}
// ------ remove old SecondaryStructures ----------
// we have to be sure not to delete a SS which has an SS as parent!
// because it would be deleted twice
vector<SecondaryStructure*> to_remove;
SecondaryStructureIterator ssit = p->beginSecondaryStructure();
for (; +ssit; ++ssit)
{
if ((*ssit).getParent() == 0 ||
!RTTI::isKindOf<SecondaryStructure>(*(*ssit).getParent()))
{
to_remove.push_back(&*ssit);
}
}
for (Position i = 0; i < to_remove.size(); i++)
{
delete to_remove[i];
}
BALL_POSTCONDITION_EXCEPTION(p->countSecondaryStructures() == 0,
"SecondaryStructureProcessor did not remove all old secondary structures!")
// ------ insert new SecondaryStructures ----------
for (Position i = 0; i < new_ss.size(); i++)
{
p->insert(*new_ss[i]);
}
BALL_POSTCONDITION_EXCEPTION(p->countSecondaryStructures() == new_ss.size(),
"SecondaryStructureProcessor did not add all new secondary structures!")
return Processor::CONTINUE;
}