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Marco Biasini authoredMarco Biasini authored
heuristic.cc 3.52 KiB
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2011 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#include <ost/log.hh>
#include <ost/profile.hh>
#include <ost/mol/xcs_editor.hh>
#include <ost/mol/bond_handle.hh>
#include <ost/mol/torsion_handle.hh>
#include <ost/mol/impl/residue_impl.hh>
#include <ost/mol/impl/atom_impl.hh>
#include <ost/mol/residue_handle.hh>
#include "heuristic.hh"
#include "conop.hh"
namespace ost { namespace conop {
void HeuristicProcessor::ProcessUnkResidue(DiagnosticsPtr diags,
mol::ResidueHandle res) const {
res.SetChemClass(GuessChemClass(res));
mol::AtomHandleList atoms = res.GetAtomList();
for (mol::AtomHandleList::iterator
i = atoms.begin(), e = atoms.end(); i != e; ++i) {
mol::AtomHandle a = *i;
if (!Conopology::Instance().IsValidElement(a.GetElement()))
a.SetElement(GuessAtomElement(a.GetName(), a.IsHetAtom()));
}
if (!this->GetConnect()) { return; }
for (mol::AtomHandleList::iterator
i = atoms.begin(), e = atoms.end(); i != e; ++i) {
this->DistanceBasedConnect(*i);
}
}
void HeuristicProcessor::DoProcess(DiagnosticsPtr diags,
mol::EntityHandle ent) const
{
Profile prof("HeuristicProcessor::Process");
mol::ChainHandleList chains=ent.GetChainList();
for (mol::ChainHandleList::iterator
i = chains.begin(), e = chains.end(); i!= e; ++i) {
mol::ChainHandle& chain = *i;
mol::ResidueHandleList residues = chain.GetResidueList();
mol::ResidueHandle prev;
for (mol::ResidueHandleList::iterator
j = residues.begin(), e2 = residues.end(); j != e2; ++j) {
mol::ResidueHandle residue = *j;
CompoundPtr compound = lib_.FindCompound(residue.GetName(), Compound::PDB);
if (!compound) {
// process unknown residue...
this->ProcessUnkResidue(diags, residue);
continue;
}
this->ReorderAtoms(residue, compound, true);
this->FillResidueProps(residue, compound);
if (this->GetConnect()) {
this->ConnectAtomsOfResidue(residue, compound, false);
if (this->GetConnectAminoAcids())
this->ConnectResidues(prev, residue);
}
prev = residue;
if (!this->GetConnect()) { continue; }
mol::AtomHandleList atoms = residue.GetAtomList();
for (mol::AtomHandleList::iterator
i = atoms.begin(), e = atoms.end(); i != e; ++i) {
if (i->GetBondCount() == 0)
this->DistanceBasedConnect(*i);
}
}
if (residues.empty() || !this->GetAssignTorsions()) {
continue;
}
AssignBackboneTorsions(residues);
}
}
}}