Something went wrong on our end
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Marco Biasini authored
It seems, just looking at the number of atoms is not enough, we also have to look at the hetatm flag. The whole element guessing code is still quite shaky and should be improved.
Marco Biasini authoredIt seems, just looking at the number of atoms is not enough, we also have to look at the hetatm flag. The whole element guessing code is still quite shaky and should be improved.
heuristic.cc 3.80 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 {
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(), atoms.size()));
}
res.SetChemClass(GuessChemClass(res));
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);
if (this->GetConnectAminoAcids())
this->ConnectResidues(prev, residue);
prev = 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);
}
}
String HeuristicProcessor::ToString() const {
std::stringstream ss;
ss << "HeuristicProcessor(" << this->OptionsToString() << ")";
return ss.str();
}
}}