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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: extractors.C,v 1.2.8.2 2007/03/27 21:16:34 amoll Exp $
//
// Author:
// Oliver Kohlbacher
//
#include <BALL/KERNEL/extractors.h>
#include <BALL/KERNEL/expression.h>
#include <BALL/KERNEL/atomContainer.h>
#include <BALL/KERNEL/residue.h>
#include <BALL/KERNEL/protein.h>
#include <BALL/KERNEL/nucleicAcid.h>
namespace BALL
{
AtomList atoms(const AtomContainer& fragment, const String& expression)
{
AtomList result;
// iterate over all atoms
AtomConstIterator it = fragment.beginAtom();
if (expression == "")
{
for (; +it; ++it)
{
// store the atom pointer in the list
result.push_back(const_cast<Atom*>(&*it));
}
}
else
{
Expression match(expression);
for (; +it; ++it)
{
if (match(*it))
{
// store the atom pointer in the list
result.push_back(const_cast<Atom*>(&*it));
}
}
}
return result;
}
AtomList atoms(const AtomList& atom_list, const String& expression)
{
AtomList result;
// iterate over all atoms
AtomList::const_iterator it = atom_list.begin();
Expression match(expression);
for (; it != atom_list.end(); ++it)
{
if (match(**it))
{
// store the atom pointer in the list
result.push_back(const_cast<Atom*>(*it));
}
}
return result;
}
PDBAtomList PDBAtoms(const AtomContainer& fragment, const String& expression)
{
PDBAtomList result;
// iterate over all atoms
AtomConstIterator it = fragment.beginAtom();
if (expression == "")
{
for (; +it; ++it)
{
const PDBAtom* pdb_atom = dynamic_cast<const PDBAtom*>(&*it);
if (pdb_atom != 0)
{
// store the pdb atom pointer in the list
result.push_back(const_cast<PDBAtom*>(pdb_atom));
}
}
}
else
{
Expression match(expression);
for (; +it; ++it)
{
const PDBAtom* pdb_atom = dynamic_cast<const PDBAtom*>(&*it);
if ((pdb_atom != 0) && match(*pdb_atom))
{
// store the pdb atom pointer in the list
result.push_back(const_cast<PDBAtom*>(pdb_atom));
}
}
}
return result;
}
BondList bonds(const AtomContainer& fragment, bool selected_only)
{
// iterate over all atoms
HashSet<Bond*> bond_set;
AtomConstIterator atom_it = fragment.beginAtom();
for (; +atom_it; ++atom_it)
{
if (atom_it->isSelected() || !selected_only)
{
// it the atom is selected or selection is irrelevant,
// insert all bonds into the bond_set
Atom::BondConstIterator bond_it = atom_it->beginBond();
for (; +bond_it; ++bond_it)
{
bond_set.insert(const_cast<Bond*>(&*bond_it));
}
}
}
// copy the results from the hash set to the list
BondList result;
for (HashSet<Bond*>::Iterator it = bond_set.begin(); +it; ++it)
{
result.push_back(*it);
}
return result;
}
BondList bonds(const Atom& atom)
{
BondList result;
Atom::BondConstIterator bond_it = atom.beginBond();
for (; +bond_it; ++bond_it)
{
result.push_back(const_cast<Bond*>(&*bond_it));
}
return result;
}
AtomContainerList atomContainers(const AtomContainer& fragment, bool selected_only)
{
AtomContainerList result;
// iterate over all base fragments
AtomContainerConstIterator it = fragment.beginAtomContainer();
for (; +it; ++it)
{
if (!selected_only || it->isSelected())
{
// store the base fragment pointer in the list
result.push_back(const_cast<AtomContainer*>(&*it));
}
}
return result;
}
FragmentList fragments(const AtomContainer& fragment, bool selected_only)
{
// iterate over all fragments
FragmentList result;
AtomContainerConstIterator it = fragment.beginAtomContainer();
for (; +it; ++it)
{
const Fragment* fragment = dynamic_cast<const Fragment*>(&*it);
if ((fragment != 0) && (it->isSelected() || !selected_only))
{
// store the fragment pointer in the list
result.push_back(const_cast<Fragment*>(fragment));
}
}
return result;
}
MoleculeList molecules(const AtomContainer& fragment, bool selected_only)
{
// iterate over all molecules
AtomContainerConstIterator it = fragment.beginAtomContainer();
MoleculeList result;
for (; +it; ++it)
{
const Molecule* molecule = dynamic_cast<const Molecule*>(&*it);
if ((molecule != 0) && (it->isSelected() || !selected_only))
{
// store the molecule pointer in the list
result.push_back(const_cast<Molecule*>(molecule));
}
}
return result;
}
ResidueList residues(const AtomContainer& fragment, bool selected_only)
{
// iterate over all residues
AtomContainerConstIterator it = fragment.beginAtomContainer();
ResidueList result;
for (; +it; ++it)
{
const Residue* residue = dynamic_cast<const Residue*>(&*it);
if ((residue != 0) && (it->isSelected() || !selected_only))
{
// store the residue pointer in the list
result.push_back(const_cast<Residue*>(residue));
}
}
return result;
}
SecondaryStructureList secondaryStructures(const AtomContainer& fragment, bool selected_only)
{
// iterate over all secondary structures
AtomContainerConstIterator it = fragment.beginAtomContainer();
SecondaryStructureList result;
for (; +it; ++it)
{
const SecondaryStructure* sec_struct = dynamic_cast<const SecondaryStructure*>(&*it);
if ((sec_struct != 0) && (it->isSelected() || !selected_only))
{
// store the sec_struct pointer in the list
result.push_back(const_cast<SecondaryStructure*>(sec_struct));
}
}
return result;
}
ChainList chains(const AtomContainer& fragment, bool selected_only)
{
// iterate over all chains
AtomContainerConstIterator it = fragment.beginAtomContainer();
ChainList result;
for (; +it; ++it)
{
const Chain* chain = dynamic_cast<const Chain*>(&*it);
if ((chain != 0) && (it->isSelected() || !selected_only))
{
// store the chain pointer in the list
result.push_back(const_cast<Chain*>(chain));
}
}
return result;
}
ProteinList proteins(const AtomContainer& fragment, bool selected_only)
{
// iterate over all proteins
AtomContainerConstIterator it = fragment.beginAtomContainer();
ProteinList result;
for (; +it; ++it)
{
const Protein* protein = dynamic_cast<const Protein*>(&*it);
if ((protein != 0) && (it->isSelected() || !selected_only))
{
// store the protein pointer in the list
result.push_back(const_cast<Protein*>(protein));
}
}
return result;
}
NucleotideList nucleotides(const AtomContainer& fragment, bool selected_only)
{
// iterate over all proteins
AtomContainerConstIterator it = fragment.beginAtomContainer();
NucleotideList result;
for (; +it; ++it)
{
const Nucleotide* nucleotide = dynamic_cast<const Nucleotide*>(&*it);
if ((nucleotide != 0) && (it->isSelected() || !selected_only))
{
// store the nucleotide pointer in the list
result.push_back(const_cast<Nucleotide*>(nucleotide));
}
}
return result;
}
NucleicAcidList nucleicAcids(const AtomContainer& fragment, bool selected_only)
{
// iterate over all proteins
AtomContainerConstIterator it = fragment.beginAtomContainer();
NucleicAcidList result;
for (; +it; ++it)
{
const NucleicAcid* nucleic_acid = dynamic_cast<const NucleicAcid*>(&*it);
if ((nucleic_acid != 0) && (it->isSelected() || !selected_only))
{
// store the nucleic acid pointer in the list
result.push_back(const_cast<NucleicAcid*>(nucleic_acid));
}
}
return result;
}
}
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