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sec_struct.cc
export_entity_view.cc 8.73 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 <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
using namespace boost::python;
#include <ost/export_helper/pair_to_tuple_conv.hh>
#include <ost/mol/entity_view.hh>
#include <ost/mol/query.hh>
#include <ost/mol/mol.hh>
#include <ost/mol/view_op.hh>
using namespace ost;
using namespace ost::mol;
#include "bounds.hh"
namespace {
template<class T>
std::vector<T> from_list(const list& seq)
{
std::vector<T> nrvo;
for (int i = 0; i < len(seq); ++i) {
nrvo.push_back(extract<T>(seq[i]));
}
return nrvo;
}
typedef ChainView (EntityView::*StringMethod)(const String&) const;
typedef ChainView (EntityView::*StringMethod)(const String&) const;
typedef EntityView (EntityView::*QueryMethod)(const Query&, uint) const;
typedef EntityView (EntityView::*QSMethod)(const String&, uint) const;
typedef ChainView (EntityView::*HandleMethod)(const ChainHandle&) const;
typedef ChainView (EntityView::*HM)(const ChainHandle&, ViewAddFlags);
typedef ChainView (EntityView::*VM)(const ChainView&, ViewAddFlags);
VM vm=&EntityView::AddChain;
HM hm=&EntityView::AddChain;
HandleMethod find_chain_hnd=&EntityView::FindChain;
StringMethod find_chain_str=&EntityView::FindChain;
QSMethod select_string=&EntityView::Select;
QueryMethod select_query=&EntityView::Select;
EntityView create_view(const list& seq)
{
if(len(seq)==0) return EntityView();
extract<AtomHandle> get_handle(seq[0]);
if(get_handle.check()) {
return CreateViewFromAtomList(from_list<AtomHandle>(seq));
}
extract<AtomView> get_view(seq[0]);
if(get_view.check()) {
return CreateViewFromAtomList(from_list<AtomView>(seq)); }
throw Error("expected sequence of atom handles or atom views");
return EntityView();
}
ResidueView (EntityView::*add_res_a)(const ResidueHandle&,
ViewAddFlags)=&EntityView::AddResidue;
ResidueView (EntityView::*add_res_b)(const ResidueView&,
ViewAddFlags)=&EntityView::AddResidue;
AtomView (EntityView::*add_atom_a)(const AtomHandle&,
ViewAddFlags)=&EntityView::AddAtom;
AtomView (EntityView::*add_atom_b)(const AtomView&,
ViewAddFlags)=&EntityView::AddAtom;
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_add_residue_overloads,
EntityView::AddResidue, 1, 2)
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_add_chain_overloads,
EntityView::AddChain, 1, 2)
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_add_atom_overloads,
EntityView::AddAtom, 1, 2)
AtomView (EntityView::*find_atom_a)(const String&, const ResNum&, const String&) const=&EntityView::FindAtom;
AtomView (EntityView::*find_atom_b)(const AtomHandle&) const=&EntityView::FindAtom;
}
void export_EntityView()
{
enum_<ViewAddFlag::Type>("ViewAddFlag")
.value("INCLUDE_ATOMS",ViewAddFlag::INCLUDE_ATOMS)
.value("INCLUDE_RESIDUES",ViewAddFlag::INCLUDE_RESIDUES)
.value("INCLUDE_CHAINS",ViewAddFlag::INCLUDE_CHAINS)
.value("INCLUDE_ALL",ViewAddFlag::INCLUDE_ALL)
.value("CHECK_DUPLICATES",ViewAddFlag::CHECK_DUPLICATES)
.export_values()
;
Real (EntityView::*get_angle1)(const AtomHandle&, const AtomHandle&, const AtomHandle&) const = &EntityView::GetAngle;
Real (EntityView::*get_angle2)(const AtomView&, const AtomView&, const AtomView&) const = &EntityView::GetAngle;
class_<EntityView, bases<EntityBase> >("EntityView", init<>())
.def("Copy", &EntityView::Copy)
.def("ExtendViewToResidues", &EntityView::ExtendViewToResidues)
.def("ExtendViewToSurrounding", &EntityView::ExtendViewToSurrounding)
.def("FindChain", find_chain_str)
.def("FindResidue", &EntityView::FindResidue)
.def("FindAtom", find_atom_a)
.def("FindAtom", find_atom_b)
.def("GetAtomCount", &EntityView::GetAtomCount)
.def("GetGeometricStart", geom_start<EntityView>)
.def("GetGeometricEnd", geom_end<EntityView>)
.def("GetGeometricCenter", geom_center<EntityView>)
.add_property("geometric_center", geom_center<EntityView>)
.def("GetCenterOfMass", &EntityView::GetCenterOfMass)
.def("GetCenterOfAtoms", &EntityView::GetCenterOfAtoms)
.def("GetMass", &EntityView::GetMass)
.def("GetResidueCount", &EntityView::GetResidueCount)
.def("GetChainCount", &EntityView::GetChainCount)
.def("GetBondCount", &EntityView::GetBondCount)
.def("GetAngle", get_angle1)
.def("GetAngle", get_angle2)
.def("FindChain", find_chain_hnd)
.def("RemoveChain", &EntityView::RemoveChain)
.def("FindWithin", &EntityView::FindWithin)
.def("RemoveResidue", &EntityView::RemoveResidue)
.def("RemoveAtom", &EntityView::RemoveAtom)
.def("CreateEmptyView", &EntityView::CreateEmptyView)
.def("IsValid", &EntityView::IsValid) .def("CreateFullView", &EntityView::CreateFullView)
.def("AddAllInclusiveBonds", &EntityView::AddAllInclusiveBonds)
.add_property("chain_count", &EntityView::GetChainCount)
.add_property("residue_count", &EntityView::GetResidueCount)
.add_property("atom_count", &EntityView::GetAtomCount)
.add_property("bond_count", &EntityView::GetBondCount)
.add_property("mass", &EntityView::GetMass)
.add_property("center_of_mass", &EntityView::GetCenterOfMass)
.add_property("center_of_atoms", &EntityView::GetCenterOfAtoms)
.add_property("valid", &EntityView::IsValid)
.def("GetResidueList", &EntityView::GetResidueList)
.def("GetAtomList", &EntityView::GetAtomList)
.add_property("atoms", &EntityView::GetAtomList)
.add_property("residues", &EntityView::GetResidueList)
.def("AddBond", &EntityView::AddBond)
.def("AddAtom", add_atom_a,
X_add_atom_overloads(args("atom_handle", "view_add_flags")))
.def("AddAtom", add_atom_b,
X_add_atom_overloads(args("atom_view", "view_add_flags")))
.def("AddResidue", add_res_a,
X_add_residue_overloads(args("residue_handle", "view_add_flags")))
.def("AddResidue", add_res_b,
X_add_residue_overloads(args("residue_view", "view_add_flags")))
.def("AddChain", hm,
X_add_chain_overloads(args("chain_handle", "view_add_flags")))
.def("AddChain", vm,
X_add_chain_overloads(args("chain_view", "view_add_flags")))
.def("Select", select_string, arg("flags")=0)
.def("Select", select_query, arg("flags")=0)
.def("GetBondList", &EntityView::GetBondList,
return_value_policy<reference_existing_object>())
.def("AddAllInclusiveBonds",&EntityView::AddAllInclusiveBonds)
.add_property("handle", &EntityView::GetHandle)
.def("GetHandle", &EntityView::GetHandle)
.add_property("bonds",
make_function(&EntityView::GetBondList,
return_value_policy<reference_existing_object>()))
.def("GetChainList", &EntityView::GetChainList,
return_value_policy<reference_existing_object>())
.add_property("chains",
make_function(&EntityView::GetChainList,
return_value_policy<reference_existing_object>()))
.def(self==self)
.def(self!=self)
.def("Dump", &EntityView::Dump)
.def("GetBounds", &EntityView::GetBounds)
.add_property("bounds", &EntityView::GetBounds)
;
to_python_converter<std::pair<EntityView, EntityView>,
PairToTupleConverter<EntityView, EntityView> >();
def("Union", &Union);
def("Difference", &Difference);
def("Intersection", &Intersection);
def("CreateViewFromAtoms", create_view);
def("CreateEntityFromView", &CreateEntityFromView,
arg("handle")=EntityHandle());
class_<EntityViewList>("EntityViewList", init<>())
.def(vector_indexing_suite<EntityViewList>())
;
}