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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 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/mol/mol.hh>
#include <ost/mol/impl/entity_impl.hh>
#include <ost/mol/impl/chain_impl.hh>
#include <ost/mol/impl/residue_impl.hh>
#include <ost/mol/impl/atom_impl.hh>
using namespace ost;
using namespace ost::mol;
namespace {
BondHandle (EditorBase::*connect_a)(const AtomHandle&,
const AtomHandle&)=&EditorBase::Connect;
BondHandle (EditorBase::*connect_c)(const AtomHandle&,
const AtomHandle&,
unsigned char)=&EditorBase::Connect;
BondHandle (EditorBase::*connect_b)(const AtomHandle&, const AtomHandle&,
Real, Real, Real)=&EditorBase::Connect;
BondHandle (EditorBase::*connect_d)(const AtomHandle&, const AtomHandle&,
Real, Real, Real,
unsigned char)=&EditorBase::Connect;
ChainHandle (EditorBase::*insert_chain_a)(const String& chain_name)=&EditorBase::InsertChain;
ChainHandle (EditorBase::*insert_chain_b)(const String& chain_name,
ChainHandle chain, bool deep)=&EditorBase::InsertChain;
ResidueHandle (EditorBase::*append_a)(ChainHandle ch,
const ResidueKey&)=&EditorBase::AppendResidue;
ResidueHandle (EditorBase::*append_b)(ChainHandle ch, const ResidueKey&,
const ResNum&)=&EditorBase::AppendResidue;
ResidueHandle (EditorBase::*append_c)(ChainHandle ch, ResidueHandle residue,
bool deep)=&EditorBase::AppendResidue;
AtomHandle (EditorBase::*insert_atom_a)(ResidueHandle residue, const String& name,
const geom::Vec3& pos, const String& ele,
Real occupancy, Real b_factor,
bool is_hetatm)=&EditorBase::InsertAtom;
AtomHandle (EditorBase::*insert_atom_b)(ResidueHandle residue, AtomHandle atom)=&EditorBase::InsertAtom;
AtomHandle (EditorBase::*insert_alt_atom_a)(ResidueHandle residue, const String& name,
const String& alt_group, const geom::Vec3& pos,
const String& ele, Real occ,
Real b_factor)=&EditorBase::InsertAltAtom;
AtomHandle (EditorBase::*insert_alt_atom_b)(ResidueHandle residue, AtomHandle atom,
const String& alt_group)=&EditorBase::InsertAltAtom;
void (ICSEditor::*set_torsion_a)(TorsionHandle, Real, bool)=&ICSEditor::SetTorsionAngle;
void (ICSEditor::*set_torsion_b)(const AtomHandle&, const AtomHandle&,
const AtomHandle&, const AtomHandle&,
Real, bool)=&ICSEditor::SetTorsionAngle;
void (ICSEditor::*rotate_torsion_a)(TorsionHandle, Real, bool)=&ICSEditor::RotateTorsionAngle;
void (ICSEditor::*rotate_torsion_b)(const AtomHandle&, const AtomHandle&,
const AtomHandle&, const AtomHandle&,
Real, bool)=&ICSEditor::RotateTorsionAngle;
void (EditorBase::*renumber_chain_a)(ChainHandle,const ResNumList&)=&EditorBase::RenumberChain;
void (EditorBase::*renumber_chain_b)(const ChainHandle&,int, bool)=&EditorBase::RenumberChain;
void set_pos(XCSEditor& e, object o1, object o2, bool trans)
{
extract<AtomHandle> eah(o1);
extract<geom::Vec3> ev3(o2);
if(eah.check() && ev3.check()) {
if(trans) {
e.SetAtomTransformedPos(eah(),ev3());
} else {
e.SetAtomOriginalPos(eah(),ev3());
}
return;
}
throw Error("SetAtom*Pos(...,ndarray) not available, because numpy support not compiled in");
}
void set_o_pos(XCSEditor& e, object o1, object o2)
{
set_pos(e,o1,o2,false);
}
void set_t_pos(XCSEditor& e, object o1, object o2)
{
set_pos(e,o1,o2,true);
}
}
void export_Editors()
{
class_<EditorBase>("EditorBase", no_init)
.def("InsertChain", insert_chain_a)
.def("InsertChain", insert_chain_b,(arg("chain_name"),arg("chain"), arg("deep")=false))
.def("InsertAtom", insert_atom_a,
(arg("residue"), arg("name"), arg("pos"), arg("element")="",
arg("occupancy")=1.0, arg("b_factor")=0.0, arg("is_hetatm")=false))
.def("InsertAtom", insert_atom_b)
.def("InsertAltAtom", insert_alt_atom_a)
.def("InsertAltAtom", insert_alt_atom_b)
.def("AddAltAtomPos", &EditorBase::AddAltAtomPos)
.def("DeleteResidue", &EditorBase::DeleteResidue)
.def("DeleteChain", &EditorBase::DeleteChain)
.def("DeleteAtom", &EditorBase::DeleteAtom)
.def("DeleteBond", &EditorBase::DeleteBond)
.def("DeleteBonds", &EditorBase::DeleteBonds)
.def("InsertResidueBefore", &EditorBase::InsertResidueBefore)
.def("InsertResidueAfter", &EditorBase::InsertResidueAfter)
.def("AppendResidue", append_a)
.def("AppendResidue", append_b)
.def("AppendResidue", append_c, (arg("chain"), arg("residue"),
arg("deep")=false))
.def("Connect", connect_a)
.def("Connect", connect_b)
.def("Connect", connect_c)
.def("Connect", connect_d)
.def("RenameChain", &EditorBase::RenameChain)
.def("SetChainType", &EditorBase::SetChainType)
.def("SetChainDescription", &EditorBase::SetChainDescription)
.def("RenameResidue", &EditorBase::RenameResidue)
.def("SetResidueNumber", &EditorBase::SetResidueNumber)
.def("RenameAtom", &EditorBase::RenameAtom)
.def("AddTorsion", &EditorBase::AddTorsion)
.def("ReorderResidues",&EditorBase::ReorderResidues)
.def("ReorderAllResidues",&EditorBase::ReorderAllResidues)
.def("RenumberAllResidues",&EditorBase::RenumberAllResidues)
.def("RenumberChain",renumber_chain_a)
.def("RenumberChain",renumber_chain_b)
.def("Prune", &EditorBase::Prune)
;
void (XCSEditor::*apply_transform1)(const geom::Mat4&) = &XCSEditor::ApplyTransform;
void (XCSEditor::*apply_transform2)(const geom::Transform&) = &XCSEditor::ApplyTransform;
void (XCSEditor::*set_transform1)(const geom::Mat4&) = &XCSEditor::SetTransform;
void (XCSEditor::*set_transform2)(const geom::Transform&) = &XCSEditor::SetTransform;
class_<XCSEditor, bases<EditorBase> >("XCSEditor", no_init)
.def("SetAtomPos", set_t_pos)
.def("SetAtomTransformedPos", set_t_pos)
.def("SetAtomOriginalPos", set_o_pos)
.def("ApplyTransform", apply_transform1)
.def("ApplyTransform", apply_transform2)
.def("SetTransform", set_transform1)
.def("SetTransform", set_transform2)
.def("UpdateICS", &XCSEditor::UpdateICS)
.def("ForceUpdate", &XCSEditor::ForceUpdate)
.def("__exit__", &XCSEditor::ForceUpdate)
.def("__del__", &XCSEditor::ForceUpdate)
;
class_<ICSEditor, bases<EditorBase> >("ICSEditor", no_init)
.def("SetAngle", &ICSEditor::SetAngle)
.def("SetBondLength", &ICSEditor::SetBondLength)
.def("SetTorsionAngle", set_torsion_a,
(arg("torsion"),arg("angle"), arg("update_others")=true))
.def("SetTorsionAngle", set_torsion_b,
(arg("atom_a"), arg("atom_b"), arg("atom_c"), arg("atom_d"),
arg("angle"), arg("update_others")))
.def("RotateTorsionAngle", rotate_torsion_a,
(arg("torsion"),arg("angle"), arg("update_others")=true))
.def("RotateTorsionAngle", rotate_torsion_b,
(arg("atom_a"), arg("atom_b"), arg("atom_c"), arg("atom_d"),
arg("angle"), arg("update_others")))
.def("UpdateXCS", &ICSEditor::UpdateXCS)
.def("__exit__", &ICSEditor::UpdateXCS)
;
}
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