//------------------------------------------------------------------------------ // This file is part of the OpenStructure project // // 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 #include using namespace boost::python; #include #include #include #include #include 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 eah(o1); extract 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", 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", 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", 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) ; }