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Studer Gabriel authoredStuder Gabriel authored
export_residue.cc 12.27 KiB
//------------------------------------------------------------------------------
// 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/chem_class.hh>
#include <ost/mol/chem_type.hh>
#include <ost/mol/mol.hh>
#include <ost/geom/export_helper/vector.hh>
using namespace ost;
using namespace ost::mol;
#include <ost/export_helper/generic_property_def.hh>
#include "bounds.hh"
namespace {
String sec_structure_as_string(SecStructure& s)
{
return String(1, char(s));
}
boost::python::list get_alt_group_names(const ost::mol::ResidueHandle& res) {
std::vector<String> v_alt_group_names = res.GetAltAtomGroupNames();
boost::python::list alt_group_names;
for(std::vector<String>::iterator it = v_alt_group_names.begin();
it != v_alt_group_names.end(); ++it) {
alt_group_names.append(*it);
}
return alt_group_names;
}
typedef EntityView (ResidueHandle::*QueryMethod)(const Query&, uint) const;
typedef EntityView (ResidueHandle::*StringMethod)(const String&, uint) const;
QueryMethod select_query=&ResidueHandle::Select;
StringMethod select_string=&ResidueHandle::Select;
void set_sec_struct1(ResidueBase* b, const SecStructure& s) {b->SetSecStructure(s);}
void set_sec_struct2(ResidueBase* b, char c) {b->SetSecStructure(SecStructure(c));}
void set_chemclass(ResidueBase* b, object po)
{
extract<ChemClass> ex1(po);
if(ex1.check()) {
b->SetChemClass(ex1());
}
extract<char> ex2(po);
if(ex2.check()) {
b->SetChemClass(ChemClass(ex2()));
}
std::string st=extract<std::string>(po);
if(st.empty()) {
throw Error("expected non-empty string as chem class"); }
b->SetChemClass(ChemClass(st[0]));
}
}
void export_Residue()
{
class_<ChemClass>("ChemClass", init<char>(args("chem_class")))
.def(self!=self)
.def(self==self)
.def(self_ns::str(self))
.def("IsPeptideLinking", &ChemClass::IsPeptideLinking)
.def("IsNucleotideLinking", &ChemClass::IsNucleotideLinking)
;
implicitly_convertible<char, ChemClass>();
object ct_class = class_<ChemType>("ChemType", init<char>(args("chem_type")))
.def(self!=self)
.def(self==self)
.def(self_ns::str(self))
.def("IsIon", &ChemType::IsIon)
.def("IsNucleotide", &ChemType::IsNucleotide)
.def("IsSaccharide", &ChemType::IsSaccharide)
.def("IsAminoAcid", &ChemType::IsAminoAcid)
.def("IsCoenzyme", &ChemType::IsCoenzyme)
.def("IsDrug", &ChemType::IsDrug)
.def("IsNonCanonical", &ChemType::IsNonCanonical)
.def("IsKnown", &ChemType::IsKnown)
.def("IsWater", &ChemType::IsWater)
;
implicitly_convertible<char, ChemType>();
ct_class.attr("IONS")=char(ChemType::IONS);
ct_class.attr("NONCANONICALMOLS")=char(ChemType::NONCANONICALMOLS);
ct_class.attr("SACCHARIDES")=char(ChemType::SACCHARIDES);
ct_class.attr("NUCLEOTIDES")=char(ChemType::NUCLEOTIDES);
ct_class.attr("AMINOACIDS")=char(ChemType::AMINOACIDS);
ct_class.attr("COENZYMES")=char(ChemType::COENZYMES);
ct_class.attr("WATERCOORDIONS")=char(ChemType::WATERCOORDIONS);
ct_class.attr("DRUGS")=char(ChemType::DRUGS);
ct_class.attr("WATERS")=char(ChemType::WATERS);
ct_class.attr("UNKNOWN")=char(ChemType::UNKNOWN);
class_<ResNum>("ResNum", init<int>(args("num")))
.def(init<int,char>(args("num", "ins_code")))
.def("GetNum", &ResNum::GetNum)
.def("GetInsCode", &ResNum::GetInsCode)
.add_property("num", &ResNum::GetNum)
.add_property("ins_code", &ResNum::GetInsCode)
.def("__str__", &ResNum::AsString)
.def("__repr__", &ResNum::AsString)
.def(self<self)
.def(self>self)
.def(self>=self)
.def(self<=self)
.def(self==self)
.def(self!=self)
.def(self+=self)
.def(self-=self)
.def(self+self)
.def(self-self)
.def(self+=int())
.def(self-=int())
.def(self+int())
.def(self-int())
;
class_<ResNumList>("ResNumList", init<>())
.def(vector_indexing_suite<ResNumList>())
.def(geom::VectorAdditions<ResNumList>())
;
implicitly_convertible<int, ResNum>();
scope().attr("PEPTIDE_LINKING")=char(ChemClass::PEPTIDE_LINKING);
scope().attr("D_PEPTIDE_LINKING")=char(ChemClass::D_PEPTIDE_LINKING);
scope().attr("L_PEPTIDE_LINKING")=char(ChemClass::L_PEPTIDE_LINKING);
scope().attr("RNA_LINKING")=char(ChemClass::RNA_LINKING);
scope().attr("DNA_LINKING")=char(ChemClass::DNA_LINKING);
scope().attr("NON_POLYMER")=char(ChemClass::NON_POLYMER);
scope().attr("L_SACCHARIDE")=char(ChemClass::L_SACCHARIDE);
scope().attr("D_SACCHARIDE")=char(ChemClass::D_SACCHARIDE);
scope().attr("SACCHARIDE")=char(ChemClass::SACCHARIDE);
scope().attr("WATER")=char(ChemClass::WATER);
scope().attr("UNKNOWN")=char(ChemClass::UNKNOWN);
{
scope sec_struct_scope=class_<SecStructure>("SecStructure", init<>())
.def(init<char>())
.def(init<SecStructure::Type>())
.def("IsHelical", &SecStructure::IsHelical)
.def("IsExtended", &SecStructure::IsExtended)
.def("IsCoil", &SecStructure::IsCoil)
.def("__str__", &sec_structure_as_string)
;
enum_<SecStructure::Type>("Type")
.value("EXTENDED", SecStructure::EXTENDED)
.value("COIL", SecStructure::COIL)
.value("THREE_TEN_HELIX", SecStructure::THREE_TEN_HELIX)
.value("ALPHA_HELIX", SecStructure::ALPHA_HELIX)
.value("BETA_BRIDGE", SecStructure::BETA_BRIDGE)
.value("BEND", SecStructure::BEND)
.value("PI_HELIX", SecStructure::PI_HELIX)
.value("TURN", SecStructure::TURN)
.export_values()
;
}
class_<ResidueBase> residue_base("ResidueBase", no_init);
residue_base
.def("GetSecStructure", &ResidueBase::GetSecStructure)
.def("SetSecStructure", set_sec_struct1)
.def("SetSecStructure", set_sec_struct2)
.def("GetPhiTorsion", &ResidueBase::GetPhiTorsion)
.def("GetPsiTorsion", &ResidueBase::GetPsiTorsion)
.def("GetOmegaTorsion", &ResidueBase::GetOmegaTorsion)
.add_property("phi_torsion", &ResidueBase::GetPhiTorsion)
.add_property("psi_torsion", &ResidueBase::GetPsiTorsion)
.add_property("omega_torsion", &ResidueBase::GetOmegaTorsion)
.def(self_ns::str(self))
.def("GetOneLetterCode", &ResidueBase::GetOneLetterCode)
.def("SetOneLetterCode", &ResidueBase::SetOneLetterCode)
.add_property("one_letter_code", &ResidueBase::GetOneLetterCode,
&ResidueBase::SetOneLetterCode)
.def("GetQualifiedName", &ResidueBase::GetQualifiedName)
.add_property("qualified_name", &ResidueBase::GetQualifiedName)
.def("IsPeptideLinking", &ResidueBase::IsPeptideLinking)
.add_property("peptide_linking", &ResidueBase::IsPeptideLinking)
.def("IsNucleotideLinking", &ResidueBase::IsNucleotideLinking)
.add_property("nucleotide_linking", &ResidueBase::IsNucleotideLinking)
.def("GetCentralAtom", &ResidueBase::GetCentralAtom)
.def("SetCentralAtom", &ResidueBase::SetCentralAtom)
.add_property("central_atom", &ResidueBase::GetCentralAtom, &ResidueBase::SetCentralAtom)
.add_property("central_normal", &ResidueBase::GetCentralNormal)
.def("GetKey", &ResidueBase::GetKey,
return_value_policy<copy_const_reference>())
.def("GetName", &ResidueBase::GetName,
return_value_policy<copy_const_reference>())
.def("GetNumber", &ResidueBase::GetNumber,
return_value_policy<copy_const_reference>())
.def("GetChemClass", &ResidueBase::GetChemClass) .add_property("chem_class", &ResidueBase::GetChemClass, set_chemclass)
.def("SetChemClass", set_chemclass)
.def("GetChemType", &ResidueBase::GetChemType)
.add_property("chem_type", &ResidueBase::GetChemType)
.add_property("is_ligand", &ResidueBase::IsLigand, &ResidueBase::SetIsLigand)
.def("IsLigand", &ResidueBase::IsLigand)
.def("SetIsLigand", &ResidueBase::SetIsLigand)
.add_property("is_protein", &ResidueBase::IsProtein,
&ResidueBase::SetIsProtein)
.def("IsProtein", &ResidueBase::IsProtein)
.def("SetIsProtein", &ResidueBase::SetIsProtein)
.add_property("number",
make_function(&ResidueBase::GetNumber,
return_value_policy<copy_const_reference>()))
.add_property("sec_structure", &ResidueBase::GetSecStructure,
&ResidueBase::SetSecStructure)
.add_property("key",
make_function(&ResidueBase::GetKey,
return_value_policy<copy_const_reference>()))
.add_property("name",
make_function(&ResidueBase::GetName,
return_value_policy<copy_const_reference>()))
.def("IsValid", &ResidueBase::IsValid)
.add_property("valid", &ResidueBase::IsValid)
;
generic_prop_def<ResidueBase>(residue_base);
class_<ResidueHandle, bases<ResidueBase> >("ResidueHandle", init<>())
.def("GetChain",&ResidueHandle::GetChain)
.add_property("chain", &ResidueHandle::GetChain)
.def("GetEntity",&ResidueHandle::GetEntity)
.add_property("entity", &ResidueHandle::GetEntity)
.def("GetAtomList", &ResidueHandle::GetAtomList)
.def("GetIndex", &ResidueHandle::GetIndex)
.def("GetNext", &ResidueHandle::GetNext)
.def("GetPrev", &ResidueHandle::GetPrev)
.def("GetTorsionList", &ResidueHandle::GetTorsionList)
.add_property("prev", &ResidueHandle::GetPrev)
.add_property("next", &ResidueHandle::GetNext)
.def("HasAltAtoms", &ResidueHandle::HasAltAtoms)
.def("GetHandle", &ResidueHandle::GetHandle)
.add_property("handle", &ResidueHandle::GetHandle)
.def("HasAltAtomGroup", &ResidueHandle::HasAltAtomGroup)
.def("GetAltAtomGroupNames", &get_alt_group_names)
.def("GetCurrentAltGroupName", &ResidueHandle::GetCurrentAltGroupName,
return_value_policy<copy_const_reference>())
.def("SwitchAtomPos", &ResidueHandle::SwitchAtomPos)
.add_property("atoms", &ResidueHandle::GetAtomList)
.def("FindAtom", &ResidueHandle::FindAtom, args("atom_name"))
.def("FindTorsion", &ResidueHandle::FindTorsion)
.def("GetAtomCount", &ResidueHandle::GetAtomCount)
.def("GetBondCount", &ResidueHandle::GetBondCount)
.add_property("atom_count", &ResidueHandle::GetAtomCount)
.add_property("index", &ResidueHandle::GetIndex)
.def("Select", select_string, arg("flags")=0)
.def("Select", select_query, arg("flags")=0)
.def("GetMass", &ResidueHandle::GetMass)
.def("GetCenterOfMass", &ResidueHandle::GetCenterOfMass)
.def("GetCenterOfAtoms", &ResidueHandle::GetCenterOfAtoms)
.def("GetGeometricCenter", geom_center<ResidueHandle>)
.add_property("mass", &ResidueHandle::GetMass)
.add_property("center_of_mass", &ResidueHandle::GetCenterOfMass)
.add_property("center_of_atoms", &ResidueHandle::GetCenterOfAtoms)
.add_property("geometric_center", geom_center<ResidueHandle>)
.def("GetGeometricStart", geom_start<ResidueHandle>)
.def("GetGeometricEnd", geom_end<ResidueHandle>)
.def(self==self)
.def(self!=self)
.def("__hash__", &ResidueHandle::GetHashCode)
.def("GetHashCode", &ResidueHandle::GetHashCode) .def("GetBounds", &ResidueHandle::GetBounds)
.add_property("bounds", &ResidueHandle::GetBounds)
.add_property("hash_code", &ResidueHandle::GetHashCode)
;
class_<ResidueHandleList>("ResidueHandleList", no_init)
.def(vector_indexing_suite<ResidueHandleList>())
.def(geom::VectorAdditions<ResidueHandleList>())
;
def("InSequence", &InSequence);
}