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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 <ost/mol/mm/block_modifiers.hh>
#include <ost/mol/mm/gromacs_block_modifiers.hh>
#include <ost/mol/mm/heuristic_block_modifiers.hh>
using namespace boost::python;
namespace{
template <typename Iterator>
void AppendToList(Iterator first, Iterator last, boost::python::list& l) {
for (Iterator i = first; i != last; ++i) {
l.append(*i);
}
}
template <typename Vec>
void AppendVectorToList(const Vec& v, boost::python::list& l) {
AppendToList(v.begin(), v.end(), l);
}
template<typename T>
std::vector<T> ListToVec(const boost::python::list& l){
std::vector<T> vec;
for (int i = 0; i < boost::python::len(l); ++i){
vec.push_back(boost::python::extract<T>(l[i]));
}
return vec;
}
void WrapAddAddRule(ost::mol::mm::GromacsBlockModifierPtr p,
int number, int method,
const boost::python::list& atom_names,
const boost::python::list& anchors,
const String& type, Real new_charge){
std::vector<String> v_atom_names = ListToVec<String>(atom_names);
std::vector<String> v_anchors = ListToVec<String>(anchors);
p->AddAddRule(number,method,v_atom_names,v_anchors,type,new_charge);
}
void WrapAddHydrogenRule(ost::mol::mm::GromacsHydrogenConstructorPtr p,
int number, int method,
const boost::python::list& hydrogen_names,
const boost::python::list& anchors){
std::vector<String> v_hydrogen_names = ListToVec<String>(hydrogen_names);
std::vector<String> v_anchors = ListToVec<String>(anchors);
p->AddHydrogenRule(number,method,v_hydrogen_names,v_anchors);
}
boost::python::list
WrapGetHydrogenRules(ost::mol::mm::GromacsHydrogenConstructorPtr p) {
// for data extraction: get all rules as list of tuples
// -> data: (number, method, names, anchors)
boost::python::list result;
for (uint i = 0; i < p->GetNumHydrogenRules(); ++i) {
int number = p->GetHydrogenRuleNumber(i);
int method = p->GetHydrogenRuleMethod(i);
boost::python::list names;
AppendVectorToList(p->GetHydrogenRuleNames(i), names);
boost::python::list anchors;
AppendVectorToList(p->GetHydrogenRuleAnchors(i), anchors);
result.append(boost::python::make_tuple(number, method, names, anchors));
}
return result;
}
boost::python::list WrapGetBonds(ost::mol::mm::GromacsBlockModifierPtr p) {
boost::python::list result;
AppendVectorToList(p->GetBonds(), result);
return result;
}
boost::python::list WrapGetAngles(ost::mol::mm::GromacsBlockModifierPtr p) {
boost::python::list result;
AppendVectorToList(p->GetAngles(), result);
return result;
}
boost::python::list WrapGetDihedrals(ost::mol::mm::GromacsBlockModifierPtr p) {
boost::python::list result;
AppendVectorToList(p->GetDihedrals(), result);
return result;
}
boost::python::list WrapGetImpropers(ost::mol::mm::GromacsBlockModifierPtr p) {
boost::python::list result;
AppendVectorToList(p->GetImpropers(), result);
return result;
}
boost::python::list WrapGetCmaps(ost::mol::mm::GromacsBlockModifierPtr p) {
boost::python::list result;
AppendVectorToList(p->GetCmaps(), result);
return result;
}
boost::python::list WrapGetDeleteAtoms(ost::mol::mm::GromacsBlockModifierPtr p) {
boost::python::list result;
AppendVectorToList(p->GetDeleteAtoms(), result);
return result;
}
boost::python::list
WrapGetReplaceRules(ost::mol::mm::GromacsBlockModifierPtr p) {
// for data extraction: get all rules as list of tuples
// -> data: (name, new_name, new_type, new_charge)
boost::python::list result;
for (uint i = 0; i < p->GetNumReplaceRules(); ++i) {
result.append(boost::python::make_tuple(p->GetReplaceRuleName(i),
p->GetReplaceRuleNewName(i),
p->GetReplaceRuleNewType(i),
p->GetReplaceRuleNewCharge(i)));
}
return result;
}
boost::python::list
WrapGetAddRules(ost::mol::mm::GromacsBlockModifierPtr p) {
// for data extraction: get all rules as list of tuples
// -> data: (number, method, names, anchors, type, charge)
boost::python::list result;
for (uint i = 0; i < p->GetNumAddRules(); ++i) {
boost::python::list names;
AppendVectorToList(p->GetAddRuleNames(i), names);
boost::python::list anchors;
AppendVectorToList(p->GetAddRuleAnchors(i), anchors);
result.append(boost::python::make_tuple(p->GetAddRuleNumber(i),
p->GetAddRuleMethod(i),
names, anchors,
p->GetAddRuleType(i),
p->GetAddRuleCharge(i)));
}
return result;
}
}
void export_BlockModifiers()
{
class_<ost::mol::mm::HydrogenConstructor, boost::noncopyable>("HydrogenConstructor",no_init);
boost::python::register_ptr_to_python<ost::mol::mm::HydrogenConstructorPtr>();
class_<ost::mol::mm::BlockModifier, boost::noncopyable>("BlockModifier",no_init);
boost::python::register_ptr_to_python<ost::mol::mm::BlockModifierPtr>();
class_<ost::mol::mm::GromacsHydrogenConstructor, bases<ost::mol::mm::HydrogenConstructor> >("GromacsHydrogenConstructor", init<>())
.def("ApplyOnBuildingBlock",&ost::mol::mm::GromacsHydrogenConstructor::ApplyOnBuildingBlock,(arg("block")))
.def("ApplyOnResidue",&ost::mol::mm::GromacsHydrogenConstructor::ApplyOnResidue,(arg("residue"),arg("editor")))
.def("AddHydrogenRule",&WrapAddHydrogenRule,(arg("number"),arg("method"),arg("hydrogen_names"),arg("anchors")))
.def("GetHydrogenRules",&WrapGetHydrogenRules)
;
class_<ost::mol::mm::GromacsBlockModifier, bases<ost::mol::mm::BlockModifier> >("GromacsBlockModifier", init<>())
.def("ApplyOnBuildingBlock",&ost::mol::mm::GromacsBlockModifier::ApplyOnBuildingBlock,(arg("block")))
.def("ApplyOnResidue",&ost::mol::mm::GromacsBlockModifier::ApplyOnResidue,(arg("residue"),arg("editor")))
.def("AddReplaceRule",&ost::mol::mm::GromacsBlockModifier::AddReplaceRule,(arg("name"),arg("new_name"),arg("new_type"),arg("new_charge")))
.def("AddAddRule",&WrapAddAddRule,(arg("number"),arg("method"),arg("atom_names"),arg("anchors"),arg("type"),arg("charge")))
.def("AddBond",&ost::mol::mm::GromacsBlockModifier::AddBond,(arg("bond")))
.def("AddAngle",&ost::mol::mm::GromacsBlockModifier::AddAngle,(arg("angle")))
.def("AddDihedral",&ost::mol::mm::GromacsBlockModifier::AddDihedral,(arg("dihedral")))
.def("AddImproper",&ost::mol::mm::GromacsBlockModifier::AddImproper,(arg("improper")))
.def("AddCMap",&ost::mol::mm::GromacsBlockModifier::AddCMap,(arg("cmap")))
.def("AddDeleteAtom",&ost::mol::mm::GromacsBlockModifier::AddDeleteAtom,(arg("name")))
.def("GetBonds", &WrapGetBonds)
.def("GetAngles", &WrapGetAngles)
.def("GetDihedrals", &WrapGetDihedrals)
.def("GetImpropers", &WrapGetImpropers)
.def("GetCmaps", &WrapGetCmaps)
.def("GetDeleteAtoms", &WrapGetDeleteAtoms)
.def("GetReplaceRules", &WrapGetReplaceRules)
.def("GetAddRules", &WrapGetAddRules)
;
class_<ost::mol::mm::HeuristicHydrogenConstructor, bases<ost::mol::mm::HydrogenConstructor> >("HeuristicHydrogenConstructor", init<ost::mol::mm::BuildingBlockPtr>())
.def("ApplyOnBuildingBlock",&ost::mol::mm::HeuristicHydrogenConstructor::ApplyOnBuildingBlock,(arg("block")))
.def("ApplyOnResidue",&ost::mol::mm::HeuristicHydrogenConstructor::ApplyOnResidue,(arg("residue"),arg("editor")))
;
boost::python::register_ptr_to_python<ost::mol::mm::GromacsHydrogenConstructorPtr>();
boost::python::register_ptr_to_python<ost::mol::mm::GromacsBlockModifierPtr>();
boost::python::register_ptr_to_python<ost::mol::mm::HeuristicHydrogenConstructorPtr>();
}
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