1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
|
//------------------------------------------------------------------------------
// 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 <limits>
#include <boost/python.hpp>
#include <ost/mol/mm/buildingblock.hh>
#include <ost/log.hh>
#include <vector>
using namespace boost::python;
namespace{
template<typename T>
boost::python::list VecToList(std::vector<T>& vec){
boost::python::list l;
for(typename std::vector<T>::iterator it=vec.begin();it!=vec.end();++it){
l.append(*it);
}
return l;
}
bool WrapMatch(ost::mol::mm::BuildingBlockPtr p, const ost::mol::ResidueHandle& res, bool match_connectivity){
String match_fail_info;
bool match = p->Match(res,match_connectivity,match_fail_info);
if(!match){
std::stringstream ss;
ss << "Residue "<< res.GetQualifiedName() << " does not match the building";
ss << "block. "<<match_fail_info;
LOG_INFO(ss.str());
}
return match;
}
boost::python::list WrapGetAtoms(ost::mol::mm::BuildingBlockPtr p){
std::vector<String> atoms = p->GetAtoms();
return VecToList<String>(atoms);
}
boost::python::list WrapGetTypes(ost::mol::mm::BuildingBlockPtr p){
std::vector<String> types = p->GetTypes();
return VecToList<String>(types);
}
boost::python::list WrapGetCharges(ost::mol::mm::BuildingBlockPtr p){
std::vector<Real> charges = p->GetCharges();
return VecToList<Real>(charges);
}
boost::python::list WrapGetMasses(ost::mol::mm::BuildingBlockPtr p){
std::vector<Real> masses = p->GetMasses();
return VecToList<Real>(masses);
}
}
void export_Buildingblock()
{
class_<ost::mol::mm::BuildingBlock>("BuildingBlock",init<>())
.def("Match",&WrapMatch,(arg("res"),arg("match_connectivity")=true))
.def("Connect",&ost::mol::mm::BuildingBlock::Connect,(arg("residue"),arg("xcs_editor")))
.def("GetAtoms",&WrapGetAtoms)
.def("GetTypes",&WrapGetTypes)
.def("GetCharges",&WrapGetCharges)
.def("GetMasses",&WrapGetMasses)
.def("GetType",&ost::mol::mm::BuildingBlock::GetType,(arg("name")))
.def("GetCharge",&ost::mol::mm::BuildingBlock::GetCharge,(arg("name")))
.def("GetMass",&ost::mol::mm::BuildingBlock::GetMass,(arg("name")))
.def("GetBonds",&ost::mol::mm::BuildingBlock::GetBonds)
.def("GetAngles",&ost::mol::mm::BuildingBlock::GetAngles)
.def("GetDihedrals",&ost::mol::mm::BuildingBlock::GetDihedrals)
.def("GetImpropers",&ost::mol::mm::BuildingBlock::GetImpropers)
.def("GetCMaps",&ost::mol::mm::BuildingBlock::GetCMaps)
.def("GetExclusions",&ost::mol::mm::BuildingBlock::GetExclusions)
.def("GetConstraints",&ost::mol::mm::BuildingBlock::GetConstraints)
.def("AddAtom",&ost::mol::mm::BuildingBlock::AddAtom,(arg("name"),arg("type"),arg("charge"),arg("mass")=std::numeric_limits<Real>::quiet_NaN()))
.def("AddBond",&ost::mol::mm::BuildingBlock::AddBond,(arg("bond"),arg("replace_existing")=false))
.def("AddAngle",&ost::mol::mm::BuildingBlock::AddAngle,(arg("angle"),arg("replace_existing")=false))
.def("AddDihedral",&ost::mol::mm::BuildingBlock::AddDihedral,(arg("dihedral"),arg("replace_existing")=false))
.def("AddImproper",&ost::mol::mm::BuildingBlock::AddImproper,(arg("improper"),arg("replace_existing")=false))
.def("AddExclusion",&ost::mol::mm::BuildingBlock::AddExclusion,(arg("exclusion"),arg("replace_existing")=false))
.def("AddCMap",&ost::mol::mm::BuildingBlock::AddCMap,(arg("cmap"),arg("replace_existing")=false))
.def("AddConstraint",&ost::mol::mm::BuildingBlock::AddConstraint,(arg("constraint"),arg("replace_existing")=false))
.def("RemoveAtom",&ost::mol::mm::BuildingBlock::RemoveAtom,(arg("name")))
.def("ReplaceAtom",&ost::mol::mm::BuildingBlock::ReplaceAtom,(arg("name"),arg("new_name"),arg("new_type"),arg("new_charge"),arg("new_mass")=std::numeric_limits<Real>::quiet_NaN()))
.def("RemoveInteractionsToNext",&ost::mol::mm::BuildingBlock::RemoveInteractionsToNext)
.def("RemoveInteractionsToPrev",&ost::mol::mm::BuildingBlock::RemoveInteractionsToPrev)
;
boost::python::register_ptr_to_python<ost::mol::mm::BuildingBlockPtr>();
}
|
