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
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
|
//------------------------------------------------------------------------------
// 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/register_ptr_to_python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
using namespace boost::python;
#include <ost/message.hh>
#include <ost/conop/compound.hh>
#include <ost/conop/compound_lib.hh>
using namespace ost::mol;
using namespace ost::conop;
namespace {
Compound::Dialect tr_dialect(const String& dialect)
{
if (dialect=="PDB") {
return Compound::PDB;
}
if (dialect=="CHARMM") {
return Compound::CHARMM;
}
if (dialect=="OPLS") {
return Compound::OPLS;
}
if (dialect=="AMBER") {
return Compound::AMBER;
}
std::stringstream ss;
ss << "unknown compound dialect '" << dialect << "'";
throw ost::Error(ss.str());
}
void set_dialect(CompoundPtr compound, const String& dialect)
{
compound->SetDialect(tr_dialect(dialect));
}
char get_chemclass(CompoundPtr compound)
{
return char(compound->GetChemClass());
}
void set_chemclass(CompoundPtr compound, char cc)
{
compound->SetChemClass(ChemClass(cc));
}
char get_chemtype(CompoundPtr compound)
{
return char(compound->GetChemType());
}
CompoundPtr find_compound(CompoundLibPtr comp_lib,
const String& id, const String& dialect)
{
return comp_lib->FindCompound(id, tr_dialect(dialect));
}
boost::python::list find_compounds(CompoundLibPtr comp_lib,
const String& query,
const String& by,
const String& dialect)
{
CompoundPtrList ptr_list = comp_lib->FindCompounds(query, by, tr_dialect(dialect));
// We can't return ptr_list directly - the list was full of non working
// compounds for no obvious reason. So we convert it to a boost python list
// of Compounds.
boost::python::list l;
for(auto it = ptr_list.begin(); it != ptr_list.end(); ++it) {
l.append(*it);
}
return l;
}
bool is_residue_complete(CompoundLibPtr comp_lib,
const ost::mol::ResidueHandle& res,
bool check_hydrogens, const String& dialect)
{
return comp_lib->IsResidueComplete(res, check_hydrogens, tr_dialect(dialect));
}
String get_creation_date(CompoundLibPtr comp_lib)
{
return comp_lib->GetCreationDate().ToString();
}
}
void export_Compound() {
class_<Compound, CompoundPtr>("Compound", no_init)
.def("GetID", &Compound::GetID,
return_value_policy<copy_const_reference>())
.def("SetOneLetterCode", &Compound::SetOneLetterCode)
.def("GetOneLetterCode", &Compound::GetOneLetterCode)
.add_property("three_letter_code", make_function(&Compound::GetID, return_value_policy<copy_const_reference>()))
.add_property("name",
make_function(&Compound::GetName,
return_value_policy<copy_const_reference>()))
.add_property("id", make_function(&Compound::GetID, return_value_policy<copy_const_reference>()))
.add_property("one_letter_code", &Compound::GetOneLetterCode,
&Compound::SetOneLetterCode)
.def("GetAtomSpecs", &Compound::GetAtomSpecs,
return_value_policy<copy_const_reference>())
.add_property("bond_specs", make_function(&Compound::GetBondSpecs,
return_value_policy<copy_const_reference>()))
.add_property("atom_specs", make_function(&Compound::GetAtomSpecs,
return_value_policy<copy_const_reference>()))
.def("AddAtom", &Compound::AddAtom)
.def("AddBond", &Compound::AddBond)
.def("IsPeptideLinking", &Compound::IsPeptideLinking)
.def("IsNucleotideLinking", &Compound::IsNucleotideLinking)
.add_property("chem_class", &get_chemclass,
&set_chemclass)
.add_property("chem_type", &get_chemtype)
.add_property("formula",make_function(&Compound::GetFormula,
return_value_policy<copy_const_reference>()),
&Compound::SetFormula)
.add_property("dialect", &Compound::GetDialectAsString,
&set_dialect)
.add_property("inchi",
make_function(&Compound::GetInchi,
return_value_policy<copy_const_reference>()))
.add_property("inchi_key",
make_function(&Compound::GetInchiKey,
return_value_policy<copy_const_reference>()))
.add_property("smiles",
make_function(&Compound::GetSMILES,
return_value_policy<copy_const_reference>()))
.add_property("obsolete", &Compound::GetObsolete)
.add_property("replaced_by",
make_function(&Compound::GetReplacedBy,
return_value_policy<copy_const_reference>()))
;
class_<AtomSpec>("AtomSpec", no_init)
.def_readonly("element", &AtomSpec::element)
.def_readonly("name", &AtomSpec::name)
.def_readonly("alt_name", &AtomSpec::alt_name)
.def_readonly("is_leaving", &AtomSpec::is_leaving)
.def_readonly("is_aromatic", &AtomSpec::is_aromatic)
.def_readonly("ordinal", &AtomSpec::ordinal)
.def_readonly("charge", &AtomSpec::charge)
;
class_<BondSpec>("BondSpec", no_init)
.def_readonly("atom_one", &BondSpec::atom_one)
.def_readonly("atom_two", &BondSpec::atom_two)
.def_readonly("order", &BondSpec::order)
;
class_<CompoundLib>("CompoundLib", no_init)
.def("Load", &CompoundLib::Load, arg("readonly")=true).staticmethod("Load")
.def("FindCompound", &find_compound,
(arg("id"), arg("dialect")="PDB"))
.def("FindCompounds", &find_compounds,
(arg("query"), arg("by"), arg("dialect")="PDB"))
.def("IsResidueComplete", &is_residue_complete, (arg("residue"),
arg("check_hydrogens")=false,
arg("dialect")="PDB"))
.def("ClearCache", &CompoundLib::ClearCache)
.def("GetOSTVersionUsed", &CompoundLib::GetOSTVersionUsed)
.def("GetCreationDate", &get_creation_date, (arg("comp_lib")))
;
class_<AtomSpecList>("AtomSpecList", init<>())
.def(vector_indexing_suite<AtomSpecList>())
;
class_<BondSpecList>("BondSpecList", init<>())
.def(vector_indexing_suite<BondSpecList>())
;
register_ptr_to_python<CompoundLibPtr>();
}
|
