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
|
// Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
// Biozentrum - University of Basel
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/loop/all_atom_env.hh>
using namespace promod3;
using namespace promod3::loop;
using namespace boost::python;
// WRAPPERS
namespace {
AllAtomEnvPtr WrapInitSeq(const ost::seq::SequenceHandle& seqres) {
ost::seq::SequenceList seq_list = ost::seq::CreateSequenceList();
seq_list.AddSequence(seqres);
AllAtomEnvPtr env(new AllAtomEnv(seq_list));
return env;
}
AllAtomEnvPtr WrapInitSeqList(const ost::seq::SequenceList& seqres) {
AllAtomEnvPtr env(new AllAtomEnv(seqres));
return env;
}
AllAtomEnvPtr WrapInitStr(const String& seqres) {
ost::seq::SequenceList seq_list = ost::seq::CreateSequenceList();
ost::seq::SequenceHandle s = ost::seq::CreateSequence("A", seqres);
seq_list.AddSequence(s);
AllAtomEnvPtr env(new AllAtomEnv(seq_list));
return env;
}
AllAtomEnvPtr WrapInitStrList(const boost::python::list& seqres) {
ost::seq::SequenceList seq_list = ost::seq::CreateSequenceList();
for (uint i = 0; i < boost::python::len(seqres); ++i) {
String s = boost::python::extract<String>(seqres[i]);
ost::seq::SequenceHandle sh = ost::seq::CreateSequence("A", s);
seq_list.AddSequence(sh);
}
AllAtomEnvPtr env(new AllAtomEnv(seq_list));
return env;
}
void (AllAtomEnv::*WrapSetEnvironment)(const AllAtomPositions&, uint, uint)
= &AllAtomEnv::SetEnvironment;
void WrapSetEnvironmentResNum(AllAtomEnvPtr env,
const AllAtomPositions& new_pos,
const ost::mol::ResNum& start_resnum,
uint chain_index) {
uint num = start_resnum.GetNum();
env->SetEnvironment(new_pos, num, chain_index);
}
void (AllAtomEnv::*WrapSetEnvironmentEnvPos)(const AllAtomEnvPositions&)
= &AllAtomEnv::SetEnvironment;
void (AllAtomEnv::*WrapSetEnvironmentBB)(const BackboneList&, uint, uint)
= &AllAtomEnv::SetEnvironment;
void WrapSetEnvironmentBBResNum(AllAtomEnvPtr env,
const BackboneList& bb_list,
const ost::mol::ResNum& start_resnum,
uint chain_index) {
uint num = start_resnum.GetNum();
env->SetEnvironment(bb_list, num, chain_index);
}
AllAtomEnvPositionsPtr (AllAtomEnv::*WrapGetEnvironment)(uint, uint, uint)
= &AllAtomEnv::GetEnvironment;
boost::python::list WrapGetResIndices(const AllAtomEnvPositions& all_env_pos) {
boost::python::list return_list;
core::AppendVectorToList(all_env_pos.res_indices, return_list);
return return_list;
}
void WrapSetResIndices(AllAtomEnvPositions& all_env_pos,
const boost::python::list& res_idx_list) {
core::ConvertListToVector(res_idx_list, all_env_pos.res_indices);
}
} // anon wrapper ns
void export_AllAtomEnv() {
class_<AllAtomEnv, AllAtomEnvPtr>("AllAtomEnv", no_init)
.def("__init__", make_constructor(&WrapInitSeq))
.def("__init__", make_constructor(&WrapInitSeqList))
.def("__init__", make_constructor(&WrapInitStr))
.def("__init__", make_constructor(&WrapInitStrList))
.def("SetInitialEnvironment", &AllAtomEnv::SetInitialEnvironment,
(arg("env_structure")))
.def("SetEnvironment", WrapSetEnvironment,
(arg("new_pos"), arg("start_resnum"), arg("chain_idx") = 0))
.def("SetEnvironment", WrapSetEnvironmentResNum,
(arg("new_pos"), arg("start_resnum"), arg("chain_idx") = 0))
.def("SetEnvironment", WrapSetEnvironmentEnvPos, (arg("new_env_pos")))
.def("SetEnvironment", WrapSetEnvironmentBB,
(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
.def("SetEnvironment", WrapSetEnvironmentBBResNum,
(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
.def("ClearEnvironment", &AllAtomEnv::ClearEnvironment,
(arg("start_resnum"), arg("num_residues"), arg("chain_idx") = 0))
.def("GetEnvironment", WrapGetEnvironment,
(arg("start_resnum"), arg("num_residues"), arg("chain_idx") = 0))
.def("GetSeqres", &AllAtomEnv::GetSeqres)
.def("GetAllAtomPositions", &AllAtomEnv::GetAllPosData)
;
class_<AllAtomEnvPositions, AllAtomEnvPositionsPtr>
("AllAtomEnvPositions", init<>())
.def_readwrite("all_pos", &AllAtomEnvPositions::all_pos)
.add_property("res_indices", &WrapGetResIndices, &WrapSetResIndices)
;
}
|
