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
|
// Copyright 2021 Global Phasing Ltd.
#include "gemmi/topo.hpp"
#include "gemmi/riding_h.hpp" // for adjust_hydrogen_distances
#include "gemmi/crd.hpp" // for prepare_refmac_crd, ...
#include "common.h"
#include <pybind11/stl.h>
#include <pybind11/stl_bind.h>
#include <pybind11/iostream.h> // for detail::pythonbuf
namespace py = pybind11;
using namespace gemmi;
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Bond>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Angle>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Torsion>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Chirality>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Plane>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Link>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::ChainInfo>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::ResInfo>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Rule>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Mod>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::FinalChemComp>)
void add_topo(py::module& m) {
py::class_<Topo> topo(m, "Topo");
py::enum_<HydrogenChange>(m, "HydrogenChange")
.value("NoChange", HydrogenChange::NoChange)
.value("Shift", HydrogenChange::Shift)
.value("Remove", HydrogenChange::Remove)
.value("ReAdd", HydrogenChange::ReAdd)
.value("ReAddButWater", HydrogenChange::ReAddButWater)
.value("ReAddKnown", HydrogenChange::ReAddKnown);
py::class_<Topo::Bond>(topo, "Bond")
.def_readonly("restr", &Topo::Bond::restr)
.def_readonly("atoms", &Topo::Bond::atoms)
.def("calculate", &Topo::Bond::calculate)
.def("calculate_z", &Topo::Bond::calculate_z)
;
py::bind_vector<std::vector<Topo::Bond>>(m, "TopoBonds");
py::class_<Topo::Angle>(topo, "Angle")
.def_readonly("restr", &Topo::Angle::restr)
.def_readonly("atoms", &Topo::Angle::atoms)
.def("calculate", &Topo::Angle::calculate)
.def("calculate_z", &Topo::Angle::calculate_z)
;
py::bind_vector<std::vector<Topo::Angle>>(m, "TopoAngles");
py::class_<Topo::Torsion>(topo, "Torsion")
.def_readonly("restr", &Topo::Torsion::restr)
.def_readonly("atoms", &Topo::Torsion::atoms)
.def("calculate", &Topo::Torsion::calculate)
.def("calculate_z", &Topo::Torsion::calculate_z)
;
py::bind_vector<std::vector<Topo::Torsion>>(m, "TopoTorsions");
py::class_<Topo::Chirality>(topo, "Chirality")
.def_readonly("restr", &Topo::Chirality::restr)
.def_readonly("atoms", &Topo::Chirality::atoms)
.def("calculate", &Topo::Chirality::calculate)
.def("calculate_z", &Topo::Chirality::calculate_z,
py::arg("ideal_abs_vol"), py::arg("esd"))
.def("check", &Topo::Chirality::check)
;
py::bind_vector<std::vector<Topo::Chirality>>(m, "TopoChirs");
py::class_<Topo::Plane>(topo, "Plane")
.def_readonly("restr", &Topo::Plane::restr)
.def_readonly("atoms", &Topo::Plane::atoms)
.def("has", &Topo::Plane::has)
;
py::bind_vector<std::vector<Topo::Plane>>(m, "TopoPlanes");
py::enum_<Topo::RKind>(m, "RKind")
.value("Bond", Topo::RKind::Bond)
.value("Angle", Topo::RKind::Angle)
.value("Torsion", Topo::RKind::Torsion)
.value("Chirality", Topo::RKind::Chirality)
.value("Plane", Topo::RKind::Plane)
;
py::class_<Topo::Rule>(topo, "Rule")
.def_readonly("rkind", &Topo::Rule::rkind)
.def_readonly("index", &Topo::Rule::index)
;
py::bind_vector<std::vector<Topo::Rule>>(m, "TopoRules");
py::class_<Topo::Mod>(topo, "Mod")
.def_readonly("id", &Topo::Mod::id)
.def_readonly("alias", &Topo::Mod::alias)
.def_readonly("altloc", &Topo::Mod::altloc)
;
py::bind_vector<std::vector<Topo::Mod>>(m, "TopoMods");
py::class_<Topo::FinalChemComp>(topo, "FinalChemComp")
.def_readonly("altloc", &Topo::FinalChemComp::altloc)
.def_readonly("cc", &Topo::FinalChemComp::cc)
;
py::bind_vector<std::vector<Topo::FinalChemComp>>(m, "TopoFinalChemComps");
py::class_<Topo::Link>(topo, "Link")
.def_readonly("link_id", &Topo::Link::link_id)
.def_readonly("res1", &Topo::Link::res1)
.def_readonly("res2", &Topo::Link::res2)
.def_readonly("alt1", &Topo::Link::alt1)
.def_readonly("alt2", &Topo::Link::alt2)
.def_readonly("link_rules", &Topo::Link::link_rules)
;
py::bind_vector<std::vector<Topo::Link>>(m, "TopoLinks");
py::class_<Topo::ResInfo>(topo, "ResInfo")
.def_readonly("res", &Topo::ResInfo::res)
.def_readonly("prev", &Topo::ResInfo::prev)
.def_readonly("mods", &Topo::ResInfo::mods)
.def_readonly("chemcomps", &Topo::ResInfo::chemcomps)
.def_readonly("monomer_rules", &Topo::ResInfo::monomer_rules)
.def("get_final_chemcomp", &Topo::ResInfo::get_final_chemcomp)
;
py::bind_vector<std::vector<Topo::ResInfo>>(m, "TopoResInfos");
py::class_<Topo::ChainInfo>(topo, "ChainInfo")
.def_property_readonly("chain_ref", [](const Topo::ChainInfo& self)
{ return &self.chain_ref; }, py::return_value_policy::reference_internal)
.def_readonly("subchain_name", &Topo::ChainInfo::subchain_name)
.def_readonly("entity_id", &Topo::ChainInfo::entity_id)
.def_readonly("polymer", &Topo::ChainInfo::polymer)
.def_readonly("polymer_type", &Topo::ChainInfo::polymer_type)
.def_readonly("res_infos", &Topo::ChainInfo::res_infos)
;
py::class_<std::vector<Topo::ChainInfo>>(m, "TopoChainInfos")
.def("__len__", &std::vector<Topo::ChainInfo>::size)
.def("__getitem__", [](const std::vector<Topo::ChainInfo> &self, size_t i) {return self.at(i);})
;
topo
.def(py::init<>())
.def("adjust_hydrogen_distances", &adjust_hydrogen_distances,
py::arg("of"), py::arg("default_scale")=1.)
.def_readonly("bonds", &Topo::bonds)
.def_readonly("angles", &Topo::angles)
.def_readonly("torsions", &Topo::torsions)
.def_readonly("chirs", &Topo::chirs)
.def_readonly("planes", &Topo::planes)
.def_readonly("extras", &Topo::extras)
.def_readonly("chain_infos", &Topo::chain_infos)
.def("ideal_chiral_abs_volume", &Topo::ideal_chiral_abs_volume)
.def("links_to_previous", [](Topo& self, Residue* res) {
if (Topo::ResInfo* ri = self.find_resinfo(res))
return ri->prev;
fail("links_to_previous(): Residue not found");
}, py::return_value_policy::reference_internal)
.def("first_bond_in_link", &Topo::first_bond_in_link,
py::return_value_policy::reference_internal)
.def("set_cispeps_in_structure", &Topo::set_cispeps_in_structure)
.def("find_missing_atoms", &find_missing_atoms,
py::arg("including_hydrogen")=false)
;
m.def("prepare_topology",
[](Structure& st, MonLib& monlib, size_t model_index,
HydrogenChange h_change, bool reorder,
const py::object& pywarnings, bool ignore_unknown_links, bool use_cispeps) {
std::ostream* warnings = nullptr;
std::ostream os(nullptr);
std::unique_ptr<py::detail::pythonbuf> buffer;
if (!pywarnings.is_none()) {
buffer.reset(new py::detail::pythonbuf(pywarnings));
os.rdbuf(buffer.get());
warnings = &os;
}
return prepare_topology(st, monlib, model_index, h_change, reorder,
warnings, ignore_unknown_links, use_cispeps);
}, py::arg("st"), py::arg("monlib"), py::arg("model_index")=0,
py::arg("h_change")=HydrogenChange::NoChange, py::arg("reorder")=false,
py::arg("warnings")=py::none(), py::arg("ignore_unknown_links")=false,
py::arg("use_cispeps")=false);
// crd.hpp
m.def("setup_for_crd", &setup_for_crd);
m.def("prepare_refmac_crd", &prepare_refmac_crd);
m.def("add_automatic_links", &add_automatic_links);
}
|
