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
|
// Copyright 2018 Global Phasing Ltd.
#include "gemmi/chemcomp.hpp" // for ChemComp
#include "gemmi/to_chemcomp.hpp" // for add_chemcomp_to_block
#include "common.h"
#include <pybind11/stl.h>
#include <pybind11/stl_bind.h>
namespace py = pybind11;
using namespace gemmi;
PYBIND11_MAKE_OPAQUE(std::vector<Restraints::Bond>)
PYBIND11_MAKE_OPAQUE(std::vector<Restraints::Angle>)
PYBIND11_MAKE_OPAQUE(std::vector<Restraints::Torsion>)
PYBIND11_MAKE_OPAQUE(std::vector<Restraints::Chirality>)
PYBIND11_MAKE_OPAQUE(std::vector<Restraints::Plane>)
PYBIND11_MAKE_OPAQUE(std::vector<ChemComp::Atom>)
void add_chemcomp(py::module& m) {
py::class_<ChemComp> chemcomp(m, "ChemComp");
py::class_<ChemComp::Atom> chemcompatom(chemcomp, "Atom");
py::class_<Restraints> restraints(m, "Restraints");
py::class_<Restraints::Bond> restraintsbond(restraints, "Bond");
py::class_<Restraints::Angle> restraintsangle(restraints, "Angle");
py::class_<Restraints::Torsion> restraintstorsion(restraints, "Torsion");
py::class_<Restraints::Chirality> restraintschirality(restraints, "Chirality");
py::class_<Restraints::Plane> restraintsplane(restraints, "Plane");
py::bind_vector<std::vector<Restraints::Bond>>(m, "RestraintsBonds");
py::bind_vector<std::vector<Restraints::Angle>>(m, "RestraintsAngles");
py::bind_vector<std::vector<Restraints::Torsion>>(m, "RestraintsTorsions");
py::bind_vector<std::vector<Restraints::Chirality>>(m, "RestraintsChirs");
py::bind_vector<std::vector<Restraints::Plane>>(m, "RestraintsPlanes");
py::bind_vector<std::vector<ChemComp::Atom>>(m, "ChemCompAtoms");
py::enum_<BondType>(m, "BondType")
.value("Unspec", BondType::Unspec)
.value("Single", BondType::Single)
.value("Double", BondType::Double)
.value("Triple", BondType::Triple)
.value("Aromatic", BondType::Aromatic)
.value("Deloc", BondType::Deloc)
.value("Metal", BondType::Metal);
py::enum_<ChiralityType>(m, "ChiralityType")
.value("Positive", ChiralityType::Positive)
.value("Negative", ChiralityType::Negative)
.value("Both", ChiralityType::Both);
py::enum_<Restraints::DistanceOf>(restraints, "DistanceOf")
.value("ElectronCloud", Restraints::DistanceOf::ElectronCloud)
.value("Nucleus", Restraints::DistanceOf::Nucleus);
py::class_<Restraints::AtomId>(restraints, "AtomId")
.def(py::init([](int comp, const std::string& atom) {
return new Restraints::AtomId{comp, atom};
}))
.def(py::init([](const std::string& atom) {
return new Restraints::AtomId{1, atom};
}))
.def_readwrite("comp", &Restraints::AtomId::comp)
.def_readwrite("atom", &Restraints::AtomId::atom)
.def("get_from",
(Atom* (Restraints::AtomId::*)(Residue&, Residue*, char) const)
&Restraints::AtomId::get_from,
py::arg("res1"), py::arg("res2"), py::arg("altloc"),
py::return_value_policy::reference)
.def("__repr__", [](const Restraints::AtomId& self) {
return cat("<gemmi.Restraints.AtomId ", self.comp, ' ', self.atom, '>');
});
restraintsbond
.def_readwrite("id1", &Restraints::Bond::id1)
.def_readwrite("id2", &Restraints::Bond::id2)
.def_readwrite("type", &Restraints::Bond::type)
.def_readwrite("aromatic", &Restraints::Bond::aromatic)
.def_readwrite("value", &Restraints::Bond::value)
.def_readwrite("esd", &Restraints::Bond::esd)
.def_readwrite("value_nucleus", &Restraints::Bond::value_nucleus)
.def_readwrite("esd_nucleus", &Restraints::Bond::esd_nucleus)
.def("lexicographic_str", &Restraints::Bond::lexicographic_str)
.def("__repr__", [](const Restraints::Bond& self) {
return "<gemmi.Restraints.Bond " + self.str() + ">";
});
restraintsangle
.def_readwrite("id1", &Restraints::Angle::id1)
.def_readwrite("id2", &Restraints::Angle::id2)
.def_readwrite("id3", &Restraints::Angle::id3)
.def_readwrite("value", &Restraints::Angle::value)
.def_readwrite("esd", &Restraints::Angle::esd)
.def("__repr__", [](const Restraints::Angle& self) {
return "<gemmi.Restraints.Angle " + self.str() + ">";
});
restraintstorsion
.def_readwrite("label", &Restraints::Torsion::label)
.def_readwrite("id1", &Restraints::Torsion::id1)
.def_readwrite("id2", &Restraints::Torsion::id2)
.def_readwrite("id3", &Restraints::Torsion::id3)
.def_readwrite("id4", &Restraints::Torsion::id4)
.def_readwrite("value", &Restraints::Torsion::value)
.def_readwrite("esd", &Restraints::Torsion::esd)
.def_readwrite("period", &Restraints::Torsion::period)
.def("__repr__", [](const Restraints::Torsion& self) {
return "<gemmi.Restraints.Torsion " + self.str() + ">";
});
restraintschirality
.def_readwrite("id_ctr", &Restraints::Chirality::id_ctr)
.def_readwrite("id1", &Restraints::Chirality::id1)
.def_readwrite("id2", &Restraints::Chirality::id2)
.def_readwrite("id3", &Restraints::Chirality::id3)
.def_readwrite("sign", &Restraints::Chirality::sign)
.def("is_wrong", &Restraints::Chirality::is_wrong)
.def("__repr__", [](const Restraints::Chirality& self) {
return "<gemmi.Restraints.Chirality " + self.str() + ">";
});
restraintsplane
.def_readwrite("label", &Restraints::Plane::label)
.def_readwrite("ids", &Restraints::Plane::ids)
.def_readwrite("esd", &Restraints::Plane::esd)
.def("__repr__", [](const Restraints::Plane& self) {
return "<gemmi.Restraints.Plane " + self.str() + ">";
});
restraints
.def_readwrite("bonds", &Restraints::bonds)
.def_readwrite("angles", &Restraints::angles)
.def_readwrite("torsions", &Restraints::torsions)
.def_readwrite("chirs", &Restraints::chirs)
.def_readwrite("planes", &Restraints::planes)
.def("empty", &Restraints::empty)
.def("get_bond", &Restraints::get_bond,
py::return_value_policy::reference_internal)
.def("get_bond", [](Restraints& self,
const std::string& a1, const std::string& a2)
-> Restraints::Bond& {
auto it = self.find_bond(a1, a2);
if (it == self.bonds.end())
fail("Bond restraint not found: " + a1 + "-" + a2);
return *it;
}, py::return_value_policy::reference_internal)
.def("find_shortest_path", &Restraints::find_shortest_path)
.def("chiral_abs_volume", &Restraints::chiral_abs_volume)
;
chemcompatom
.def_readonly("id", &ChemComp::Atom::id)
.def_readonly("el", &ChemComp::Atom::el)
.def_readonly("charge", &ChemComp::Atom::charge)
.def_readonly("chem_type", &ChemComp::Atom::chem_type)
.def("is_hydrogen", &ChemComp::Atom::is_hydrogen)
;
chemcomp
.def_readwrite("name", &ChemComp::name)
.def_readwrite("group", &ChemComp::group)
.def_readonly("atoms", &ChemComp::atoms)
.def_readonly("rt", &ChemComp::rt)
.def("get_atom", &ChemComp::get_atom)
.def("find_atom", [](ChemComp& self, const std::string& atom_id) {
auto it = self.find_atom(atom_id);
return it != self.atoms.end() ? &*it : nullptr;
}, py::return_value_policy::reference_internal)
.def("remove_hydrogens", &ChemComp::remove_hydrogens)
;
m.def("make_chemcomp_from_block", &make_chemcomp_from_block);
m.def("add_chemcomp_to_block", &add_chemcomp_to_block);
m.def("make_chemcomp_with_restraints", &make_chemcomp_with_restraints);
}
|
