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
|
// $Id$
//
// Copyright (C) 2016 Sereina Riniker, Paolo Tosco
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDBoost/python.h>
#include <RDBoost/Wrap.h>
#include "GraphMol/Trajectory/Trajectory.h"
#include "GraphMol/ROMol.h"
namespace python = boost::python;
namespace RDKit {
Snapshot *getSnapshot_wrap(Trajectory *traj, unsigned int snapshotNum) {
return new Snapshot(traj->getSnapshot(snapshotNum));
}
Snapshot *constructSnapshot_wrap(python::list &coordList, double energy) {
unsigned int l = python::len(coordList);
boost::shared_array<double> c;
if (l)
c.reset(new double[l]);
for (unsigned int i = 0; i < l; ++i)
c[i] = python::extract<double>(coordList[i]);
return new Snapshot(c, energy);
}
Snapshot *copyConstructSnapshot_wrap(Snapshot *other) {
return new Snapshot(*other);
}
Trajectory *constructTrajectory_wrap(unsigned int dimension, unsigned int numPoints, python::list snapshotList) {
unsigned int l = python::len(snapshotList);
auto *traj = new Trajectory(dimension, numPoints);
for (unsigned int i = 0; i < l; ++i) {
Snapshot *s = python::extract<Snapshot *>(snapshotList[i]);
traj->addSnapshot(*s);
}
return traj;
}
Trajectory *copyConstructTrajectory_wrap(Trajectory *other) {
return new Trajectory(*other);
}
struct Trajectory_wrapper {
static void wrap() {
python::class_<Trajectory>(
"Trajectory", "A class which allows storing Snapshots from a trajectory", python::no_init)
.def("Dimension", &Trajectory::dimension, (python::arg("self")),
"returns the dimensionality of this Trajectory's coordinate tuples")
.def("NumPoints", &Trajectory::numPoints, (python::arg("self")),
"returns the number of coordinate tuples associated to each Snapshot")
.def("__len__", &Trajectory::size)
.def("AddSnapshot", &Trajectory::addSnapshot,
(python::arg("self"), python::arg("s")),
"appends Snapshot s to this Trajectory; returns the zero-based index "
"position of the added snapshot\n")
.def("GetSnapshot", getSnapshot_wrap,
(python::arg("self"), python::arg("snapshotNum")),
"returns the Snapshot snapshotNum, where the latter is the zero-based "
"index of the retrieved Snapshot\n",
python::return_value_policy<python::manage_new_object>())
.def("InsertSnapshot", &Trajectory::insertSnapshot,
(python::arg("self"), python::arg("snapshotNum"), python::arg("s")),
"inserts Snapshot s into the Trajectory at the position snapshotNum, "
"where the latter is the zero-based index of the Trajectory's Snapshot "
"before which the Snapshot s will be inserted; returns the zero-based "
"index position of the inserted snapshot\n")
.def("RemoveSnapshot", &Trajectory::removeSnapshot,
(python::arg("self"), python::arg("snapshotNum")),
"removes Snapshot snapshotNum from the Trajectory, where "
"snapshotNum is the zero-based index of Snapshot to be removed\n")
.def("Clear", &Trajectory::clear,
(python::arg("self")),
"removes all Snapshots from the Trajectory\n")
.def("AddConformersToMol", &Trajectory::addConformersToMol,
(python::arg("self"), python::arg("mol"),
python::arg("from") = -1, python::arg("to") = -1),
"adds conformations from the Trajectory to mol\n"
"from is the first Snapshot that will be added as a Conformer; "
"defaults to -1 (first available)\n"
"to is the last Snapshot that will be added as a Conformer; "
"defaults to -1 (all)\n");
python::def("Trajectory", constructTrajectory_wrap,
(python::arg("dimension"), python::arg("numPoints"),
python::arg("snapshotList") = python::list()),
"Constructor;\n"
"dimension: dimensionality of this Trajectory's coordinate tuples;\n"
"numPoints: number of coordinate tuples associated to each Snapshot;\n"
"snapshotList: list of Snapshot objects used to initialize the Trajectory (optional; defaults to []).\n",
python::return_value_policy<python::manage_new_object>());
python::def("Trajectory", copyConstructTrajectory_wrap, (python::arg("other")),
"Copy constructor", python::return_value_policy<python::manage_new_object>());
python::class_<Snapshot>(
"Snapshot", "A class which allows storing coordinates from a trajectory", python::no_init)
.def("GetPoint2D", &Snapshot::getPoint2D, (python::arg("self"), python::arg("pointNum")),
"return the coordinates at pointNum as a Point2D object; "
"requires the Trajectory dimension to be == 2")
.def("GetPoint3D", &Snapshot::getPoint3D, (python::arg("self"), python::arg("pointNum")),
"return the coordinates at pointNum as a Point3D object; "
"requires the Trajectory dimension to be >= 2")
.def("GetEnergy", &Snapshot::getEnergy, (python::arg("self")),
"returns the energy for this Snapshot")
.def("SetEnergy", &Snapshot::setEnergy, (python::arg("self"), python::arg("energy")),
"sets the energy for this Snapshot");
python::def("Snapshot", constructSnapshot_wrap,
(python::arg("coordList"), python::arg("energy") = 0.0),
"Constructor;\n"
"coordList: list of floats containing the coordinates for this Snapshot;\n"
"energy: the energy for this Snapshot.\n",
python::return_value_policy<python::manage_new_object>());
python::def("Snapshot", copyConstructSnapshot_wrap, (python::arg("other")),
"Copy constructor", python::return_value_policy<python::manage_new_object>());
python::def("ReadAmberTrajectory", &readAmberTrajectory,
(python::arg("fName"), python::arg("traj")),
"reads coordinates from an AMBER trajectory file into the Trajectory object; "
"returns the number of Snapshot objects read in\n");
python::def("ReadGromosTrajectory", &readGromosTrajectory,
(python::arg("fName"), python::arg("traj")),
"reads coordinates from a GROMOS trajectory file into the Trajectory object; "
"returns the number of Snapshot objects read in\n");
};
};
}
void wrap_trajectory() { RDKit::Trajectory_wrapper::wrap(); }
|
