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// $Id$
//
// 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("__init__",
python::make_constructor(
&constructTrajectory_wrap, python::default_call_policies(),
(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")
.def("__init__",
python::make_constructor(©ConstructTrajectory_wrap,
python::default_call_policies(),
python::arg("other")),
"Copy constructor")
.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, python::args("self"))
.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("fromCid") = -1, python::arg("toCid") = -1),
"adds conformations from the Trajectory to mol\n"
"fromCid is the first Snapshot that will be added as a Conformer; "
"defaults to -1 (first available)\n"
"toCid is the last Snapshot that will be added as a Conformer; "
"defaults to -1 (all)\n");
python::class_<Snapshot>(
"Snapshot",
"A class which allows storing coordinates from a trajectory",
python::no_init)
.def("__init__",
python::make_constructor(
&constructSnapshot_wrap, python::default_call_policies(),
(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")
.def("__init__",
python::make_constructor(©ConstructSnapshot_wrap,
python::default_call_policies(),
python::arg("other")),
"Copy constructor")
.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("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");
};
};
} // namespace RDKit
void wrap_trajectory() { RDKit::Trajectory_wrapper::wrap(); }
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