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py_numeric.C File Reference

#include "py_commands.h"
#include "numpy/ndarrayobject.h"
#include "AtomSel.h"
#include "VMDApp.h"
#include "MoleculeList.h"

Go to the source code of this file.

Defines
#define	NPY_NO_DEPRECATED_API   NPY_1_7_API_VERSION
Functions
PyObject *	py_timestep (PyObject *self, PyObject *args, PyObject *kwargs)
PyObject *	py_velocities (PyObject *self, PyObject *args, PyObject *kwargs)
PyObject *	py_atomselect (PyObject *self, PyObject *args, PyObject *kwargs)
PyObject *	initvmdnumpy ()
Variables
const char	timestep_doc []
const char	velocities_doc []
const char	atomselect_doc []
PyMethodDef	methods []
const char	vnumpy_moddoc []

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Define Documentation

#define NPY_NO_DEPRECATED_API   NPY_1_7_API_VERSION

Definition at line 25 of file py_numeric.C.

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Function Documentation

PyObject* initvmdnumpy (    )

Definition at line 200 of file py_numeric.C. References methods, NULL, and vnumpy_moddoc.

PyObject* py_atomselect (  PyObject *    self, PyObject *    args, PyObject *    kwargs )  [static]

Definition at line 132 of file py_numeric.C. References VMDApp::atomSelParser, AtomSel::change, get_vmdapp, BaseMolecule::id, MoleculeList::mol_from_id, VMDApp::molecule_top, VMDApp::moleculeList, BaseMolecule::nAtoms, AtomSel::NO_PARSE, NULL, AtomSel::on, result, valid_molid, and AtomSel::which_frame.

PyObject* py_timestep (  PyObject *    self, PyObject *    args, PyObject *    kwargs )  [static]

Definition at line 45 of file py_numeric.C. References get_vmdapp, VMDApp::molecule_top, NULL, Timestep::num, parse_timestep, Timestep::pos, result, and valid_molid.

PyObject* py_velocities (  PyObject *    self, PyObject *    args, PyObject *    kwargs )  [static]

Definition at line 84 of file py_numeric.C. References get_vmdapp, VMDApp::molecule_top, NULL, Timestep::num, parse_timestep, result, valid_molid, and Timestep::vel.

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Variable Documentation

const char atomselect_doc[] [static]

Initial value: "Return an array of ints representing flags for on/off atoms in an atom\n" "selection\n\n" "Args:\n" " selection (str): Atom selection string\n" " molid (int): Molecule ID. Defaults to -1 (top molecule)\n" " frame (int): Frame to select. Defaults to -1 (current frame)\n" "Returns:\n" " (N, int ndarray): Flags for atoms, where N is the number of atoms\n" " in the molecule. The value for an atom will be 1 if it is in the\n" " selection, 0 otherwise" Definition at line 121 of file py_numeric.C.

PyMethodDef methods[] [static]

Initial value: { {"timestep", (PyCFunction)py_timestep, METH_VARARGS | METH_KEYWORDS, timestep_doc}, {"positions", (PyCFunction)py_timestep, METH_VARARGS | METH_KEYWORDS, timestep_doc}, {"velocities", (PyCFunction)py_velocities, METH_VARARGS | METH_KEYWORDS, velocities_doc}, {"atomselect", (PyCFunction)py_atomselect, METH_VARARGS | METH_KEYWORDS, atomselect_doc}, {NULL, NULL} } Definition at line 175 of file py_numeric.C. Referenced by initvmdnumpy.

const char timestep_doc[] [static]

Initial value: "Return a zero-copy reference to atomic coordinates\n\n" "Args:\n" " molid (int): Molecule ID. Defaults to -1 (top molecule)\n" " frame (int): Frame to select. Defaults to -1 (current frame)\n" "Returns:\n" " (N x 3 float32 ndarray): Reference to coordinates, where N is the\n" " number of atoms in the molecule" Definition at line 37 of file py_numeric.C.

const char velocities_doc[] [static]

Initial value: "Return a zero-copy reference to atomic velocites, or None if no velocity\n" "information is present\n\n" "Args:\n" " molid (int): Molecule ID. Defaults to -1 (top molecule)\n" " frame (int): Frame to select. Defaults to -1 (current frame)\n" "Returns:\n" " (N x 3 float32 ndarray): Reference to velocities, where N is the\n" " number of atoms in the molecule" Definition at line 75 of file py_numeric.C.

const char vnumpy_moddoc[] [static]

Initial value: "Methods for interacting with atomic positions or velocities as numpy arrays. " "This can offer significant performance gains over using atomsel types" Definition at line 184 of file py_numeric.C. Referenced by initvmdnumpy.

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