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py_measure.C File Reference

#include "py_commands.h"
#include "VMDApp.h"
#include "Measure.h"

Go to the source code of this file.

Functions
PyObject *	py_measure_bond (PyObject *self, PyObject *args, PyObject *kwargs)
PyObject *	py_measure_angle (PyObject *self, PyObject *args, PyObject *kwargs)
PyObject *	py_measure_dihed (PyObject *self, PyObject *args, PyObject *kwargs)
PyObject *	initmeasure ()
Variables
const char	bond_doc []
const char	angle_doc []
const char	dihed_doc []
PyMethodDef	methods []
const char	measure_moddoc []

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Function Documentation

PyObject* initmeasure (    )

Definition at line 287 of file py_measure.C. References measure_moddoc, and methods.

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

Definition at line 117 of file py_measure.C. References get_vmdapp, MEASURE_ANGLE, measure_error, measure_geom, VMDApp::molecule_top, VMDApp::moleculeList, NULL, and ResizeArray::num.

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

Definition at line 39 of file py_measure.C. References get_vmdapp, MEASURE_BOND, measure_error, measure_geom, VMDApp::molecule_top, VMDApp::moleculeList, NULL, and ResizeArray::num.

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

Definition at line 197 of file py_measure.C. References get_vmdapp, MEASURE_DIHED, measure_error, measure_geom, VMDApp::molecule_top, VMDApp::moleculeList, NULL, and ResizeArray::num.

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Variable Documentation

const char angle_doc[] [static]

Initial value: "Measure angles between given atoms over a trajectory. Can specify multiple\n" "molids to measure angles between atoms in different molecules.\n\n" "Args:\n" " atom1 (int): Index of first atom\n" " atom2 (int): Index of second atom\n" " atom3 (int): Index of third atom\n" " molid (int): Molecule ID of first atom. Defaults to top molecule\n" " molid2 (int): Molecule ID of second atom, if different from first molid\n" " molid3 (int): Molecule ID of third atom, if different from first molid\n" " frame (int): Single frame to measure angle in. Defaults to current frame\n" " first (int): First frame in range to measure in, for multiple frames\n" " last (int): Last frame in range to measure in, for multiple frames\n" "Returns:\n" " (list of float): Angle as measured in frame(s)" Definition at line 102 of file py_measure.C.

const char bond_doc[] [static]

Initial value: "Measures the distance between the atom1 and atom2 over the trajectory, either\n" "at the given frame or over frames from first to last. Distances between atoms\n" "in different molecules can be measured by giving specific molids\n\n" "Args:\n" " atom1 (int): Index of first atom\n" " atom2 (int): Index of second atom\n" " molid (int): Molecule ID of first atom, defaults to top molecule\n" " molid2 (int): Molecule ID of second atom, if different. (optional)\n" " frame (int): Measure distance in this single frame. Defaults to current\n" " first (int): For measuring multiple frames, first frame to measure\n" " last (int): For measuring multiple, last frame to measure\n" "Returns:\n" " (list of float): Distance between atoms for given frame(s)" Definition at line 25 of file py_measure.C.

const char dihed_doc[] [static]

Initial value: "Measures the dihedral angle between atoms over the trajectory. Can specify\n" "multiple molecule IDs to measure over different loaded molecules.\n\n" "Args:\n" " atom1 (int): First atom in dihedral\n" " atom2 (int): Second atom in dihedral\n" " atom3 (int): Third atom in dihedral\n" " atom4 (int): Fourth atom in dihedral\n" " molid (int): Molecule ID to measure in. Defaults to top molecule\n" " molid2 (int): Molecule ID for second atom, if different from molid\n" " molid3 (int): Molecule ID for third atom, if different from molid\n" " molid4 (int): Molecule ID for fourth atom, if different from molid\n" " frame (int): Single frame to measure angle in. Defaults to current frame\n" " first (int): First frame in range to measure in, for multiple frames\n" " last (int): Last frame in range to measure in, for multiple frames\n" "Returns:\n" " (list of float): Dihedral as measured in frame(s)" Definition at line 180 of file py_measure.C.

const char measure_moddoc[] [static]

Initial value: "Methods to measure bonds, angles, or dihedrals in loaded molecules" Definition at line 272 of file py_measure.C. Referenced by initmeasure.

PyMethodDef methods[] [static]

Initial value: { {"bond", (PyCFunction)py_measure_bond, METH_VARARGS | METH_KEYWORDS, bond_doc}, {"angle", (PyCFunction)py_measure_angle, METH_VARARGS | METH_KEYWORDS, angle_doc}, {"dihedral", (PyCFunction)py_measure_dihed, METH_VARARGS | METH_KEYWORDS, dihed_doc}, {NULL, NULL} } Definition at line 264 of file py_measure.C. Referenced by initmeasure.

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