measure.md

Measurements

Among other utilities pyvmd provides also functions to measure properties of system. The utilities reside in module pyvmd.measure.

List of functions

• distance(a, b) - returns distance between two atoms a and b.
• angle(a, b, c) - returns angle between three atoms a, b and c.
• dihedral(a, b, c, d) - returns dihedral or improper dihedral angle of four atoms a, b, c and d.
• center(selection) - returns coordinates of geometric center of the selection or iterable of atoms.

Examples

from pyvmd import measure
from pyvmd.atoms import Atom, Residue, Selection

# Measure distance between atoms
measure.distance(Atom(0), Atom(42))  #>>> 4.578

# Measure angle between atoms
measure.angle(Atom(0), Atom(42), Atom(1))  #>>> 73.278

# Measure dihedral angle of atoms
measure.dihedral(Atom(0), Atom(42), Atom(1), Atom(2))  #>>> -58.378

# Measure center of selection
measure.center(Selection('all and noh'))  #>>> array([0.25, 0.78, 80.58])
# Measure center of residue
measure.center(Residue(12))  #>>> array([12.89, 57.32, 75.38])
# Measure center of atom iterable
my_atoms = (Atom(i) for i in xrange(10))
measure.center(my_atoms)  #>>> array([8.95, 3.9, -59.3])
# Center of atom is equal to its coordinates
measure.center(Atom(0)) == Atom(0).coords  #>>> array([ True,  True,  True])