Get angles#

Calculating bond and valence angles defined by atom triplets.

The function molsysmt.structure.get_angles() computes planar angles formed by sequences of three atoms \((A, B, C)\) where \(B\) is the central apex atom.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.structure.get_angles().

Basic usage#

Let’s calculate the valence angle formed by three consecutive atoms in Met-enkephalin:

import molsysmt as msm
import pyunitwizard as puw
import matplotlib.pyplot as plt

molsys = msm.convert(msm.systems['Met-enkephalin']['met_enkephalin.h5msm'])

Note

Demo Systems Catalog

This tutorial uses demonstration datasets provided by MolSysMT. To explore the full catalog of bundled systems, forms, and file paths, visit the Demo Systems guide.

We select the first three atoms and evaluate their angle with molsysmt.structure.get_angles():

triplet = [0, 1, 2]
angle = msm.structure.get_angles(molsys, triplets=triplet)
print('Valence angle (radians):', angle)
print('Valence angle (degrees):', puw.convert(angle, to_unit='degrees'))

Valence angle (radians): [[0.6446696079651566]] radian
Valence angle (degrees): [[36.93684771675683]] degree

Angle evolution across structural ensembles#

When evaluating angles across multi-structure systems or molecular dynamics simulations, molsysmt.structure.get_angles() tracks the angular fluctuation profile:

traj = msm.convert(msm.systems['pentalanine']['traj_pentalanine.h5msm'])
time = msm.get(traj, time=True)
angles_series = msm.structure.get_angles(traj, triplets=[0, 1, 2])
angles_deg = puw.get_value(puw.convert(angles_series[:, 0], to_unit='degrees'))
time_ns = puw.get_value(puw.convert(time, to_unit='ns'))

fig, ax = plt.subplots(figsize=(7, 3.5))
ax.plot(time_ns, angles_deg, color='teal', lw=1.0)
ax.set_xlabel('Time (ns)')
ax.set_ylabel('Angle (degrees)')
ax.set_title('Valence Angle Fluctuations Across Structures')
plt.tight_layout()
plt.show()

../../../../_images/ad8dd7b722fd56c170462c41a08e9a36941537af231f0c17b4fa65fbc987cba5.png

Computing multiple angle triplets concurrently#

Multiple atom triplets can be passed simultaneously as a list of 3-tuples:

triplets = [[0, 1, 2], [1, 2, 3], [2, 3, 4]]
angles_multi = msm.structure.get_angles(molsys, triplets=triplets)
print('Multiple angles (degrees):', puw.convert(angles_multi, to_unit='degrees'))

Multiple angles (degrees): [[36.93684771675683 120.03546704196674 42.49416671770135]] degree