Center#

Centering a molecular system around coordinate origin or reference points.

The function molsysmt.structure.center() translates a molecular system so that its center of geometry (or center of mass) coincides with a specified target point (such as the coordinate origin [0.0, 0.0, 0.0] nm).

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.center().

Basic usage#

Let’s show how to center a pentalanine trajectory around the coordinate origin:

import molsysmt as msm
import numpy as np
import matplotlib.pyplot as plt

molsys = msm.convert(msm.systems['pentalanine']['traj_pentalanine.h5'], to_form='molsysmt.MolSys')

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 compute the geometric center before centering and plot its coordinate trajectories across simulation frames:

center_before = msm.structure.get_center(molsys)
time = msm.get(molsys, element='system', time=True)

plt.figure(figsize=(6, 4))
plt.plot(center_before[:, 0, 0], label='x')
plt.plot(center_before[:, 0, 1], label='y')
plt.plot(center_before[:, 0, 2], label='z')
plt.xlabel('Structure index')
plt.ylabel('Center position [nm]')
plt.legend()
plt.show()

../../../../_images/d0bf3b0909195357c886e692952b9209f2bb62f2b3d1d091c5821721eeef4d27.png

Now we center the molecular system using molsysmt.structure.center():

molsys_centered = msm.structure.center(molsys)
center_after = msm.structure.get_center(molsys_centered)

We verify that the distance of the geometric center from the origin is now zero across all frames:

dist_before = np.linalg.norm(center_before[:, 0, :], axis=1)
dist_after = np.linalg.norm(center_after[:, 0, :], axis=1)

plt.figure(figsize=(6, 4))
plt.plot(dist_before, label='Before centering', color='coral')
plt.plot(dist_after, label='After centering', color='teal')
plt.xlabel('Structure index')
plt.ylabel('Distance to origin [nm]')
plt.legend()
plt.show()

../../../../_images/075e953c612de1661539773c08338c35b718cd61c529a1be4852701d337342c1.png

Centering on a sub-selection or custom point#

We can center the whole system based on the center of a specific sub-selection (such as only C-alpha atoms) using center_of_selection, or relocate it to custom coordinates using center_coordinates:

molsys_ca_centered = msm.structure.center(molsys, selection='all', center_of_selection='atom_name=="CA"')
ca_center = msm.structure.get_center(molsys_ca_centered, selection='atom_name=="CA"')
print('CA center at frame 0:', ca_center[0])

CA center at frame 0: [[0.0 0.0 -1.1102230246251566e-17]] nanometer

molsys_custom = msm.structure.center(molsys, center_coordinates='[1.0, 1.0, 1.0] nm')
custom_center = msm.structure.get_center(molsys_custom)
print('System center at custom coordinates:', custom_center[0])

System center at custom coordinates: [[0.9999999999999993 1.0000000000000007 1.0000000000000009]] nanometer