Get volume#

Querying amino acid sidechain steric volumes from reference scales.

The function molsysmt.physchem.get_volume() evaluates residue sidechain volumes using established biochemical scales (e.g. Grantham).

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.physchem.get_volume().

Basic usage#

Let’s extract Grantham sidechain volumes for residues in a molecular system:

import molsysmt as msm

molsys = msm.convert(msm.systems['Trp-Cage']['1l2y.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 query sidechain volumes using the Grantham scale:

volumes = msm.physchem.get_volume(molsys, definition='grantham')
print('Sidechain volumes (Grantham):\n', volumes)

Sidechain volumes (Grantham):
 [ 56.  111.  136.  111.   85.  170.  111.  119.   54.    3.    3.   32.5
  32.   32.    3.  124.   32.5  32.5  32.5  32. ]