%load_ext autoreload
%autoreload 2

import molsysmt as msm
from matplotlib import pyplot as plt

Get SASA#

molecular_system = msm.convert('1tcd')

molecular_system = msm.remove(molecular_system, selection='molecule_type==["water", "ion", "cosolute"]')

msm.info(molecular_system)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_proteins	n_structures
molsysmt.MolSys	3818	497	2	2	2	1	2	1

sasa_per_residue = msm.physchem.get_sasa(molecular_system, element='group')

group_index = msm.get(molecular_system, element='group', index=True)
plt.scatter(group_index, sasa_per_residue[0])

/home/diego/Myopt/miniconda3/envs/MolSysMT@uibcdf_3.12/lib/python3.12/site-packages/numpy/ma/core.py:2820: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
  _data = np.array(data, dtype=dtype, copy=copy,

<matplotlib.collections.PathCollection at 0x7f342d66f290>

../../../../_images/67d84e9a95e0dc35d6b287c61e73398ae8b1011def8b6b66ae40a897d885bceb.png

sasa_per_molecule = msm.physchem.get_sasa(molecular_system, element='molecule')

sasa_per_molecule

Magnitude	[[96.37336730957031 98.58065795898438]]
Units	nanometer²