schrodinger.application.matsci.msmembrane module

Utilities for complex bilayer and membrane systems.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.msmembrane.get_transmembrane_atom_indices(protein_st, normal_axis=2)

Get the atom indices of protein atoms in the transmembrane region

Parameters:

  • protein_st (Structure) – Protein structure

  • normal_axis (int) – Axis normal to the membrane.

Return type:

np.array(int)

Returns:

0-based atom indices in transmembrane region

schrodinger.application.matsci.msmembrane.get_protein_xyz_transmembrane(protein_st, normal_axis=2)

Get the protein coordinates in the transmembrane region

Parameters:

  • protein_st (Structure) – Protein structure

  • normal_axis (int) – Axis normal to the membrane.

Return type:

numpy.array

Returns:

Protein coordinates in the transmembrane region

schrodinger.application.matsci.msmembrane.get_protein_xyz_per_leaflet(protein_st, normal_axis=2)

Get the protein coordinates in the upper and lower leaflets

Parameters:

  • protein_st (Structure) – Protein structure

  • normal_axis (int) – Axis normal to the membrane.

Return type:

tuple(numpy.array)

Returns:

(protein coordinates in upper leaflet, protein coordinates in lower leaflet)

schrodinger.application.matsci.msmembrane.estimate_protein_area(protein_st, normal_axis=2)

Estimate the area of the protein in the upper and lower leaflets

Parameters:

  • protein_st (Structure) – Protein structure

  • normal_axis (int) – Axis normal to the membrane.

Return type:

dict

Returns:

Dictionary of protein area (in square angstrom) in upper and lower leaflets