schrodinger.protein.membrane module

Module for displaying and manipulating a membrane.

Used by Prime panel, System Builder, and thermal_mmgbsa.py

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.protein.membrane.Membrane_Model(ct=None)[source]

Bases: object

__init__(ct=None)[source]

Initialize self. See help(type(self)) for accurate signature.

get_vector_atoms_from_internal_coords()[source]
update_internal_coords_to_vector_atoms(coords1, coords2)[source]

Update internal coordinates from 2 numpy arrays containing the x,y,z coordinates of two atoms defining the membrane.

getCenterOrientationOfAtoms(atom_list)[source]
autoPlaceByMolecule(mol_atom_lists)[source]

Auto places the membrane based on the average vector between all specified molecules (list of atom iterators)

placeFromExplicitMembrane()[source]

Attempt to detect explicit membrane atoms in the structure, and set self.center and self.orientation based on its orientation.

writePrimeProperties()[source]

Add implicit membrane properties to the structure, based on the current membrane orientation.

findHydrophobicCenter()[source]

Returns coordinates of center of mass of all hydrophobic residues

autoPlace()[source]

Automatically orient the membrane according to the protein in self.ct

rotateProteinToMembrane()[source]

Translate the protein so that the membrane will be located at the origin and rotate the protein so that membrane is along the z-axis. Assumes that center/orientation/thickness are set.

At the end the protein will not have vector atoms.

calculateMembraneBox()[source]

Creates 3D objects for the representation of the membrane box (2 red squares) in this instance.

The membrane info is taken from center/orientation/thickness

show()[source]

Show the membrane group

hide()[source]

Hide the membrane.

clear()[source]

Remove the 3D objects from the group, which removes them from Maestro’s fit bounds.

isDefined()[source]

Return True if the membrane dimensions are defined.

write_structure(filename)[source]