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)

Bases: object

__init__(ct=None)

get_vector_atoms_from_internal_coords()

update_internal_coords_to_vector_atoms(coords1, coords2)

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

getCenterOrientationOfAtoms(atom_list)

autoPlaceByMolecule(mol_atom_lists)

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

placeFromExplicitMembrane()

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

writePrimeProperties()

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

findHydrophobicCenter()

Returns coordinates of center of mass of all hydrophobic residues

autoPlace()

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

rotateProteinToMembrane()

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()

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()

Show the membrane group

hide()

Hide the membrane.

clear()

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

isDefined()

Return True if the membrane dimensions are defined.

write_structure(filename)