schrodinger.protein.membrane module

Module for displaying and manipulating a membrane.

Used by Prime panel and System Builder

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.protein.membrane.Membrane_Model(ct=None)

Bases: object

__init__(ct=None)

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

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)

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()

Stores OpenGL representation of the membrane box (2 red squares) in this instance. These boxes can later be drawn to the workspace by calling the draw() method.

The membrane info is taken from center/orientation/thickness

draw()

Draws the red membrane squires to the workspace. Should be invoked within a workspace_draw routine.

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)