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)

autoPlace()

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

autoPlaceByMolecule(mol_atom_lists)

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

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

clear()

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

createVectorAtoms()

Add vector dummy atoms to the specified Structure based on membrane coordinates

deleteVectorAtoms()

Delete the vector atoms

draw()

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

findHydrophobicCenter()

Returns coordinates of center of mass of all hydrophobic residues

findVectorAtoms()

Return a list of 2 atom numbers for the vector dummy atoms

generate_dummy_atoms()

getCenterOrientationOfAtoms(atom_list)

get_vector_atoms_from_internal_coords()

isDefined()

Return True if the membrane dimensions are defined.

remove_dummy_atoms()

Delete the vector atoms and other dummy atoms

rotateProteinToMembrane(rotate_membrane=True)

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.

rotate_membrane = whether to adjust self.center/self.orientation according to the new position (orientation along z-axis).

updateFromVector()

Update internal coordinates from vector dummy atoms in self.ct

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.

write_parameter_file(filename)

write_structure(filename)