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
()¶ 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)¶
-