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)¶