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.
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class
schrodinger.protein.membrane.
Membrane_Model
(ct=None)[source]¶ Bases:
object
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update_internal_coords_to_vector_atoms
(coords1, coords2)[source]¶ Update internal coordinates from 2 numpy arrays containing the x,y,z coordinates of two atoms defining the membrane.
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autoPlaceByMolecule
(mol_atom_lists)[source]¶ Auto places the membrane based on the average vector between all specified molecules (list of atom iterators)
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placeFromExplicitMembrane
()[source]¶ Attempt to detect explicit membrane atoms in the structure, and set self.center and self.orientation based on its orientation.
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writePrimeProperties
()[source]¶ Add implicit membrane properties to the structure, based on the current membrane orientation.
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rotateProteinToMembrane
()[source]¶ 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.
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calculateMembraneBox
()[source]¶ 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
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