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.

generate_dummy_atoms()

findVectorAtoms()

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

remove_dummy_atoms()

Delete the vector atoms and other dummy atoms

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.

updateFromVector()

Update internal coordinates from vector dummy atoms in self.ct

createVectorAtoms()

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

deleteVectorAtoms()

Delete the vector atoms

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(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).

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)

write_parameter_file(filename)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.membrane', '__init__': <function Membrane_Model.__init__>, 'generate_dummy_atoms': <function Membrane_Model.generate_dummy_atoms>, 'findVectorAtoms': <function Membrane_Model.findVectorAtoms>, 'remove_dummy_atoms': <function Membrane_Model.remove_dummy_atoms>, 'get_vector_atoms_from_internal_coords': <function Membrane_Model.get_vector_atoms_from_internal_coords>, 'update_internal_coords_to_vector_atoms': <function Membrane_Model.update_internal_coords_to_vector_atoms>, 'updateFromVector': <function Membrane_Model.updateFromVector>, 'createVectorAtoms': <function Membrane_Model.createVectorAtoms>, 'deleteVectorAtoms': <function Membrane_Model.deleteVectorAtoms>, 'getCenterOrientationOfAtoms': <function Membrane_Model.getCenterOrientationOfAtoms>, 'autoPlaceByMolecule': <function Membrane_Model.autoPlaceByMolecule>, 'findHydrophobicCenter': <function Membrane_Model.findHydrophobicCenter>, 'autoPlace': <function Membrane_Model.autoPlace>, 'rotateProteinToMembrane': <function Membrane_Model.rotateProteinToMembrane>, 'calculateMembraneBox': <function Membrane_Model.calculateMembraneBox>, 'draw': <function Membrane_Model.draw>, 'show': <function Membrane_Model.show>, 'hide': <function Membrane_Model.hide>, 'clear': <function Membrane_Model.clear>, 'isDefined': <function Membrane_Model.isDefined>, 'write_structure': <function Membrane_Model.write_structure>, 'write_parameter_file': <function Membrane_Model.write_parameter_file>, '__dict__': <attribute '__dict__' of 'Membrane_Model' objects>, '__weakref__': <attribute '__weakref__' of 'Membrane_Model' objects>, '__doc__': None})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.membrane'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)