IMP Reference Guide
2.20.2
The Integrative Modeling Platform
|
Restrain particles to be above, below, or inside a planar membrane. More...
Inherits RestraintBase.
Restrain particles to be above, below, or inside a planar membrane.
The membrane is defined to lie on the xy plane with a given z coordinate and thickness, and particles are restrained (by their z coordinates) with a simple sigmoid score.
Definition at line 309 of file restraints/basic.py.
Public Member Functions | |
def | __init__ |
Setup the restraint. More... | |
def | create_membrane_density |
Create an MRC density file to visualize the membrane. More... | |
def IMP.pmi.restraints.basic.MembraneRestraint.__init__ | ( | self, | |
hier, | |||
objects_above = None , |
|||
objects_inside = None , |
|||
objects_below = None , |
|||
center = 0.0 , |
|||
thickness = 30.0 , |
|||
softness = 3.0 , |
|||
plateau = 1e-10 , |
|||
resolution = 1 , |
|||
weight = 1.0 , |
|||
label = None |
|||
) |
Setup the restraint.
objects_inside | list or tuples of objects in membrane (e.g. ['p1', (10, 30,'p2')]) |
objects_above | list or tuples of objects above membrane |
objects_below | list or tuples of objects below membrane |
thickness | Thickness of the membrane along the z-axis |
softness | Softness of the limiter in the sigmoid function |
plateau | Parameter to set the probability (=1- plateau)) at the plateau phase of the sigmoid |
weight | Weight of restraint |
label | A unique label to be used in outputs and particle/restraint names. |
Definition at line 323 of file restraints/basic.py.
def IMP.pmi.restraints.basic.MembraneRestraint.create_membrane_density | ( | self, | |
file_out = 'membrane_localization.mrc' |
|||
) |
Create an MRC density file to visualize the membrane.
Definition at line 416 of file restraints/basic.py.