IMP.pmi.dof.dof Class Reference

Degrees of Freedom. More...

Inherits object.

Detailed Description

Degrees of Freedom.

Tasks: define rigid bodies and super rigid bodies define symmetries (see representation.py) create nuisances and their parameters generate lists of MC or MD movers

Note

This class is only available in Python.

Definition at line 12 of file dof.py.

Public Member Functions
def	remove_floppy_bodies
	give a list of hierarchies, get the leaves and remove the corresponding particles from the floppy bodies list. More...
def	set_chain_of_super_rigid_bodies
	this function takes a linear list of hierarchies (they are supposed to be sequence-contiguous) and produces a chain of super rigid bodies with given length range, specified by min_length and max_length More...
def	set_rigid_bodies
	This method allows the construction of a rigid body given a list of tuples, that identify the residue ranges and the subunit names (the names used to create the component by using create_component. More...
def	set_rigid_body_from_hierarchies
	This method allows the construction of a rigid body given a list of hierarchies and or a list of particles. More...

Member Function Documentation

def IMP.pmi.dof.dof.remove_floppy_bodies	(		self,
			hierarchies
	)

give a list of hierarchies, get the leaves and remove the corresponding particles from the floppy bodies list.

We need this function because sometimes we want to constraint the floppy bodies in a rigid body. For instance when you want to associate a bead with a density particle.

Definition at line 198 of file dof.py.

def IMP.pmi.dof.dof.set_chain_of_super_rigid_bodies	(		self,
			hiers,
			min_length = None,
			max_length = None,
			axis = None
	)

this function takes a linear list of hierarchies (they are supposed to be sequence-contiguous) and produces a chain of super rigid bodies with given length range, specified by min_length and max_length

Definition at line 147 of file dof.py.

def IMP.pmi.dof.dof.set_rigid_bodies	(		self,
			subunits
	)

This method allows the construction of a rigid body given a list of tuples, that identify the residue ranges and the subunit names (the names used to create the component by using create_component.

subunits: [(name_1,(first_residue_1,last_residue_1)),(name_2,(first_residue_2,last_residue_2)),.....] or [name_1,name_2,(name_3,(first_residue_3,last_residue_3)),.....]

example: ["prot1","prot2",("prot3",(1,10))]

sometimes, we know about structure of an interaction and here we make such PPIs rigid

Definition at line 63 of file dof.py.

def IMP.pmi.dof.dof.set_rigid_body_from_hierarchies	(		self,
			hiers,
			particles = None
	)

This method allows the construction of a rigid body given a list of hierarchies and or a list of particles.

hiers: list of hierarchies particles: (optional, default=None) list of particles to add to the rigid body

Definition at line 31 of file dof.py.

---

The documentation for this class was generated from the following file:

• dof.py