Simplify creation of constraints and movers for an IMP Hierarchy. More...

Detailed Description

Simplify creation of constraints and movers for an IMP Hierarchy.

The various "create X" functions make movers for system components as well as set up necessary constraints. For each of these functions, you can generally pass PMI objects like Molecule or slices thereof.
DegreesOfFreedom.create_rigid_body() lets you rigidify a molecule (but allows you to also pass "nonrigid" components which move with the body and also independently).
DegreesOfFreedom.create_super_rigid_body() sets up a special "Super Rigid Body" which moves rigidly but is not always constrained to be rigid (so you can later move the parts separately). This is good for speeding up sampling.
DegreesOfFreedom.create_flexible_beads() sets up particles to move individually.
DegreesOfFreedom.setup_md() sets up particles to move with molecular dynamics. Note that this is not (yet) compatible with rigid bodies, and only works with some restraints.
DegreesOfFreedom.constrain_symmetry() makes a symmetry constraint so that clones automatically move with their references. If instead you want a softer restraint, check out the SymmetryRestraint.
When you are done you can access all movers with DegreesOfFreedom.get_movers(). If you have set up rigid, super rigid, or flexible beads, pass the movers to the monte_carlo_sample_objects argument of ReplicaExchange.
If you are running MD, you have to separately pass the particles (also returned from DegreesOfFreedom.setup_md()) to the molecular_dynamics_sample_objects argument of ReplicaExchange. Check out an MD example here.

Note: This class is only available in Python.

Definition at line 39 of file pmi/dof/__init__.py.

Public Member Functions
def	constrain_symmetry
	Create a symmetry constraint. More...

def	create_flexible_beads
	Create a chain of flexible beads. More...

def	create_main_chain_mover
	Create crankshaft moves from a set of SUPER rigid body mover from one molecule. More...

def	create_nuisance_mover
	Create MC normal mover for nuisance particles. More...

def	create_rigid_body
	Create rigid body constraint and mover. More...

def	create_super_rigid_body
	Create SUPER rigid body mover from one or more hierarchies. More...

def	disable_movers
	Fix the position of the particles by disabling the corresponding movers. More...

def	enable_all_movers
	Re-enable all movers: previously fixed particles will be released. More...

def	get_flexible_beads
	Return all flexible beads, including nonrigid members of rigid bodies. More...

def	get_floppy_body_movers
	Return all movers corresponding to individual beads. More...

def	get_movers
	Returns Enabled movers. More...

def	get_nuisances_from_restraint
	Extract the nuisances from get_particles_to_sample() More...

def	get_rigid_bodies
	Return list of rigid body objects. More...

def	optimize_flexible_beads
	Set up MC run with just flexible beads. More...

def	setup_md
	Setup particles for MD simulation. More...

Member Function Documentation

def IMP.pmi.dof.DegreesOfFreedom.constrain_symmetry	(	self,
		references,
		clones,
		transform,
		resolution = `'all'`,
		type = `'AXIAL'`
	)

Create a symmetry constraint.

Checks: same number of particles disable ANY movers involving symmetry copies (later may support moving them WITH references, but requires code to propagate constraint)

Parameters

references	Can be one of the following inputs: IMP Hierarchy, PMI System/State/Molecule/TempResidue, or a list/set (of list/set) of them
clones	Same format as references
transform	The transform that moves a clone onto a reference IMP.algebra.Transformation3D
resolution	Only used if you pass PMI objects. If you have a multires system, assuming each are rigid bodies you probably only need one resolution.
type	of symmetry. Implemented = AXIAL, RIGID_BODY

Definition at line 403 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.create_flexible_beads	(	self,
		flex_parts,
		max_trans = `3.0`,
		resolution = `'all'`
	)

Create a chain of flexible beads.

Parameters

flex_parts	Can be one of the following inputs: IMP Hierarchy, PMI System/State/Molecule/TempResidue, or a list/set (of list/set) of them. Must be uniform input, however. No mixing object types.
max_trans	Maximum flexible bead translation
resolution	Only used if you pass PMI objects. Probably you want 'all'.

Definition at line 327 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.create_main_chain_mover	(	self,
		molecule,
		resolution = `10`,
		lengths = `[5`
	)

Create crankshaft moves from a set of SUPER rigid body mover from one molecule.

See http://scfbm.biomedcentral.com/articles/10.1186/1751-0473-3-12

Definition at line 207 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.create_nuisance_mover	(	self,
		nuisance_p,
		step_size,
		name = `None`
	)

Create MC normal mover for nuisance particles.

We will add an easier interface to add all of them from a PMI restraint

Parameters

nuisance_p	The Nuisance particle (an ISD::Scale)
step_size	The maximum step size for Monte Carlo
name	The name of the mover, useful for better output reading.

Definition at line 366 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.create_rigid_body	(	self,
		rigid_parts,
		nonrigid_parts = `None`,
		max_trans = `4.0`,
		max_rot = `0.5`,
		nonrigid_max_trans = `4.0`,
		resolution = `'all'`,
		name = `None`
	)

Create rigid body constraint and mover.

Parameters

rigid_parts	Can be one of the following inputs: IMP Hierarchy, PMI System/State/Molecule/TempResidue, a list/set (of list/set) of them or a RigidBody object. Must be uniform input, however. No mixing object types.
nonrigid_parts	Same input format as rigid_parts. Must be a subset of rigid_parts particles.
max_trans	Maximum rigid body translation
max_rot	Maximum rigid body rotation
nonrigid_max_trans	Maximum step for the nonrigid (bead) particles
resolution	Only used if you pass PMI objects. Probably you want 'all'.
name	Rigid body name (if None, use IMP default)

Returns: (rb_movers,rb_object)

Note: If you want all resolutions, pass PMI objects because this function will get them all. Alternatively you can do your selection elsewhere and just pass hierarchies.

Definition at line 92 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.create_super_rigid_body	(	self,
		srb_parts,
		max_trans = `1.0`,
		max_rot = `0.1`,
		chain_min_length = `None`,
		chain_max_length = `None`,
		resolution = `'all'`,
		name = `None`,
		axis = `None`
	)

Create SUPER rigid body mover from one or more hierarchies.

Can also create chain of SRBs. If you don't pass chain min/max, it'll treat everything you pass as ONE rigid body. If you DO pass chain min/max, it'll expect srb_parts is a list and break it into bits.

Parameters

srb_parts	Can be one of the following inputs: IMP Hierarchy, PMI System/State/Molecule/TempResidue, or a list/set (of list/set) of them. Must be uniform input, however. No mixing object types.
max_trans	Maximum super rigid body translation
max_rot	Maximum super rigid body rotation
chain_min_length	Create a CHAIN of super rigid bodies - must provide list; this parameter is the minimum chain length.
chain_max_length	Maximum chain length
resolution	Only used if you pass PMI objects. Probably you want 'all'.
name	The name of the SRB (hard to assign a good one automatically)
axis	A tuple containing two particles which are used to compute the rotation axis of the SRB. The default is None, meaning that the rotation axis is random.

Note: If you set the chain parameters, will NOT create an SRB from all of them together, but rather in groups made from the outermost list.

Definition at line 236 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.disable_movers	(	self,
		objects,
		mover_types = `None`
	)

Fix the position of the particles by disabling the corresponding movers.

Parameters

objects	Can be one of the following inputs: IMP Hierarchy, PMI System/State/Molecule/TempResidue, or a list/set (of list/set) of them. Must be uniform input, however. No mixing object types.
mover_types	further filter the mover type that will be disabled; it can be a list of IMP.core.RigidBodyMover, IMP.core.BallMover etc etc if one wants to fix the corresponding rigid body, or the floppy bodies. An empty mover_types list is interpreted as all possible movers. It returns the list of fixed xyz particles (ie, floppy bodies/beads) and rigid bodies whose movers were disabled

Definition at line 542 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.enable_all_movers ( self )

Re-enable all movers: previously fixed particles will be released.

Definition at line 576 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.get_flexible_beads ( self )

Return all flexible beads, including nonrigid members of rigid bodies.

Definition at line 527 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.get_floppy_body_movers ( self )

Return all movers corresponding to individual beads.

Definition at line 519 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.get_movers ( self )

Returns Enabled movers.

Definition at line 508 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.get_nuisances_from_restraint	(	self,
		r
	)

Extract the nuisances from get_particles_to_sample()

Definition at line 580 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.get_rigid_bodies ( self )

Return list of rigid body objects.

Definition at line 523 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.optimize_flexible_beads	(	self,
		nsteps,
		temperature = `1.0`
	)

Set up MC run with just flexible beads.

Optimization works much better when restraints are already set up.

Definition at line 495 of file pmi/dof/__init__.py.

def IMP.pmi.dof.DegreesOfFreedom.setup_md	(	self,
		hspec
	)

Setup particles for MD simulation.

Returns all particles, just pass this to molecular_dynamics_sample_objects in ReplicaExchange.

Parameters

hspec Can be one of the following inputs: IMP Hierarchy, PMI System/State/Molecule/TempResidue, or a list/set (of list/set) of them. Must be uniform input, however. No mixing object types.

Definition at line 383 of file pmi/dof/__init__.py.

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

pmi/dof/__init__.py

Detailed Description

Public Member Functions

Member Function Documentation