IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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Simplify creation of constraints and movers for an IMP Hierarchy. More...
Inherits object.
Simplify creation of constraints and movers for an IMP Hierarchy.
monte_carlo_sample_objects
argument of ReplicaExchange0.molecular_dynamics_sample_objects
argument of ReplicaExchange0. Check out an MD example here.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 |
Reenable 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... | |
def IMP.pmi.dof.DegreesOfFreedom.constrain_symmetry | ( | self, | |
references, | |||
clones, | |||
transform, | |||
resolution = 'all' , |
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type = 'AXIAL' |
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) |
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)
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 404 of file pmi/dof/__init__.py.
def IMP.pmi.dof.DegreesOfFreedom.create_flexible_beads | ( | self, | |
flex_parts, | |||
max_trans = 3.0 , |
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resolution = 'all' |
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) |
Create a chain of flexible beads.
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 321 of file pmi/dof/__init__.py.
def IMP.pmi.dof.DegreesOfFreedom.create_main_chain_mover | ( | self, | |
molecule, | |||
resolution = 10 , |
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lengths = [5 |
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) |
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 201 of file pmi/dof/__init__.py.
def IMP.pmi.dof.DegreesOfFreedom.create_nuisance_mover | ( | self, | |
nuisance_p, | |||
step_size, | |||
name = None |
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) |
Create MC normal mover for nuisance particles.
We will add an easier interface to add all of them from a PMI restraint
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 360 of file pmi/dof/__init__.py.
def IMP.pmi.dof.DegreesOfFreedom.create_rigid_body | ( | self, | |
rigid_parts, | |||
nonrigid_parts = None , |
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max_trans = 4.0 , |
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max_rot = 0.5 , |
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nonrigid_max_trans = 4.0 , |
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resolution = 'all' , |
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name = None |
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) |
Create rigid body constraint and mover.
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) |
Definition at line 94 of file pmi/dof/__init__.py.
def IMP.pmi.dof.DegreesOfFreedom.create_super_rigid_body | ( | self, | |
srb_parts, | |||
max_trans = 1.0 , |
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max_rot = 0.1 , |
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chain_min_length = None , |
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chain_max_length = None , |
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resolution = 'all' , |
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name = None , |
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axis = None |
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) |
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.
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. |
Definition at line 229 of file pmi/dof/__init__.py.
def IMP.pmi.dof.DegreesOfFreedom.disable_movers | ( | self, | |
objects, | |||
mover_types = None |
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) |
Fix the position of the particles by disabling the corresponding movers.
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 552 of file pmi/dof/__init__.py.
def IMP.pmi.dof.DegreesOfFreedom.enable_all_movers | ( | self | ) |
Reenable all movers: previously fixed particles will be released.
Definition at line 583 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 541 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 533 of file pmi/dof/__init__.py.
def IMP.pmi.dof.DegreesOfFreedom.get_movers | ( | self | ) |
Returns Enabled movers.
Definition at line 522 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 587 of file pmi/dof/__init__.py.
def IMP.pmi.dof.DegreesOfFreedom.get_rigid_bodies | ( | self | ) |
Return list of rigid body objects.
Definition at line 537 of file pmi/dof/__init__.py.
def IMP.pmi.dof.DegreesOfFreedom.optimize_flexible_beads | ( | self, | |
nsteps, | |||
temperature = 1.0 |
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) |
Set up MC run with just flexible beads.
Optimization works much better when restraints are already set up.
Definition at line 508 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 ReplicaExchange0.
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 380 of file pmi/dof/__init__.py.