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IMP Reference Guide
2.8.0
The Integrative Modeling Platform
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A class to simplify create of constraints and movers for an IMP Hierarchy. More...
Inherits object.
A class to simplify create of constraints and movers for an IMP Hierarchy.
Call the various create() functions to get started. Can get all enabled movers with get_movers(). Pass this to ReplicaExchange0.
Definition at line 35 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 350 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 272 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 164 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 306 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) |
ote 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. Returns tuple (rb_movers,rb_object)
Definition at line 58 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. |
ote 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 185 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 498 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 529 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 487 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 479 of file pmi/dof/__init__.py.
| def IMP.pmi.dof.DegreesOfFreedom.get_movers | ( | self | ) |
Returns Enabled movers.
Definition at line 468 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 533 of file pmi/dof/__init__.py.
| def IMP.pmi.dof.DegreesOfFreedom.get_rigid_bodies | ( | self | ) |
Return list of rigid body objects.
Definition at line 483 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 454 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 326 of file pmi/dof/__init__.py.
