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IMP
2.3.1
The Integrative Modeling Platform
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IMP
2.3.1
The Integrative Modeling Platform
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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. More...
Inherits object.
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.
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... | |
| 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.
| def IMP.pmi.dof.dof.set_chain_of_super_rigid_bodies | ( | self, | |
| hiers, | |||
min_length = None, |
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max_length = None, |
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axis = None |
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| ) |
| 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
| def IMP.pmi.dof.dof.set_rigid_body_from_hierarchies | ( | self, | |
| hiers, | |||
particles = None |
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| ) |