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IMP Reference Guide
2.12.0
The Integrative Modeling Platform
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Setup cross-link distance restraints at atomic level The "atomic" aspect is that it models the particle uncertainty with a Gaussian The noise in the data and the structural uncertainty of cross-linked amino-acids is inferred using Bayes' theory of probability. More...
Inheritance diagram for IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint:Setup cross-link distance restraints at atomic level The "atomic" aspect is that it models the particle uncertainty with a Gaussian The noise in the data and the structural uncertainty of cross-linked amino-acids is inferred using Bayes' theory of probability.
Definition at line 473 of file restraints/crosslinking.py.
Public Member Functions | |
| def | __init__ |
| Constructor. More... | |
| def | create_restraints_for_rmf |
| create dummy harmonic restraints for each XL but don't add to model Makes it easy to see each contribution to each XL in RMF More... | |
| def | get_best_stats |
| return the probability, best distance, two coords, and possibly the psi for each xl More... | |
| def | get_particles_to_sample |
| Get the particles to be sampled by the IMP.pmi.sampler object. More... | |
| def | load_nuisances_from_stat_file |
| Read a stat file and load all the sigmas. More... | |
| def | plot_violations |
| Create CMM files, one for each state, of all crosslinks. More... | |
| Public Member Functions inherited from IMP.pmi.restraints.RestraintBase | |
| def | __init__ |
| Constructor. More... | |
| def | add_to_model |
| Add the restraint to the model. More... | |
| def | evaluate |
| Evaluate the score of the restraint. More... | |
| def | get_output |
| Get outputs to write to stat files. More... | |
| def | get_particles_to_sample |
| Get any created particles which should be sampled. More... | |
| def | get_restraint |
| Get the primary restraint set. More... | |
| def | get_restraint_for_rmf |
| Get the restraint for visualization in an RMF file. More... | |
| def | get_restraint_set |
| Get the primary restraint set. More... | |
| def | set_label |
| Set the unique label used in outputs and particle/restraint names. More... | |
| def | set_weight |
| Set the weight to apply to all internal restraints. More... | |
| def IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint.__init__ | ( | self, | |
| root_hier, | |||
| xldb, | |||
atom_type = 'NZ', |
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length = 10.0, |
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slope = 0.01, |
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nstates = None, |
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label = None, |
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nuisances_are_optimized = True, |
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sigma_init = 5.0, |
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psi_init = 0.01, |
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one_psi = True, |
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filelabel = None, |
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weight = 1.0 |
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| ) |
Constructor.
Automatically creates one "sigma" per crosslinked residue and one "psis" per pair. Other nuisance options are available.
| root_hier | The root hierarchy on which you'll do selection |
| xldb | CrossLinkDataBase object |
| atom_type | Can either be "NZ" or "CA" |
| length | The XL linker length |
| slope | Linear term to add to the restraint function to help when far away |
| nstates | The number of states to model. Defaults to the number of states in root. |
| label | The output label for the restraint |
| nuisances_are_optimized | Whether to optimize nuisances |
| sigma_init | The initial value for all the sigmas |
| psi_init | The initial value for all the psis |
| one_psi | Use a single psi for all restraints (if False, creates one per XL) |
| filelabel | automatically generated file containing missing/included/excluded cross-links will be labeled using this text |
| weight | Weight of restraint |
Definition at line 492 of file restraints/crosslinking.py.
| def IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint.create_restraints_for_rmf | ( | self | ) |
create dummy harmonic restraints for each XL but don't add to model Makes it easy to see each contribution to each XL in RMF
Definition at line 734 of file restraints/crosslinking.py.
| def IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint.get_best_stats | ( | self, | |
limit_to_state = None, |
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limit_to_chains = None, |
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exclude_chains = '', |
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use_CA = False |
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| ) |
return the probability, best distance, two coords, and possibly the psi for each xl
| limit_to_state | Only examine contributions from one state |
| limit_to_chains | Returns the particles for certain "easy to visualize" chains |
| exclude_chains | Even if you limit, don't let one end be in this list. Only works if you also limit chains |
| use_CA | Limit to CA particles |
Definition at line 926 of file restraints/crosslinking.py.
| def IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint.get_particles_to_sample | ( | self | ) |
Get the particles to be sampled by the IMP.pmi.sampler object.
Definition at line 759 of file restraints/crosslinking.py.
| def IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint.load_nuisances_from_stat_file | ( | self, | |
| in_fn, | |||
| nframe | |||
| ) |
Read a stat file and load all the sigmas.
This is potentially quite stupid. It's also a hack since the sigmas should be stored in the RMF file. Also, requires one sigma and one psi for ALL XLs.
Definition at line 785 of file restraints/crosslinking.py.
| def IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint.plot_violations | ( | self, | |
| out_prefix, | |||
max_prob_for_violation = 0.1, |
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min_dist_for_violation = 1000000000.0, |
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coarsen = False, |
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limit_to_chains = None, |
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exclude_chains = '' |
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| ) |
Create CMM files, one for each state, of all crosslinks.
will draw in GREEN if non-violated in all states (or if only one state) will draw in PURPLE if non-violated only in a subset of states (draws nothing elsewhere) will draw in RED in ALL states if all violated (if only one state, you'll only see green and red)
| out_prefix | Output xlink files prefix |
| max_prob_for_violation | It's a violation if the probability is below this |
| min_dist_for_violation | It's a violation if the min dist is above this |
| coarsen | Use CA positions |
| limit_to_chains | Try to visualize just these chains |
| exclude_to_chains | Try to NOT visualize these chains |
Definition at line 806 of file restraints/crosslinking.py.