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IMP Reference Guide
2.13.0
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.pmi1.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.
ote Wraps an IMP::isd::AtomicCrossLinkMSRestraint
Definition at line 495 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.pmi1.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.pmi1.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.pmi1.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.
ote Will return an error if the data+extra_sel don't specify two particles per XL pair.
| 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 517 of file /restraints/crosslinking.py.
| def IMP.pmi1.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 752 of file /restraints/crosslinking.py.
| def IMP.pmi1.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 944 of file /restraints/crosslinking.py.
| def IMP.pmi1.restraints.crosslinking.AtomicCrossLinkMSRestraint.get_particles_to_sample | ( | self | ) |
Get the particles to be sampled by the IMP.pmi1.sampler object.
Definition at line 777 of file /restraints/crosslinking.py.
| def IMP.pmi1.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 803 of file /restraints/crosslinking.py.
| def IMP.pmi1.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 824 of file /restraints/crosslinking.py.