IMP Reference Guide
2.20.2
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...
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.