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IMP Reference Guide
develop.d97d4ead1f,2024/11/22
The Integrative Modeling Platform
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Setup cross-link distance restraints from mass spectrometry data. More...
Inherits RestraintBase.
Setup cross-link distance restraints from mass spectrometry data.
The noise in the data and the structural uncertainty of cross-linked amino-acids is inferred using Bayes theory of probability
Definition at line 22 of file crosslinking.py.
Public Member Functions | |
| def | __init__ |
| Constructor. More... | |
| def | create_psi |
| This is called internally. More... | |
| def | create_sigma |
| This is called internally. More... | |
| def | get_hierarchies |
| get the hierarchy More... | |
| def | get_likelihood |
| Get the unweighted likelihood of the restraint. More... | |
| def | get_movers |
| Get all need data to construct a mover in IMP.pmi.dof class. More... | |
| def | get_output |
| Get the output of the restraint to be used by the IMP.pmi.output object. More... | |
| def | get_particle_pairs |
| Get a list of tuples containing the particle pairs. More... | |
| def | get_particles_to_sample |
| Get the particles to be sampled by the IMP.pmi.sampler object. More... | |
| def | get_restraint_for_rmf |
| get the dummy restraints to be displayed in the rmf file More... | |
| def | get_restraint_sets |
| get the restraint set More... | |
| def | get_restraints |
| get the restraints in a list More... | |
| def | set_output_level |
| Set the output level of the output. More... | |
| def | set_psi_is_sampled |
| Switch on/off the sampling of psi particles. More... | |
| def | set_sigma_is_sampled |
| Switch on/off the sampling of sigma particles. More... | |
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.__init__ | ( | self, | |
| root_hier, | |||
database = None, |
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length = 10.0, |
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resolution = None, |
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slope = 0.02, |
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label = None, |
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filelabel = 'None', |
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attributes_for_label = None, |
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linker = None, |
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weight = 1.0 |
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| ) |
Constructor.
| root_hier | The canonical hierarchy containing all the states |
| database | The IMP.pmi.io.crosslink.CrossLinkDataBase object that contains the cross-link dataset |
| length | maximal cross-linker length (including the residue sidechains) |
| resolution | what representation resolution should the cross-link restraint be applied to. |
| slope | The slope of a distance-linear scoring function that funnels the score when the particles are too far away. Suggested value 0.02. |
| label | the extra text to label the restraint so that it is searchable in the output |
| filelabel | automatically generated file containing missing/included/excluded cross-links will be labeled using this text |
| attributes_for_label | |
| weight | Weight of restraint |
| linker | description of the chemistry of the linker itself, as an ihm.ChemDescriptor object (see https://python-ihm.readthedocs.io/en/latest/main.html#ihm.ChemDescriptor). Common cross-linkers can be found in the ihm.cross_linkers module. |
Definition at line 46 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.create_psi | ( | self, | |
| name | |||
| ) |
This is called internally.
Creates a nuisance on the data uncertainty
Definition at line 401 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.create_sigma | ( | self, | |
| name | |||
| ) |
This is called internally.
Creates a nuisance on the structural uncertainty
Definition at line 373 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_hierarchies | ( | self | ) |
get the hierarchy
Definition at line 336 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_likelihood | ( | self | ) |
Get the unweighted likelihood of the restraint.
Definition at line 456 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_movers | ( | self | ) |
Get all need data to construct a mover in IMP.pmi.dof class.
Definition at line 464 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_output | ( | self | ) |
Get the output of the restraint to be used by the IMP.pmi.output object.
Definition at line 425 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_particle_pairs | ( | self | ) |
Get a list of tuples containing the particle pairs.
Definition at line 352 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_particles_to_sample | ( | self | ) |
Get the particles to be sampled by the IMP.pmi.sampler object.
Definition at line 495 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_restraint_for_rmf | ( | self | ) |
get the dummy restraints to be displayed in the rmf file
Definition at line 348 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_restraint_sets | ( | self | ) |
get the restraint set
Definition at line 340 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_restraints | ( | self | ) |
get the restraints in a list
Definition at line 344 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.set_output_level | ( | self, | |
level = 'low' |
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| ) |
Set the output level of the output.
Definition at line 361 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.set_psi_is_sampled | ( | self, | |
is_sampled = True |
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| ) |
Switch on/off the sampling of psi particles.
Definition at line 365 of file crosslinking.py.
| def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.set_sigma_is_sampled | ( | self, | |
is_sampled = True |
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| ) |
Switch on/off the sampling of sigma particles.
Definition at line 369 of file crosslinking.py.