Miscellaneous utilities.
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def | add_restraint_to_model |
| Add a PMI restraint to the model. More...
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def | cross_link_db_filter_parser |
| example '"{ID_Score}" > 28 AND "{Sample}" == "%10_1%" OR ":Sample}" == "%10_2%" OR ":Sample}" == "%10_3%" OR ":Sample}" == "%8_1%" OR ":Sample}" == "%8_2%"' More...
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def | get_closest_residue_position |
| this function works with plain hierarchies, as read from the pdb, no multi-scale hierarchies More...
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def | get_prot_name_from_particle |
| Return the component name provided a particle and a list of names. More...
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def | get_random_cross_link_dataset |
| Return a random cross-link dataset as a string. More...
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def | get_residue_gaps_in_hierarchy |
| Return the residue index gaps and contiguous segments in the hierarchy. More...
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def | get_residue_indexes |
| Retrieve the residue indexes for the given particle. More...
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def | get_restraint_set |
| Get a RestraintSet containing all PMI restraints added to the model. More...
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def | get_terminal_residue |
| Get the particle of the terminal residue at the GIVEN resolution (NOTE: not the closest resolution!). More...
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def | get_terminal_residue_position |
| Get XYZ coordinates of the terminal residue at the GIVEN resolution. More...
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def | scatter_and_gather |
| Synchronize data over a parallel run. More...
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def | select |
| this function uses representation=SimplifiedModel it returns the corresponding selected particles representation_type="Beads", "Res:X", "Densities", "Representation", "Molecule" More...
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def | select_by_tuple_2 |
| New tuple format: molname OR (start,stop,molname,copynum,statenum) Copy and state are optional. More...
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def IMP.pmi.tools.add_restraint_to_model |
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model, |
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restraint, |
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add_to_rmf = False |
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Add a PMI restraint to the model.
Since Model.add_restraint() no longer exists (in modern IMP restraints should be added to a ScoringFunction instead) store them instead in a RestraintSet, and keep a reference to it in the Model.
If add_to_rmf
is True, also add the restraint to a separate list of restraints that will be written out to RMF files (by default, most PMI restraints are not).
- Note
- This function is only available in Python.
Definition at line 69 of file tools.py.
def IMP.pmi.tools.cross_link_db_filter_parser |
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inputstring | ) |
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example '"{ID_Score}" > 28 AND "{Sample}" == "%10_1%" OR ":Sample}" == "%10_2%" OR ":Sample}" == "%10_3%" OR ":Sample}" == "%8_1%" OR ":Sample}" == "%8_2%"'
- Note
- This function is only available in Python.
Definition at line 501 of file tools.py.
def IMP.pmi.tools.get_closest_residue_position |
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hier, |
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resindex, |
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terminus = 'N' |
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this function works with plain hierarchies, as read from the pdb, no multi-scale hierarchies
- Note
- This function is only available in Python.
Definition at line 571 of file tools.py.
def IMP.pmi.tools.get_prot_name_from_particle |
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p, |
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list_of_names |
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Return the component name provided a particle and a list of names.
- Note
- This function is only available in Python.
Definition at line 1043 of file tools.py.
def IMP.pmi.tools.get_random_cross_link_dataset |
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representation, |
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resolution = 1.0 , |
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number_of_cross_links = 10 , |
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ambiguity_probability = 0.1 , |
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confidence_score_range = [0 , |
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avoid_same_particles = False |
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Return a random cross-link dataset as a string.
Every line is a residue pair, together with UniqueIdentifier and XL score.
- Note
- This function is only available in Python.
Definition at line 394 of file tools.py.
def IMP.pmi.tools.get_residue_gaps_in_hierarchy |
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hierarchy, |
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start, |
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end |
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Return the residue index gaps and contiguous segments in the hierarchy.
- Parameters
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hierarchy | hierarchy to examine |
start | first residue index |
end | last residue index |
- Returns
- A list of lists of the form [[1,100,"cont"],[101,120,"gap"],[121,200,"cont"]]
- Note
- This function is only available in Python.
Definition at line 655 of file tools.py.
def IMP.pmi.tools.get_residue_indexes |
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hier | ) |
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Retrieve the residue indexes for the given particle.
The particle must be an instance of Fragment,Residue, Atom or Molecule or else returns an empty list
- Note
- This function is only available in Python.
Definition at line 1063 of file tools.py.
def IMP.pmi.tools.get_restraint_set |
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model, |
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rmf = False |
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Get a RestraintSet containing all PMI restraints added to the model.
If rmf
is True, return only the subset of these restraints that should be written out to RMF files.
- Note
- This function is only available in Python.
Definition at line 88 of file tools.py.
def IMP.pmi.tools.get_terminal_residue |
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representation, |
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hier, |
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terminus = 'C' , |
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resolution = 1 |
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Get the particle of the terminal residue at the GIVEN resolution (NOTE: not the closest resolution!).
To get the terminal residue at the closest resolution use: particles=IMP.pmi.tools.select_by_tuple(representation,molecule_name) particles[0] and particles[-1] will be the first and last particles corresponding to the two termini. It is needed for instance to determine the last residue of a pdb.
- Parameters
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hier | hierarchy containing the terminal residue |
terminus | either 'N' or 'C' |
resolution | resolution to use. |
- Note
- This function is only available in Python.
Definition at line 602 of file tools.py.
def IMP.pmi.tools.get_terminal_residue_position |
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representation, |
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hier, |
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terminus = 'C' , |
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resolution = 1 |
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Get XYZ coordinates of the terminal residue at the GIVEN resolution.
- Note
- This function is only available in Python.
Definition at line 643 of file tools.py.
def IMP.pmi.tools.scatter_and_gather |
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data | ) |
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Synchronize data over a parallel run.
- Note
- This function is only available in Python.
Definition at line 1115 of file tools.py.
def IMP.pmi.tools.select |
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representation, |
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resolution = None , |
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hierarchies = None , |
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selection_arguments = None , |
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name = None , |
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name_is_ambiguous = False , |
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first_residue = None , |
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last_residue = None , |
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residue = None , |
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representation_type = None |
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this function uses representation=SimplifiedModel it returns the corresponding selected particles representation_type="Beads", "Res:X", "Densities", "Representation", "Molecule"
- Note
- This function is only available in Python.
Definition at line 726 of file tools.py.
def IMP.pmi.tools.select_by_tuple_2 |
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hier, |
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tuple_selection, |
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resolution |
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New tuple format: molname OR (start,stop,molname,copynum,statenum) Copy and state are optional.
Can also use 'None' for them which will get all. You can also pass -1 for stop which will go to the end. Returns the particles
- Note
- This function is only available in Python.
Definition at line 845 of file tools.py.