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IMP Reference Guide
develop.6f18bfa751,2025/09/20
The Integrative Modeling Platform
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Miscellaneous utilities. More...
Miscellaneous utilities.
Classes | |
| class | ColorChange |
| Change color code to hexadecimal to rgb. More... | |
| class | OrderedDefaultDict |
| Store objects in order they were added, but with default type. More... | |
| class | Segments |
| This class stores integers in ordered compact lists eg: [[1,2,3],[6,7,8]] the methods help splitting and merging the internal lists Example: s=Segments([1,2,3]) is [[1,2,3]] s.add(4) is [[1,2,3,4]] (add right) s.add(3) is [[1,2,3,4]] (item already existing) s.add(7) is [[1,2,3,4],[7]] (new list) s.add([8,9]) is [[1,2,3,4],[7,8,9]] (add item right) s.add([5,6]) is [[1,2,3,4,5,6,7,8,9]] (merge) s.remove(3) is [[1,2],[4,5,6,7,8,9]] (split) etc. More... | |
| class | Stopwatch |
| Collect timing information. More... | |
Functions | |
| def | add_restraint_to_model |
| Add a PMI restraint to the model. More... | |
| def | color2rgb |
| Given a Chimera color name or hex color value, return RGB. More... | |
| 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... | |
| def | display_bonds |
| Decorate the sequence-consecutive particles from a PMI2 molecule with a bond, so that they appear connected in the rmf file. More... | |
| def | get_all_leaves |
| Just get the leaves from a list of hierarchies. More... | |
| def | get_closest_residue_position |
| this function works with plain hierarchies, as read from the pdb, no multi-scale hierarchies More... | |
| def | get_densities |
| Given a list of PMI objects, returns all density hierarchies within these objects. More... | |
| def | get_molecules |
| This function returns the parent molecule hierarchies of given objects. More... | |
| def | get_particles_within_zone |
| Utility to retrieve particles from a hierarchy within a zone around a set of ps. More... | |
| def | get_prot_name_from_particle |
| Return the component name provided a particle and a list of names. More... | |
| def | get_rbs_and_beads |
| Returns unique objects in original order. More... | |
| def | get_residue_gaps_in_hierarchy |
| Return the residue index gaps and contiguous segments in the hierarchy. More... | |
| def | get_residue_indexes |
| Retrieve the residue indexes for the given particle. More... | |
| def | get_restraint_set |
| Get a RestraintSet containing all PMI restraints added to the model. More... | |
| def | get_sorted_segments |
| Returns sequence-sorted segments array, each containing the first particle the last particle and the first residue index. More... | |
| def | input_adaptor |
| Adapt things for PMI (degrees of freedom, restraints, ...) Returns list of list of hierarchies, separated into Molecules if possible. More... | |
| def | list_chunks_iterator |
| Yield successive length-sized chunks from a list. More... | |
| def | scatter_and_gather |
| Synchronize data over a parallel run. More... | |
| def | select_at_all_resolutions |
| Perform selection using the usual keywords but return ALL resolutions (BEADS and GAUSSIANS). More... | |
| def | select_by_tuple_2 |
| New tuple format: molname OR (start,stop,molname,copynum,statenum) Copy and state are optional. More... | |
| def | set_coordinates_from_rmf |
| Extract frame from RMF file and fill coordinates. More... | |
| def | shuffle_configuration |
| Shuffle particles. More... | |
| def | sublist_iterator |
| Yield all sublists of length >= lmin and <= lmax. More... | |
| def IMP.pmi.tools.add_restraint_to_model | ( | model, | |
| restraint, | |||
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).
Definition at line 84 of file pmi/tools.py.
| def IMP.pmi.tools.color2rgb | ( | colorname | ) |
Given a Chimera color name or hex color value, return RGB.
Definition at line 1558 of file pmi/tools.py.
| def IMP.pmi.tools.cross_link_db_filter_parser | ( | inputstring | ) |
example '"{ID_Score}" > 28 AND "{Sample}" == "%10_1%" OR ":Sample}" == "%10_2%" OR ":Sample}" == "%10_3%" OR ":Sample}" == "%8_1%" OR ":Sample}" == "%8_2%"'
Definition at line 261 of file pmi/tools.py.
| def IMP.pmi.tools.display_bonds | ( | mol | ) |
Decorate the sequence-consecutive particles from a PMI2 molecule with a bond, so that they appear connected in the rmf file.
Definition at line 1033 of file pmi/tools.py.
| def IMP.pmi.tools.get_all_leaves | ( | list_of_hs | ) |
Just get the leaves from a list of hierarchies.
Definition at line 1055 of file pmi/tools.py.
| def IMP.pmi.tools.get_closest_residue_position | ( | hier, | |
| resindex, | |||
terminus = 'N' |
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| ) |
this function works with plain hierarchies, as read from the pdb, no multi-scale hierarchies
Definition at line 315 of file pmi/tools.py.
| def IMP.pmi.tools.get_densities | ( | input_objects | ) |
Given a list of PMI objects, returns all density hierarchies within these objects.
The output of this function can be inputted into things such as EM restraints. This function is intended to gather density particles appended to molecules (and not other hierarchies which might have been appended to the root node directly).
Definition at line 1206 of file pmi/tools.py.
| def IMP.pmi.tools.get_molecules | ( | input_objects | ) |
This function returns the parent molecule hierarchies of given objects.
Definition at line 1159 of file pmi/tools.py.
| def IMP.pmi.tools.get_particles_within_zone | ( | hier, | |
| target_ps, | |||
| sel_zone, | |||
| entire_residues, | |||
| exclude_backbone | |||
| ) |
Utility to retrieve particles from a hierarchy within a zone around a set of ps.
| hier | The hierarchy in which to look for neighbors |
| target_ps | The particles for zoning |
| sel_zone | The maximum distance |
| entire_residues | If True, will grab entire residues |
| exclude_backbone | If True, will only return sidechain particles |
Definition at line 1100 of file pmi/tools.py.
| def IMP.pmi.tools.get_prot_name_from_particle | ( | p, | |
| list_of_names | |||
| ) |
Return the component name provided a particle and a list of names.
Definition at line 479 of file pmi/tools.py.
| def IMP.pmi.tools.get_rbs_and_beads | ( | hiers | ) |
Returns unique objects in original order.
Definition at line 1135 of file pmi/tools.py.
| def IMP.pmi.tools.get_residue_gaps_in_hierarchy | ( | hierarchy, | |
| start, | |||
| end | |||
| ) |
Return the residue index gaps and contiguous segments in the hierarchy.
| hierarchy | hierarchy to examine |
| start | first residue index |
| end | last residue index |
Definition at line 353 of file pmi/tools.py.
| def IMP.pmi.tools.get_residue_indexes | ( | hier | ) |
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
Definition at line 499 of file pmi/tools.py.
| def IMP.pmi.tools.get_restraint_set | ( | model, | |
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.
Definition at line 104 of file pmi/tools.py.
| def IMP.pmi.tools.get_sorted_segments | ( | mol | ) |
Returns sequence-sorted segments array, each containing the first particle the last particle and the first residue index.
Definition at line 1007 of file pmi/tools.py.
| def IMP.pmi.tools.input_adaptor | ( | stuff, | |
pmi_resolution = 0, |
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flatten = False, |
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selection_tuple = None, |
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warn_about_slices = True |
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| ) |
Adapt things for PMI (degrees of freedom, restraints, ...) Returns list of list of hierarchies, separated into Molecules if possible.
The input can be a list, or a list of lists (iterable of ^1 or iterable of ^2) (iterable of ^2) Hierarchy -> returns input as list of list of hierarchies, only one entry, not grouped by molecules. (iterable of ^2) PMI::System/State/Molecule/TempResidue -> returns residue hierarchies, grouped in molecules, at requested resolution
| stuff | Can be one of the following inputs: IMP Hierarchy, PMI System/State/Molecule/TempResidue, or a list/set (of list/set) of them. Must be uniform input, however. No mixing object types. |
| pmi_resolution | For selecting, only does it if you pass PMI objects. Set it to "all" if you want all resolutions! |
| flatten | Set to True if you just want all hierarchies in one list. |
| warn_about_slices | Print a warning if you are requesting only part of a bead. Sometimes you just don't care! |
Definition at line 872 of file pmi/tools.py.
| def IMP.pmi.tools.list_chunks_iterator | ( | list, | |
| length | |||
| ) |
Yield successive length-sized chunks from a list.
Definition at line 590 of file pmi/tools.py.
| def IMP.pmi.tools.scatter_and_gather | ( | data | ) |
Synchronize data over a parallel run.
Definition at line 542 of file pmi/tools.py.
| def IMP.pmi.tools.select_at_all_resolutions | ( | hier = None, |
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hiers = None, |
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| kwargs | |||
| ) |
Perform selection using the usual keywords but return ALL resolutions (BEADS and GAUSSIANS).
Returns in flat list!
Definition at line 1062 of file pmi/tools.py.
| def IMP.pmi.tools.select_by_tuple_2 | ( | hier, | |
| tuple_selection, | |||
| resolution | |||
| ) |
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
Definition at line 430 of file pmi/tools.py.
| def IMP.pmi.tools.set_coordinates_from_rmf | ( | hier, | |
| rmf_fn, | |||
frame_num = 0 |
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| ) |
Extract frame from RMF file and fill coordinates.
Must be identical topology.
| hier | The (System) hierarchy to fill (e.g. after you've built it) |
| rmf_fn | The file to extract from |
| frame_num | The frame number to extract |
Definition at line 846 of file pmi/tools.py.
| def IMP.pmi.tools.shuffle_configuration | ( | objects, | |
max_translation = 300.0, |
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max_rotation = 2.0 * math.pi, |
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avoidcollision_rb = True, |
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avoidcollision_fb = False, |
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cutoff = 10.0, |
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niterations = 100, |
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bounding_box = None, |
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excluded_rigid_bodies = [], |
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hierarchies_excluded_from_collision = [], |
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hierarchies_included_in_collision = [], |
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verbose = False, |
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return_debug = False |
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| ) |
Shuffle particles.
Used to restart the optimization. The configuration of the system is initialized by placing each rigid body and each bead randomly in a box. If bounding_box is specified, the particles are placed inside this box; otherwise, each particle is displaced by up to max_translation angstroms, and randomly rotated. Effort is made to place particles far enough from each other to prevent any steric clashes.
| objects | Can be one of the following inputs: IMP Hierarchy, PMI System/State/Molecule/TempResidue, or a list/set of them |
| max_translation | Max translation (rbs and flexible beads) |
| max_rotation | Max rotation (rbs only) |
| avoidcollision_rb | check if the particle/rigid body was placed close to another particle; uses the optional arguments cutoff and niterations |
| avoidcollision_fb | Advanced. Generally you want this False because it's hard to shuffle beads. |
| cutoff | Distance less than this is a collision |
| niterations | How many times to try avoiding collision |
| bounding_box | Only shuffle particles within this box. Defined by ((x1,y1,z1),(x2,y2,z2)). |
| excluded_rigid_bodies | Don't shuffle these rigid body objects |
| hierarchies_excluded_from_collision | Don't count collision with these bodies |
| hierarchies_included_in_collision | Hierarchies that are not shuffled, but should be included in collision calculation (for fixed regions) |
| verbose | Give more output |
Definition at line 1242 of file pmi/tools.py.
| def IMP.pmi.tools.sublist_iterator | ( | ls, | |
lmin = 1, |
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lmax = None |
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| ) |
Yield all sublists of length >= lmin and <= lmax.
Definition at line 574 of file pmi/tools.py.