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IMP Reference Guide
2.7.0
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 | HierarchyDatabase |
| Store the representations for a system. 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... | |
Functions | |
| def | add_restraint_to_model |
| Add a PMI restraint to the model. More... | |
| def | color2rgb |
| Given a chimera color name, 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, return all density hierarchies within these 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_position_terminal_residue |
| Get the xyz position of the terminal residue at the given resolution. More... | |
| def | get_prot_name_from_particle |
| Return the component name provided a particle and a list of names. More... | |
| def | get_random_cross_link_dataset |
| Return a random cross-link dataset as a string. 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 | get_terminal_residue |
| Get the particle of the terminal residue at the GIVEN resolution (NOTE: not the closest resolution!). More... | |
| def | get_terminal_residue_position |
| Get XYZ coordinates of the terminal residue at the GIVEN resolution. 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 | scatter_and_gather_dict_append |
| Synchronize data over a parallel run. More... | |
| def | select |
| this function uses representation=SimplifiedModel it returns the corresponding selected particles representation_type="Beads", "Res:X", "Densities", "Representation", "Molecule" 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 | translate_hierarchy |
| Apply a translation to a hierarchy along the input vector. More... | |
| def IMP.pmi.tools.add_restraint_to_model | ( | model, | |
| restraint | |||
| ) |
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.
| def IMP.pmi.tools.color2rgb | ( | colorname | ) |
| def IMP.pmi.tools.cross_link_db_filter_parser | ( | inputstring | ) |
| def IMP.pmi.tools.display_bonds | ( | mol | ) |
| def IMP.pmi.tools.get_all_leaves | ( | list_of_hs | ) |
| def IMP.pmi.tools.get_closest_residue_position | ( | hier, | |
| resindex, | |||
terminus = 'N' |
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| ) |
| def IMP.pmi.tools.get_densities | ( | input_objects | ) |
| 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 |
| def IMP.pmi.tools.get_position_terminal_residue | ( | hier, | |
terminus = 'C', |
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resolution = 1 |
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| ) |
Get the xyz position of the terminal residue at the given resolution.
| hier | hierarchy containing the terminal residue |
| terminus | either 'N' or 'C' |
| resolution | resolution to use. |
| def IMP.pmi.tools.get_prot_name_from_particle | ( | p, | |
| list_of_names | |||
| ) |
| def IMP.pmi.tools.get_random_cross_link_dataset | ( | representation, | |
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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| ) |
| def IMP.pmi.tools.get_rbs_and_beads | ( | hiers | ) |
| 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 |
| def IMP.pmi.tools.get_residue_indexes | ( | hier | ) |
| def IMP.pmi.tools.get_restraint_set | ( | model | ) |
Get a RestraintSet containing all PMI restraints added to the model.
| def IMP.pmi.tools.get_sorted_segments | ( | mol | ) |
| def IMP.pmi.tools.get_terminal_residue | ( | representation, | |
| hier, | |||
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.
| hier | hierarchy containing the terminal residue |
| terminus | either 'N' or 'C' |
| resolution | resolution to use. |
| def IMP.pmi.tools.get_terminal_residue_position | ( | representation, | |
| hier, | |||
terminus = 'C', |
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resolution = 1 |
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| ) |
| 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.
(iterable of ^2) hierarchy -> returns input as list of list of hierarchies, only one entry. (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! |
ote since this relies on IMP::atom::Selection, this will not return any objects if they weren't built! But there should be no problem if you request unbuilt residues, they should be ignored.
| def IMP.pmi.tools.list_chunks_iterator | ( | list, | |
| length | |||
| ) |
| def IMP.pmi.tools.scatter_and_gather | ( | data | ) |
| def IMP.pmi.tools.scatter_and_gather_dict_append | ( | data | ) |
| def IMP.pmi.tools.select | ( | representation, | |
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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| ) |
| def IMP.pmi.tools.select_at_all_resolutions | ( | hier = None, |
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hiers = None, |
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| kwargs | |||
| ) |
| 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
| 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 |
| def IMP.pmi.tools.shuffle_configuration | ( | objects, | |
max_translation = 300.0, |
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max_rotation = 2.0 * 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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| ) |
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 with a side of max_translation angstroms, and far enough from each other to prevent any steric clashes. The rigid bodies are also randomly rotated.
| 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 |
ote Best to only call this function after you've set up degrees of freedom For debugging purposes, returns: <shuffled indexes>="">, <collision avoided="" indexes>="">
| def IMP.pmi.tools.sublist_iterator | ( | l, | |
lmin = None, |
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lmax = None |
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| ) |