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IMP Reference Guide  develop.b79bf0c255,2019/12/05
The Integrative Modeling Platform
IMP.pmi.tools Namespace Reference

Miscellaneous utilities. More...

Detailed Description

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...
 
class  ThreeToOneConverter
 This class converts three to one letter codes, and return X for any unknown codes. 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...
 

Function Documentation

def IMP.pmi.tools.add_restraint_to_model (   model,
  restraint,
  add_to_rmf = False 
)

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 89 of file tools.py.

def IMP.pmi.tools.color2rgb (   colorname)

Given a Chimera color name or hex color value, return RGB.

Note
This function is only available in Python.

Definition at line 1580 of file 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%"'

Note
This function is only available in Python.

Definition at line 322 of file 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.

Note
This function is only available in Python.

Definition at line 1070 of file tools.py.

def IMP.pmi.tools.get_all_leaves (   list_of_hs)

Just get the leaves from a list of hierarchies.

Note
This function is only available in Python.

Definition at line 1119 of file tools.py.

def IMP.pmi.tools.get_closest_residue_position (   hier,
  resindex,
  terminus = 'N' 
)

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 375 of file 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).

Note
This function is only available in Python.

Definition at line 1259 of file tools.py.

def IMP.pmi.tools.get_molecules (   input_objects)

This function returns the parent molecule hierarchies of given objects.

Note
This function is only available in Python.

Definition at line 1216 of file 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.

Parameters
hierThe hierarchy in which to look for neighbors
target_psThe particles for zoning
sel_zoneThe maximum distance
entire_residuesIf True, will grab entire residues
exclude_backboneIf True, will only return sidechain particles
Note
This function is only available in Python.

Definition at line 1159 of file 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.

Note
This function is only available in Python.

Definition at line 534 of file tools.py.

def IMP.pmi.tools.get_rbs_and_beads (   hiers)

Returns unique objects in original order.

Note
This function is only available in Python.

Definition at line 1193 of file 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.

Parameters
hierarchyhierarchy to examine
startfirst residue index
endlast 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 407 of file 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

Note
This function is only available in Python.

Definition at line 554 of file tools.py.

def IMP.pmi.tools.get_restraint_set (   model,
  rmf = False 
)

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 108 of file 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.

Note
This function is only available in Python.

Definition at line 1044 of file tools.py.

def IMP.pmi.tools.input_adaptor (   stuff,
  pmi_resolution = 0,
  flatten = False,
  selection_tuple = None,
  warn_about_slices = True 
)

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

Parameters
stuffCan 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_resolutionFor selecting, only does it if you pass PMI objects. Set it to "all" if you want all resolutions!
flattenSet to True if you just want all hierarchies in one list.
warn_about_slicesPrint a warning if you are requesting only part of a bead. Sometimes you just don't care!
Note
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.
This function is only available in Python.

Definition at line 918 of file tools.py.

def IMP.pmi.tools.list_chunks_iterator (   list,
  length 
)

Yield successive length-sized chunks from a list.

Note
This function is only available in Python.

Definition at line 646 of file tools.py.

def IMP.pmi.tools.scatter_and_gather (   data)

Synchronize data over a parallel run.

Note
This function is only available in Python.

Definition at line 596 of file tools.py.

def IMP.pmi.tools.select_at_all_resolutions (   hier = None,
  hiers = None,
  kwargs 
)

Perform selection using the usual keywords but return ALL resolutions (BEADS and GAUSSIANS).

Returns in flat list!

Note
This function is only available in Python.

Definition at line 1125 of file 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

Note
This function is only available in Python.

Definition at line 484 of file tools.py.

def IMP.pmi.tools.set_coordinates_from_rmf (   hier,
  rmf_fn,
  frame_num = 0 
)

Extract frame from RMF file and fill coordinates.

Must be identical topology.

Parameters
hierThe (System) hierarchy to fill (e.g. after you've built it)
rmf_fnThe file to extract from
frame_numThe frame number to extract
Note
This function is only available in Python.

Definition at line 896 of file tools.py.

def IMP.pmi.tools.shuffle_configuration (   objects,
  max_translation = 300.0,
  max_rotation = 2.0 * pi,
  avoidcollision_rb = True,
  avoidcollision_fb = False,
  cutoff = 10.0,
  niterations = 100,
  bounding_box = None,
  excluded_rigid_bodies = [],
  hierarchies_excluded_from_collision = [],
  hierarchies_included_in_collision = [],
  verbose = False,
  return_debug = False 
)

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.

Parameters
objectsCan be one of the following inputs: IMP Hierarchy, PMI System/State/Molecule/TempResidue, or a list/set of them
max_translationMax translation (rbs and flexible beads)
max_rotationMax rotation (rbs only)
avoidcollision_rbcheck if the particle/rigid body was placed close to another particle; uses the optional arguments cutoff and niterations
avoidcollision_fbAdvanced. Generally you want this False because it's hard to shuffle beads.
cutoffDistance less than this is a collision
niterationsHow many times to try avoiding collision
bounding_boxOnly shuffle particles within this box. Defined by ((x1,y1,z1),(x2,y2,z2)).
excluded_rigid_bodiesDon't shuffle these rigid body objects
hierarchies_excluded_from_collisionDon't count collision with these bodies
hierarchies_included_in_collisionHierarchies that are not shuffled, but should be included in collision calculation (for fixed regions)
verboseGive more output
Note
Best to only call this function after you've set up degrees of freedom For debugging purposes, returns: <shuffled indexes>="">, <collision avoided="" indexes>="">
This function is only available in Python.

Definition at line 1287 of file tools.py.

def IMP.pmi.tools.sublist_iterator (   l,
  lmin = None,
  lmax = None 
)

Yield all sublists of length >= lmin and <= lmax.

Note
This function is only available in Python.

Definition at line 627 of file tools.py.