IMP Reference Guide  develop.63e71f5352,2022/07/06 The Integrative Modeling Platform
IMP.pmi1.representation.Representation Class Reference

Set up the representation of all proteins and nucleic acid macromolecules. More...

Inherits object.

## Detailed Description

Set up the representation of all proteins and nucleic acid macromolecules.

Create the molecular hierarchies, representation, sequence connectivity for the various involved proteins and nucleic acid macromolecules:

Create a protein, DNA or RNA, represent it as a set of connected balls of appropriate radii and number of residues, PDB at given resolution(s), or ideal helices.

How to use the SimplifiedModel class (typical use):

see test/test_hierarchy_contruction.py

examples:

1) Create a chain of helices and flexible parts

self.set_rigid_body_from_hierarchies(c_120_131) self.set_rigid_body_from_hierarchies(c_139_156) self.set_rigid_body_from_hierarchies(c_175_182) self.set_rigid_body_from_hierarchies(c_195_216)

clist=[c_1_119,c_120_131,c_132_138,c_139_156,c_157_174,c_175_182,c_183_194,c_195_216, c_217_250]

self.set_chain_of_super_rigid_bodies(clist,2,3)

self.set_super_rigid_bodies(["prot1"])

Note
This class is only available in Python.

Definition at line 45 of file pmi1/representation.py.

## Public Member Functions

def __init__
Constructor. More...

Decorates all specified particles as Gaussians directly. More...

Sets up a Gaussian Mixture Model for this component. More...

Make a copy of a hierarchy and append it to a component. More...

Generates a string of beads with given length. More...

Add a component that has an associated 3D structure in a PDB file. More...

Add the primary sequence for a single component. More...

Associate some metadata with this modeling. More...

Capture details of the modeling protocol. More...

def check_root
If the root hierarchy does not exist, construct it. More...

def coarse_hierarchy
Generate all needed coarse grained layers. More...

def create_components_from_rmf
still not working. More...

def create_non_modeled_component
Create a component that isn't used in the modeling. More...

def create_rotational_symmetry
The copies must not contain rigid bodies. More...

def create_transformed_component
Create a transformed view of a component. More...

def get_file_dataset
Get the dataset associated with a filename, or None. More...

def get_hierarchies_at_given_resolution
Get the hierarchies at the given resolution. More...

def get_particles_from_selection_tuples
selection tuples must be [(r1,r2,"name1"),(r1,r2,"name2"),.... More...

Load coordinates in the current representation. More...

def remove_floppy_bodies
Remove leaves of hierarchies from the floppy bodies list. More...

def remove_floppy_bodies_from_component
Remove leaves of hierarchies from the floppy bodies list based on the component name. More...

def set_chain_of_super_rigid_bodies
Make a chain of super rigid bodies from a list of hierarchies. More...

def set_coordinates_from_rmf
Read and replace coordinates from an RMF file. More...

def set_file_dataset
Associate a dataset with a filename. More...

def set_floppy_bodies_as_fixed
Fix floppy bodies in their actual position. More...

def set_rigid_bodies
Construct a rigid body from a list of subunits. More...

def set_rigid_bodies_as_fixed
Fix rigid bodies in their actual position. More...

def set_rigid_body_from_hierarchies
Construct a rigid body from hierarchies (and optionally particles). More...

def setup_component_sequence_connectivity
Generate restraints between contiguous fragments in the hierarchy. More...

def shuffle_configuration
Shuffle configuration; used to restart the optimization. More...

## Constructor & Destructor Documentation

 def IMP.pmi1.representation.Representation.__init__ ( self, model, upperharmonic = True, disorderedlength = True )

Constructor.

Parameters
 model the model upperharmonic This flag uses either harmonic (False) or upperharmonic (True) in the intra-pair connectivity restraint. disorderedlength This flag uses either disordered length calculated for random coil peptides (True) or zero surface-to-surface distance between beads (False) as optimal distance for the sequence connectivity restraint.

Definition at line 85 of file pmi1/representation.py.

## Member Function Documentation

 def IMP.pmi1.representation.Representation.add_all_atom_densities ( self, name, hierarchies = None, selection_tuples = None, particles = None, resolution = 0, output_map = None, voxel_size = 1.0 )

Decorates all specified particles as Gaussians directly.

Parameters
 name component name hierarchies set up GMM for some hierarchies selection_tuples (list of tuples) example (first_residue,last_residue,component_name) particles set up GMM for particles directly resolution usual PMI resolution for selecting particles from the hierarchies

Definition at line 857 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.add_component_beads ( self, name, ds, colors = None, incoord = None )

Parameters
 name the component name ds a list of tuples corresponding to the residue ranges of the beads colors a list of colors associated to the beads incoord the coordinate tuple corresponding to the position of the beads

Definition at line 608 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.add_component_density ( self, name, hierarchies = None, selection_tuples = None, particles = None, resolution = 0.0, num_components = 10, inputfile = None, outputfile = None, outputmap = None, kernel_type = None, covariance_type = 'full', voxel_size = 1.0, out_hier_name = '', sampled_points = 1000000, num_iter = 100, simulation_res = 1.0, multiply_by_total_mass = True, transform = None, intermediate_map_fn = None, density_ps_to_copy = None, use_precomputed_gaussians = False )

Sets up a Gaussian Mixture Model for this component.

Can specify input GMM file or it will be computed.

Parameters
 name component name hierarchies set up GMM for some hierarchies selection_tuples (list of tuples) example (first_residue,last_residue,component_name) particles set up GMM for particles directly resolution usual PMI resolution for selecting particles from the hierarchies inputfile read the GMM from this file outputfile fit and write the GMM to this file (text) outputmap after fitting, create GMM density file (mrc) kernel_type for creating the intermediate density (points are sampled to make GMM). Options are IMP.em.GAUSSIAN, IMP.em.SPHERE, and IMP.em.BINARIZED_SPHERE covariance_type for fitting the GMM. options are 'full', 'diagonal' and 'spherical' voxel_size for creating the intermediate density map and output map. lower number increases accuracy but also rasterizing time grows out_hier_name name of the output density hierarchy sampled_points number of points to sample. more will increase accuracy and fitting time num_iter num GMM iterations. more will increase accuracy and fitting time multiply_by_total_mass multiply the weights of the GMM by this value (only works on creation!) transform for input file only, apply a transformation (eg for multiple copies same GMM) intermediate_map_fn for debugging, this will write the intermediate (simulated) map density_ps_to_copy in case you already created the appropriate GMM (eg, for beads) use_precomputed_gaussians Set this flag and pass fragments - will use roughly spherical Gaussian setup

Definition at line 730 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.add_component_hierarchy_clone ( self, name, hierarchy )

Make a copy of a hierarchy and append it to a component.

Definition at line 917 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.add_component_necklace ( self, name, begin, end, length, color = None, incoord = None )

Generates a string of beads with given length.

Definition at line 706 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.add_component_pdb ( self, name, pdbname, chain, resolutions, color = None, resrange = None, offset = 0, cacenters = True, show = False, isnucleicacid = False, readnonwateratoms = False, read_ca_cb_only = False )

Add a component that has an associated 3D structure in a PDB file.

Reads the PDB, and constructs the fragments corresponding to contiguous sequence stretches.

Returns
a list of hierarchies.
Parameters
 name (string) the name of the component pdbname (string) the name of the PDB file chain (string or integer) can be either a string (eg, "A") or an integer (eg, 0 or 1) in case you want to get the corresponding chain number in the PDB. resolutions (integers) a list of integers that corresponds to the resolutions that have to be generated color (float from 0 to 1) the color applied to the hierarchies generated resrange (tuple of integers): the residue range to extract from the PDB. It is a tuple (beg,end). If not specified, all residues belonging to the specified chain are read. offset (integer) specifies the residue index offset to be applied when reading the PDB (the FASTA sequence is assumed to start from residue 1, so use this parameter if the PDB file does not start at residue 1) cacenters (boolean) if True generates resolution=1 beads centered on C-alpha atoms. show (boolean) print out the molecular hierarchy at the end. isnucleicacid (boolean) use True if you're reading a PDB with nucleic acids. readnonwateratoms (boolean) if True fixes some pathological PDB. read_ca_cb_only (boolean) if True, only reads CA/CB

Definition at line 391 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.add_component_sequence ( self, name, filename, id = None, offs = None, format = 'FASTA' )

Add the primary sequence for a single component.

Parameters
 name Human-readable name of the component filename Name of the FASTA file id Identifier of the sequence in the FASTA file header (if not provided, use name instead)

Definition at line 267 of file pmi1/representation.py.

Associate some metadata with this modeling.

Parameters

Definition at line 177 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.add_protocol_output ( self, p )

Capture details of the modeling protocol.

Parameters
 p an instance of IMP.pmi1.output.ProtocolOutput or a subclass.

Definition at line 202 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.check_root ( self, name, protein_h, resolution )

If the root hierarchy does not exist, construct it.

Definition at line 1228 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.coarse_hierarchy ( self, name, start, end, resolutions, isnucleicacid, input_hierarchy, protein_h, type, color )

Generate all needed coarse grained layers.

Parameters
 name name of the protein resolutions list of resolutions protein_h root hierarchy input_hierarchy hierarchy to coarse grain type a string, typically "pdb" or "helix"

Definition at line 1239 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.create_components_from_rmf ( self, rmfname, frameindex )

still not working.

create the representation (i.e. hierarchies) from the rmf file. it will be stored in self.prot, which will be overwritten. load the coordinates from the rmf file at frameindex.

Definition at line 1876 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.create_non_modeled_component ( self, name )

Create a component that isn't used in the modeling.

No coordinates or other structural data for this component will be read or written, but a primary sequence can be assigned. This is useful if the input experimental data is of a system larger than that modeled. Any references to these non-modeled components can then be correctly resolved later.

Definition at line 246 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.create_rotational_symmetry ( self, maincopy, copies, rotational_axis = IMP.algebra.Vector3D(0, 0, nSymmetry = None, skip_gaussian_in_clones = False )

The copies must not contain rigid bodies.

The symmetry restraints are applied at each leaf.

Definition at line 1723 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.create_transformed_component ( self, name, original, transform )

Create a transformed view of a component.

This does not copy the coordinates or representation of the component, and the transformed component is not visible to IMP, but when the model is written to a ProtocolOutput, the transformed component is added. This can be used to easily add symmetry-related 'copies' of a component without copying the underlying IMP objects.

Definition at line 235 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.get_file_dataset ( self, fname )

Get the dataset associated with a filename, or None.

Parameters
 fname filename
Returns
an ihm.dataset.Dataset, or None.

Definition at line 195 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.get_hierarchies_at_given_resolution ( self, resolution )

Get the hierarchies at the given resolution.

The map between resolution and hierarchies is cached to accelerate the selection algorithm. The cache is invalidated when the representation was changed by any add_component_xxx.

Definition at line 1380 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.get_particles_from_selection_tuples ( self, selection_tuples, resolution = None )

selection tuples must be [(r1,r2,"name1"),(r1,r2,"name2"),....

]

Returns
the particles

Definition at line 2123 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.link_components_to_rmf ( self, rmfname, frameindex )

Load coordinates in the current representation.

This should be done only if the hierarchy self.prot is identical to the one as stored in the rmf i.e. all components were added.

Definition at line 1862 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.remove_floppy_bodies ( self, hierarchies )

Remove leaves of hierarchies from the floppy bodies list.

Given a list of hierarchies, get the leaves and remove the corresponding particles from the floppy bodies list. We need this function because sometimes we want to constrain the floppy bodies in a rigid body - for instance when you want to associate a bead with a density particle.

Definition at line 2084 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.remove_floppy_bodies_from_component ( self, component_name )

Remove leaves of hierarchies from the floppy bodies list based on the component name.

Definition at line 2069 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.set_chain_of_super_rigid_bodies ( self, hiers, min_length = None, max_length = None, axis = None )

Make a chain of super rigid bodies from a list of hierarchies.

Takes a linear list of hierarchies (they are supposed to be sequence-contiguous) and produces a chain of super rigid bodies with given length range, specified by min_length and max_length.

Definition at line 2021 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.set_coordinates_from_rmf ( self, component_name, rmf_file_name, rmf_frame_number, rmf_component_name = None, check_number_particles = True, representation_name_to_rmf_name_map = None, state_number = 0, skip_gaussian_in_rmf = False, skip_gaussian_in_representation = False, save_file = False, force_rigid_update = False )

Read and replace coordinates from an RMF file.

Replace the coordinates of particles with the same name. It assumes that the RMF and the representation have the particles in the same order.

Parameters
 component_name Component name rmf_component_name Name of the component in the RMF file (if not specified, use component_name) representation_name_to_rmf_name_map a dictionary that map the original rmf particle name to the recipient particle component name save_file save a file with the names of particles of the component force_rigid_update update the coordinates of rigid bodies (normally this should be called before rigid bodies are set up)

Definition at line 1084 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.set_file_dataset ( self, fname, dataset )

Associate a dataset with a filename.

This can be used to identify how the file was produced (in many cases IMP can determine this automatically from a file header or other metadata, but not always). For example, a manually-produced PDB file (not from the PDB database or Modeller) can be identified this way.

Parameters
 fname filename the ihm.dataset.Dataset object to associate.

Definition at line 187 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.set_floppy_bodies_as_fixed ( self, floppybodiesarefixed = True )

Fix floppy bodies in their actual position.

The get_particles_to_sample() function will return just the rigid bodies (if they are not fixed).

Definition at line 2166 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.set_rigid_bodies ( self, subunits )

Construct a rigid body from a list of subunits.

Each subunit is a tuple that identifies the residue ranges and the component name (as used in create_component()).

subunits: [(name_1,(first_residue_1,last_residue_1)),(name_2,(first_residue_2,last_residue_2)),.....] or [name_1,name_2,(name_3,(first_residue_3,last_residue_3)),.....]

example: ["prot1","prot2",("prot3",(1,10))]

sometimes, we know about structure of an interaction and here we make such PPIs rigid

Definition at line 1935 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.set_rigid_bodies_as_fixed ( self, rigidbodiesarefixed = True )

Fix rigid bodies in their actual position.

The get_particles_to_sample() function will return just the floppy bodies (if they are not fixed).

Definition at line 2158 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.set_rigid_body_from_hierarchies ( self, hiers, particles = None )

Construct a rigid body from hierarchies (and optionally particles).

Parameters
 hiers list of hierarchies to make rigid particles list of particles to add to the rigid body

Definition at line 1898 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.setup_component_sequence_connectivity ( self, name, resolution = 10, scale = 1.0 )

Generate restraints between contiguous fragments in the hierarchy.

The linkers are generated at resolution 10 by default.

Definition at line 1631 of file pmi1/representation.py.

 def IMP.pmi1.representation.Representation.shuffle_configuration ( self, max_translation = 300.0, max_rotation = 2.0 * pi, avoidcollision = True, cutoff = 10.0, niterations = 100, bounding_box = None, excluded_rigid_bodies = None, ignore_initial_coordinates = False, hierarchies_excluded_from_collision = None )

Shuffle configuration; 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.

Parameters
 avoidcollision check if the particle/rigid body was placed close to another particle; uses the optional arguments cutoff and niterations bounding_box defined by ((x1,y1,z1),(x2,y2,z2))

Definition at line 1404 of file pmi1/representation.py.

The documentation for this class was generated from the following file: