IMP  2.4.0 The Integrative Modeling Platform
IMP.EMageFit.imp_general.representation Namespace Reference

Utility functions to handle representation. More...

## Detailed Description

Utility functions to handle representation.

## Functions

def apply_rotation_around_centroid
Rotates the reference frame of a rigid body around the centroid. More...

def apply_transformation_around_centroid
Aplies a transformation around the centroid of a rigid body. More...

def create_assembly
Read all the PDBs given in the list of names fn_pdbs and adds the hierarchies to the model. More...

def create_assembly_from_pdb
Builds the assembly setting the chains in the PDB file as components. More...

def create_rigid_bodies
set the children of a molecule type hierarchy as rigid bodies In this case, all the children are the components of the complex. More...

def create_simplified_assembly
Simplifies an assembly, by creating a hierarchy with one ball per n_res residues. More...

def create_simplified_dna
Gets a hierarchy containing a molecule of DNA and simplifies it, generating a coarse representation of spheres. More...

def get_all_chains
Gets all the chains in a set of hierarchies. More...

def get_all_members
Gets all the members of a set of rigid bodies, removing the subrigid bodies. More...

def get_backbone
Get the backbone atoms for a hierarchy. More...

def get_coarse_selection
The function returns the particles (fragments) in the coarse hierarchy that were created by summarizing the residues_numbers. More...

def get_component
Select a component of the assembly using the name. More...

def get_nucleic_acid_backbone
Returns the atoms in the backbone of the nucleic acid contained in the hierarchy. More...

def get_rb_name
Name to use for the rigid body of a hierarch. More...

def get_residue_coordinates
Get the coordinates of a residue (the coordinates of the first particle) More...

def get_residue_particle
Get the particle for a residue in a hierarchy. More...

def get_residues_distance
Distance between two residues. More...

def get_rigid_body
Select a rigid body from the rigid_bodies using the name. More...

def get_selection_as_atom_hierarchy
Gets a selection of particles and decorates them as Atoms. More...

def get_selection_rigid_body
Build the rigid body for all the particles in the selection S. More...

def rename_chains
Rename all the chains of an assembly so there are no conflicts with the ids. More...

## Function Documentation

 def IMP.EMageFit.imp_general.representation.apply_rotation_around_centroid ( rb, rot )

Rotates the reference frame of a rigid body around the centroid.

Definition at line 303 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.apply_transformation_around_centroid ( rb, T )

Aplies a transformation around the centroid of a rigid body.

First does the rotation around the centroid and then applies the transformation.

Parameters
 rb A IMP.core.RigidBody object T a IMP.algebra.Transformation3D object

Definition at line 316 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.create_assembly ( model, fn_pdbs, names = False )

Read all the PDBs given in the list of names fn_pdbs and adds the hierarchies to the model.

Definition at line 44 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.create_assembly_from_pdb ( model, fn_pdb, names = False )

Builds the assembly setting the chains in the PDB file as components.

Definition at line 27 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.create_rigid_bodies ( assembly )

set the children of a molecule type hierarchy as rigid bodies In this case, all the children are the components of the complex.

I use the function create_rigid_body(), that creates a lot of sub-rigid bodies.

I have changed the function and now build the rigid body directly from the leaves of each of the components. With this I guarantee that the number of rigid members is going to be the same if the components have the same number of atoms.

Definition at line 74 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.create_simplified_assembly ( assembly, components_rbs, n_res )

Simplifies an assembly, by creating a hierarchy with one ball per n_res residues.

Each of the chains in the new hierarchy are added to the rigid bodies for each of the components. There must be correspondence between the children of the assembly (components) and the rigid bodies. I check for the ids.

Definition at line 177 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.create_simplified_dna ( dna_hierarchy, n_res )

Gets a hierarchy containing a molecule of DNA and simplifies it, generating a coarse representation of spheres.

The function returns a hierarchy with the spheres. n_res - Number of residues to use per sphere.

Definition at line 119 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_all_chains ( hierarchies )

Gets all the chains in a set of hierarchies.

Parameters
 hierarchies A set of IMP.atom.Hierarchy objects

Definition at line 371 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_all_members ( rigid_bodies )

Gets all the members of a set of rigid bodies, removing the subrigid bodies.

Returns all the plain atom or bead members

Definition at line 444 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_backbone ( hierarchy )

Get the backbone atoms for a hierarchy.

It can be a protein or a nucleic acid

Definition at line 427 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_coarse_selection ( coarse_h, residues_numbers )

The function returns the particles (fragments) in the coarse hierarchy that were created by summarizing the residues_numbers.

Coarse hierarchy - Hierarchy formed by a bunch of fragments. Each fragment must have the residue numbers that it contains residue_numbers - list with the number of the residues that need to be recovered. The function returns the set of particles that are atom.Fragments

Definition at line 281 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_component ( assembly, name )

Select a component of the assembly using the name.

Definition at line 228 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_nucleic_acid_backbone ( hierarchy, backbone = 'minimal' )

Returns the atoms in the backbone of the nucleic acid contained in the hierarchy.

backbone 'minimal' returns the atoms: ["P", "O5'", "C5'", "C4'", "C3'", "O3'"] backbone 'trace' returns the atoms C4'

Definition at line 388 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_rb_name ( name )

Name to use for the rigid body of a hierarch.

Definition at line 246 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_residue_coordinates ( h, chain_id = False, res = 1 )

Get the coordinates of a residue (the coordinates of the first particle)

Parameters
 h Hierarchy chain See help for get_residue_particle() res See help for get_residue_particle()

Definition at line 343 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_residue_particle ( h, chain_id = False, res = 1 )

Get the particle for a residue in a hierarchy.

Parameters
 h The hierarchy chain_id If chain_id == False, just search for the residue res Number of residue in the chain

Definition at line 328 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_residues_distance ( hierarchy1, chain_id1, residue1, hierarchy2, chain_id2, residue2 )

Distance between two residues.

See the help for get_residue_particle()

Parameters
 hierarchy1 chain_id1 residue1 hierarchy2 chain_id2 residue2

Definition at line 354 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_rigid_body ( rigid_bodies, name )

Select a rigid body from the rigid_bodies using the name.

Definition at line 238 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_selection_as_atom_hierarchy ( model, S )

Gets a selection of particles and decorates them as Atoms.

Then all of them are put into a big residue. I have this to use with the multifit.create_coarse_molecule_from_molecule() function

Definition at line 269 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.get_selection_rigid_body ( model, S )

Build the rigid body for all the particles in the selection S.

Definition at line 251 of file EMageFit/imp_general/representation.py.

 def IMP.EMageFit.imp_general.representation.read_component ( model, fn_pdb, name = False )