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
	Applies 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	read_component
	Read a PDB molecule, add atoms, and set a name. 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.

Note: This function is only available in Python.

Definition at line 300 of file EMageFit/imp_general/representation.py.

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

Applies 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

Note: This function is only available in Python.

Definition at line 313 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.

Note: This function is only available in Python.

Definition at line 41 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.

Note: This function is only available in Python.

Definition at line 24 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.

Note: This function is only available in Python.

Definition at line 71 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.

Note: This function is only available in Python.

Definition at line 173 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.

Note: This function is only available in Python.

Definition at line 116 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

Note: This function is only available in Python.

Definition at line 368 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

Note: This function is only available in Python.

Definition at line 441 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

Note: This function is only available in Python.

Definition at line 424 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 IMP.atom.Fragments

Note: This function is only available in Python.

Definition at line 278 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.

Note: This function is only available in Python.

Definition at line 225 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'

Note: This function is only available in Python.

Definition at line 385 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.

Note: This function is only available in Python.

Definition at line 243 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_id	See help for get_residue_particle()
res	See help for get_residue_particle()

Note: This function is only available in Python.

Definition at line 340 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

Note: This function is only available in Python.

Definition at line 325 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

Note: This function is only available in Python.

Definition at line 351 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.

Note: This function is only available in Python.

Definition at line 235 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

Note: This function is only available in Python.

Definition at line 266 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.

Note: This function is only available in Python.

Definition at line 248 of file EMageFit/imp_general/representation.py.

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

Read a PDB molecule, add atoms, and set a name.

Note: This function is only available in Python.

Definition at line 55 of file EMageFit/imp_general/representation.py.

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

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

The names are added sequentially.

Note: This function is only available in Python.

Definition at line 97 of file EMageFit/imp_general/representation.py.

Detailed Description

Functions

Function Documentation