Management of a model using DOMINO. More...

Public Member Functions
def	add_branch_and_bound_assignments_table
	BranchAndBoundAssignmentsTable enumerate states based on provided filtered using the provided the subset filter tables.

def	add_exclusion_filter_table
	ExclusionSubsetFilterTable ensures that two particles are not given the same state at the same time.

def	add_restraint
	Adds a restraint to the model. More...

def	add_restraint_score_filter_table
	Add a RestraintScoreSubsetFilterTable to DOMINO that allows to reject assignments that have score worse than the thresholds for the restraints.

def	align_rigid_bodies_states
	Aligns the set of structures considered for DOMINO sampling. More...

def	create_coarse_assembly
	Simplify the assembly with a coarse representation. More...

def	create_merge_tree
	Creates a merge tree from the restraints that are set already.

def	do_sampling
	Do Domino sampling. More...

def	get_assignment_and_RFs
	Return a line with texts for an assignment and the the reference frames of the RigidBodies in the subset. More...

def	get_assignment_info
	Info related to an assignment. More...

def	get_assignment_scores
	Returns a list with the values for the restraints on a subset of the components of the assembly. More...

def	get_assignment_text
	Get the formatted text for an assignment. More...

def	get_assignments_with_heap
	Domino sampling that recovers the assignments for the root of the merge tree, but conserving only the best k scores for each vertex of the tree. More...

def	get_restraint_value_for_assignment
	Recover the value of a restraint. More...

def	get_restraints_for_native
	Get values of the restraints for the native structure. More...

def	get_restraints_names_used
	Get the names of the restraints used for a subset. More...

def	load_state
	Load the positions of the components given by the assignment. More...

def	read_merge_tree
	Read and create a merge tree from a file. More...

def	set_assembly
	Sets an assembly from a single PDB file. More...

def	set_assembly_components
	Sets the components of an assembly, each one given as a separate PDB file. More...

def	set_close_pairs_excluded_volume_restraint
	Creates an excluded volume restraint between all the components of the coarse assembly.See help for. More...

def	set_complementarity_restraint
	Set a restraint for geometric complementarity between 2 components. More...

def	set_connectivity_restraint
	Set a connectivity restraint between the elements of the assembly. More...

def	set_em2d_restraint
	Set a Restraint computing the em2d score. More...

def	set_native_assembly_for_benchmark
	Sets the native model for benchmark, by reading the native structure and set the rigid bodies. More...

def	set_not_optimized
	Set a part of the model as not optimized (it does not move during the model optimization) More...

def	set_pair_score_restraint
	Set a pair_score restraint between the coarse representation of two components. More...

def	set_rb_states
	Add a set of reference frames as possible states for a rigid body. More...

def	set_xlink_restraint
	Set a restraint on the maximum distance between 2 residues. More...

def	setup_domino_sampler
	Creates a DOMINO sampler and adds the required filter tables.

def	write_merge_tree
	Writes the current merge tree to file. More...

def	write_monte_carlo_solution
	Write the solution of a MonteCarlo run. More...

def	write_pdb_for_assignment
	Write the solution in the assignment. More...

def	write_pdb_for_component
	Write one component of the assembly. More...

def	write_pdb_for_configuration
	Write a file with a configuration for the model (configuration here means a configuration in DOMINO) More...

def	write_pdb_for_reference_frames
	Write a PDB file with a solution given by a set of reference frames. More...

def	write_pdbs_for_reference_frames
	Write a separate PDB for each of the elements. More...

def	write_solutions_database
	Write the results of the DOMINO sampling to a SQLite database. More...

def	write_subset
	Writes lines describing a subset (vertex of a merge tree) More...

Detailed Description

Note: This class is only available in Python.

Definition at line 4 of file DominoModel.py.

Member Function Documentation

def IMP.em2d.DominoModel.DominoModel.add_restraint	(	self,
		r,
		name,
		weight,
		max_score = `False`
	)

Parameters

r	An IMP.Restraint object
name	Name for the restraint
weight	Weight for the restraint
max_score	Maximum score allowed for the restraint. If max_score is False, there is no limit for the value of the restraint

Definition at line 11 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.align_rigid_bodies_states ( self )

The function: 1) reads the possible reference frames that the rb_states_table stores for each rigid body. This table must be filled before using this function. Usually it is filled with the results from a previous Monte Carlo sampling. If the solutions from Monte Carlo seem to have the same structure but they are not aligned to each other, this function can help setting better starting positions to use with DOMINO. 2) Gets the first state for each of the rigid bodies and sets a reference structure using such states. 3) Aligns all the rest of the structures respect to the reference 4) Replaces the values of the reference frames stored in the rb_states_table with the new values obtained from the alignments. It does it for all states of a rigid body.

Note: : If this function is applied, the parameters "anchor" and "fixed" are ignored, as they are superseded by the use of the aligments calculated here.

Definition at line 32 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.create_coarse_assembly	(	self,
		n_residues,
		write = `False`
	)

Parameters

n_residues	Number of residues used for a coarse particle
write	If True, write the coarse assembly to a format that Chimera can display

Definition at line 67 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.do_sampling	(	self,
		mode = `'assignments_heap_container'`,
		params = `None`
	)

Parameters

mode The mode used to recover solutions from domino. It can have the value "configuration", "assignments", or "assignments_heap_container". The mode "configuration" recovers all possible configurations (takes a while to generate them). The mode "assignments" only provides the assignments (state numbers) of the solutions. It is faster but requires generating the solutions afterwards The mode "assignments_heap_container" selects the best solutions after ecah merging in DOMINO, discarding the rest. In practice I used the mode "assignments_heap_container"

Definition at line 83 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.get_assignment_and_RFs	(	self,
		assignment,
		subset
	)

Parameters

subset	Subset of components of the assembly
assignment	Assignment class with the states for the subset

Note: : see the get_assignment_assignment_text() note.

Definition at line 100 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.get_assignment_info	(	self,
		assignment,
		subset
	)

Returns a list with text for the assignment and all the scores for the restraints

Parameters

subset	Subset of components of the assembly
assignment	Assignment class with the states for the subset

Definition at line 107 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.get_assignment_scores	(	self,
		assignment,
		subset
	)

Parameters

subset	Subset of components of the assembly
assignment	Assignment class with the states for the subset

Definition at line 114 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.get_assignment_text	(	self,
		assignment,
		subset
	)

Parameters

subset	Subset of components of the assembly
assignment	Assignment class with the states for the subset

Note: : The order in assignment and subset is not always the order of the rigid bodies in self.components_rbs. The function reorders the terms in the assignment so there is correspondence.

Definition at line 92 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.get_assignments_with_heap	(	self,
		vertex,
		k = `0`
	)

Parameters

vertex Vertex with the root of the current merge tree. This function is recursive.

Definition at line 127 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.get_restraint_value_for_assignment	(	self,
		assignment,
		name
	)

Parameters

name	of the restraint
assignment	Assignment class containing the assignment for the solution desired

Definition at line 134 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.get_restraints_for_native	(	self,
		restraints_names
	)

Parameters

restraints_names Names of the restraints requested

Returns: a list with the values of all scores, and the total score

Definition at line 295 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.get_restraints_names_used	(	self,
		subset
	)

Parameters

subset Subset of components of the assembly

Definition at line 289 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.load_state	(	self,
		assignment
	)

Parameters

assignment Assignment class

Definition at line 119 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.read_merge_tree	(	self,
		fn
	)

The format of the file is the format written by write merge_tree() It does not matter the order of the indices in the file, as they are sorted by this function. The only condition is that the index for the vertex that is the root of the tree MUST be the largest. This is guaranteed when creating a merge tree with create_merge_tree()

Parameters

fn	File containing the merge tree

Definition at line 197 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.set_assembly	(	self,
		fn_pdb,
		names
	)

The function assumes that the components of the assembly are the chains of the PDB file.

Parameters

fn_pdb	PDB with the file for the asembly
names	Names for each of the components (chains) of the asembly

Definition at line 172 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.set_assembly_components	(	self,
		fn_pdbs,
		names
	)

Parameters

fn_pdbs	List with the names of the pdb files
names	List with the names of the components of the assembly.

Definition at line 164 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.set_close_pairs_excluded_volume_restraint	(	self,
		distance = `10`,
		weight = `1.0`,
		ratio = `0.05`,
		stddev = `2`,
		max_score = `False`
	)

Parameters

distance	Maximum distance tolerated between particles
weight	Weight for the restraint
max_score	Maximum value for the restraint. If the parameter is None, an automatic value is computed (using the ratio).
ratio	Fraction of the number of possible pairs of particles that are tolerated to overlap. The maximum score is modified according to this ratio. I have found that ratios of 0.05-0.1 work well allowing for some interpenetration
stddev	Standard deviation used to approximate the HarmonicUpperBound function to a Gaussian

Definition at line 266 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.set_complementarity_restraint	(	self,
		name1,
		name2,
		rname,
		max_sep_distance,
		max_penetration,
		weight,
		max_score = `10000000000.0`
	)

Parameters

name1	name of
name2	- The restraint is applied to this components rname - The name given to the restraint max_sep_distance - maximum distance between molecules tolerated by the restraint max_penetration - Maximum penetration allowd (angstrom)

Definition at line 60 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.set_connectivity_restraint	(	self,
		names,
		rname,
		distance = `10`,
		weight = `1.0`,
		max_score = `None`,
		n_pairs = `1`,
		stddev = `2`
	)

Parameters

names	List with all the elements to be connected
distance	Maximum distance tolerated by the restraint
rname	Name for the restraint
weight	Weight for the restraint
max_score	Maximum score for the restraint
n_pairs	Number of pairs of particles used in the KClosePairScore of the connecitivity restraint
stddev	Standard deviation used to approximate the HarmonicUpperBound function to a Gaussian

Definition at line 226 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.set_em2d_restraint	(	self,
		name,
		fn_images_sel,
		pixel_size,
		resolution,
		n_projections,
		weight,
		max_score = `False`,
		mode = `'fast'`,
		n_optimized = `1`
	)

Parameters

name	Name for the restraint
fn_images_sel	Selection file with the names of the images used for the restraint
pixel_size	- pixel size in the images
resolution	- resolution used to downsample the projections of the model when projecting
weight	Weight of the restraint
max_score	- Maximum value tolerated for the restraint
n_projections	- Number of projections to generate when projecting the model to do the coarse alignments
mode	- Mode used for computing the restraints.
n_optimized	- number of results from the coarse alignment that are refined with the Simplex algorithm to get a more accurate value for the restraint

Definition at line 244 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.set_native_assembly_for_benchmark	(	self,
		params
	)

Parameters

fn_pdb_native	PDB with the native structure
anchored	List of True/False values indicating if the components of the assembly are anchored. The function sets the FIRST anchored component in the (0,0,0) coordinate and moves the other components with the same translation

Definition at line 144 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.set_not_optimized	(	self,
		name
	)

Parameters

Name	of the component to optimized

Definition at line 250 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.set_pair_score_restraint	(	self,
		name1,
		name2,
		restraint_name,
		distance = `10`,
		weight = `1.0`,
		n_pairs = `1`,
		stddev = `2`,
		max_score = `None`
	)

Parameters

name1	Name of the first component
name2	Name of the second component
restraint_name	Name for the restraint
distance	Maximum distance tolerated between particles
weight.	Weight of the restraint
max_score	Maximum value tolerated for the restraint
stddev	Standard deviation used to approximate the HarmonicUpperBound function to a Gaussian

Definition at line 279 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.set_rb_states	(	self,
		rb,
		transformations
	)

Parameters

rb	The rigid body
transformations	Transformations are used to build the reference frames for the rigid body.

Definition at line 151 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.set_xlink_restraint	(	self,
		id1,
		chain1,
		residue1,
		id2,
		chain2,
		residue2,
		distance,
		weight,
		stddev,
		max_score = `False`
	)

Parameters

id1	Name of the first component
residue1	Residue number for the aminoacid in the first component.The number is the number in the PDB file, not the number relative to the beginning of the chain
id2	Name of the second component
residue2	Residue number for the aminoacid in the second component.
distance	Maximum distance tolerated
weight	Weight of the restraint
stddev	Standard deviation used to approximate the HarmonicUpperBound function to a Gaussian
max_score	See help for add_restraint(). If none is given, the maximum score is set to allow a maximum distance of 10 Angstrom greater than the parameter "distance".

Definition at line 50 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.write_merge_tree	(	self,
		fn
	)

The format is: parent | child_left | child_right | labels

Parameters

fn	File for storing the merge tree

Definition at line 207 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.write_monte_carlo_solution	(	self,
		fn_database
	)

Parameters

fn_database Database file with the solution. The database will contain only one record

Definition at line 332 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.write_pdb_for_assignment	(	self,
		assignment,
		fn_pdb
	)

Parameters

assignment	Assignment class with the states for the subset
fn_pdb	File to write the model

Definition at line 301 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.write_pdb_for_component	(	self,
		component_index,
		ref,
		fn_pdb
	)

Parameters

component_index	Position of the component in the assembly
ref	Reference frame of the component
fn_pdb	Output PDB

Definition at line 326 of file DominoModel.py.

def IMP.em2d.DominoModel.DominoModel.write_pdb_for_configuration	(	self,
		n,
		fn_pdb
	)

Parameters

n	Index of the configuration desired.

Definition at line 307 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.write_pdb_for_reference_frames	(	self,
		RFs,
		fn_pdb
	)

Parameters

RFs	Reference frames for the elements of the complex
fn_pdb	File to write the solution

Definition at line 313 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.write_pdbs_for_reference_frames	(	self,
		RFs,
		fn_base
	)

Parameters

RFs	Reference frames for the elements of the complex
fn_base	base string to buid the names of the PDBs files

Definition at line 319 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.write_solutions_database	(	self,
		fn_database,
		max_number = `None`
	)

Parameters

max_number Maximum number of results to write

Definition at line 284 of file DominoModel.py.

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def IMP.em2d.DominoModel.DominoModel.write_subset	(	self,
		v,
		w
	)

Parameters

w	A csv.writer
v	Vertex index

Definition at line 213 of file DominoModel.py.

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

DominoModel.py

Public Member Functions

Detailed Description

Member Function Documentation