This class contains analysis utilities to investigate ReplicaExchange results. More...

Detailed Description

This class contains analysis utilities to investigate ReplicaExchange results.

Note: This class is only available in Python.

Definition at line 1625 of file macros.py.

Public Member Functions
def	__init__
	Construction of the Class. More...

def	aggregate
	initial filling of the clusters. More...

def	apply_molecular_assignments
	compute the molecular assignments between multiple copies of the same sequence. More...

def	bipartite_precision
	Compute the bipartite precision (ie the cross-precision) between two clusters. More...

def	cluster
	Cluster the models based on RMSD. More...

def	compute_cluster_center
	Compute the cluster center for a given cluster. More...

def	get_cluster_data
	Return the model data from a cluster. More...

def	have_close_members
	returns true if c0 and c1 have members that are closer than rmsd_cutoff More...

def	load_clusters
	Load the clusters from a pickle file. More...

def	load_data
	Load the data from an external pickled file. More...

def	merge
	merge two clusters More...

def	merge_aggregates
	merge the clusters that have close members More...

def	precision
	Compute the precision of a cluster. More...

def	prune_redundant_structures
	remove structures that are similar append it to a new cluster More...

def	refine
	Refine the clusters by merging the ones whose centers are close. More...

def	rmsd
	Computes the RMSD. More...

def	rmsd_helper
	a function that returns the permutation best_sel of sels0 that minimizes metric More...

def	rmsf
	Compute the Root mean square fluctuations of a molecule in a cluster Returns an IMP.pmi.tools.OrderedDict() where the keys are the residue indexes and the value is the rmsf. More...

def	save_clusters
	Save the clusters into a pickle file. More...

def	save_coordinates
	Save the coordinates of the current cluster a single rmf file. More...

def	save_data
	Save the data for the whole models into a pickle file. More...

def	set_alignment_selection
	Setup the selection onto which the alignment is computed. More...

def	set_data
	Set the data from an external IMP.pmi.output.Data. More...

def	set_reference
	Fix the reference structure for structural alignment, rmsd and chain assignment. More...

def	set_rmsd_selection
	Setup the selection onto which the rmsd is computed. More...

def	set_symmetric
	Store names of symmetric molecules. More...

def	undo_apply_molecular_assignments
	Undo the Copy index assignment. More...

def	update_clusters
	Update the cluster id numbers. More...

def	update_seldicts
	Update the seldicts. More...

Constructor & Destructor Documentation

def IMP.pmi.macros.AnalysisReplicaExchange.__init__	(	self,
		model,
		stat_files,
		best_models = `None`,
		score_key = `None`,
		alignment = `True`
	)

Construction of the Class.

Parameters

model	IMP.Model()
stat_files	list of string. Can be ascii stat files, rmf files names
best_models	Integer. Number of best scoring models, if None: all models will be read
score_key	Use the provided stat key keyword as the score (by default, the total score is used)
alignment	boolean (Default=True). Align before computing the rmsd.

Definition at line 1636 of file macros.py.

Member Function Documentation

def IMP.pmi.macros.AnalysisReplicaExchange.aggregate	(	self,
		idxs,
		rmsd_cutoff = `10`,
		metric = `IMP.atom.get_rmsd`
	)

initial filling of the clusters.

Definition at line 2377 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.apply_molecular_assignments	(	self,
		n1
	)

compute the molecular assignments between multiple copies of the same sequence.

It changes the Copy index of Molecules

Definition at line 2561 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.bipartite_precision	(	self,
		cluster1,
		cluster2,
		verbose = `False`
	)

Compute the bipartite precision (ie the cross-precision) between two clusters.

Definition at line 1950 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.cluster	(	self,
		rmsd_cutoff = `10`,
		metric = `IMP.atom.get_rmsd`
	)

Cluster the models based on RMSD.

Parameters

rmsd_cutoff	Float the distance cutoff in Angstrom
metric	(Default=IMP.atom.get_rmsd) the metric that will be used to compute rmsds

Definition at line 1715 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.compute_cluster_center	(	self,
		cluster
	)

Compute the cluster center for a given cluster.

Definition at line 1843 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.get_cluster_data	(	self,
		cluster
	)

Return the model data from a cluster.

Parameters

cluster IMP.pmi.output.Cluster object

Definition at line 1764 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.have_close_members	(	self,
		c0,
		c1,
		rmsd_cutoff,
		metric
	)

returns true if c0 and c1 have members that are closer than rmsd_cutoff

Definition at line 2435 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.load_clusters	(	self,
		filename = `'clusters.pkl'`,
		append = `False`
	)

Load the clusters from a pickle file.

Parameters

filename	string
append	bool (Default=False), if True. append the clusters to the ones currently present

Definition at line 1823 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.load_data	(	self,
		filename = `'data.pkl'`
	)

Load the data from an external pickled file.

Parameters

filename string

Definition at line 1789 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.merge	(	self,
		c0,
		c1
	)

merge two clusters

Definition at line 2450 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.merge_aggregates	(	self,
		rmsd_cutoff,
		metric = `IMP.atom.get_rmsd`
	)

merge the clusters that have close members

Parameters

rmsd_cutoff	cutoff distance in Angstorms
metric	Function to calculate distance between two Selections (by default, IMP.atom.get_rmsd is used)

Definition at line 2404 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.precision	(	self,
		cluster
	)

Compute the precision of a cluster.

Definition at line 1921 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.prune_redundant_structures	(	self,
		rmsd_cutoff = `10`
	)

remove structures that are similar append it to a new cluster

Definition at line 1886 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.refine	(	self,
		rmsd_cutoff = `10`
	)

Refine the clusters by merging the ones whose centers are close.

Parameters

rmsd_cutoff cutoff distance in Angstorms

Definition at line 1728 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.rmsd	(	self,
		metric = `IMP.atom.get_rmsd`
	)

Computes the RMSD.

Resolves ambiguous pairs assignments

Definition at line 2494 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.rmsd_helper	(	self,
		sels0,
		sels1,
		metric
	)

a function that returns the permutation best_sel of sels0 that minimizes metric

Definition at line 2458 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.rmsf	(	self,
		cluster,
		molecule,
		copy_index = `0`,
		state_index = `0`,
		cluster_ref = `None`,
		step = `1`
	)

Compute the Root mean square fluctuations of a molecule in a cluster Returns an IMP.pmi.tools.OrderedDict() where the keys are the residue indexes and the value is the rmsf.

Definition at line 1970 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.save_clusters	(	self,
		filename = `'clusters.pkl'`
	)

Save the clusters into a pickle file.

Parameters

filename string

Definition at line 1814 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.save_coordinates	(	self,
		cluster,
		rmf_name = `None`,
		reference = `'Absolute'`,
		prefix = `'./'`
	)

Save the coordinates of the current cluster a single rmf file.

Definition at line 1861 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.save_data	(	self,
		filename = `'data.pkl'`
	)

Save the data for the whole models into a pickle file.

Parameters

filename string

Definition at line 1774 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.set_alignment_selection	(	self,
		kwargs
	)

Setup the selection onto which the alignment is computed.

Parameters

kwargs use IMP.atom.Selection keywords

Definition at line 1699 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.set_data	(	self,
		data
	)

Set the data from an external IMP.pmi.output.Data.

Parameters

data	IMP.pmi.output.Data

Definition at line 1781 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.set_reference	(	self,
		reference,
		cluster
	)

Fix the reference structure for structural alignment, rmsd and chain assignment.

Parameters

reference can be either "Absolute" (cluster center of the first cluster) or Relative (cluster center of the current cluster) #param cluster the reference IMP.pmi.output.Cluster object

Definition at line 2542 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.set_rmsd_selection	(	self,
		kwargs
	)

Setup the selection onto which the rmsd is computed.

Parameters

kwargs use IMP.atom.Selection keywords

Definition at line 1683 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.set_symmetric	(	self,
		molecule_name
	)

Store names of symmetric molecules.

Definition at line 1692 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.undo_apply_molecular_assignments	(	self,
		n1
	)

Undo the Copy index assignment.

Definition at line 2575 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.update_clusters ( self )

Update the cluster id numbers.

Definition at line 2335 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange.update_seldicts ( self )

Update the seldicts.

Definition at line 2346 of file macros.py.

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

macros.py

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation