IMP.pmi.analysis.Precision Class Reference

A class to evaluate the precision of an ensemble. More...

Inherits object.

Detailed Description

A class to evaluate the precision of an ensemble.

Also can evaluate the cross-precision of multiple ensembles. Supports MPI for coordinate reading. Recommended procedure:

1. initialize object and pass the selection for evaluating precision
2. call add_structures() to read in the data (specify group name)
3. call get_precision() to evaluate inter/intra precision
4. call get_rmsf() to evaluate within-group fluctuations

Note

This class is only available in Python.

Definition at line 473 of file pmi/Analysis.py.

Public Member Functions
def	__init__
	Constructor. More...
def	add_structure
	Read a structure into the ensemble and store (as coordinates). More...
def	add_structures
	Read a list of RMFs, supports parallel. More...
def	get_average_distance_wrt_reference_structure
	Compare the structure set to the reference structure. More...
def	get_precision
	Evaluate the precision of two named structure groups. More...
def	get_rmsd_wrt_reference_structure_with_alignment
	First align then calculate RMSD. More...
def	get_rmsf
	Calculate the residue mean square fluctuations (RMSF). More...
def	set_reference_structure
	Read in a structure used for reference computation. More...

Constructor & Destructor Documentation

def IMP.pmi.analysis.Precision.__init__	(		self,
			model,
			resolution = 1,
			selection_dictionary = {}
	)

Constructor.

Parameters

model	The IMP Model
resolution	Use 1 or 10 (kluge: requires that "_Res:X" is part of the hier name)
selection_dictionary	Dictionary where keys are names for selections and values are selection tuples for scoring precision. "All" is automatically made as well

Definition at line 484 of file pmi/Analysis.py.

Member Function Documentation

def IMP.pmi.analysis.Precision.add_structure	(		self,
			rmf_name,
			rmf_frame_index,
			structure_set_name,
			setup_index_map = False
	)

Read a structure into the ensemble and store (as coordinates).

Parameters

rmf_name	The name of the RMF file
rmf_frame_index	The frame to read
structure_set_name	Name for the set that includes this structure (e.g. "cluster 1")
setup_index_map	if requested, set up a dictionary to help find residue indexes

Definition at line 563 of file pmi/Analysis.py.

def IMP.pmi.analysis.Precision.add_structures	(		self,
			rmf_name_frame_tuples,
			structure_set_name
	)

Read a list of RMFs, supports parallel.

Parameters

rmf_name_frame_tuples	list of (rmf_file_name,frame_number)
structure_set_name	Name this set of structures (e.g. "cluster.1")

Definition at line 614 of file pmi/Analysis.py.

def IMP.pmi.analysis.Precision.get_average_distance_wrt_reference_structure	(		self,
			structure_set_name
	)

Compare the structure set to the reference structure.

Parameters

structure_set_name

The structure set to compute this on

Note

First call set_reference_structure()

Definition at line 947 of file pmi/Analysis.py.

def IMP.pmi.analysis.Precision.get_precision	(		self,
			structure_set_name1,
			structure_set_name2,
			outfile = None,
			skip = 1,
			selection_keywords = None
	)

Evaluate the precision of two named structure groups.

Supports MPI. When the structure_set_name1 is different from the structure_set_name2, this evaluates the cross-precision (average pairwise distances).

Parameters

outfile	Name of the precision output file
structure_set_name1	string name of the first structure set
structure_set_name2	string name of the second structure set
skip	analyze every (skip) structure for the distance matrix calculation
selection_keywords	Specify the selection name you want to calculate on. By default this is computed for everything you provided in the constructor, plus all the subunits together.

Definition at line 735 of file pmi/Analysis.py.

def IMP.pmi.analysis.Precision.get_rmsd_wrt_reference_structure_with_alignment	(		self,
			structure_set_name,
			alignment_selection_key
	)

First align then calculate RMSD.

Parameters

structure_set_name	the name of the structure set
alignment_selection	the key containing the selection tuples needed to make the alignment stored in self.selection_dictionary

Returns

: for each structure in the structure set, returns the rmsd

Definition at line 917 of file pmi/Analysis.py.

def IMP.pmi.analysis.Precision.get_rmsf	(		self,
			structure_set_name,
			outdir = './',
			skip = 1,
			set_plot_yaxis_range = None
	)

Calculate the residue mean square fluctuations (RMSF).

Automatically outputs as data file and pdf

Parameters

structure_set_name	Which structure set to calculate RMSF for
outdir	Where to write the files
skip	Skip this number of structures
set_plot_yaxis_range	In case you need to change the plot

Definition at line 844 of file pmi/Analysis.py.

def IMP.pmi.analysis.Precision.set_reference_structure	(		self,
			rmf_name,
			rmf_frame_index
	)

Read in a structure used for reference computation.

Needed before calling get_average_distance_wrt_reference_structure()

Parameters

rmf_name	The RMF file to read the reference
rmf_frame_index	The index in that file

Definition at line 902 of file pmi/Analysis.py.

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

• pmi/Analysis.py