IMP Reference Guide  develop.9f755902c2,2022/12/07 The Integrative Modeling Platform
IMP.pmi1.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
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 593 of file pmi1/Analysis.py.

Public Member Functions

def __init__
Constructor. More...

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

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.pmi1.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 604 of file pmi1/Analysis.py.

Member Function Documentation

 def IMP.pmi1.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 683 of file pmi1/Analysis.py.

 def IMP.pmi1.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 734 of file pmi1/Analysis.py.

 def IMP.pmi1.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 1056 of file pmi1/Analysis.py.

 def IMP.pmi1.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 844 of file pmi1/Analysis.py.

 def IMP.pmi1.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 1026 of file pmi1/Analysis.py.

 def IMP.pmi1.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 953 of file pmi1/Analysis.py.

 def IMP.pmi1.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 1011 of file pmi1/Analysis.py.

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