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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
  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 593 of file pmi1/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.pmi1.analysis.Precision.__init__ (   self,
  model,
  resolution = 1,
  selection_dictionary = {} 
)

Constructor.

Parameters
modelThe IMP Model
resolutionUse 1 or 10 (kluge: requires that "_Res:X" is part of the hier name)
selection_dictionaryDictionary 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_nameThe name of the RMF file
rmf_frame_indexThe frame to read
structure_set_nameName for the set that includes this structure (e.g. "cluster 1")
setup_index_mapif 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_tupleslist of (rmf_file_name,frame_number)
structure_set_nameName 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_nameThe 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
outfileName of the precision output file
structure_set_name1string name of the first structure set
structure_set_name2string name of the second structure set
skipanalyze every (skip) structure for the distance matrix calculation
selection_keywordsSpecify 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_namethe name of the structure set
alignment_selectionthe 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_nameWhich structure set to calculate RMSF for
outdirWhere to write the files
skipSkip this number of structures
set_plot_yaxis_rangeIn 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_nameThe RMF file to read the reference
rmf_frame_indexThe index in that file

Definition at line 1011 of file pmi1/Analysis.py.


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