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IMP Reference Guide  develop.9f755902c2,2022/12/07
The Integrative Modeling Platform
IMP.pmi.analysis.Clustering Class Reference

A class to cluster structures. More...

Inherits object.

Detailed Description

A class to cluster structures.

Uses scipy's cdist function to compute distance matrices and sklearn's kmeans clustering module.

Note
This class is only available in Python.

Definition at line 184 of file pmi/Analysis.py.

Public Member Functions

def __init__
 Constructor. More...
 
def do_cluster
 Run K-means clustering. More...
 
def fill
 Add coordinates for a single model. More...
 

Constructor & Destructor Documentation

def IMP.pmi.analysis.Clustering.__init__ (   self,
  rmsd_weights = None 
)

Constructor.

Parameters
rmsd_weightsFlat list of weights for each particle (if they're coarse)

Definition at line 189 of file pmi/Analysis.py.

Member Function Documentation

def IMP.pmi.analysis.Clustering.do_cluster (   self,
  number_of_clusters,
  seed = None 
)

Run K-means clustering.

Parameters
number_of_clustersNum means
seedthe random seed

Definition at line 253 of file pmi/Analysis.py.

def IMP.pmi.analysis.Clustering.fill (   self,
  frame,
  Coords 
)

Add coordinates for a single model.

Definition at line 210 of file pmi/Analysis.py.


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