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IMP Reference Guide  develop.cc86c9801d,2022/11/22
The Integrative Modeling Platform
IMP.pmi.macros.AnalysisReplicaExchange Class Reference

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

Inherits object.

Detailed Description

This class contains analysis utilities to investigate ReplicaExchange results.

Note
This class is only available in Python.

Definition at line 1584 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 assignemnts 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 assignemnt. 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
modelIMP.Model()
stat_fileslist of string. Can be ascii stat files, rmf files names
best_modelsInteger. Number of best scoring models, if None: all models will be read
alignmentboolean (Default=True). Align before computing the rmsd.

Definition at line 1595 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 2340 of file macros.py.

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

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

It changes the Copy index of Molecules

Definition at line 2520 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 1913 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_cutoffFloat the distance cutoff in Angstrom
metric(Default=IMP.atom.get_rmsd) the metric that will be used to compute rmsds

Definition at line 1672 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 1806 of file macros.py.

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

Return the model data from a cluster.

Parameters
clusterIMP.pmi.output.Cluster object

Definition at line 1721 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 2395 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
filenamestring
appendbool (Default=False), if True. append the clusters to the ones currently present

Definition at line 1783 of file macros.py.

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

Load the data from an external pickled file.

Parameters
filenamestring

Definition at line 1746 of file macros.py.

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

merge two clusters

Definition at line 2410 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_cutoffcutoff distance in Angstorms

Definition at line 2367 of file macros.py.

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

Compute the precision of a cluster.

Definition at line 1884 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 1849 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_cutoffcutoff distance in Angstorms

Definition at line 1685 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 2454 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 2418 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 1933 of file macros.py.

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

Save the clusters into a pickle file.

Parameters
filenamestring

Definition at line 1771 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 1824 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
filenamestring

Definition at line 1731 of file macros.py.

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

Setup the selection onto which the alignment is computed.

Parameters
kwargsuse IMP.atom.Selection keywords

Definition at line 1656 of file macros.py.

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

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

Parameters
dataIMP.pmi.output.Data

Definition at line 1738 of file macros.py.

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

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

Parameters
referencecan be either "Absolute" (cluster center of the first cluster) or Relative (cluster center of the current cluster)

Definition at line 2502 of file macros.py.

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

Setup the selection onto which the rmsd is computed.

Parameters
kwargsuse IMP.atom.Selection keywords

Definition at line 1640 of file macros.py.

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

Store names of symmetric molecules.

Definition at line 1649 of file macros.py.

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

Undo the Copy index assignment.

Definition at line 2534 of file macros.py.

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

Update the cluster id numbers.

Definition at line 2298 of file macros.py.

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

Update the seldicts.

Definition at line 2309 of file macros.py.


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