IMP Reference Guide
develop.62cd6b8d93,2024/10/30
The Integrative Modeling Platform
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This class contains analysis utilities to investigate ReplicaExchange results. More...
Inherits object.
This class contains analysis utilities to investigate ReplicaExchange results.
Definition at line 1901 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 assignments 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.pmi1.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.pmi1.output.Data. More... | |
def | set_reference |
Fix the reference structure for structural alignment, rmsd and chain assignment. 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... | |
def IMP.pmi1.macros.AnalysisReplicaExchange.__init__ | ( | self, | |
model, | |||
stat_files, | |||
best_models = None , |
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score_key = None , |
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alignment = True |
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) |
Construction of the Class.
model | IMP.Model() |
stat_files | list of string. Can be ascii stat files, rmf files names |
best_models | Integer. Number of best scoring models, if None: all models will be read |
alignment | boolean (Default=True). Align before computing the rmsd. |
Definition at line 1911 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.aggregate | ( | self, | |
idxs, | |||
rmsd_cutoff = 10 , |
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metric = IMP.atom.get_rmsd |
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) |
initial filling of the clusters.
Definition at line 2625 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.apply_molecular_assignments | ( | self, | |
n1 | |||
) |
compute the molecular assignments between multiple copies of the same sequence.
It changes the Copy index of Molecules
Definition at line 2805 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.bipartite_precision | ( | self, | |
cluster1, | |||
cluster2, | |||
verbose = False |
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) |
Compute the bipartite precision (ie the cross-precision) between two clusters.
Definition at line 2217 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.cluster | ( | self, | |
rmsd_cutoff = 10 , |
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metric = IMP.atom.get_rmsd |
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) |
Cluster the models based on RMSD.
rmsd_cutoff | Float the distance cutoff in Angstrom |
metric | (Default=IMP.atom.get_rmsd) the metric that will be used to compute rmsds |
Definition at line 1982 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.compute_cluster_center | ( | self, | |
cluster | |||
) |
Compute the cluster center for a given cluster.
Definition at line 2115 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.get_cluster_data | ( | self, | |
cluster | |||
) |
Return the model data from a cluster.
cluster | IMP.pmi1.output.Cluster object |
Definition at line 2031 of file /macros.py.
def IMP.pmi1.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 2674 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.load_clusters | ( | self, | |
filename = 'clusters.pkl' , |
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append = False |
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) |
Load the clusters from a pickle file.
filename | string |
append | bool (Default=False), if True. append the clusters to the ones currently present |
Definition at line 2093 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.load_data | ( | self, | |
filename = 'data.pkl' |
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) |
Load the data from an external pickled file.
filename | string |
Definition at line 2056 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.merge | ( | self, | |
c0, | |||
c1 | |||
) |
merge two clusters
Definition at line 2689 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.merge_aggregates | ( | self, | |
rmsd_cutoff, | |||
metric = IMP.atom.get_rmsd |
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) |
merge the clusters that have close members
rmsd_cutoff | cutoff distance in Angstorms |
Definition at line 2650 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.precision | ( | self, | |
cluster | |||
) |
Compute the precision of a cluster.
Definition at line 2188 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.prune_redundant_structures | ( | self, | |
rmsd_cutoff = 10 |
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) |
remove structures that are similar append it to a new cluster
Definition at line 2154 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.refine | ( | self, | |
rmsd_cutoff = 10 |
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) |
Refine the clusters by merging the ones whose centers are close.
rmsd_cutoff | cutoff distance in Angstorms |
Definition at line 1995 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.rmsd | ( | self, | |
metric = IMP.atom.get_rmsd |
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) |
def IMP.pmi1.macros.AnalysisReplicaExchange.rmsd_helper | ( | self, | |
sels0, | |||
sels1, | |||
metric | |||
) |
a function that returns the permutation best_sel of sels0 that minimizes metric
Definition at line 2697 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.rmsf | ( | self, | |
cluster, | |||
molecule, | |||
copy_index = 0 , |
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state_index = 0 , |
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cluster_ref = None , |
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step = 1 |
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) |
Compute the Root mean square fluctuations of a molecule in a cluster Returns an IMP.pmi1.tools.OrderedDict() where the keys are the residue indexes and the value is the rmsf.
Definition at line 2235 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.save_clusters | ( | self, | |
filename = 'clusters.pkl' |
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) |
Save the clusters into a pickle file.
filename | string |
Definition at line 2081 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.save_coordinates | ( | self, | |
cluster, | |||
rmf_name = None , |
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reference = 'Absolute' , |
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prefix = './' |
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) |
Save the coordinates of the current cluster a single rmf file.
Definition at line 2132 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.save_data | ( | self, | |
filename = 'data.pkl' |
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) |
Save the data for the whole models into a pickle file.
filename | string |
Definition at line 2041 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.set_alignment_selection | ( | self, | |
kwargs | |||
) |
Setup the selection onto which the alignment is computed.
kwargs | use IMP.atom.Selection keywords |
Definition at line 1966 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.set_data | ( | self, | |
data | |||
) |
Set the data from an external IMP.pmi1.output.Data.
data | IMP.pmi1.output.Data |
Definition at line 2048 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.set_reference | ( | self, | |
reference, | |||
cluster | |||
) |
Fix the reference structure for structural alignment, rmsd and chain assignment.
reference | can be either "Absolute" (cluster center of the first cluster) or Relative (cluster center of the current cluster) |
Definition at line 2790 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.set_rmsd_selection | ( | self, | |
kwargs | |||
) |
Setup the selection onto which the rmsd is computed.
kwargs | use IMP.atom.Selection keywords |
Definition at line 1950 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.set_symmetric | ( | self, | |
molecule_name | |||
) |
Store names of symmetric molecules.
Definition at line 1959 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.undo_apply_molecular_assignments | ( | self, | |
n1 | |||
) |
Undo the Copy index assignment.
Definition at line 2819 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.update_clusters | ( | self | ) |
Update the cluster id numbers.
Definition at line 2587 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange.update_seldicts | ( | self | ) |
Update the seldicts.
Definition at line 2598 of file /macros.py.