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IMP Reference Guide
develop.d4e9f3251e,2024/04/26
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.