This class contains analysis utilities to investigate ReplicaExchange results.
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Inherits object.
This class contains analysis utilities to investigate ReplicaExchange results.
- Note
- This class is only available in Python.
Definition at line 1576 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.__init__ |
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self, |
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model, |
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stat_files, |
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best_models = None , |
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score_key = None , |
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alignment = True |
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Construction of the Class.
- Parameters
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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 1587 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.aggregate |
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self, |
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idxs, |
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rmsd_cutoff = 10 , |
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metric = IMP.atom.get_rmsd |
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initial filling of the clusters.
Definition at line 2332 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.apply_molecular_assignments |
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self, |
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n1 |
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compute the molecular assignments between multiple copies of the same sequence.
It changes the Copy index of Molecules
Definition at line 2512 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.bipartite_precision |
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self, |
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cluster1, |
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cluster2, |
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verbose = False |
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Compute the bipartite precision (ie the cross-precision) between two clusters.
Definition at line 1905 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.cluster |
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self, |
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rmsd_cutoff = 10 , |
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metric = IMP.atom.get_rmsd |
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Cluster the models based on RMSD.
- Parameters
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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 1664 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.compute_cluster_center |
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self, |
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cluster |
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Compute the cluster center for a given cluster.
Definition at line 1798 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.get_cluster_data |
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self, |
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cluster |
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Return the model data from a cluster.
- Parameters
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Definition at line 1713 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.have_close_members |
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self, |
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c0, |
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c1, |
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rmsd_cutoff, |
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metric |
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returns true if c0 and c1 have members that are closer than rmsd_cutoff
Definition at line 2387 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.load_clusters |
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self, |
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filename = 'clusters.pkl' , |
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append = False |
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Load the clusters from a pickle file.
- Parameters
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filename | string |
append | bool (Default=False), if True. append the clusters to the ones currently present |
Definition at line 1775 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.load_data |
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self, |
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filename = 'data.pkl' |
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Load the data from an external pickled file.
- Parameters
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Definition at line 1738 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.merge |
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self, |
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c0, |
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c1 |
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def IMP.pmi.macros.AnalysisReplicaExchange.merge_aggregates |
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self, |
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rmsd_cutoff, |
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metric = IMP.atom.get_rmsd |
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merge the clusters that have close members
- Parameters
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rmsd_cutoff | cutoff distance in Angstorms |
Definition at line 2359 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.precision |
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self, |
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cluster |
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Compute the precision of a cluster.
Definition at line 1876 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.prune_redundant_structures |
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self, |
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rmsd_cutoff = 10 |
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remove structures that are similar append it to a new cluster
Definition at line 1841 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.refine |
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self, |
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rmsd_cutoff = 10 |
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Refine the clusters by merging the ones whose centers are close.
- Parameters
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rmsd_cutoff | cutoff distance in Angstorms |
Definition at line 1677 of file macros.py.
Computes the RMSD.
Resolves ambiguous pairs assignments
Definition at line 2446 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.rmsd_helper |
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self, |
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sels0, |
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sels1, |
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metric |
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a function that returns the permutation best_sel of sels0 that minimizes metric
Definition at line 2410 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.rmsf |
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self, |
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cluster, |
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molecule, |
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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.pmi.tools.OrderedDict() where the keys are the residue indexes and the value is the rmsf.
Definition at line 1925 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.save_clusters |
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self, |
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filename = 'clusters.pkl' |
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Save the clusters into a pickle file.
- Parameters
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Definition at line 1763 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.save_coordinates |
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self, |
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cluster, |
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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 1816 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.save_data |
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self, |
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filename = 'data.pkl' |
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Save the data for the whole models into a pickle file.
- Parameters
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Definition at line 1723 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.set_alignment_selection |
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self, |
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kwargs |
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Setup the selection onto which the alignment is computed.
- Parameters
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Definition at line 1648 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.set_data |
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self, |
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data |
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Set the data from an external IMP.pmi.output.Data.
- Parameters
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Definition at line 1730 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.set_reference |
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self, |
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reference, |
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cluster |
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Fix the reference structure for structural alignment, rmsd and chain assignment.
- Parameters
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reference | can be either "Absolute" (cluster center of the first cluster) or Relative (cluster center of the current cluster) |
Definition at line 2494 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.set_rmsd_selection |
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self, |
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kwargs |
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Setup the selection onto which the rmsd is computed.
- Parameters
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Definition at line 1632 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.set_symmetric |
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self, |
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molecule_name |
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Store names of symmetric molecules.
Definition at line 1641 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.undo_apply_molecular_assignments |
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self, |
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n1 |
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Undo the Copy index assignment.
Definition at line 2526 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.update_clusters |
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self | ) |
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Update the cluster id numbers.
Definition at line 2290 of file macros.py.
def IMP.pmi.macros.AnalysisReplicaExchange.update_seldicts |
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self | ) |
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The documentation for this class was generated from the following file: