IMP Reference Guide
2.20.2
The Integrative Modeling Platform
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A class to evaluate the precision of an ensemble. More...
Inherits object.
A class to evaluate the precision of an ensemble.
Also can evaluate the cross-precision of multiple ensembles. Supports MPI for coordinate reading. Recommended procedure:
Definition at line 593 of file pmi1/Analysis.py.
Public Member Functions | |
def | __init__ |
Constructor. More... | |
def | add_structure |
Read a structure into the ensemble and store (as coordinates). More... | |
def | add_structures |
Read a list of RMFs, supports parallel. More... | |
def | get_average_distance_wrt_reference_structure |
Compare the structure set to the reference structure. More... | |
def | get_precision |
Evaluate the precision of two named structure groups. More... | |
def | get_rmsd_wrt_reference_structure_with_alignment |
First align then calculate RMSD. More... | |
def | get_rmsf |
Calculate the residue mean square fluctuations (RMSF). More... | |
def | set_reference_structure |
Read in a structure used for reference computation. More... | |
def IMP.pmi1.analysis.Precision.__init__ | ( | self, | |
model, | |||
resolution = 1 , |
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selection_dictionary = {} |
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) |
Constructor.
model | The IMP Model |
resolution | Use 1 or 10 (kluge: requires that "_Res:X" is part of the hier name) |
selection_dictionary | Dictionary where keys are names for selections and values are selection tuples for scoring precision. "All" is automatically made as well |
Definition at line 604 of file pmi1/Analysis.py.
def IMP.pmi1.analysis.Precision.add_structure | ( | self, | |
rmf_name, | |||
rmf_frame_index, | |||
structure_set_name, | |||
setup_index_map = False |
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) |
Read a structure into the ensemble and store (as coordinates).
rmf_name | The name of the RMF file |
rmf_frame_index | The frame to read |
structure_set_name | Name for the set that includes this structure (e.g. "cluster 1") |
setup_index_map | if requested, set up a dictionary to help find residue indexes |
Definition at line 683 of file pmi1/Analysis.py.
def IMP.pmi1.analysis.Precision.add_structures | ( | self, | |
rmf_name_frame_tuples, | |||
structure_set_name | |||
) |
Read a list of RMFs, supports parallel.
rmf_name_frame_tuples | list of (rmf_file_name,frame_number) |
structure_set_name | Name this set of structures (e.g. "cluster.1") |
Definition at line 734 of file pmi1/Analysis.py.
def IMP.pmi1.analysis.Precision.get_average_distance_wrt_reference_structure | ( | self, | |
structure_set_name | |||
) |
Compare the structure set to the reference structure.
structure_set_name | The structure set to compute this on |
Definition at line 1056 of file pmi1/Analysis.py.
def IMP.pmi1.analysis.Precision.get_precision | ( | self, | |
structure_set_name1, | |||
structure_set_name2, | |||
outfile = None , |
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skip = 1 , |
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selection_keywords = None |
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) |
Evaluate the precision of two named structure groups.
Supports MPI. When the structure_set_name1 is different from the structure_set_name2, this evaluates the cross-precision (average pairwise distances).
outfile | Name of the precision output file |
structure_set_name1 | string name of the first structure set |
structure_set_name2 | string name of the second structure set |
skip | analyze every (skip) structure for the distance matrix calculation |
selection_keywords | Specify the selection name you want to calculate on. By default this is computed for everything you provided in the constructor, plus all the subunits together. |
Definition at line 844 of file pmi1/Analysis.py.
def IMP.pmi1.analysis.Precision.get_rmsd_wrt_reference_structure_with_alignment | ( | self, | |
structure_set_name, | |||
alignment_selection_key | |||
) |
First align then calculate RMSD.
structure_set_name | the name of the structure set |
alignment_selection | the key containing the selection tuples needed to make the alignment stored in self.selection_dictionary |
Definition at line 1026 of file pmi1/Analysis.py.
def IMP.pmi1.analysis.Precision.get_rmsf | ( | self, | |
structure_set_name, | |||
outdir = './' , |
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skip = 1 , |
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set_plot_yaxis_range = None |
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) |
Calculate the residue mean square fluctuations (RMSF).
Automatically outputs as data file and pdf
structure_set_name | Which structure set to calculate RMSF for |
outdir | Where to write the files |
skip | Skip this number of structures |
set_plot_yaxis_range | In case you need to change the plot |
Definition at line 953 of file pmi1/Analysis.py.
def IMP.pmi1.analysis.Precision.set_reference_structure | ( | self, | |
rmf_name, | |||
rmf_frame_index | |||
) |
Read in a structure used for reference computation.
Needed before calling get_average_distance_wrt_reference_structure()
rmf_name | The RMF file to read the reference |
rmf_frame_index | The index in that file |
Definition at line 1011 of file pmi1/Analysis.py.