IMP Reference Guide
2.6.1
The Integrative Modeling Platform
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Utility classes and functions for reading and storing PMI files. More...
Utility classes and functions for reading and storing PMI files.
Namespaces | |
crosslink | |
Handles cross-link data sets. | |
utilities | |
Utility classes and functions for IO. | |
xltable | |
Tools to plot a contact map overlaid with cross-links. | |
Classes | |
class | RMSDOutput |
A helper output based on dist to initial coordinates. More... | |
class | TotalScoreOutput |
A helper output for model evaluation. More... | |
Functions | |
def | get_bead_sizes |
def | get_best_models |
Given a list of stat files, read them all and find the best models. More... | |
def | get_trajectory_models |
Given a list of stat files, read them all and find a trajectory of models. More... | |
def | parse_dssp |
read dssp file, get SSEs. More... | |
def | read_coordinates_of_rmfs |
Read in coordinates of a set of RMF tuples. More... | |
def | save_best_models |
Given a list of stat files, read them all and find the best models. More... | |
def IMP.pmi.io.get_bead_sizes | ( | model, | |
rmf_tuple, | |||
rmsd_calculation_components = None , |
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state_number = 0 |
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) |
model | The IMP model |
rmf_tuple | score,filename,frame number,original order number, rank |
rmsd_calculation_components | Tuples to specify what components are used for RMSD calc |
Definition at line 438 of file pmi/io/__init__.py.
def IMP.pmi.io.get_best_models | ( | stat_files, | |
score_key = 'SimplifiedModel_Total_Score_None' , |
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feature_keys = None , |
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rmf_file_key = 'rmf_file' , |
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rmf_file_frame_key = 'rmf_frame_index' , |
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prefiltervalue = None , |
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get_every = 1 |
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) |
Given a list of stat files, read them all and find the best models.
Returns the best rmf filenames, frame numbers, scores, and values for feature keywords
Definition at line 234 of file pmi/io/__init__.py.
def IMP.pmi.io.get_trajectory_models | ( | stat_files, | |
score_key = 'SimplifiedModel_Total_Score_None' , |
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rmf_file_key = 'rmf_file' , |
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rmf_file_frame_key = 'rmf_frame_index' , |
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get_every = 1 |
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) |
Given a list of stat files, read them all and find a trajectory of models.
Returns the rmf filenames, frame numbers, scores, and values for feature keywords
Definition at line 301 of file pmi/io/__init__.py.
def IMP.pmi.io.parse_dssp | ( | dssp_fn, | |
limit_to_chains = '' |
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) |
read dssp file, get SSEs.
values are all PDB residue numbering. Returns a dictionary with keys helix, beta, loop Each contains a list of SSEs. Each SSE is a list of elements (e.g. strands in a sheet) Each element is a pair (chain,(residue_indexes))
Example for a structure with helix A:5-7 and Beta strands A:1-3,A:9-11: ret = { 'helix' : [ [ ('A',5,7 ) ],... ] 'beta' : [ [ ('A',1,3), ('A',9,11),...],...] 'loop' : same format as helix }
Definition at line 21 of file pmi/io/__init__.py.
def IMP.pmi.io.read_coordinates_of_rmfs | ( | model, | |
rmf_tuples, | |||
alignment_components = None , |
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rmsd_calculation_components = None , |
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state_number = 0 |
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) |
Read in coordinates of a set of RMF tuples.
Returns the coordinates split as requested (all, alignment only, rmsd only) as well as RMF file names (as keys in a dictionary, with values being the rank number) and just a plain list
model | The IMP model |
rmf_tuples | [score,filename,frame number,original order number, rank] |
alignment_components | Tuples to specify what you're aligning on |
rmsd_calculation_components | Tuples to specify what components are used for RMSD calc |
Definition at line 348 of file pmi/io/__init__.py.
def IMP.pmi.io.save_best_models | ( | mdl, | |
out_dir, | |||
stat_files, | |||
number_of_best_scoring_models = 10 , |
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get_every = 1 , |
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score_key = 'SimplifiedModel_Total_Score_None' , |
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feature_keys = None , |
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rmf_file_key = 'rmf_file' , |
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rmf_file_frame_key = 'rmf_frame_index' , |
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override_rmf_dir = None |
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) |
Given a list of stat files, read them all and find the best models.
Save to a single RMF along with a stat file.
mdl | The IMP Model |
out_dir | The output directory. Will save 3 files (RMF, stat, summary) |
stat_files | List of all stat files to collect |
number_of_best_scoring_models | Num best models to gather |
get_every | Skip frames |
score_key | Used for the ranking |
feature_keys | Keys to keep around |
rmf_file_key | The key that says RMF file name |
rmf_file_frame_key | The key that says RMF frame number |
override_rmf_dir | For output, change the name of the RMF directory (experiment) |
Definition at line 111 of file pmi/io/__init__.py.