IMP Reference Guide
develop.36b5e40f34,2024/10/13
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 | add_provenance |
Add provenance information in prov (a list of _TempProvenance objects) to each of the IMP hierarchies provided. More... | |
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 a DSSP file, and return secondary structure elements (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.pmi1.io.add_provenance | ( | prov, | |
hiers | |||
) |
Add provenance information in prov
(a list of _TempProvenance objects) to each of the IMP hierarchies provided.
Note that we do this all at once since we typically don't preserve the IMP::Model object throughout a PMI protocol.
Definition at line 287 of file pmi1/io/__init__.py.
def IMP.pmi1.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 511 of file pmi1/io/__init__.py.
def IMP.pmi1.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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provenance = None |
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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 298 of file pmi1/io/__init__.py.
def IMP.pmi1.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 390 of file pmi1/io/__init__.py.
def IMP.pmi1.io.parse_dssp | ( | dssp_fn, | |
limit_to_chains = '' , |
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name_map = None |
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) |
Read a DSSP file, and return secondary structure elements (SSEs).
Values are all PDB residue numbering.
dssp_fn | The file to read |
limit_to_chains | Only read/return these chain IDs |
name_map | If passed, return tuples organized by molecule name (name_map should be a dictionary with chain IDs as keys and molecule names as values). |
Example for a structure with helix A:5-7 and Beta strands A:1-3,A:9-11:
Definition at line 28 of file pmi1/io/__init__.py.
def IMP.pmi1.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 437 of file pmi1/io/__init__.py.
def IMP.pmi1.io.save_best_models | ( | model, | |
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.
model | 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 132 of file pmi1/io/__init__.py.