IMP  2.4.0
The Integrative Modeling Platform
Classes | Functions
IMP.pmi.io Namespace Reference

Utility classes and functions for reading and storing PMI files. More...

Detailed Description

Utility classes and functions for reading and storing PMI files.

Classes

class  CrossLink
 A class to store the selection commands for a single crosslink. More...
 
class  CrossLinkData
 A class for storing groups of crosslinks. More...
 
class  Subsequence
 A light class to store multiple not-necessarily-contiguous residue ranges. More...
 
class  SubsequenceData
 Group a bunch of subsequences with certain labels Use cases: storing lists of secondary structures from DSSP or PSIPRED storing lists of molecules that should be made symmetric. 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 parse_xlinks_davis
 Format from Trisha Davis. 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...
 

Function Documentation

def IMP.pmi.io.get_bead_sizes (   model,
  rmf_tuple,
  rmsd_calculation_components = None 
)
Parameters
modelThe IMP model
rmf_tuplescore,filename,frame number,original order number, rank
rmsd_calculation_componentsTuples to specify what components are used for RMSD calc

Definition at line 683 of file pmi/io/__init__.py.

def IMP.pmi.io.get_best_models (   stat_files,
  score_key = 'SimplifiedModel_Total_Score_None',
  feature_keys = None,
  rmf_file_key = 'rmf_file',
  rmf_file_frame_key = 'rmf_frame_index',
  prefiltervalue = None,
  get_every = 1 
)

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 495 of file pmi/io/__init__.py.

def IMP.pmi.io.get_trajectory_models (   stat_files,
  score_key = 'SimplifiedModel_Total_Score_None',
  rmf_file_key = 'rmf_file',
  rmf_file_frame_key = 'rmf_frame_index',
  get_every = 1 
)

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 558 of file pmi/io/__init__.py.

def IMP.pmi.io.parse_dssp (   dssp_fn,
  limit_to_chains = '' 
)

read dssp file, get SSEs.

values are all PDB residue numbering. Returns a SubsequenceData object containing labels helix, beta, loop. Each one is a list of SelectionDictionaries

Example for a structure with helix A:5-7 and Beta strands A:1-3,A:9-11: helix : [ [ {'chain':'A','residue_indexes': [5,6,7]} ] ] beta : [ [ {'chain':'A','residue_indexes': [1,2,3]}, {'chain':'A','residue_indexes': [9,10,11]} ] ] loop : same format as helix

Definition at line 20 of file pmi/io/__init__.py.

def IMP.pmi.io.parse_xlinks_davis (   data_fn,
  max_num = -1,
  name_map = {},
  named_offsets = {},
  use_chains = {} 
)

Format from Trisha Davis.

Lines are: ignore ignore seq1 seq2 >Name(res) >Name(res) score

Parameters
modelAn IMP model
data_fnThe data file name
max_numMaximum number of XL to read (-1 is all)
name_mapDictionary mapping text file names to the molecule name
named_offsetsInteger offsets to apply to the indexing in the file Output is a CrossLinkData object containing SelectionDictionaries data[unique_id] = [ { 'r1': {'molecule':'A','residue_index':5}, 'r2': {'molecule':'B','residue_index':100}, 'score': 123 }, { 'r1': {'molecule':'C','residue_index':63}, 'r2': {'molecule':'D','residue_index':94}, 'score': 600 } ]

Definition at line 107 of file pmi/io/__init__.py.

def IMP.pmi.io.read_coordinates_of_rmfs (   model,
  rmf_tuples,
  alignment_components = None,
  rmsd_calculation_components = None 
)

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

Parameters
modelThe IMP model
rmf_tuples[score,filename,frame number,original order number, rank]
alignment_componentsTuples to specify what you're aligning on
rmsd_calculation_componentsTuples to specify what components are used for RMSD calc

Definition at line 605 of file pmi/io/__init__.py.

def IMP.pmi.io.save_best_models (   mdl,
  out_dir,
  stat_files,
  number_of_best_scoring_models = 10,
  get_every = 1,
  score_key = 'SimplifiedModel_Total_Score_None',
  feature_keys = None,
  rmf_file_key = 'rmf_file',
  rmf_file_frame_key = 'rmf_frame_index',
  override_rmf_dir = None 
)

Given a list of stat files, read them all and find the best models.

Save to a single RMF along with a stat file.

Parameters
mdlThe IMP Model
out_dirThe output directory. Will save 3 files (RMF, stat, summary)
stat_filesList of all stat files to collect
number_of_best_scoring_modelsNum best models to gather
get_everySkip frames
score_keyUsed for the ranking
feature_keysKeys to keep around
rmf_file_keyThe key that says RMF file name
rmf_file_frame_keyThe key that says RMF frame number
override_rmf_dirFor output, change the name of the RMF directory (experiment)

Definition at line 373 of file pmi/io/__init__.py.