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.

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	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,
			state_number = 0
	)

Parameters

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

Note

This function is only available in Python.

Definition at line 689 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

Note

This function is only available in Python.

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

Note

This function is only available in Python.

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

Note

This function is only available in Python.

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

data_fn	The data file name
max_num	Maximum number of XL to read (-1 is all)
name_map	Dictionary mapping text file names to the molecule name
named_offsets	Integer 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 } ]

Note

This function is only available in Python.

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,
			state_number = 0
	)

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

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

Note

This function is only available in Python.

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

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)

Note

This function is only available in Python.

Definition at line 372 of file pmi/io/__init__.py.