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	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...

Function Documentation

def IMP.pmi.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.

Note

This function is only available in Python.

Definition at line 287 of file pmi/io/__init__.py.

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 522 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,
			provenance = None
	)

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 298 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 390 of file pmi/io/__init__.py.

def IMP.pmi.io.parse_dssp	(		dssp_fn,
			limit_to_chains = '',
			name_map = None
	)

Read a DSSP file, and return secondary structure elements (SSEs).

Values are all PDB residue numbering.

Parameters

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).

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 tuple (residue start, residue end, chain)

Example for a structure with helix A:5-7 and Beta strands A:1-3,A:9-11:

ret = { 'helix' : [ [ (5,7,'A') ],... ]
        'beta'  : [ [ (1,3,'A'),
                      (9,11,'A'),...],...]
        'loop'  : same format as helix
      }

Note

This function is only available in Python.

Definition at line 28 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 437 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 132 of file pmi/io/__init__.py.