IMP.pmi.tools Namespace Reference

Miscellaneous utilities. More...

Detailed Description

Miscellaneous utilities.

Classes
class	ColorChange
	Change color code to hexadecimal to rgb. More...
class	HierarchyDatabase
	Store the representations for a system. More...

Functions
def	cross_link_db_filter_parser
	example '"{ID_Score}" > 28 AND "{Sample}" == "%10_1%" OR ":Sample}" == "%10_2%" OR ":Sample}" == "%10_3%" OR ":Sample}" == "%8_1%" OR ":Sample}" == "%8_2%"' More...
def	get_closest_residue_position
	this function works with plain hierarchies, as read from the pdb, no multi-scale hierarchies More...
def	get_position_terminal_residue
	Get the xyz position of the terminal residue at the given resolution. More...
def	get_prot_name_from_particle
	Return the component name provided a particle and a list of names. More...
def	get_random_cross_link_dataset
	Return a random cross-link dataset as a string. More...
def	get_residue_gaps_in_hierarchy
	Return the residue index gaps and contiguous segments in the hierarchy. More...
def	get_residue_indexes
	Retrieve the residue indexes for the given particle. More...
def	list_chunks_iterator
	Yield successive length-sized chunks from a list. More...
def	parse_dssp
	Read dssp file and get secondary structure information. More...
def	scatter_and_gather
	Synchronize data over a parallel run. More...
def	scatter_and_gather_dict_append
	Synchronize data over a parallel run. More...
def	select
	this function uses representation=SimplifiedModel it returns the corresponding selected particles representation_type="Beads", "Res:X", "Densities", "Representation", "Molecule" More...
def	sse_selections_to_chimera_colors
	get chimera command to check if you've correctly made the dssp dictionary colors each helix and beta sheet More...
def	sublist_iterator
	Yield all sublists of length >= lmin and <= lmax. More...
def	translate_hierarchy
	Apply a translation to a hierarchy along the input vector. More...

Function Documentation

def IMP.pmi.tools.cross_link_db_filter_parser

(

inputstring

)

example '"{ID_Score}" > 28 AND "{Sample}" == "%10_1%" OR ":Sample}" == "%10_2%" OR ":Sample}" == "%10_3%" OR ":Sample}" == "%8_1%" OR ":Sample}" == "%8_2%"'

Definition at line 425 of file tools.py.

def IMP.pmi.tools.get_closest_residue_position	(		hier,
			resindex,
			terminus = 'N'
	)

this function works with plain hierarchies, as read from the pdb, no multi-scale hierarchies

Definition at line 493 of file tools.py.

def IMP.pmi.tools.get_position_terminal_residue	(		hier,
			terminus = 'C',
			resolution = 1
	)

Get the xyz position of the terminal residue at the given resolution.

Parameters

hier	hierarchy containing the terminal residue
terminus	either 'N' or 'C'
resolution	resolution to use.

Definition at line 524 of file tools.py.

def IMP.pmi.tools.get_prot_name_from_particle	(		p,
			list_of_names
	)

Return the component name provided a particle and a list of names.

Definition at line 910 of file tools.py.

def IMP.pmi.tools.get_random_cross_link_dataset	(		representation,
			resolution = 1.0,
			number_of_cross_links = 10,
			ambiguity_probability = 0.1,
			confidence_score_range = [0,
			avoid_same_particles = False
	)

Return a random cross-link dataset as a string.

Every line is a residue pair, together with UniqueIdentifier and XL score.

Definition at line 313 of file tools.py.

def IMP.pmi.tools.get_residue_gaps_in_hierarchy	(		hierarchy,
			start,
			end
	)

Return the residue index gaps and contiguous segments in the hierarchy.

Parameters

hierarchy	hierarchy to examine
start	first residue index
end	last residue index

Returns

A list of lists of the form [[1,100,"cont"],[101,120,"gap"],[121,200,"cont"]]

Definition at line 556 of file tools.py.

def IMP.pmi.tools.get_residue_indexes

(

hier

)

Retrieve the residue indexes for the given particle.

The particle must be an instance of Fragment,Residue or Atom

Definition at line 930 of file tools.py.

def IMP.pmi.tools.list_chunks_iterator	(		list,
			length
	)

Yield successive length-sized chunks from a list.

Definition at line 1045 of file tools.py.

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

Read dssp file and get secondary structure information.

Values are all PDB residue numbering.

Returns

dict of sel tuples helix : [ [ ['A',5,7] ] , [['B',15,17]] , ...] two helices A:5-7,B:15-17 beta : [ [ ['A',1,3] , ['A',100,102] ] , ...] one sheet: A:1-3 & A:100-102 loop : same format as helix, it's the contiguous loops

Definition at line 1269 of file tools.py.

def IMP.pmi.tools.scatter_and_gather

(

data

)

Synchronize data over a parallel run.

Definition at line 972 of file tools.py.

def IMP.pmi.tools.scatter_and_gather_dict_append

(

data

)

Synchronize data over a parallel run.

Definition at line 999 of file tools.py.

def IMP.pmi.tools.select	(		representation,
			resolution = None,
			hierarchies = None,
			selection_arguments = None,
			name = None,
			name_is_ambiguous = False,
			first_residue = None,
			last_residue = None,
			residue = None,
			representation_type = None
	)

this function uses representation=SimplifiedModel it returns the corresponding selected particles representation_type="Beads", "Res:X", "Densities", "Representation", "Molecule"

Definition at line 633 of file tools.py.

def IMP.pmi.tools.sse_selections_to_chimera_colors	(		dssp_dict,
			chimera_model_num = 0
	)

get chimera command to check if you've correctly made the dssp dictionary colors each helix and beta sheet

Definition at line 1358 of file tools.py.

def IMP.pmi.tools.sublist_iterator	(		l,
			lmin = None,
			lmax = None
	)

Yield all sublists of length >= lmin and <= lmax.

Definition at line 1026 of file tools.py.

def IMP.pmi.tools.translate_hierarchy	(		hierarchy,
			translation_vector
	)

Apply a translation to a hierarchy along the input vector.

Definition at line 1069 of file tools.py.