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	add_restraint_to_model
	Add a PMI restraint to the model. More...

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	get_restraint_set
	Get a RestraintSet containing all PMI restraints added to the model. 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.add_restraint_to_model	(	model,
		restraint
	)

Add a PMI restraint to the model.

Since Model.add_restraint() no longer exists (in modern IMP restraints should be added to a ScoringFunction instead) store them instead in a RestraintSet, and keep a reference to it in the Model.

Note: This function is only available in Python.

Definition at line 22 of file tools.py.

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%"'

Note: This function is only available in Python.

Definition at line 454 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

Note: This function is only available in Python.

Definition at line 522 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.

Note: This function is only available in Python.

Definition at line 553 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.

Note: This function is only available in Python.

Definition at line 939 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.

Note: This function is only available in Python.

Definition at line 342 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"]]

Note: This function is only available in Python.

Definition at line 585 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

Note: This function is only available in Python.

Definition at line 959 of file tools.py.

def IMP.pmi.tools.get_restraint_set ( model )

Get a RestraintSet containing all PMI restraints added to the model.

Note: This function is only available in Python.

Definition at line 34 of file tools.py.

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

Yield successive length-sized chunks from a list.

Note: This function is only available in Python.

Definition at line 1074 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

Note: This function is only available in Python.

Definition at line 1298 of file tools.py.

def IMP.pmi.tools.scatter_and_gather ( data )

Synchronize data over a parallel run.

Note: This function is only available in Python.

Definition at line 1001 of file tools.py.

def IMP.pmi.tools.scatter_and_gather_dict_append ( data )

Synchronize data over a parallel run.

Note: This function is only available in Python.

Definition at line 1028 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"

Note: This function is only available in Python.

Definition at line 662 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

Note: This function is only available in Python.

Definition at line 1387 of file tools.py.

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

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

Note: This function is only available in Python.

Definition at line 1055 of file tools.py.

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

Apply a translation to a hierarchy along the input vector.

Note: This function is only available in Python.

Definition at line 1098 of file tools.py.

Detailed Description

Classes

Functions

Function Documentation