Miscellaneous utilities. More...

Detailed Description

Miscellaneous utilities.

Classes
class	HierarchyDatabase
	Store the representations for a system. More...

class	Stopwatch
	Collect timing information. 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_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	get_terminal_residue
	Get the particle of the terminal residue at the GIVEN resolution (NOTE: not the closest resolution!). More...

def	get_terminal_residue_position
	Get XYZ coordinates of the terminal residue at the GIVEN resolution. More...

def	scatter_and_gather
	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	select_by_tuple_2
	New tuple format: molname OR (start,stop,molname,copynum,statenum) Copy and state are optional. More...

Function Documentation

def IMP.pmi.tools.add_restraint_to_model	(	model,
		restraint,
		add_to_rmf = `False`
	)

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.

If add_to_rmf is True, also add the restraint to a separate list of restraints that will be written out to RMF files (by default, most PMI restraints are not).

Note: This function is only available in Python.

Definition at line 69 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 501 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 571 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 1043 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 394 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 655 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, Atom or Molecule or else returns an empty list

Note: This function is only available in Python.

Definition at line 1063 of file tools.py.

def IMP.pmi.tools.get_restraint_set	(	model,
		rmf = `False`
	)

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

If rmf is True, return only the subset of these restraints that should be written out to RMF files.

Note: This function is only available in Python.

Definition at line 88 of file tools.py.

def IMP.pmi.tools.get_terminal_residue	(	representation,
		hier,
		terminus = `'C'`,
		resolution = `1`
	)

Get the particle of the terminal residue at the GIVEN resolution (NOTE: not the closest resolution!).

To get the terminal residue at the closest resolution use: particles=IMP.pmi.tools.select_by_tuple(representation,molecule_name) particles[0] and particles[-1] will be the first and last particles corresponding to the two termini. It is needed for instance to determine the last residue of a pdb.

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 602 of file tools.py.

def IMP.pmi.tools.get_terminal_residue_position	(	representation,
		hier,
		terminus = `'C'`,
		resolution = `1`
	)

Get XYZ coordinates of the terminal residue at the GIVEN resolution.

Note: This function is only available in Python.

Definition at line 643 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 1115 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 726 of file tools.py.

def IMP.pmi.tools.select_by_tuple_2	(	hier,
		tuple_selection,
		resolution
	)

New tuple format: molname OR (start,stop,molname,copynum,statenum) Copy and state are optional.

Can also use 'None' for them which will get all. You can also pass -1 for stop which will go to the end. Returns the particles

Note: This function is only available in Python.

Definition at line 845 of file tools.py.

Detailed Description

Classes

Functions

Function Documentation