ample.util.contact_util module¶

Wrapper module for the ConKit package

class ContactUtil(sequence_file, sequence_format, contact_file=None, contact_format=None, bbcontacts_file=None, bbcontacts_format=’bbcontacts’, cutoff_factor=1.0, distance_to_neighbor=5)[source]¶

Bases: object

Attributes:

Attributes:	bbcontacts_file : str The path to the bbcontacts contact file bbcontacts_format : str The format of `bbcontacts_file` contact_file : str The path to the contact file contact_format : str The format of `contact_file` cutoff_factor : float The contact list truncation factor distance_to_neighbor : int The minimum distance between contacting residues sequence_file : str The path to the sequence file sequence_format : str The format of the `sequence_file`

bbcontacts_file : str: The path to the bbcontacts contact file
bbcontacts_format : str: The format of bbcontacts_file
contact_file : str: The path to the contact file
contact_format : str: The format of contact_file
cutoff_factor : float: The contact list truncation factor
distance_to_neighbor : int: The minimum distance between contacting residues
sequence_file : str: The path to the sequence file
sequence_format : str: The format of the sequence_file

Methods

`compute_precision_by_range`(decoys, …)	Compute restraint precision score by sequence separation range
`subselect_decoys`(decoys, decoy_format[, mode])	Subselect decoys excluding those not satisfying long-distance restraints
`summarize`(plot_file[, structure_file, …])	Process the contact file etc
`write_restraints`(restraint_file, …)	Write a list of restraints

check_options
predict_contacts_from_sequence

bbcontacts_file¶

bbcontacts_format¶

static check_options(optd)[source]¶

compute_precision_by_range(decoys, decoy_format, **kwargs)[source]¶

Compute restraint precision score by sequence separation range

Parameters:	decoys : list, tuple A list containing paths to decoy files decoy_format : str The file format of `decoys` **kwargs Job submission related keyword arguments
Returns:	list A list of short-range scores of all decoys list A list of medium-range scores of all decoys list A list of long-range scores of all decoys

contact_format¶

contact_map¶

contacts_file¶

cutoff_factor¶

distance_to_neighbor¶

do_contact_analysis¶

found_ccmpred_contact_prediction_deps¶

predict_contacts_from_sequence(wdir=’.’, min_neff=200)[source]¶

require_contact_prediction¶

sequence_file¶

sequence_format¶

subselect_decoys(decoys, decoy_format, mode=’linear’, **kwargs)[source]¶

Subselect decoys excluding those not satisfying long-distance restraints

Parameters:

Parameters:	decoys : list, tuple A list containing paths to decoy files decoy_format : str The file format of `decoys` mode : str, optional The subselection mode to use scaled: keep the decoys with scaled scores of >= 0.5 linear: keep the top half of decoys cutoff: keep all decoys with precision scores of >= 0.287 ignore: keep all decoys **kwargs Job submission related keyword arguments
Returns:	list A 2-D list of paths and scores of all sub-selected decoys

decoys : list, tuple

A list containing paths to decoy files

decoy_format : str

The file format of decoys

mode : str, optional

The subselection mode to use

scaled: keep the decoys with scaled scores of >= 0.5
linear: keep the top half of decoys
cutoff: keep all decoys with precision scores of >= 0.287
ignore: keep all decoys

**kwargs

Job submission related keyword arguments

Returns:

list: A 2-D list of paths and scores of all sub-selected decoys

summarize(plot_file, structure_file=None, structure_format=None, native_cutoff=8)[source]¶

Process the contact file etc

Parameters:	plot_file : str The path to the contact map plot structure_file : str A reference structure file structure_format : str The format of `structure_file` native_cutoff : int The distance cutoff for contact extraction from `structure_file`
Returns:	str The path to the contact map plot float The precision score, if calculated, else 0.0
Raises:	ValueError A structure file also needs a structure format ValueError A structure format also needs structure file ValueError Unknown structure format

write_restraints(restraint_file, restraint_format, energy_function)[source]¶

Write a list of restraints

Parameters:	restraint_file : str The file to write the restraints to restraint_format : str The restraints format, depends primarily on the program for which the restraints will be used energy_function : str The energy function
Returns:	str The file the restraints were written to
Raises:	ValueError Unknown restraint format ValueError Unknown Rosetta energy function ValueError Unknown SAINT2 energy function

class SubselectionAlgorithm[source]¶

Bases: object

A class to collect all subselection algorithms

Methods

`cutoff`(data[, cutoff])	A cutoff-defined subselection algorithm
`ignore`(data)	“A subselection algorithm to keep all
`linear`(data[, cutoff])	A linearly-defined subselection algorithm
`scaled`(data[, cutoff])	A scaling-defined subselection algorithm

static cutoff(data, cutoff=0.287)[source]¶

A cutoff-defined subselection algorithm

Parameters:	data : list, tuple A 1D array of scores cutoff : float, optional The cutoff of keeping decoys
Returns:	list The decoy indices to keep list The decoy indices to throw

static ignore(data)[source]¶

“A subselection algorithm to keep all

Parameters:	data : list, tuple A 1D array of scores
Returns:	list The decoy indices to keep list The decoy indices to throw

static linear(data, cutoff=0.5)[source]¶

A linearly-defined subselection algorithm

Parameters:	data : list, tuple A 1D array of scores cutoff : float, optional The porportion of the total number of decoys to keep
Returns:	list The decoy indices to keep list The decoy indices to throw

static scaled(data, cutoff=0.5)[source]¶

A scaling-defined subselection algorithm

Parameters:	data : list, tuple A 1D array of scores cutoff : float, optional The cutoff of keeping decoys
Returns:	list The decoy indices to keep list The decoy indices to throw