ample.util.contact_util module¶

Wrapper module for the ConKit package

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

Bases: object

Attributes:

Attributes:	`bbcontacts_file` : str The path to `bbcontacts_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 neighboring contacts `sequence_file` : str The path to `sequence_file` `sequence_format` : str The format of `sequence_file`

bbcontacts_file : str: The path to bbcontacts_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 neighboring contacts
sequence_file : str: The path to sequence_file
sequence_format : str: The format of sequence_file

Methods

`check_options`(optd)	Function to check that all contact files are available
`subselect_decoys`(decoys, decoy_format[, …])	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

bbcontacts_file¶: The path to bbcontacts_file

bbcontacts_format¶: The format of bbcontacts_file

static check_options(optd)[source]¶

Function to check that all contact files are available

Raises:	ValueError You must provide `-contact_file` when using `-bbcontacts_file` or use as `-contact_file` instead ValueError Cannot find contact file ValueError Rosetta energy function unavailable

contact_format¶: The format of contact_file

contacts_file¶: The path to contacts_file

cutoff_factor¶: The contact list truncation factor

distance_to_neighbor¶: The minimum distance between neighboring contacts

sequence_file¶: The path to sequence_file

sequence_format¶: The format of sequence_file

subselect_decoys(decoys, decoy_format, mode=’linear’, subdistance_to_neighbor=24, **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 satisfaction scores of >= 0.287 subdistance_to_neighbor : int, optional The minimum distance between neighboring residues in the subselection [default: 24] **kwargs Job submission related keyword arguments
Returns:	list A list of paths to the 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 satisfaction scores of >= 0.287

subdistance_to_neighbor : int, optional

The minimum distance between neighboring residues in the subselection [default: 24]

**kwargs

Job submission related keyword arguments

Returns:

list: A list of paths to the 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
`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 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