Jess

class pyjess.Jess

A handle to run Jess over a list of templates.

Added in version 0.4.0: Equality, hashing and pickle protocol support.

__init__(templates=())

Create a new Jess database containing the given templates.

Parameters:

templates (sequence of Template) – The templates to index in the database for further querying.

Caution

The Template objects given in argument will be copied because the internal C data structure requires ownership of the data. Modification to the original Template objects will not have an effect on the newly created Jess templates.

copy()

Create a copy of the Jess object.

Returns:

Jess – A Jess object containing the same templates.

Added in version 0.4.0.

query(molecule, rmsd_threshold, distance_cutoff, max_dynamic_distance, *, max_candidates=1000, ignore_chain=False, best_match=False)

Scan for templates matching the given molecule.

Parameters:

• molecule (Molecule) – The protein to match the templates to.

• rmsd_threshold (float) – The RMSD threshold for reporting results.

• distance_cutoff (float) – The global distance cutoff used to guide the search.

• max_dynamic_distance (float) – The maximum template/query dynamic distance after adding the global distance cutoff and the individual atom distance cutoff defined for each atom of the template.

• ignore_chain (bool) – Whether to check or ignore the chain of the atoms to match.

• best_match (bool) – Pass True to return only the best match to each template.

Returns:

Query – An iterator over the query hits.

class pyjess.Query

A query over templates with a given molecule.

Jess iterates over the templates and attempt matches the query molecule, so the hits can actually be generated iteratively. This class allows accessing the hits as a Python iterator.

jess

The templates this object is currently scanning.

Type:

Jess

molecule

The query molecule to align to the templates.

Type:

Molecule

rmsd_threshold

The RMSD threshold for reporting results.

Type:

float

max_candidates

The maximum number of candidate hits to report.

Type:

int

ignore_chain

Whether to check or ignore the chain of the atoms to match.

Type:

bool

best_match

Whether the query will return only the best match to each template.

Type:

bool

__iter__()

Implement iter(self).

class pyjess.Hit

A hit identified between a query molecule and a target template.

rmsd

The RMSD between the aligned structures.

Type:

float

template

The template that matched the query molecule.

Type:

Template

molecule

The query molecule.

Type:

Molecule

__new__(**kwargs)

__reduce__()

Helper for pickle.

atoms(transform=True)

Get the list of query atoms matching the template.

Parameters:

transform (bool) – Whether or not to transform coordinates of hits into template frame.

Returns:

list of Atom – The list of matching atoms.

molecule(transform=False)

Get the molecule matching the template.

Parameters:

transform (bool) – Whether or not to transform coordinates of the molecule atoms into template frame.

Returns:

Molecule – The matching molecule, optionally rotated to match the template coordinate.

Added in version 0.5.0.

determinant

The determinant of the rotation matrix.

Type:

float

evalue

The E-value estimated for the hit.

Type:

float

log_evalue

The logarithm of the E-value estimated for the hit.

Type:

float