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.. MacSyFinder - Detection of macromolecular systems in protein datasets
using systems modelling and similarity search.
Authors: Sophie Abby, Bertrand Néron
Copyright © 2014-2023 Institut Pasteur (Paris), and CNRS.
See the COPYRIGHT file for details
MacsyFinder is distributed under the terms of the GNU General Public License (GPLv3).
See the COPYING file for details.
.. _system:
******
system
******
This module classes and functions which a given set of hits and a model
compute if this set satisfy the model or not
The object which check the compliance of hits to a model is MatchMaker
which have 2 sub-classes for ordered and unordered replicons
MatchMaker.match method link hit to a model (:class:`macsypy.hit.ValidHit`)
and then check if these valid hit satisfy the quorum constraints defined
in the model. According this it instanciate a :class:`macsypy.system.System`
or :class:`macsypy.system.RejectedCandidate` for ordered replicons
or :class:`macsypy.system.LikelySystem` or :class:`macsypy.system.UnlikelySystem`
for unordered replicons
below the inheritance diagram:
.. inheritance-diagram::
macsypy.system.AbstractSetOfHits
macsypy.system.AbstractClusterizedHits
macsypy.system.System
macsypy.system.RejectedCandidate
macsypy.system.AbstractUnordered
macsypy.system.LikelySystem
macsypy.system.UnlikelySystem
:parts: 1
.. warning::
The abstract class :class:`macsypy.system.AbstractSetOfHits` is controlled by the metaclass
:class:`macsypy.system.MetaSetOfHits` which inject on the fly several private attributes and
public properties (see more in :class:`macsypy.system.MetaSetOfHits` documentation)
.. inheritance-diagram::
macsypy.system.MatchMaker
macsypy.system.OrderedMatchMaker
macsypy.system.UnorderedMatchMaker
:parts: 1
.. _system_api:
system reference api
====================
MatchMaker
==========
.. autoclass:: macsypy.system.MatchMaker
:members:
:private-members:
:special-members:
OrderedMatchMaker
=================
.. autoclass:: macsypy.system.OrderedMatchMaker
:members:
:private-members:
:special-members:
UnorderedMatchMaker
===================
.. autoclass:: macsypy.system.UnorderedMatchMaker
:members:
:private-members:
:special-members:
HitSystemTracker
================
.. autoclass:: macsypy.system.HitSystemTracker
:members:
:private-members:
:special-members:
MetaSetOfHits
=============
.. autoclass:: macsypy.system.MetaSetOfHits
:members:
:private-members:
:special-members:
AbstractSetOfHits
=================
.. autoclass:: macsypy.system.AbstractSetOfHits
:members:
:private-members:
:special-members:
AbstractClusterizedHits
=======================
.. autoclass:: macsypy.system.AbstractClusterizedHits
:members:
:private-members:
:special-members:
System
======
.. autoclass:: macsypy.system.System
:members:
:private-members:
:special-members:
RejectedCandidate
=================
.. autoclass:: macsypy.system.RejectedCandidate
:members:
:private-members:
:special-members:
AbstractUnordered
=================
.. autoclass:: macsypy.system.AbstractUnordered
:members:
:private-members:
:special-members:
LikelySystem
============
.. autoclass:: macsypy.system.LikelySystem
:members:
:private-members:
:special-members:
UnlikelySystem
==============
.. autoclass:: macsypy.system.UnlikelySystem
:members:
:private-members:
:special-members:
|
