<commit_before>"""
Statements representing mechanistic relationships between biological agents.

Statement classes follow an inheritance hierarchy, with all Statement types
inheriting from the parent class :py:class:`Statement`. At
the next level in the hierarchy are the following classes:

- :py:class:`Complex`
- :py:class:`Modification`
- :py:class:`SelfModification`
- :py:class:`RegulateActivity`
- :py:class:`RegulateAmount`
- :py:class:`ActiveForm`
- :py:class:`Translocation`
- :py:class:`RasGef`
- :py:class:`RasGap`

There are several types of Statements representing post-translational
modifications that further inherit from
:py:class:`Modification`:

- :py:class:`Phosphorylation`
- :py:class:`Dephosphorylation`
- :py:class:`Ubiquitination`
- :py:class:`Debiquitination`
- :py:class:`Sumoylation`
- :py:class:`Desumoylation`
- :py:class:`Hydroxylation`
- :py:class:`Dehydroxylation`
- :py:class:`Acetylation`
- :py:class:`Deacetylation`
- :py:class:`Glycosylation`
- :py:class:`Deglycosylation`
- :py:class:`Farnesylation`
- :py:class:`Defarnesylation`
- :py:class:`Geranylgeranylation`
- :py:class:`Degeranylgeranylation`
- :py:class:`Palmitoylation`
- :py:class:`Depalmitoylation`
- :py:class:`Myristoylation`
- :py:class:`Demyristoylation`
- :py:class:`Ribosylation`
- :py:class:`Deribosylation`

There are additional subtypes of :py:class:`SelfModification`:

- :py:class:`Autophosphorylation`
- :py:class:`Transphosphorylation`

Interactions between proteins are often described simply in terms of their
effect on a protein's "activity", e.g., "Active MEK activates ERK", or "DUSP6
inactives ERK".  These types of relationships are indicated by the
:py:class:`RegulateActivity` abstract base class which has subtypes

- :py:class:`Activation`
- :py:class:`Inhibition`

while the :py:class:`RegulateAmount` abstract base class has subtypes

- :py:class:`IncreaseAmount`
- :py:class:`DecreaseAmount`

Statements involve one or more biological *Agents*, typically proteins,
represented by the class :py:class:`Agent`. Agents can have several types
of context specified on them including

- a specific post-translational modification state (indicated by one or<commit_msg>Update statements docs for methylation<commit_after>"""
Statements representing mechanistic relationships between biological agents.

Statement classes follow an inheritance hierarchy, with all Statement types
inheriting from the parent class :py:class:`Statement`. At
the next level in the hierarchy are the following classes:

- :py:class:`Complex`
- :py:class:`Modification`
- :py:class:`SelfModification`
- :py:class:`RegulateActivity`
- :py:class:`RegulateAmount`
- :py:class:`ActiveForm`
- :py:class:`Translocation`
- :py:class:`RasGef`
- :py:class:`RasGap`

There are several types of Statements representing post-translational
modifications that further inherit from
:py:class:`Modification`:

- :py:class:`Phosphorylation`
- :py:class:`Dephosphorylation`
- :py:class:`Ubiquitination`
- :py:class:`Debiquitination`
- :py:class:`Sumoylation`
- :py:class:`Desumoylation`
- :py:class:`Hydroxylation`
- :py:class:`Dehydroxylation`
- :py:class:`Acetylation`
- :py:class:`Deacetylation`
- :py:class:`Glycosylation`
- :py:class:`Deglycosylation`
- :py:class:`Farnesylation`
- :py:class:`Defarnesylation`
- :py:class:`Geranylgeranylation`
- :py:class:`Degeranylgeranylation`
- :py:class:`Palmitoylation`
- :py:class:`Depalmitoylation`
- :py:class:`Myristoylation`
- :py:class:`Demyristoylation`
- :py:class:`Ribosylation`
- :py:class:`Deribosylation`
- :py:class:`Methylation`
- :py:class:`Demethylation`

There are additional subtypes of :py:class:`SelfModification`:

- :py:class:`Autophosphorylation`
- :py:class:`Transphosphorylation`

Interactions between proteins are often described simply in terms of their
effect on a protein's "activity", e.g., "Active MEK activates ERK", or "DUSP6
inactives ERK".  These types of relationships are indicated by the
:py:class:`RegulateActivity` abstract base class which has subtypes

- :py:class:`Activation`
- :py:class:`Inhibition`

while the :py:class:`RegulateAmount` abstract base class has subtypes

- :py:class:`IncreaseAmount`
- :py:class:`DecreaseAmount`

Statements involve one or more biological *Agents*, typically proteins,
represented by the class :py:class:`Agent`. Agents can have several types
of context specified on them including

- a specific post-translational modification state (indicated by one or
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