.. Autogenerated in conf.py

.. _examples-dg:

Derivations and Reaction Networks
################################################################################



Rule Application
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Transformation rules (reaction patterns) can be applied to graphs
(molecules) to create new graphs (molecules). The transformations
(reactions) implicitly form a directed (multi-)hypergraph (chemical
reaction network).

`Explore in the playground
<https://cheminf-live.imada.sdu.dk/mod?example=0210_dgFixed.py>`__.

.. literalinclude:: /_static/examples/py/0210_dgFixed.py
	:language: python
	:linenos:
	:lines: 1-14
	:tab-width: 3


Repetition
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

A sub-strategy can be repeated.

`Explore in the playground
<https://cheminf-live.imada.sdu.dk/mod?example=0211_dgRepeat.py>`__.

.. literalinclude:: /_static/examples/py/0211_dgRepeat.py
	:language: python
	:linenos:
	:lines: 1-12
	:tab-width: 3


Application Constraints
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

We may want to impose constraints on which reactions are accepted.
E.g., in formose the molecules should not have too many carbon atoms.

`Explore in the playground
<https://cheminf-live.imada.sdu.dk/mod?example=0212_dgPredicate.py>`__.

.. literalinclude:: /_static/examples/py/0212_dgPredicate.py
	:language: python
	:linenos:
	:lines: 1-18
	:tab-width: 3


Advanced Printing
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Reaction networks can become large, and often it is necessary to hide
parts of the network, or in general change the appearance.

`Explore in the playground
<https://cheminf-live.imada.sdu.dk/mod?example=0250_dgPrinting.py>`__.

.. literalinclude:: /_static/examples/py/0250_dgPrinting.py
	:language: python
	:linenos:
	:lines: 1-17
	:tab-width: 3


Double Pushout Printing
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Each reaction/derivation can be visualised as a DPO diagram.

`Explore in the playground
<https://cheminf-live.imada.sdu.dk/mod?example=0260_dpoPrinting.py>`__.

.. literalinclude:: /_static/examples/py/0260_dpoPrinting.py
	:language: python
	:linenos:
	:lines: 1-3
	:tab-width: 3