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Update userguide's ligand network wording for how scores are used. #1382

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atravitz merged 2 commits into from
Jun 25, 2025
Merged

Update userguide's ligand network wording for how scores are used. #1382

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5b3c456
Update userguide's ligand network wording for how scores are used.
IAlibay Jun 24, 2025
68f5394
Update creating_ligand_networks.rst
IAlibay Jun 25, 2025
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5 changes: 2 additions & 3 deletions docs/guide/setup/creating_ligand_networks.rst
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Expand Up @@ -8,9 +8,8 @@ For example, a :class:`.LigandNetwork` with drug candidates as nodes can be used
**openfe** includes an interface to common :any:`Ligand Network Planners`, which are implemented in OpenFE's `konnektor <https://github.com/OpenFreeEnergy/konnektor>`_ package.
(See `konnektor's documentation <https://konnektor.openfree.energy/en/latest/>`_ for more information on network generators.)

Because each edge in a :class:`.LigandNetwork` is a :class:`.LigandAtomMapping`, each edge can be assigned a score that indicates the mapping's quality.
Some network generators use these scores to construct more efficient network topologies.

A :class:`.LigandNetwork` is constructed from :class:`.SmallMoleculeComponent`, which represent the nodes and optionally :class:`.LigandAtomMapping`, which represent the edges of the network.
A :class:`.LigandAtomMapping` can have a :ref:`score associated with the mapping <Scoring Atom Mappings>` which can be used by some network generators to construct more efficient network topologies.

Below is an example of a ``LigandNetwork`` with scores assigned to each atom mapping:

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