From 5b3c456a6b0c2e6ecc31a804295d6f895f0dc08f Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Tue, 24 Jun 2025 14:50:49 +0100 Subject: [PATCH 1/2] Update userguide's ligand network wording for how scores are used. --- docs/guide/setup/creating_ligand_networks.rst | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/guide/setup/creating_ligand_networks.rst b/docs/guide/setup/creating_ligand_networks.rst index c01e9b979..32d94b04a 100644 --- a/docs/guide/setup/creating_ligand_networks.rst +++ b/docs/guide/setup/creating_ligand_networks.rst @@ -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 `_ package. (See `konnektor's documentation `_ 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:`.LigandAtomMapping`, which represent the edges of the network. +A :class:`.LigandAtomMapping` can have a :ref:`score associated with the mapping ` 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: From 68f5394903064e22076ae3cff9a6e20cb45bf586 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Wed, 25 Jun 2025 17:02:05 +0100 Subject: [PATCH 2/2] Update creating_ligand_networks.rst --- docs/guide/setup/creating_ligand_networks.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/guide/setup/creating_ligand_networks.rst b/docs/guide/setup/creating_ligand_networks.rst index 32d94b04a..5f6d96ff8 100644 --- a/docs/guide/setup/creating_ligand_networks.rst +++ b/docs/guide/setup/creating_ligand_networks.rst @@ -8,7 +8,7 @@ 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 `_ package. (See `konnektor's documentation `_ for more information on network generators.) -A :class:`.LigandNetwork` is constructed from :class:`.LigandAtomMapping`, which represent the edges of the network. +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 ` 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: