diff --git a/docs/guide/setup/creating_ligand_networks.rst b/docs/guide/setup/creating_ligand_networks.rst index a6cb7b02f..25d7379e2 100644 --- a/docs/guide/setup/creating_ligand_networks.rst +++ b/docs/guide/setup/creating_ligand_networks.rst @@ -1,18 +1,17 @@ -.. _define_ligand_network: .. _userguide_ligand_network: Defining the Ligand Network =========================== -A ligand network is a set of small molecules connected by mappings of two ligands. -Such a network can represent a set of drug candidates derived from molecule enumeration that should -be ranked by free energy calculations, in order to prioritize molecule synthesis efforts. -The ligand networks are a tool that is used to orchestrate the free energy calculations to efficiently +A :class:`.LigandNetwork` is a set of small molecules connected by mappings of two small molecules. +One example for such a network could be a set of drug candidates, that should be ranked using alchemical transformations. +The :class:`.LigandNetwork` is a tool that is used to orchestrate the free energy calculations to efficiently compute a ligand ranking. -It is of course possible to calculate all possible transformations defined by all possible mappings connecting all small molecules with a ''maximal network'', -but it is much more efficient to use a network with less transformations like a ''radial network'' (also known as a star map) -or a ''minimimal spanning network''. +It is of course possible to calculate all possible :class:`.Transformation` defined by all possible :class:`.AtomMappings` +connecting all :class:`.SmallMoleculeComponent` with a ''maximal network'' (using :func:`.generate_maximal_network`), +but it is much more efficient to use a network with less transformations like a ''radial network'' (also known as a star map, using :func:`.generate_radial_network`) +or a ''minimimal spanning network'' (using :func:`.generate_minimal_spanning_network`). -Any ``LigandNetwork`` generation can be generally conceptualized into three steps: +Any :class:`.LigandNetwork`` generation can be generally conceptualized into three steps: * Generate the :ref:`Atom Mappings` of all pairwise combinations of ligands * :ref:`Score all resulting Atom Mappings` @@ -47,5 +46,7 @@ In the following code, we will show how a ``LigandNetwork`` can be planned: # Now let's plan the Network ligand_network = network_planner(ligands=mols, mappers=[mapper], scorer=scorer) +Practical information on generating ligand networks can be found in our :ref:`cookbook for ligand network generation ` . + .. note:: Like the Component objects, a ``LigandNetwork`` object is immutable once created!