From 8729fe0004e4eb037c8b7b3d075ad40656d6d2c5 Mon Sep 17 00:00:00 2001 From: riesben Date: Sat, 6 Apr 2024 09:13:40 +0200 Subject: [PATCH 1/3] including comments from #793 --- docs/guide/setup/creating_ligand_networks.rst | 20 ++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/docs/guide/setup/creating_ligand_networks.rst b/docs/guide/setup/creating_ligand_networks.rst index a6cb7b02f..8774f3b61 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 +46,8 @@ 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) +More on generating ligand networks you can find in our generate_ligand_network_cookbook_ . +.. _generate_ligand_network_cookbook: cookbook/generate_ligand_network + .. note:: Like the Component objects, a ``LigandNetwork`` object is immutable once created! From 717778bc70dbb3a8e34d1c0aaba1a5536f8c1b6a Mon Sep 17 00:00:00 2001 From: Benjamin Ries Date: Thu, 11 Apr 2024 11:34:24 +0200 Subject: [PATCH 2/3] Update docs/guide/setup/creating_ligand_networks.rst Co-authored-by: Irfan Alibay --- docs/guide/setup/creating_ligand_networks.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/guide/setup/creating_ligand_networks.rst b/docs/guide/setup/creating_ligand_networks.rst index 8774f3b61..025b3a325 100644 --- a/docs/guide/setup/creating_ligand_networks.rst +++ b/docs/guide/setup/creating_ligand_networks.rst @@ -46,8 +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) -More on generating ligand networks you can find in our generate_ligand_network_cookbook_ . -.. _generate_ligand_network_cookbook: cookbook/generate_ligand_network +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! From 3e9b847c1c3519e9581b9954d1c0f166cd78fe50 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Thu, 11 Apr 2024 12:27:58 +0100 Subject: [PATCH 3/3] Update docs/guide/setup/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 025b3a325..25d7379e2 100644 --- a/docs/guide/setup/creating_ligand_networks.rst +++ b/docs/guide/setup/creating_ligand_networks.rst @@ -46,7 +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 ` . +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!