From 15394414e20441780486d3695b6fcd95a732757c Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Wed, 16 Oct 2024 07:44:19 -0700 Subject: [PATCH 1/4] formatting fixes to cli_basics --- docs/guide/cli/cli_basics.rst | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/guide/cli/cli_basics.rst b/docs/guide/cli/cli_basics.rst index 56f5602d0..14aa5997f 100644 --- a/docs/guide/cli/cli_basics.rst +++ b/docs/guide/cli/cli_basics.rst @@ -3,11 +3,12 @@ CLI basics The ``openfe`` command consists of several subcommands. This is similar to tools like ``gmx``, which has subcommands like ``gmx mdrun``, or ``conda``, -which has subcommands like ``conda install``. To get a list of the -subcommands and a brief description of them, use ``openfe (or -``openfe -h``), which will give: +which has subcommands like ``conda install``. -.. TODO autogemerate using sphinxcontrib-programoutput +To get a list of the subcommands and their descriptions, call ``openfe`` (or +``openfe -h``): + +.. TODO autogenerate using sphinxcontrib-programoutput .. code:: none From 24ef31952366edbbf996e5cc3d2d13a2f49b38aa Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Wed, 16 Oct 2024 08:23:09 -0700 Subject: [PATCH 2/4] clarity edits to cli_yaml docs --- docs/guide/cli/cli_yaml.rst | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/docs/guide/cli/cli_yaml.rst b/docs/guide/cli/cli_yaml.rst index b69493686..297888c20 100644 --- a/docs/guide/cli/cli_yaml.rst +++ b/docs/guide/cli/cli_yaml.rst @@ -2,9 +2,10 @@ Customising CLI planning with yaml settings =========================================== The planning commands in the CLI can be made more powerful by supplying -"yaml" formatted files to customise the planning algorithms. -This settings file has a series of sections for customising the different algorithms, -as an example, the settings file which re-specifies the default behaviour would look like :: +``yaml``-formatted files to customise the planning algorithms. + +This settings file has a series of sections for customising the different algorithms. +For example, the settings file which re-specifies the default behaviour would look like :: network: method: plan_minimal_spanning_tree @@ -18,9 +19,9 @@ as an example, the settings file which re-specifies the default behaviour would The name of the algorithm is given behind the ``method:`` key and the arguments to the algorithm are then optionally given behind the ``settings:`` key. -Both the `network:` and `mapper:` sections are optional. +Both the ``network:`` and ``mapper:`` sections are optional. -This is then provided to the ``openfe plan-rbfe-network`` command as :: +The settings yaml file is then provided to the ``-s`` option of ``openfe plan-rbfe-network``: :: openfe plan-rbfe-network -M molecules.sdf -P protein.pdb -s settings.yaml @@ -28,8 +29,13 @@ Customising the atom mapper --------------------------- There is a choice to be made as to which atom mapper is used, -currently included are the :class:`.LomapAtomMapper` and the :class:`.KartografAtomMapper` -For example to switch to using the ``Kartograf`` atom mapper, this settings yaml could be used :: +currently included are the :class:`.LomapAtomMapper` and the :class:`.KartografAtomMapper`. + +Full details on these options can be found in the `Kartograf documentation`_. + +.. _Kartograf documentation: https://kartograf.readthedocs.io/en/latest/api/kartograf.mappers.html#kartograf.atom_mapper.KartografAtomMapper + +For example, to switch to using the ``Kartograf`` atom mapper, this settings yaml could be used :: mapper: method: KartografAtomMapper @@ -39,9 +45,6 @@ For example to switch to using the ``Kartograf`` atom mapper, this settings yaml map_hydrogens_on_hydrogens_only: False map_exact_ring_matches_only: True -Full details on these options can be found in the `Kartograf documentation`_. - -.. _Kartograf documentation: https://kartograf.readthedocs.io/en/latest/api/kartograf.mappers.html#kartograf.atom_mapper.KartografAtomMapper Customising the network planner ------------------------------- @@ -51,7 +54,7 @@ There are a variety of network planning options available, including :func:`.generate_minimal_spanning_network`, and :func:`.generate_minimal_redundant_network`. -For example to plan a radial network using a ligand called 'CHEMBL1078774' as the central ligand, this settings yaml +For example, to plan a radial network using a ligand called 'CHEMBL1078774' as the central ligand, this settings yaml could be given :: network: From bbc535f14d440127fe95c4d2756abd935d9dd6f7 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Wed, 16 Oct 2024 08:43:35 -0700 Subject: [PATCH 3/4] moving Kartograf link) --- docs/guide/cli/cli_yaml.rst | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/guide/cli/cli_yaml.rst b/docs/guide/cli/cli_yaml.rst index 297888c20..279f7b547 100644 --- a/docs/guide/cli/cli_yaml.rst +++ b/docs/guide/cli/cli_yaml.rst @@ -2,7 +2,7 @@ Customising CLI planning with yaml settings =========================================== The planning commands in the CLI can be made more powerful by supplying -``yaml``-formatted files to customise the planning algorithms. +yaml-formatted files to customise the planning algorithms. This settings file has a series of sections for customising the different algorithms. For example, the settings file which re-specifies the default behaviour would look like :: @@ -29,9 +29,7 @@ Customising the atom mapper --------------------------- There is a choice to be made as to which atom mapper is used, -currently included are the :class:`.LomapAtomMapper` and the :class:`.KartografAtomMapper`. - -Full details on these options can be found in the `Kartograf documentation`_. +currently included are the :class:`.LomapAtomMapper` and the :class:`.KartografAtomMapper` (full details in the `Kartograf documentation`_.) .. _Kartograf documentation: https://kartograf.readthedocs.io/en/latest/api/kartograf.mappers.html#kartograf.atom_mapper.KartografAtomMapper From 69f2d0b25b72caa546ebbbc24e11ca237510eabb Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 18 Oct 2024 11:24:17 -0700 Subject: [PATCH 4/4] capitalize YAML --- docs/guide/cli/cli_yaml.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/guide/cli/cli_yaml.rst b/docs/guide/cli/cli_yaml.rst index 279f7b547..6e047e774 100644 --- a/docs/guide/cli/cli_yaml.rst +++ b/docs/guide/cli/cli_yaml.rst @@ -1,8 +1,8 @@ -Customising CLI planning with yaml settings +Customising CLI planning with YAML settings =========================================== The planning commands in the CLI can be made more powerful by supplying -yaml-formatted files to customise the planning algorithms. +YAML-formatted files to customise the planning algorithms. This settings file has a series of sections for customising the different algorithms. For example, the settings file which re-specifies the default behaviour would look like :: @@ -21,7 +21,7 @@ The name of the algorithm is given behind the ``method:`` key and the arguments algorithm are then optionally given behind the ``settings:`` key. Both the ``network:`` and ``mapper:`` sections are optional. -The settings yaml file is then provided to the ``-s`` option of ``openfe plan-rbfe-network``: :: +The settings YAML file is then provided to the ``-s`` option of ``openfe plan-rbfe-network``: :: openfe plan-rbfe-network -M molecules.sdf -P protein.pdb -s settings.yaml @@ -33,7 +33,7 @@ currently included are the :class:`.LomapAtomMapper` and the :class:`.KartografA .. _Kartograf documentation: https://kartograf.readthedocs.io/en/latest/api/kartograf.mappers.html#kartograf.atom_mapper.KartografAtomMapper -For example, to switch to using the ``Kartograf`` atom mapper, this settings yaml could be used :: +For example, to switch to using the ``Kartograf`` atom mapper, this settings YAML could be used :: mapper: method: KartografAtomMapper @@ -52,7 +52,7 @@ There are a variety of network planning options available, including :func:`.generate_minimal_spanning_network`, and :func:`.generate_minimal_redundant_network`. -For example, to plan a radial network using a ligand called 'CHEMBL1078774' as the central ligand, this settings yaml +For example, to plan a radial network using a ligand called 'CHEMBL1078774' as the central ligand, this settings YAML could be given :: network: @@ -70,7 +70,7 @@ To select the first ligand, the **integer** 0 can be given :: settings: central_ligand: 0 -Whereas if we wanted to specify the ligand named "0", we would instead explicitly pass this as **a string** to the yaml +Whereas if we wanted to specify the ligand named "0", we would instead explicitly pass this as **a string** to the YAML settings file :: network: