From 02a0cbd58bdbf3ae454ff6f6bfdc10654184a8a3 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Fri, 19 Jun 2020 22:04:05 -0700 Subject: [PATCH] link to the propka3 command page --- docs/source/command.rst | 8 +++++--- docs/source/index.rst | 4 ++-- docs/source/quickstart.rst | 12 +++++++----- 3 files changed, 14 insertions(+), 10 deletions(-) diff --git a/docs/source/command.rst b/docs/source/command.rst index 9bd8466..48cd3ae 100644 --- a/docs/source/command.rst +++ b/docs/source/command.rst @@ -1,8 +1,10 @@ .. -*- coding: utf-8 -*- -================================ - The :program:`propka3` command -================================ +.. _propka3-command: + +============================ + :program:`propka3` command +============================ PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure. The diff --git a/docs/source/index.rst b/docs/source/index.rst index 5301882..72f19b3 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -18,8 +18,8 @@ PROPKA 3 predicts the |pKa| values of ionizable groups in proteins [Sondergaard2011]_ and protein-ligand complexes based on the 3D structure [Olsson2011]_. -This package installs the :program:`propka3` command and the -:mod:`propka` Python package. +This package installs the :ref:`propka3 command ` and +the :mod:`propka` Python package. License and source code diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst index f30b17f..8b80dfe 100644 --- a/docs/source/quickstart.rst +++ b/docs/source/quickstart.rst @@ -8,19 +8,21 @@ Quickstart Guide ================== -PROPKA can be used either as a module or via the installed script :program:`propka3`; i.e., either +PROPKA can be used either via the installed script :program:`propka3` +or as a Python module. When using the :ref:`propka3-command`, use .. code-block:: bash - propka3 + propka3 FILENAME -or :mod:`propka` +As a module (:mod:`propka`), also provide the input filename .. code-block:: bash - python -m propka + python -m propka FILENAME -works for invoking PROPKA. +In both cases, additional options may be added, as described in more +detail for the :ref:`propka3-command`. Predicting protein residue |pKa| values