From 68e5cb6c6d895f7d410bcfeeaed6164c976029f2 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 11 Dec 2023 16:23:00 +0000 Subject: [PATCH] Update docstrings. --- python/BioSimSpace/Parameters/_Protocol/_amber.py | 7 +++++-- python/BioSimSpace/Parameters/_parameters.py | 14 ++++++++++---- .../Exscientia/Parameters/_Protocol/_amber.py | 7 +++++-- .../Sandpit/Exscientia/Parameters/_parameters.py | 14 ++++++++++---- 4 files changed, 30 insertions(+), 12 deletions(-) diff --git a/python/BioSimSpace/Parameters/_Protocol/_amber.py b/python/BioSimSpace/Parameters/_Protocol/_amber.py index 639f33465..1bb9e64fe 100644 --- a/python/BioSimSpace/Parameters/_Protocol/_amber.py +++ b/python/BioSimSpace/Parameters/_Protocol/_amber.py @@ -156,8 +156,11 @@ def __init__( water models. custom_parameters: [str] - A list of paths to custom parameter files. When this option is set, - we can no longer fall back on GROMACS's pdb2gmx. + A list of paths to custom parameter files. These can be user-defined + parameter files files that are loaded with loadAmberParams, or the names + of additional internal leaprc scripts, which will be sourced, e.g. + 'leaprc.gaff'. When this option is set, we can no longer fall back on + GROMACS's pdb2gmx. leap_commands : [str] An optional list of extra commands for the LEaP program. These diff --git a/python/BioSimSpace/Parameters/_parameters.py b/python/BioSimSpace/Parameters/_parameters.py index 26f0199b9..0a40ff520 100644 --- a/python/BioSimSpace/Parameters/_parameters.py +++ b/python/BioSimSpace/Parameters/_parameters.py @@ -173,8 +173,11 @@ def _parameterise_amber_protein( molecules. custom_parameters: [str] - A list of paths to custom parameter files. When this option is set, - we can no longer fall back on GROMACS's pdb2gmx. + A list of paths to custom parameter files. These can be user-defined + parameter files files that are loaded with loadAmberParams, or the names + of additional internal leaprc scripts, which will be sourced, e.g. + 'leaprc.gaff'. When this option is set, we can no longer fall back on + GROMACS's pdb2gmx. leap_commands : [str] An optional list of extra commands for the LEaP program. These @@ -1018,8 +1021,11 @@ def _function( molecules. custom_parameters: [str] - A list of paths to custom parameter files. When this option is set, - we can no longer fall back on GROMACS's pdb2gmx. + A list of paths to custom parameter files. These can be user-defined + parameter files files that are loaded with loadAmberParams, or the names + of additional internal leaprc scripts, which will be sourced, e.g. + 'leaprc.gaff'. When this option is set, we can no longer fall back on + GROMACS's pdb2gmx. leap_commands : [str] An optional list of extra commands for the LEaP program. These diff --git a/python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_amber.py b/python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_amber.py index 639f33465..1bb9e64fe 100644 --- a/python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_amber.py +++ b/python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_amber.py @@ -156,8 +156,11 @@ def __init__( water models. custom_parameters: [str] - A list of paths to custom parameter files. When this option is set, - we can no longer fall back on GROMACS's pdb2gmx. + A list of paths to custom parameter files. These can be user-defined + parameter files files that are loaded with loadAmberParams, or the names + of additional internal leaprc scripts, which will be sourced, e.g. + 'leaprc.gaff'. When this option is set, we can no longer fall back on + GROMACS's pdb2gmx. leap_commands : [str] An optional list of extra commands for the LEaP program. These diff --git a/python/BioSimSpace/Sandpit/Exscientia/Parameters/_parameters.py b/python/BioSimSpace/Sandpit/Exscientia/Parameters/_parameters.py index 26f0199b9..0a40ff520 100644 --- a/python/BioSimSpace/Sandpit/Exscientia/Parameters/_parameters.py +++ b/python/BioSimSpace/Sandpit/Exscientia/Parameters/_parameters.py @@ -173,8 +173,11 @@ def _parameterise_amber_protein( molecules. custom_parameters: [str] - A list of paths to custom parameter files. When this option is set, - we can no longer fall back on GROMACS's pdb2gmx. + A list of paths to custom parameter files. These can be user-defined + parameter files files that are loaded with loadAmberParams, or the names + of additional internal leaprc scripts, which will be sourced, e.g. + 'leaprc.gaff'. When this option is set, we can no longer fall back on + GROMACS's pdb2gmx. leap_commands : [str] An optional list of extra commands for the LEaP program. These @@ -1018,8 +1021,11 @@ def _function( molecules. custom_parameters: [str] - A list of paths to custom parameter files. When this option is set, - we can no longer fall back on GROMACS's pdb2gmx. + A list of paths to custom parameter files. These can be user-defined + parameter files files that are loaded with loadAmberParams, or the names + of additional internal leaprc scripts, which will be sourced, e.g. + 'leaprc.gaff'. When this option is set, we can no longer fall back on + GROMACS's pdb2gmx. leap_commands : [str] An optional list of extra commands for the LEaP program. These