Update docstrings.

OpenBioSim · Dec 11, 2023 · 68e5cb6 · 68e5cb6
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diff --git 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
@@ -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
@@ -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
@@ -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