From 6b0e22b7c53ae8603a4a7e4c6c011e1c0f125c7b Mon Sep 17 00:00:00 2001 From: CuadradoBenavent Date: Wed, 25 Feb 2026 17:26:09 +0100 Subject: [PATCH 1/2] Update HydrogenBondsFromMD documentation Added code block with command to execute get_water_indices.py --- doc/source/examples/HydrogenBondsFromMD.rst | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/doc/source/examples/HydrogenBondsFromMD.rst b/doc/source/examples/HydrogenBondsFromMD.rst index a1e4bf296..9a945a630 100644 --- a/doc/source/examples/HydrogenBondsFromMD.rst +++ b/doc/source/examples/HydrogenBondsFromMD.rst @@ -29,10 +29,18 @@ The script ``get_hbonds.py``. .. literalinclude:: ../../../examples/get_hbonds.py :language: python +**Example usage:** (:download:`Download get_water_indices.py <../../../examples/get_water_indices.py>`) -The script ``get_water_indices`` can create the file ``indices.txt`` that is required by the ``get_hbonds.py`` script, for the specific case where the indices of all water oxygen atoms are required. The script accepts the name of the MD trajectory RKF file. +The script ``get_water_indices`` can create the file ``indices.txt`` that is required by the ``get_hbonds.py`` script, for the specific case where the indices of all water oxygen atoms are required. The script accepts the name of the MD trajectory RKF file and can be called from the command line as follows. + +.. code-block:: bash + + amspython get_water_indices.py path/to/ams.rkf + +The script ``get_water_indices.py``. .. literalinclude:: ../../../examples/get_water_indices.py :language: python + From 3b9024ff5c23647bbe1c4813c167931da570610a Mon Sep 17 00:00:00 2001 From: CuadradoBenavent Date: Thu, 26 Feb 2026 10:09:24 +0100 Subject: [PATCH 2/2] Changed amspython to $AMSBIN/amspython --- doc/source/examples/HydrogenBondsFromMD.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/source/examples/HydrogenBondsFromMD.rst b/doc/source/examples/HydrogenBondsFromMD.rst index 9a945a630..a1747cc11 100644 --- a/doc/source/examples/HydrogenBondsFromMD.rst +++ b/doc/source/examples/HydrogenBondsFromMD.rst @@ -12,7 +12,7 @@ The script ``get_hbonds.py`` accepts the name of an MD trajectory RKF file, and .. code-block:: bash - amspython get_hbonds.py path/to/ams.rkf path/to/indices.txt + $AMSBIN/amspython get_hbonds.py path/to/ams.rkf path/to/indices.txt In its simplest form, the input file indices.txt will contain only one or more element names. @@ -36,7 +36,7 @@ The script ``get_water_indices`` can create the file ``indices.txt`` that is req .. code-block:: bash - amspython get_water_indices.py path/to/ams.rkf + $AMSBIN/amspython get_water_indices.py path/to/ams.rkf The script ``get_water_indices.py``. @@ -44,3 +44,4 @@ The script ``get_water_indices.py``. :language: python +