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Merged
dormrod merged 2 commits into from
Feb 26, 2026
Merged

Update HydrogenBondsFromMD documentation #367

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6b0e22b
Update HydrogenBondsFromMD documentation
CuadradoBenavent Feb 25, 2026
3b9024f
Changed amspython to $AMSBIN/amspython
CuadradoBenavent Feb 26, 2026
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13 changes: 11 additions & 2 deletions doc/source/examples/HydrogenBondsFromMD.rst
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Expand Up @@ -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.

Expand All @@ -29,10 +29,19 @@ 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

$AMSBIN/amspython get_water_indices.py path/to/ams.rkf

The script ``get_water_indices.py``.

.. literalinclude:: ../../../examples/get_water_indices.py
:language: python



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