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fix punctuation and clear text
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lilyminium committed Jan 29, 2024
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Expand Up @@ -11,17 +11,24 @@ Finding your hole executable

``mdahole2`` is a Python package that interfaces with the HOLE_ program.
This necessitates having a HOLE executable on your system.
``mdahole2`` will be able to find your executable if it is on your ``PATH``,
``mdahole2`` will be able to automatically find your executable if it is in your ``PATH``,
i.e. if it can be discovered by calling ``which hole``.
This should be the case for the vast majority of installations
through the recommended pathway of ``conda-forge``.

However, if you have installed HOLE_ through a nonstandard pathway,
then you will need to specify a path to your ``hole`` executable.
then you will need to specify a path to your ``hole`` executable like so::

from MDAnalysis.tests.datafiles import PDB_HOLE
from mdahole2.analysis import hole

profiles = hole(PDB_HOLE, executable='/path/to/hole')

For example, if you installed HOLE from the original source,
If you have installed HOLE from the original source, the executable
may be in your home directory instead, e.g. a path such as ``~/hole2/exe/hole``.
For example, if you installed HOLE from the original source, the executable
may be in your home directory, e.g. a path such as ``~/hole2/exe/hole``.

Throughout the rest of this documentation, we will assume that your executable
is in your ``PATH``, and will not specify a path..
is in your ``PATH``, and will not specify a different path.


Using HOLE on a PDB file
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