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lilyminium merged 1 commit into from
May 19, 2021
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Update install and selection notes #127

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17 changes: 17 additions & 0 deletions doc/source/installation.rst
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Expand Up @@ -55,6 +55,14 @@ To install the tests:

conda install -c conda-forge MDAnalysisTests

If you intend to use MDAnalysis in JupyterLab, you will have to install
an extra package for the progress bar in analysis classes:

.. code-block:: bash

conda install -c conda-forge nodejs
jupyter labextension install @jupyter-widgets/jupyterlab-manager

pip
=====
The following command will install or upgrade the latest stable version of MDAnalysis via ``pip``, with core dependencies. This means that some packages required by specific analysis modules will not be installed.
Expand All @@ -75,6 +83,15 @@ To install/upgrade tests:

pip install --upgrade MDAnalysisTests

If you intend to use MDAnalysis in JupyterLab, you will have to install
an extra package for the progress bar in analysis classes:

.. code-block:: bash

pip install nodejs
jupyter labextension install @jupyter-widgets/jupyterlab-manager


Development versions
====================
To install development versions of MDAnalysis, you can compile it from source. In order to install from source, you will need ``numpy`` and ``cython``. See :ref:`create-virtual-environment` for instructions on how to create a full development environment.
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18 changes: 14 additions & 4 deletions doc/source/selections.rst
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Expand Up @@ -69,10 +69,15 @@ selection parser. The following applies to all selections:


* String selections such as names and residue names can be
matched with Unix shell-style wildcards. Using ``*``
in a string matches any number of any characters; ``?``
matches any single character; ``[seq]`` matches any character in *seq*;
and ``[!seq]`` matches any character not in *seq*. For example,
matched with Unix shell-style wildcards. These rules include:

* Using ``*`` in a string matches any number of any characters
* ``?`` matches any single character
* ``[seq]`` matches any character in *seq*;
* ``[!seq]`` matches any character not in *seq*
* ``[!?]`` selects empty strings

For example,
the string ``GL*`` selects all strings that start with "GL",
such as "GLU", "GLY", "GLX29", "GLN". ``GL[YN]`` will select all "GLY" and
"GLN" strings. Any number of patterns can be included in the search.
Expand Down Expand Up @@ -141,6 +146,11 @@ altloc *alternative-location*
e.g. :code:`resid 4 and resname ALA and altloc B` selects only the atoms of ALA-4
that have an altloc B record.

icode *icode*
a selector for atoms where insertion codes are available. This can be combined
with residue numbers using the ``resid`` selector above.
e.g. :code:`icode [!?]` selects atoms *without* insertion codes.

moltype *molecule-type*
select by the ``moltype`` :ref:`topology attribute <topology-attributes>`, e.g. ``moltype Protein_A``. At the moment, only the TPR format defines the ``moltype``.

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