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update PyMol URLs

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This commit is contained in:
Axel Kohlmeyer
2020-03-12 00:21:20 -04:00
parent 23569e67a0
commit 6dd9a507ef
2 changed files with 10 additions and 10 deletions
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8
doc/src/Python_examples.rst
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@ -61,12 +61,12 @@ from a Python script. See the PyMol WWW pages `here <pymolhome_>`_ or
.. parsed-literal::
http://www.pymol.org
http://sourceforge.net/scm/?type=svn&group_id=4546
https://www.pymol.org
https://github.com/schrodinger/pymol-open-source
.. _pymolhome: http://www.pymol.org
.. _pymolhome: https://www.pymol.org
.. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546
.. _pymolopen: https://github.com/schrodinger/pymol-open-source
The latter link is to the open-source version.

12
doc/src/Tools.rst
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@ -6,17 +6,17 @@ molecular dynamics computations. Additional pre- and post-processing
steps are often necessary to setup and analyze a simulation. A list
of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links:
* `Pre/Post processing <http://lammps.sandia.gov/prepost.html>`_
* `Offsite LAMMPS packages & tools <http://lammps.sandia.gov/offsite.html>`_
* `Pre/Post processing <https://lammps.sandia.gov/prepost.html>`_
* `Offsite LAMMPS packages & tools <https://lammps.sandia.gov/offsite.html>`_
* `Pizza.py toolkit <pizza_>`_
The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at
Sandia which provides tools for doing setup, analysis, plotting, and
visualization for LAMMPS simulations.
.. _lws: http://lammps.sandia.gov
.. _lws: https://lammps.sandia.gov
.. _pizza: https://pizza.sandia.gov
.. _python: http://www.python.org
.. _python: https://www.python.org
Additional tools included in the LAMMPS distribution are described on
this page.
@ -519,9 +519,9 @@ The pymol\_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
particles into an input file for the `PyMol visualization package <pymolhome_>`_ or its `open source variant <pymolopen_>`_.
.. _pymolhome: http://www.pymol.org
.. _pymolhome: https://www.pymol.org
.. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546
.. _pymolopen: https://github.com/schrodinger/pymol-open-source
Specifically, the tool triangulates the ellipsoids so they can be
viewed as true ellipsoidal particles within PyMol. See the README and