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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:: .. parsed-literal::
http://www.pymol.org https://www.pymol.org
http://sourceforge.net/scm/?type=svn&group_id=4546 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. 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 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: of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links:
* `Pre/Post processing <http://lammps.sandia.gov/prepost.html>`_ * `Pre/Post processing <https://lammps.sandia.gov/prepost.html>`_
* `Offsite LAMMPS packages & tools <http://lammps.sandia.gov/offsite.html>`_ * `Offsite LAMMPS packages & tools <https://lammps.sandia.gov/offsite.html>`_
* `Pizza.py toolkit <pizza_>`_ * `Pizza.py toolkit <pizza_>`_
The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at
Sandia which provides tools for doing setup, analysis, plotting, and Sandia which provides tools for doing setup, analysis, plotting, and
visualization for LAMMPS simulations. visualization for LAMMPS simulations.
.. _lws: http://lammps.sandia.gov .. _lws: https://lammps.sandia.gov
.. _pizza: https://pizza.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 Additional tools included in the LAMMPS distribution are described on
this page. 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 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_>`_. 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 Specifically, the tool triangulates the ellipsoids so they can be
viewed as true ellipsoidal particles within PyMol. See the README and viewed as true ellipsoidal particles within PyMol. See the README and