From 853b5ea5769534f4b3f2b84ead0d40c5adafbc05 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 16 Oct 2020 17:13:31 -0400 Subject: [PATCH] Remove redundant links and wording --- doc/src/Python_examples.rst | 29 +++++++++++++---------------- 1 file changed, 13 insertions(+), 16 deletions(-) diff --git a/doc/src/Python_examples.rst b/doc/src/Python_examples.rst index 25cb4f8a77..94b3e7e2ff 100644 --- a/doc/src/Python_examples.rst +++ b/doc/src/Python_examples.rst @@ -27,7 +27,7 @@ distribution. +----------------------------------------------------------------+--------------------------------------------------+ | real-time viz via some viz package | vizplotgui_tool.py | +----------------------------------------------------------------+--------------------------------------------------+ -| combination of viz_tool.py and plot.py and gui.py | | +| combination of viz_tool.py and plot.py and gui.py | | +----------------------------------------------------------------+--------------------------------------------------+ ---------- @@ -37,18 +37,18 @@ with "gl" or "atomeye" or "pymol" or "vmd", depending on what visualization package you have installed. Note that for GL, you need to be able to run the Pizza.py GL tool, -which is included in the pizza sub-directory. See the `Pizza.py doc pages `_ for more info: +which is included in the pizza sub-directory. See the Pizza.py doc pages for more info: + +* `https://pizza.sandia.gov `_ .. _pizza: https://pizza.sandia.gov Note that for AtomEye, you need version 3, and there is a line in the scripts that specifies the path and name of the executable. See the -AtomEye WWW pages `here `_ or `here `_ for more details: +AtomEye webpages for more details: -.. parsed-literal:: - - http://li.mit.edu/Archive/Graphics/A/ - http://li.mit.edu/Archive/Graphics/A3/A3.html +* `http://li.mit.edu/Archive/Graphics/A/ `_ +* `http://li.mit.edu/Archive/Graphics/A3/A3.html `_ .. _atomeye: http://li.mit.edu/Archive/Graphics/A/ @@ -59,13 +59,10 @@ capability needed by these Python scripts. Note that for PyMol, you need to have built and installed the open-source version of PyMol in your Python, so that you can import it -from a Python script. See the PyMol WWW pages `here `_ or -`here `_ for more details: +from a Python script. See the PyMol webpages for more details: -.. parsed-literal:: - - https://www.pymol.org - https://github.com/schrodinger/pymol-open-source + * `https://www.pymol.org `_ + * `https://github.com/schrodinger/pymol-open-source `_ .. _pymolhome: https://www.pymol.org @@ -74,15 +71,15 @@ from a Python script. See the PyMol WWW pages `here `_ or The latter link is to the open-source version. Note that for VMD, you need a fairly current version (1.8.7 works for -me) and there are some lines in the pizza/vmd.py script for 4 PIZZA +me) and there are some lines in the ``pizza/vmd.py`` script for 4 PIZZA variables that have to match the VMD installation on your system. ---------- -See the python/README file for instructions on how to run them and the +See the ``python/README`` file for instructions on how to run them and the source code for individual scripts for comments about what they do. -Here are screenshots of the vizplotgui_tool.py script in action for +Here are screenshots of the ``vizplotgui_tool.py`` script in action for different visualization package options: .. |pyex1| image:: img/screenshot_gl.jpg