[PyMOL] Learning Python for PyMOL

[DeLano, W. <wa...@su...>]

David Schuller asked about the best books for learning Python.  There
are two key resources:

(1) Guido's online tutorial is a good starting point for learning the
language.

http://www.python.org/doc/current/tut/tut.html

and (2) "Python Essential Reference" by David M. Beazley, (New Riders)
is a must-have reference for writing Python code.

These tare what got me going a couple years back along with the other
documentation files on the Python web site.=20
http://www.python.org/doc/current/

NOTE: In order to write Python effectively, you need an editor which
supports its indentation scheme.  The top choices are (1) emacs running
python-mode, or (2) IDLE, the editor included with most Python
distributions. =20

Writing Python without a Python-aware editor is a thankless task due to
Python's sensitive block structures which would be a chore to maintain.
I recommend that you use spaces instead of tabs to indent Python code --
PyMOL's convention is 3 spaces per block.

The relavent portions of my .emacs file are included below in case
anyone is interested.  I think most modern Linux distrubutions include a
python mode in emacs by default.

For simple tasks, the PyMOL command language (.pml files) is easier than
Python because you can ignore the identation issue.  However, .pml files
are suited for real programming.

Cheers,
Warren

-- BEGIN .emacs excerpt

(setq-default visible-bell t)
(setq-default backup-inhibited t)
(setq-default auto-save-default nil)

(global-set-key "\C-c\C-w" 'goto-line)

(setq-default tab-stop-list '(3 6 9 12 15 18 21 24 27 30 33 36 39 42) )

(setq-default tab-width 3)
(setq-default py-indent-offset 3)
(setq-default indent-tabs-mode nil)

(setq auto-save-default nil)
(setq auto-save nil)
(setq load-path (cons "/usr/share/emacs/site-lisp/" load-path))
(autoload 'python-mode "python-mode" "Python editing mode." t)
(setq auto-mode-alist
	  (cons '("\\.py$" . python-mode) auto-mode-alist))
(setq auto-mode-alist
	  (cons '("\\.pym$" . python-mode) auto-mode-alist))
(setq interpreter-mode-alist
	  (cons '("python" . python-mode) interpreter-mode-alist))
(global-font-lock-mode)

-- END .emacs excerpt

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501



> -----Original Message-----
> From: DeLano, Warren=20
> Sent: Monday, December 10, 2001 7:40 AM
> To: Glen L. Prosise
> Cc: pym...@li...
> Subject: [PyMOL] PyMOL 0.73 Released (Win,Linux)
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> Gang,
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> Last night I posted binaries of PyMOL 0.73 for Windows and=20
> Linux to the
> downloads page.  Read more at http://www.pymol.org
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> This is the first version to support fragment and residue-based
> molecular building.  However, you may find the process=20
> challenging with
> the current rudimentary interface. =20
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> Cheers,
> Warren
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>=20
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
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