RE: [ccp4bb]: scripting

["DeLano, Warren" <warren@sunesis.com>]

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Learn Python! 

It is already directly supported by useful packages such as VMD, PyMOL, PMV, Chimera, and MMTK as well as development projects like Birdwash, CCP43D, and PHENIX.  In my opinion, Python has already emerged as the preferred the language for structural biology and computational chemistry, just as Perl long ago emerged as the de facto language for bioinformatics and web development.

Most will agree that we all stand to benefit by switching from away from shell scripts and application-specific languages to standard, well-known scripting languages.  

While Perl would be a fine choice, Python is easier for novices to learn, has better support for multi-dimensional objects (atoms, bonds, coordinates), and is better for code sharing because it is so simple, obvious, and consistent.

So just learn Python -- it will help your Science as well as your graphics.

And who knows?  Maybe it will even inspire you to write an open-source script, module, or program in your spare time.  It does have that effect upon some of us...

--
mailto:warren@sunesis.com
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: Frank Vondelft [mailto:Frank.Vondelft@syrrx.com]
> Sent: Friday, July 19, 2002 3:24 PM
> To: Bernhard Rupp; ccp4bb@dl.ac.uk
> Subject: RE: [ccp4bb]: scripting
> 
> 
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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Don't think this has been answered: 
> 
> I really would not bother with anything apart from python, and I've
> almost completely abandoned silly csh scripts.  Apparently, everybody
> who has made the small effort agrees.  (For those people that 
> don't, it
> usually seems to be that they cannot be bothered to change;  
> I found it
> *well* worth the effort, however.)
> 
> I didn't find it to be a steep learning curve at all - in 
> fact, I think
> I had a lot more trouble with Perl, because of all perl's 
> 'magic'.  The
> tutorial on the website gets you up to speed pretty quickly:
> www.python.org, just search around. 
> 
> And then there's the wonderful concise reference book - for 
> people that
> know what they want to do:  "Python, Essential Reference", 
> 2nd edition;
> David M. Beazley.
> 
> In short:  do yourself the favour.
> 
> phx.
> 
> 
> 
> -----Original Message-----
> From: Bernhard Rupp [mailto:br@llnl.gov]
> Sent: Thursday, July 18, 2002 1:39 PM
> To: ccp4bb@dl.ac.uk
> Subject: [ccp4bb]: scripting
> 
> 
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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Dear All:
> 
> This is a call for advice to the scripting pros:
> 
> I have come to the limit of what at least I personally can do
> with csh scripts (although admittedly Jim Holton's Elves attest
> to their power - given a competent scripter).
> 
> Is there a preference for lets say Python or something in the
> crystallographic programmer's community? Can I also use python
> instead of my perl or java or vbs scripts, for example?
> Is there something like a csh2python etc converter to speed
> the process up? How steep is the learning/transition curve?
> Good book?
> 
> I am sure someone went through the same pains already -
> any advice would be appreciated.
> 
> br
> 
> ------------------------------------
> Bernhard Rupp
> Dept. of Biochemistry and Biophysics
> 2128 Texas A&M University
> College Station, TX 77843-2128
> cell 925 209 7429
> lab  979 862 7639
> sec  979 862 7636
> ------------------------------------
>