[MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd)

Gustavo Mercier gamercier@yahoo.com
Thu, 12 Dec 2002 10:30:33 -0800 (PST)


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Hi!
I think the comments below are right on the money.
I believe that a molecular modeling package powered by Python is a great idea, particularly for those who would like to teach computational chemistry.
For example, many popular modeling packages allow the students to perform simulations using a black box approach. This is fine for introductory courses where the focus is on the end results relevant to the chemistry of a problem. In advanced undergraduate course, an instructor may wish to breakthrough the "black box". The scripting power of Python together with a set of modules would be the best tool for such a course. The students could program simulations using objects available through the modules. Each layer of the black box can be peeled by programming with lower level objects.
Although I've been a bit away from Python (my last heavy use was with version 1.5x!), I certainly will support and even contribute to this effort. Unfortunately, the issue is one of leadership to initiate such a project. May be those who mantain MMTK,  PyQuante, PyMol, etc. may be willing to take the initiative.
The definition of a common object/data structure for the "molecule" is a first step. This is a critical step and a little bit of thought may go along way to make development not only easier but useful. It would be best not to rediscover the wheel.
As a suggestion, let's consider the chemistry implementation of XML -- CML. Whatever the details of the object "molecule", it would be beneficial to input and output to/from CML. A specification of "molecule" based on CML would make it easier to interface with other technologies. I recognize that there are problems with CML, but this should not stop the community from considering this "standard".
Gustavo
 Eugen Leitl <eugen@leitl.org> wrote:


-- 
-- Eugen* Leitl leitl
______________________________________________________________
ICBMTO: N48 04'14.8'' E11 36'41.2'' http://eugen.leitl.org
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http://moleculardevices.org http://nanomachines.net

---------- Forwarded message ----------
Date: Thu, 12 Dec 2002 16:58:47 +1030
From: Michael Sorich 
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] improving interoperability between python molecule toolkits

Hello all,

I share in Warren's vision of extending PyMol into a "complete platform
for crystallography, computational chemistry, modeling, and
informatics". However, I believe this can only come about by cooperation
and integration with other python based molecule toolkits. 

<cut stuff ...> 

It seems to be in everyone's interest to allow easy interoperation
between the toolkits. However, in my experience it is a frustrating and
difficult task, even for relatively simple tasks. 

Does anyone else feel the same frustration? And if so, does anyone have
a solution?

I believe that a common set of core modules is required. The most
important feature is the molecule. 

<cut stuff ...>

 


--
Gustavo A. Mercier, Jr., MD,PhD
Seattle Nuclear Medicine & U/S Associates
1229 Madison, Suite 1150
Seattle, WA 98104-1377
voice: 206-386-6300; fax: 206-386-6312
gamercier@yahoo.com 


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<P>Hi!
<P>I think the comments below are right on the money.
<P>I believe that&nbsp;a molecular modeling package powered by Python is a great idea, particularly for those who would like to teach computational chemistry.
<P>For example, many popular modeling packages allow the students to perform simulations using a black box approach. This is fine for introductory courses where the focus is on the end results relevant to the chemistry of a problem. In advanced undergraduate course, an instructor may wish to breakthrough the&nbsp;"black box".&nbsp;The scripting power of Python together with a set of modules&nbsp;would be the best tool for such a course. The&nbsp;students could program simulations using objects available through the modules. Each layer of the black box can be peeled by programming with lower level objects.
<P>Although I've been a bit away from Python (my last heavy use was with version 1.5x!), I certainly will support and even contribute to this effort. Unfortunately, the issue is one of leadership to initiate such a project. May be those who mantain&nbsp;MMTK, &nbsp;PyQuante, PyMol, etc. may be willing to take the initiative.
<P>The definition of a common object/data structure for the "molecule" is a first step. This is a critical step and&nbsp;a little bit of thought may go along way to make development not only easier but useful. It would be best not to rediscover the wheel.
<P>As a suggestion, let's consider the chemistry implementation of XML -- CML. Whatever the details of the object "molecule", it would be beneficial to input and output to/from CML. A specification of "molecule" based on CML would make it easier to interface with other technologies. I recognize that there are problems with CML, but this should not stop the community from considering this "standard".
<P>Gustavo
<P>&nbsp;<B><I>Eugen Leitl &lt;eugen@leitl.org&gt;</I></B> wrote:
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">
<P><BR><BR>-- <BR>-- Eugen* Leitl <A href="http://leitl.org/">leitl</A><BR>______________________________________________________________<BR>ICBMTO: N48 04'14.8'' E11 36'41.2'' http://eugen.leitl.org<BR>83E5CA02: EDE4 7193 0833 A96B 07A7 1A88 AA58 0E89 83E5 CA02<BR>http://moleculardevices.org http://nanomachines.net<BR><BR>---------- Forwarded message ----------<BR>Date: Thu, 12 Dec 2002 16:58:47 +1030<BR>From: Michael Sorich <MIKE_SORICH@HOTMAIL.COM><BR>To: pymol-users@lists.sourceforge.net<BR>Subject: [PyMOL] improving interoperability between python molecule toolkits<BR><BR>Hello all,<BR><BR>I share in Warren's vision of extending PyMol into a "complete platform<BR>for crystallography, computational chemistry, modeling, and<BR>informatics". However, I believe this can only come about by cooperation<BR>and integration with other python based molecule toolkits. </P>
<P>&lt;cut stuff ...&gt; </P>
<P>It seems to be in everyone's interest to allow easy interoperation<BR>between the toolkits. However, in my experience it is a frustrating and<BR>difficult task, even for relatively simple tasks. <BR><BR>Does anyone else feel the same frustration? And if so, does anyone have<BR>a solution?<BR><BR>I believe that a common set of core modules is required. The most<BR>important feature is the molecule. </P>
<P>&lt;cut stuff ...&gt;</P>
<P>&nbsp;</P></BLOCKQUOTE><BR><BR>--<BR><FONT style="BACKGROUND-COLOR: white">Gustavo A. Mercier, Jr., MD,PhD<BR>Seattle Nuclear Medicine &amp; U/S Associates<BR>1229 Madison, Suite 1150<BR>Seattle, WA 98104-1377<BR>voice: 206-386-6300; fax: 206-386-6312<BR></FONT><A href="mailto:gamercier@yahoo.com"><FONT style="BACKGROUND-COLOR: white">gamercier@yahoo.com</FONT></A>&nbsp;<IMG src="http://us.i1.yimg.com/us.yimg.com/i/mesg/tsmileys/c.gif"><p><br><hr size=1>Do you Yahoo!?<br>
New <a href="http://rd.yahoo.com/evt=1207/*http://sbc.yahoo.com/">DSL Internet Access</a> from SBC & Yahoo!</a>
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