From owner-chemistry@ccl.net Sat Jun  2 04:41:00 2012
From: "Andrew Dalke dalke!=!dalkescientific.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: fmcs-1.0 - maximum common substructure search
Message-Id: <-47022-120601201111-20988-EEHYao/OGjctcXuO9i3fkQ * server.ccl.net>
X-Original-From: Andrew Dalke <dalke||dalkescientific.com>
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Date: Sat, 2 Jun 2012 02:10:52 +0200
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Sent to CCL by: Andrew Dalke [dalke^-^dalkescientific.com]
Dear CCL'ers,

 I've just released fmcs-1.0. It finds a maximum common substructure of
two or more structures. Some of the features are:

  o handles 1,000s of structures
  o several different atom and bond comparison schemes
  o modifiers to require ring bonds only match ring bonds, or
     that incomplete rings are not allowed in the MCS
  o user-defined atom class typing through isotope labels (SMILES)
     or through an SD tag field
  o uses an exact solution to find a maximum common substructure
  o reports the current best solution if the timeout is reached

The software is distributed under the 2-clause BSD license and
available for no charge from
 https://bitbucket.org/dalke/fmcs/downloads/fmcs-1.0.tar.gz

You must have the Python bindings to RDKit in order to run fmcs.


Usage details are in the README, shown also in the project page at:
  https://bitbucket.org/dalke/fmcs/

For an additional usage overview, see:
  http://www.dalkescientific.com/writings/diary/archive/2012/05/13/fmcs.html

Here's an example of using fmcs to analyze the ChEBI substructure ontology:
  http://dalkescientific.com/writings/diary/archive/2012/05/13/mcs_chebi.html
and the view from the curator's side:
  http://metabolights.blogspot.com/2012/05/chebi-smarts-and-maximum-common.html


Many thanks to Roche for funding this work, and their effort to promote
more open source software in cheminformatics. Thanks also to Greg
Landrum for RDKit, the Indigo developers for their extractCommonScaffold
multiple-structure MCS methods, Asad Rahman for SMSD (Indigo and SMSD
were used for cross-validation testing), Karen Schomburg for the
SMARTSviewer server, Daylight for the depictmatch.cgi server, and the
ChEBI team for manual inspection work.


I am available for consulting and software training in computational
chemistry. Contact me if you want help extending fmcs or integrating
it within your organization.

				Andrew Dalke
				dalke__dalkescientific.com


From owner-chemistry@ccl.net Sat Jun  2 11:17:00 2012
From: "Jimmy Stewart MrMOPAC|*|att.net" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: New MOPAC2012, Beta Test
Message-Id: <-47023-120602095319-29325-/2Yjx9iXqY0OgxKNhFzDng{}server.ccl.net>
X-Original-From: Jimmy Stewart <MrMOPAC|*|att.net>
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Date: Sat, 02 Jun 2012 07:53:24 -0600
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Sent to CCL by: Jimmy Stewart [MrMOPAC-x-att.net]
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Volunteers are needed for beta-testing a new version of MOPAC called 
MOPAC2012. The beta test will run until the end of August.  MOPAC2012 
contains the new methods PM7 and PM7-TS.  Details of the accuracy of 
these methods can be seen at:

HTTP://OpenMOPAC.net/PM7_accuracy/PM7_accuracy.html

Currently, only users familiar with MOPAC should try using MOPAC2012.  
The default method in MOPAC2012 is PM7.  If PM6 is needed, add keyword 
PM6.  Executable files (binary files) can be downloaded from:

http://openmopac.net/Download_MOPAC_Executable_Step2.html

Please send feedback and any suggestions for improvements to 
MrMOPAC:OpenMOPAC.net <mailto:MrMOPAC:OpenMOPAC.net>
Thank you


-- 

James J. P. Stewart
Stewart Computational Chemistry
15210 Paddington Circle
Colorado Springs, CO 80921
USA
Tel: (719) 488-9416, E-mail: MrMOPAC:OpenMOPAC.net
SKYPE: Jimmy.Stewart2, URL: HTTP://OpenMOPAC.net


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    <font face="Arial"><font color="#000099">Volunteers are needed for
        beta-testing a new version of MOPAC called MOPAC2012. The beta
        test will run until the end of August.&nbsp; MOPAC2012 contains the
        new methods PM7 and PM7-TS.&nbsp; Details of the accuracy of these
        methods can be seen at:<br>
        <br>
        <a rel="nofollow" target="_blank"
          href="HTTP://OpenMOPAC.net/PM7_accuracy/PM7_accuracy.html">HTTP://OpenMOPAC.net/PM7_accuracy/PM7_accuracy.html</a><br>
        <br>
        Currently, only users familiar with MOPAC should try using
        MOPAC2012.&nbsp; The default method in MOPAC2012 is PM7.&nbsp; If PM6 is
        needed, add keyword PM6.&nbsp; Executable files (binary files) can be
        downloaded from:<br>
        <br>
        <a rel="nofollow" target="_blank"
          href="http://openmopac.net/Download_MOPAC_Executable_Step2.html"><span
            class="yshortcuts" id="lw_1338645033_0">http://openmopac.net/Download_MOPAC_Executable_Step2.html</span></a><br>
        <br>
        Please send feedback and any suggestions for improvements to <a
          rel="nofollow" class="yiv959653468moz-txt-link-abbreviated"
          ymailto="mailto:MrMOPAC:OpenMOPAC.net" target="_blank"
          href="mailto:MrMOPAC:OpenMOPAC.net"><span class="yshortcuts"
            id="lw_1338645033_1">MrMOPAC:OpenMOPAC.net</span></a>&nbsp; <br>
        Thank you</font><br>
    </font><br>
    <br>
    <pre class="moz-signature" cols="72">-- 

James J. P. Stewart
Stewart Computational Chemistry
15210 Paddington Circle
Colorado Springs, CO 80921
USA
Tel: (719) 488-9416, E-mail: <a class="moz-txt-link-abbreviated" href="mailto:MrMOPAC:OpenMOPAC.net">MrMOPAC:OpenMOPAC.net</a>
SKYPE: Jimmy.Stewart2, URL: <a class="moz-txt-link-freetext" href="HTTP://OpenMOPAC.net">HTTP://OpenMOPAC.net</a>
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