Re: [Blue-obelisk] Re: 3D structure generator
I would like to add that the CDK *did* develop a 3D generator in the mean time. It works similar to the the Bustr3d approach and can be tested on http://www.chemistry-development-kit.org Note that there is currently a bug with the ring perception. Cambridge and the CDK team had plans of merging the two approaches, but so far we did not do that. Cheers, Chris peter murray-rust wrote: At 21:08 13/01/2007, Dan Willenbring wrote: Dear Dr. Peter Murray Rust, Thanks very much - I'm taking the liberty of copying your message to the Blue Obelisk list I ran across a pretty old Cdk-devel message ( http://sourceforge.net/ mailarchive/message.php?msg_id=5267361 ) where you were discussing a possible open source implementation of 3D structure generation. I am working on a project where I need to generate several thousand sets of crude 3D coordinates (for further optimization with Gaussian03) from structures presently in a ChemDraw document. I am assuming these are primarily organic Sam Adams here created Bustr3D - which used a fragment-based approach derived from the NCI dataset. BUSTR is being rewritten to allow for easier distribution and maintenance. Nick Day has a library of many thousand fragments from the crystallographic literature which we are soon going to release. Do you know if there has been any progress made in this area? Is there a project I have yet to run across that I could work on to suit my needs? We would be delighted if you were able to give some help in this area. It might be an idea to see the sorts of molecules you have. Our approach is particularly geared to ring nuclei joined by short linkers - it is not a conformational analysis system. Best P. Thank you, Dan Willenbring Tantillo Group University of California, Davis Department of Chemistry One Shields Ave Davis, CA 95616 [EMAIL PROTECTED] 530 304 0971 Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, I, Mudd, stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Relocation of mailing list?
As the owner of the domain blueobelisk.org and current host of the BO sites, I agree with all that has been said. The most important thing: We need a stable location. My choice would be SourceForge and I've taken the freedom to register the project *blueobelisk* at SourceForge. SF allows us to assign as many admins, developers, etc. as we like. Everyone has access and the stability is excellent - certainly better than any of our local sites. Provided that the project gets approved, we can start moving things over, if everyone agrees. Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, I, Mudd, stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Relocation of mailing list?
Daniel Leidert wrote: Am Dienstag, den 08.05.2007, 13:52 +0200 schrieb Christoph Steinbeck: Egon already registered bodr.sourceforge.net. http://sourceforge.net/projects/bodr Sure, but this has a different and more limited scope (dr) as the name implies. You should talk with Egon and decide, which project of both to use/remove :) Not necessary - we are in telepathic connection :-) Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, I, Mudd, stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Blue Obelisk SF project approved. Ready to start moving.
Our SF project blueobelisk.sf.net has been approved and we now have a SF-based platform. Let me know who wants to take responsibilities. I have added PeterMR and EgonW to the project as project admins, but clearly, we need more here. A minor question: Is [EMAIL PROTECTED] ok for our new mailing list. It needs to be [EMAIL PROTECTED] We can only choose the something part :-) I' going to submit a support request regarding the move of the archives. Hope that'll work, but since both systems are mailman based, it might. Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, I, Mudd, stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Status on SF.net move?
Geoff, I added you as an admin. I did not have time to do anything else. Cheers, Chris Geoffrey Hutchison wrote: Hi guys, I'd be happy to help with the SF.net migration (ghutchis) -- are we waiting for a mailing list archive migration? Thanks, -Geoff ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, I, Mudd, stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Move of mailing list to SourceForge
Dear all, I've created the mailing list blueobelisk-discuss on sourceforge and will file a support request to mass-add the members of the current list to the new one (SF does only allow to add one member at a time to prevent misuse of the platform for SPAM). Just in case: Please let me know if you do *not* want to be a member of the new list. Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, I, Mudd, stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] SourceForge and WikiSpaces
sorry for crossposting. SourceForge now provides a Wiki for every project. http://web.sourceforge.com/news_archive/2007/1820.php The cdk wiki would, for example, be at cdk.wiki.sourceforge.net. It's not Mediawiki, but maybe it is usable. If we can find tools for migrating things from Wiki type to another, maybe it is easier to use the build-in one for the new CDK wiki. Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, I, Mudd, stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] RE: Blue-obelisk wiki redesign and planet BO
I don't seem to have this information, but I contacted Wendy Warr to see if we can recover it. Very soon, the manuscript will be freely accessible anyway. Cheers, Chris Rajarshi Guha wrote: On Jun 19, 2007, at 1:54 AM, Egon Willighagen wrote: I also find it rather intriguing that the Blue Obelisk manifesto is published in a journal which only subscribers (aka da club) can access. The Blue Obelisk - Interoperability in Chemical Informatics, J. Chem. Inf. Model., 2006, 46, 991-998. http://dx.doi.org/10.1021/ci050400b Is there any way to liberate the content? Well, there would be no reason in targeting the readers who already are into ODOSOS :) Seriously, we should have a link that allows 50 free downloads, and unlimited downloads after a year or so (as reprints). I guess Rajarshi knows those details. Actually I think Christoph will have those details (he was the corresponding author) -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Lecturer in Chemoinformatics Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax: (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, I, Mudd, stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
