openmolecules.org Forum - RDF feed
https://openmolecules.org/forum/index.php
Why is clustering limited up to 10000 molecules?
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=75&th=29#msg_75
Nastasia2015-07-22T14:37:15-00:00Re: Why is clustering limited up to 10000 molecules?
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=78&th=29#msg_78
Kind regards, Thomas]]>thomas2015-07-23T19:40:59-00:00Re: Why is clustering limited up to 10000 molecules?
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=154&th=29#msg_154
I understand that it could consume huge amount of time and ram.
Best,
Nikita]]>avkitex2016-02-28T18:03:50-00:00Re: Why is clustering limited up to 10000 molecules?
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=157&th=29#msg_157
Regards, Thomas]]>thomas2016-03-03T20:49:57-00:00Re: Why is clustering limited up to 10000 molecules?
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=158&th=29#msg_158
I have servers with about 30Gb ram and a lot of time. And I woult like to try doing it.
Can you tell me how to patch and recompile jar file? And what is the best way to run it in console mode? (I have molecules in sdf or mol2 format. I would like to have a clusterisation tree in newick or compatable format.)
Looking forward to hear from you.
Best,
Nikita ]]>avkitex2016-03-03T20:54:28-00:00Re: Why is clustering limited up to 10000 molecules?
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=159&th=29#msg_159
if you use Linux or OSX, I will send you a customized datawarrior.jar file without limitation. But don't complain, if the clustering process seems to take forever...
If your server runs Linux, you can install the datawarrior directory on the server and login from remote via 'ssh -X' and then launch datawarrior the usual way. Then you all DataWarrior windows open on the client machine while it executes on the server and uses server RAM and server cores.
Best wishes, Thomas]]>thomas2016-03-04T21:24:48-00:00Re: Why is clustering limited up to 10000 molecules?
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=252&th=29#msg_252
it is indeed true that to be able to run the cluster function on a dataset larger than 10,000 would be really great considering all the new data available today... This can be done externally but Warrior is so convenient that in a future release, it really would be nice...
Sincerely]]>dataviz2017-03-22T10:34:15-00:00Re: Why is clustering limited up to 10000 molecules?
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=255&th=29#msg_255
I have lifted the limit from 10.000 to 100.000 structures, but display a warning above 20.000 compounds. Nevertheless, clustering of significantly more structures than 20.000 will require a Linux or Macintosh computer, where it is easy to increase the memory maximum that DataWarrior is allowed to use. The change will be available with the next update.
Regards, Thomas]]>thomas2017-03-30T18:35:00-00:00Re: Why is clustering limited up to 10000 molecules?
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=437&th=29#msg_437
Many thanks!
Mike]]>E3ubiquitinligase2019-01-10T20:46:46-00:00Re: Why is clustering limited up to 10000 molecules?
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=438&th=29#msg_438
http://www.openmolecules.org/help/installation.html#Installa tion
Thomas]]>thomas2019-01-10T23:00:48-00:00Re: Why is clustering limited up to 10000 molecules?
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=439&th=29#msg_439
Mike]]>E3ubiquitinligase2019-01-11T06:21:38-00:00