From: <D.G...@gm...> - 2006-12-06 13:55:36
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Hello everybody, I'm currently working on a java project in which, after loading a pdb-file, I need to add Hydrogens to the molecules. Since Pymol has an implemented method for this problem, I'd be interested in the algorithm used, so I can reimplement it in java. Does anybody know if there is a publication, where I can find it? Another approach I am following is the usage of the CDK package, but I'm not really sure how to apply it to my problem and how good the method works. I'd be thankful for any help I can get ;). greetings, Danrik -- "Ein Herz für Kinder" - Ihre Spende hilft! Aktion: www.deutschlandsegelt.de Unser Dankeschön: Ihr Name auf dem Segel der 1. deutschen America's Cup-Yacht! |
From: Stuart Endo-S. <stu...@du...> - 2006-12-06 14:18:01
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You should take a look at the program Reduce from the Richardson lab at Duke, it adds protons and is written in C++. It will take a pdb and without requiring modification or formating add protons to it. Versions exist for Linux, Windows, MacOS X, Irix, and Sun-SPARC, and the source code is available as well. It can be used as a plug-in program, just call out to it with whatever options are required, then get back the protenated pdb. Information and references (including algorithms published in JMB) at http://kinemage.biochem.duke.edu/software/reduce.php Note: not a member of the Richardson lab, but a (program using) collaborator. S. Endo-Streeter On Wednesday 06 December 2006 08:55, D.G...@gm... wrote: > Hello everybody, > > I'm currently working on a java project in which, after loading a pdb-file, > I need to add Hydrogens to the molecules. Since Pymol has an implemented > method for this problem, I'd be interested in the algorithm used, so I can > reimplement it in java. Does anybody know if there is a publication, where > I can find it? Another approach I am following is the usage of the CDK > package, but I'm not really sure how to apply it to my problem and how good > the method works. I'd be thankful for any help I can get ;). > > greetings, Danrik -- ______________________________________ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 stu...@du... |
From: gilleain t. <gil...@gm...> - 2006-12-06 14:48:28
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Hi, I also would vote for using reduce, since it is very good. If you have to do it in pure java (ie: not calling reduce from java somehow) then cdk would also be a good choice. A quick scan through the api gives: org.openscience.cdk.tools.HydrogenAdder which "Provides methods for adding missing hydrogen atoms." - seems perfect :) gilleain torrance On 12/6/06, Stuart Endo-Streeter <stu...@du...> wrote: > You should take a look at the program Reduce from the Richardson lab at Duke, > it adds protons and is written in C++. It will take a pdb and without > requiring modification or formating add protons to it. Versions exist for > Linux, Windows, MacOS X, Irix, and Sun-SPARC, and the source code is > available as well. It can be used as a plug-in program, just call out to it > with whatever options are required, then get back the protenated pdb. > > Information and references (including algorithms published in JMB) at > > http://kinemage.biochem.duke.edu/software/reduce.php > > > Note: not a member of the Richardson lab, but a (program using) collaborator. > > > S. Endo-Streeter > > > On Wednesday 06 December 2006 08:55, D.G...@gm... wrote: > > Hello everybody, > > > > I'm currently working on a java project in which, after loading a pdb-file, > > I need to add Hydrogens to the molecules. Since Pymol has an implemented > > method for this problem, I'd be interested in the algorithm used, so I can > > reimplement it in java. Does anybody know if there is a publication, where > > I can find it? Another approach I am following is the usage of the CDK > > package, but I'm not really sure how to apply it to my problem and how good > > the method works. I'd be thankful for any help I can get ;). > > > > greetings, Danrik > > -- > > > > > > > > > ______________________________________ > Stuart T. Endo-Streeter > Structural Biology and Biophysics > Dept. Biochemistry > LSRC C266 > Duke University > 919-681-1668 > stu...@du... > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |