Re: [Blueobelisk-discuss] GNU-Darwin: Molecules and Molecule of the Day, [EMAIL PROTECTED] .org
On Aug 22, 2008, at 4:43 PM, [EMAIL PROTECTED] wrote: It is my understanding that Babel is FOSS. If this is incorrect, please be sure to let me know. No, it is not. The original Babel (which you used) does not have any sort of open source license. It's free to distribute, but was blocked from Debian because of the license. This is separate from Open Babel, which is true GPL. (It's also better.) http://openbabel.org/ beautifully. In order to address this problem of poor geometry, we plan to provide high quality minimized structures based on the pdb files that we generate. You may find Open Babel 2.2 interesting, since it offers conformer searching and molecular mechanics. For drug-like molecules (i.e., no exotic elements), you could easily take the tools/obconformer code and run it over your PDB files. This will run MMFF94 conformer searching and geometry optimization. If you're likely to encounter more elements, you will probably want to try changing the force field to UFF. You may also want to consider working with Rajarshi and Indiana about their Pub3D database: http://www.chembiogrid.org/products/index.html Cheers, -Geoff - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [Blueobelisk-discuss] GNU-Darwin: Molecules and Molecule of the Day, [EMAIL PROTECTED] .org
There is no indication in the babel-1.6 source tree that I could find to indicate that it is not FOSS. It looks like openbabel-2.1.1 is in the package tree, and it would be worth checking out I take it. In fact, thank you for the excellent suggestions! Regards, On 25 Aug, Geoffrey Hutchison wrote: On Aug 22, 2008, at 4:43 PM, [EMAIL PROTECTED] wrote: It is my understanding that Babel is FOSS. If this is incorrect, please be sure to let me know. No, it is not. The original Babel (which you used) does not have any sort of open source license. It's free to distribute, but was blocked from Debian because of the license. This is separate from Open Babel, which is true GPL. (It's also better.) http://openbabel.org/ beautifully. In order to address this problem of poor geometry, we plan to provide high quality minimized structures based on the pdb files that we generate. You may find Open Babel 2.2 interesting, since it offers conformer searching and molecular mechanics. For drug-like molecules (i.e., no exotic elements), you could easily take the tools/obconformer code and run it over your PDB files. This will run MMFF94 conformer searching and geometry optimization. If you're likely to encounter more elements, you will probably want to try changing the force field to UFF. You may also want to consider working with Rajarshi and Indiana about their Pub3D database: http://www.chembiogrid.org/products/index.html Cheers, -Geoff -- Michael L. Love Ph.D Department of Biophysics and Biophysical Chemistry School of Medicine Johns Hopkins University 725 N. Wolfe Street Room 608B WBSB Baltimore MD 21205-2185 Interoffice Mail: 608B WBSB, SoM office: 410-614-2267 lab:410-614-3179 fax:410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ Visit proclus realm! http://proclus.tripod.com/ -BEGIN GEEK CODE BLOCK- Version: 3.1 GMU/S d+@ s: a+ C UBULI$ P+ L+++() E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e h--- r+++ y --END GEEK CODE BLOCK-- pgpW7zYya217s.pgp Description: PGP signature - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [Blueobelisk-discuss] GNU-Darwin: Molecules and Molecule of the Day, [EMAIL PROTECTED] .org
On Aug 25, 2008, at 3:56 PM, [EMAIL PROTECTED] wrote: There is no indication in the babel-1.6 source tree that I could find to indicate that it is not FOSS. If you take a look at any source file: This file is part of the Babel Program Copyright (C) 1992-96 W. Patrick Walters and Matthew T. Stahl All Rights Reserved To me, that pretty much rules out open source. It looks like openbabel-2.1.1 is in the package tree, and it would be worth checking out I take it. In I'd certainly suggest Open Babel 2.2.0. Trust me, it has a lot of fixes over 2.1.1. :-) Cheers, -Geoff - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [Blueobelisk-discuss] GNU-Darwin: Molecules and Molecule of the Day, [EMAIL PROTECTED] .org
On 25 Aug, Geoffrey Hutchison wrote: On Aug 25, 2008, at 3:56 PM, [EMAIL PROTECTED] wrote: There is no indication in the babel-1.6 source tree that I could find to indicate that it is not FOSS. If you take a look at any source file: This file is part of the Babel Program Copyright (C) 1992-96 W. Patrick Walters and Matthew T. Stahl All Rights Reserved This common perception about the rights reserved clause is mistaken, and many free software sources have such a clause. They nonetheless satisfy every definition of software freedom, unless the copyright holder has stipulated some restriction, on distribution for example, or moved to quell the inclusion of the code in other programs. It is clear to me from the readme file that the authors intended to encourage downloading and redistribution, etc. To me, that pretty much rules out open source. It looks like openbabel-2.1.1 is in the package tree, and it would be worth checking out I take it. In I'd certainly suggest Open Babel 2.2.0. Trust me, it has a lot of fixes over 2.1.1. :-) Thanks again! Regards, Michael L. Love Cheers, -Geoff -- Michael L. Love Ph.D Department of Biophysics and Biophysical Chemistry School of Medicine Johns Hopkins University 725 N. Wolfe Street Room 608B WBSB Baltimore MD 21205-2185 Interoffice Mail: 608B WBSB, SoM office: 410-614-2267 lab:410-614-3179 fax:410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ Visit proclus realm! http://proclus.tripod.com/ -BEGIN GEEK CODE BLOCK- Version: 3.1 GMU/S d+@ s: a+ C UBULI$ P+ L+++() E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e h--- r+++ y --END GEEK CODE BLOCK-- pgpstagntdpWF.pgp Description: PGP signature - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
