Hi David, The following describes the "gen3d" operation in Open Babel.
The 3D structure generator builds linear components from scratch following geometrical rules based on the hybridisation of the atoms. (Single conformer) ring templates are used for ring systems. Stereochemistry (cis/trans and tetrahedral) is honoured where possible (it may not be possible in the case of tetrahedral stereochemistry involving a ring system, if the ring template for a particular stereochemistry does not exist; a warning will be issued in this case). The structure generation is followed by an energy minimisation using a MMFF94 forcefield and a weighted rotor search for an energy minimised conformer using the same forcefield. Please note that the current builder in Open Babel is not recommended as a substitute for programs like CORINA if a molecule contains a complex ring system. This is an inherent limitation of a template ring system. Is this sufficient information? (We will add some more text on the builder to our documentation.) - Noel On 5 October 2010 13:20, David Lagorce <david.lago...@univ-paris-diderot.fr> wrote: > Dear Noel, > > ... 3D structure generation softwares... > > But I could not find any documentation about which kind of algorithm is > involved in the last version of OpenBabel. > Please, could you give me more informations about it ? > > Thanks for all > > Regards > > > David > > -- > > David Lagorce > > INSERM UMR-S 973 – Molécules Thérapeutiques In Silico > > Université Paris Diderot > > Bâtiment Lamarck > > 35, rue Hélène Brion > > 75013 PARIS > > 01 57 27 83 89 > > david.lago...@univ-paris-diderot.fr > > http://www.mti.univ-paris-diderot.fr ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
