From: Egon W. <eg...@sc...> - 2002-09-11 19:52:59
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Hi all, I've had a few hours to do further work on the IUPAC name generator... The design seems to be working: I've (partly) implemented two rules in Section A (1.1 and 2.1), and the current version can name these compounds in two languages (English and Dutch): methane, ethane, up to, decane (rule 1.1) and isobutane (rule 2.1) Before I will do a first release I want to implement naming of Fragment class types, aka radicals... like ethyl, etc... The output of the program is the IUPAC name (yes, of course ;), but also the applied rules... the latter is of much interest of you need to know which were applied (and in which order)... future version will even be able to map fragments of the named molecule with parts of the name, and the applicable rule... Egon |
From: Egon W. <eg...@sc...> - 2002-09-16 05:08:00
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On Wednesday 11 September 2002 22:00, Egon Willighagen wrote: > I've had a few hours to do further work on the IUPAC name generator... > The design seems to be working: > > I've (partly) implemented two rules in Section A (1.1 and 2.1), and the > current version can name these compounds in two languages (English > and Dutch): > > methane, ethane, up to, decane (rule 1.1) > > and > > isobutane (rule 2.1) Added isopentane and isohexane. > Before I will do a first release I want to implement naming of Fragment > class types, aka radicals... like ethyl, etc... Done. It will now properly name methyl - decyl... It acutually already is a recursive algorithm... that is, it can now handle structures that need to be split in smaller parts to be named. To be specific, it can name branched alkanes now, but only the fragments, the output is not correctly ordered yet ;) Neither does it add localization numbers defining how the fragments are connected yet... > The output of the program is the IUPAC name (yes, of course ;), but also > the applied rules... the latter is of much interest of you need to know > which were applied (and in which order)... future version will even be able > to map fragments of the named molecule with parts of the name, and the > applicable rule... I've been rewriting the data structures for the IUPAC name result. This is almost done. The software *will* include a mechanism that shows you which part of the molecule resulted in which IUPAC name part (which I am very happy about) But, I have two questions: Can CDK: 1. ... saturate the molecule with hydrogen? How? (And remove them?) 2. ... draw 2D images with colored atoms? The latter I want to use to color each IUPAC name part with a different color. (Preferably, I want to highlight only one part, which you could select with the mouse... but I must start somewhere ;) Egon |
From: Christoph S. <ste...@ic...> - 2002-09-17 15:02:21
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Egon Willighagen wrote: > Can CDK: > 1. ... saturate the molecule with hydrogen? How? (And remove them?) > 2. ... draw 2D images with colored atoms? I'm stunned by this progress :-) To answer your questions: 1. I do not remeber any method for adding hydrogens to saturate a molecule. There is, however, as method "saturate" in org.openscience.cdk.tools.SaturationChecker, which adjusts bond orders in order to saturate a molecule. This can be used in case on does not have bond orders but only connectivities (pdb file, or output of some structure generators) This method should be copied to saturateWithHydrogens() and adjusted to add Hydrogens instead of increasing bondorders. 2. Atoms can be colored by using the ColorHashtable in the Renderer2DModel. This allows you to assign arbitrary colors to arbitrary atoms by throwing the atom object to be colored into the hashtable as a key together with the java.awt.Color to be used for coloring this atom. Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 Jena, Germany Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |