I've run into a problem with an SD file generated by OB with atomic aliases. This file could not be opened by CambridgeSoft ChemBioDraw, or displayed correctly by ChemAxxon MarvinSketch. CamridgeSoft support tells me the atom numbers should be right-justified, where they are left-justified in OB output. Akos Papp from ChemAxxon says that there is not enough white space between "A" and the atom number. Here is an example of OB output and what Akos corrected: OB output -
A 8 R5 A 10 R4 A 11 R3 A 14 R2 A 16 R1 Corrected - A 8 R5 A 10 R4 A 11 R3 A 14 R2 A 16 R1 the corrected file can be opened by ChemDraw, MarvinSketch, as well as Symyx Draw and CACTVS csbr. Could we correct the output of atomic aliases in the next OB release? Igor On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote: > On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote: > > >> So far I see only SetAtomicNum to specify atom type, but nothing to set > >> the atomic label to something like "R1". > > > > You can use AliasData for this. > > See src/formats/mdlformat.cpp for an exact example. > > Hope that helps, > -Geoff ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
