Absolutely could be a regression but having done a fair bit of work on ChemDraw processing (old poster <https://www.nextmovesoftware.com/posters/May_SketchySketches_Sheffield_201607.pdf>) did you confirm it with the same file in both cases?
ChemDraw actually stores the expansions (fragments) in the file, if you right click and "Interpret chemically" the expansion will not be save and you'll get a '*' unless the reader does extra processing. On Wed, 28 Aug 2019 at 23:08, Geoffrey Hutchison <geoff.hutchi...@gmail.com> wrote: > Can you please file bug reports - ideally with an example file? > https://github.com/openbabel/openbabel/issues > > Noel overhauled the alias processing as part of the 3.0 effort, and I > suspect that's the problem with #1. I'm not sure about the name question.. > but please file that as a separate issue for tracking. > > As far as processing the largest fragment, you want the '-r' command-line > option: > https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html > "-r Remove all but the largest contiguous fragment (strip salts)" > > Hope that helps, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geo...@pitt.edu <geo...@pitt.edu> > twitter: @ghutchis > web: https://hutchison.chem.pitt.edu/ > > On Aug 23, 2019, at 1:03 PM, Fant, Andrew (NIH/NIDA) [E] via > OpenBabel-discuss <openbabel-discuss@lists.sourceforge.net> wrote: > > Hello, > I’m using openbabel to convert a bunch of old Chemdraw files into > SMILES strings for further processing, and I came across a pair of what > appear to be regressions in the chemdraw structure handling that I was > curious if anyone else had run into. > > Many of the files have fairly standard chemical abbreviations in them, > such as SO3 for a sulfate or N3 for an azide or COOCH2CH3 for an ethyl > ester. When I converted the files to SMILES using 2.3.2, these > abbreviations were mostly brought along and correctly parsed (the charges > on the azide were absurd, but easily set right with sed). But now, when I > try the same conversions in the latest release from github (2.4.90, it > appears), on these molecules, I get an asterisk and an error message that > the alias was not chemically interpreted. It seems like this is a loss of > functionality from the earlier version. Is there a way to get the earlier > behavior back, or have I stumbled over a dark corner where I was not meant > to go? > > Also, the chemdraw files are not named with the name of the molecule, > but rather with an obscure numbering system. Nevertheless, the name of the > molecule being extracted is present in the file, and it gets output with > the SMILES string in 2.3.2. Once again, this functionality seems to be > lost in 2.4.90. Is there an option to restore the behavior, or should I > just grin and keep using 2.3.2? > > Finally, as a last question, is there a good way to tell openbabel to only > process the largest molecule present? I have a lot of counterions that are > coming through that I would gladly ignore for this project. > > Thanks, > Andy > > -- > Andrew Fant | Systems Administrator > andrew.f...@nih.gov | Lei Shi Lab , NIH/NIDA/IRP > (443)740-2849 | > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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