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 <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 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 <mailto:andrew.f...@nih.gov> | Lei Shi Lab , > NIH/NIDA/IRP > (443)740-2849 | > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > <mailto:OpenBabel-discuss@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > <https://lists.sourceforge.net/lists/listinfo/openbabel-discuss>
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