Dear Alan, While I don’t quite understand the purpose of converting molecules on an Android phone, of course you can use Open Babel as you wish.
A few concerns, however: 1. You mention Open Babel 2.3.1, which is at this point ancient. 2. I would not indicate the SourceForge page as it is no longer used. 3. Since you are directly using GPLv2 code (Open Babel), you must include a link to the source code (your whole app). I don’t see the code for the GUI? You mention a potential issue with multiple fragments, which doesn’t seem to be an issue with the current versions, e.g. obabel -:'CCC.C=O' -O test.xyz —gen3d See attached. Best, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchisonlab.org/ On Jul 25, 2023 at 1:58:18 PM, Alan Liška <alan.li...@jh-inst.cas.cz> wrote: > Dear OpenBabel developers, > > me and my friend Veronika Ruzickova focus at porting professional > open-source chemistry codes to Android. Already in the past, we > published the standalone OpenBabel app > (https://play.google.com/store/apps/details?id=cz.jh.openbabel). > Recently, we have published 3 new free apps: > PHREEQC plus > https://play.google.com/store/apps/details?id=cz.p > https://github.com/alanliska/PHREEQC-plus > DFTB+ > https://play.google.com/store/apps/details?id=cz.jh.dftb > https://github.com/alanliska/DFTB > XTB > https://play.google.com/store/apps/details?id=cz.jh.xtb > https://github.com/alanliska/XTB > where we utilized your OpenBabel binary for SMILES to XYZ translation. > Because we plan to upgrade also some other similar apps, it is highly > probable that we integrate OpenBabel there as well. > Inside of each app as well as in the individual package descriptions, we > cited your software as follows: > > * OPENBABEL > Ref.: N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G > R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), > 3, 33. DOI:10.1186/1758-2946-3-33 > The Open Babel Package, version 2.3.1 http://openbabel.org > (accessed Oct 2011) > Source code: http://openbabel.org/wiki/Main_Page, > https://github.com/openbabel/openbabel, > https://sourceforge.net/projects/openbabel/ > > Please let me know if you would like to enhance the reference to you, or > specify the citation in a more detailed way. > Thank you :-). > > My second question concerns the SMILES to structure conversion in case > of molecular complexes, i.e. entities which contain the dot '.' between > the individual parts. OpenBabel seems to place all the separated > molecules in the same cartesian origin which makes the conversion of > type > > obabel -ismi File-with-smiles.smi -oxyz --gen3D (where SMILES could be > anything like "CCC.C=O") > > useless, as the resulting XYZ file describes a bundle of atoms coming > from both overlapping structures, often collided together. Of course, > the desired separation distance is generally unambiguous. On the other > hand, I could imagine that there would be a function to define the > distance of both molecular centres manually e.g. in form of a switch. > Don´t you consider to implement something like that in the future > versions of OpenBabel? Thanks in advance for the answer. > > Sincerely, > > Alan > > -- > RNDr. Alan Liška, Ph.D. > Ústav fyzikální chemie J. Heyrovského AV ČR, v.v.i. / J. Heyrovský > Institute of Physical Chemistry of the CAS, v.v.i. > Dolejškova 3/2155, 18223 Praha 8 > Česká republika / Czech Republic > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
test.xyz.gz
Description: GNU Zip compressed data
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