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
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