Dear Geoff,
thank you for the answer. I´m happy that the most recent versions of
Open Babel can handle structures consisting of multiple fragments quite
well. However, I found out that in the case of planar fragments like
cyclopentadienyl rings in ferrocene
obabel -:'[CH-]1C=CC=C1.[CH-]1C=CC=C1.[Fe+2]' -O test.xyz --gen3d
or benzene molecules
obabel -:'c1ccccc1.c1ccccc1' -O test.xyz --gen3d
the resulting XYZ structure still contains both moieties located in the
same positions (overlapping).
Concerning our Android applications, we appreciate Open Babel a lot, as
it makes the first (input) part of the quantum chemical calculations
fast and comfortable. In most cases, the user can define the desired
structure (to be calculated) easily by the IUPAC name, which is
converted by OPSIN to SMILES, and subsequentely by Open Babel to XYZ in
background. Thus, generating an input file takes few taps on the
phone/tablet touch screen instead of complicated drawing atom by atom.
Our applications enable performing typically semiempirical calculations
natively in the mobile device (offline) which is nowadays possible due
to the sufficient computational power of a typical hardware employed in
almost any smartphone.
As for your question, our source code repositories already contain the
GUI inside. Generally, the Android app sources are distributed as whole
Android Studio project which can be easily compiled to create the
installer identical to that one which can be accessed in the Google Play
Store. You can find the most relevant parts as follows:
-Java source files (individual functions and their connectivity)
/app/src/main/java/name/of/the/app/
-graphical and resource files (defining the graphical layout and styles
employed in each app screen - that is maybe the answer for your request)
/app/src/main/res/layout/ and /app/src/main/res/drawable/
-other files needed in the application (as the data files for Open
Babel)
/app/src/main/assets/
-precompiled binary stuff (binaries - executables and libraries which
run on the UNIX core of Android = in the case of Open Babel it is the
obabel binary)
/app/src/main/jniLibs/[architecture= arm, aarch64, x86, x86_64 - the
installer picks the one which is matching the device processor and OS
architecture automatically]; executables in this folder have to be saved
under the lib-XXX-.so names although they are not libraries - like
obabel is renamed here to libobabel.so although it is a static
executable (due to Google Android policy)
I also updated the info on Open Babel sources inside of the app - the
sourceforge entry was removed.
I´m looking forward to hearing from you.
Best,
Alan
Am 2023-08-03 20:55, schrieb Geoffrey Hutchison:
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:
* You mention Open Babel 2.3.1, which is at this point ancient.
* I would not indicate the SourceForge page as it is no longer used.
* 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 [1] —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
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