Dear Geoff,
in line with my previous letter (please see below - mailer-daemon
returned it to me several days after sending, so I don´t know if you
received it), I updated the OpenBABEL binaries in our apps. The most
recent versions should work better.
The installers and full sources are available in the corresponding
Google Play links and in Github repositories.
...
-------- Originalnachricht --------
Betreff: Re: [Open Babel] OpenBabel SMILES to XYZ conversion
Datum: 2023-08-11 16:43
Von: Alan Liška <alan.li...@jh-inst.cas.cz>
An: Geoffrey Hutchison <geoff.hutchi...@gmail.com>
Kopie: openbabel-disc...@lists.sf.net
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/
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