On 03/03/2020 17:46, Noel O'Boyle wrote:
Well, I don't really agree. They could just add it to obabel in the
first place and get the feedback from the development version. The
problem is that people find it easier to add new executables, rather
than spending a bit of time figuring out how to add a plugin for
obabel.
I once worked somewhere where there was a very big chemoinformatics
executable
able to do many things; instead of having a nice library used by several
rather simple programs.
Trying to do any task using the big executable was a nightmare in terms
of
finding the long list of options and values that you had to pass to it.
The one big program/executable approach is against the Unix philosophy
of
having rather simple programs that can be combined easily.
For those interested in the Unix philosophy and its not so trivial many
implications,
there is an interesting book:
---
Raymond, E. S. (2003). The art of Unix programming. Addison-Wesley
Professional.
---
Regards,
F.
Regards,
- Noel
On Tue, 3 Mar 2020 at 07:52, Chris Swain <sw...@mac.com> wrote:
Hi,
It is clear that a number of the obtools have been incorporated into
obabel, however I’m not sure they are all suitable for every file
type.
It is perhaps better to think of obtools as way to develop new tools
that others can hopefully try out and provide feedback. Tools that
are regularly used and prove to be robust and useful could then be
rolled into obabel.
And no I don’t know of a process to do this.
Cheers,
Chris
On 2 Mar 2020, at 20:11, Noel O'Boyle <baoille...@gmail.com> wrote:
It's not a popular opinion, but I think we should have a single
robust executable. I've never used any of the others, and they are
mostly untested.
On Sat, 29 Feb 2020, 18:21 Chris Swain via OpenBabel-discuss,
<openbabel-discuss@lists.sourceforge.net> wrote:
Hi,
I’m working on an update to iBabel, and was hoping to clear out
the tools tab particularly as I’m not sure if some are now
supported with OpenBabel 3.0
Looking through the directory of openbabel tools that are installed
we have
obconformer equiv to obabel --conformer
obdistgen (generate rough 3D coordinates) now use obabel --gen3D
obenergy equiv to obabel --energy
obfit equiv to --obabel --align
obfitall not sure what this is?
obgen equiv to obabel --gen3D (fastest --ff MMFF94s)
obgrep equiv to obabel structure searching
obminimize equiv to obabel --minimize (--ff MMFF94s --steps 1000
--sd)
obmm apparently this is a this is a 'full featured' MM program but
may not be generally useful
obprobe (create electrostatic probe grid)
obprop (print standard molecular properties), would be more useful
if we could get individual properties, e.g. obabel —props
<options> (MW LogP TPSA HBA HBD RBC)
obrms (Calculate the heavy-atom RMSD between two chemically
identical structures) perhaps this should be an obabel option?
obrotamer (generate conformer/rotamer coordinates, not minimized)
better to use —conformer?
obrotate (batch-rotate dihedral angles matching SMARTS patterns)
obspectrophore (calculate spectrophore)
obsym (detect 3D point group symmetry, only cif files?) sounds like
it is to deprecated
obtautomer (enumerate tautomer SMILES and canonical tautomer SMILES)
obthermo (extract the thermochemistry for a molecule, what file
format is needed?)
Any insights very welcome,
Cheers,
Chris
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
