Hi
Le 8 mai 2013 à 16:41, Patrick Fuller a écrit :
> You're right about this unit-cell-filling approach being different than
> OBUnitCell.FillUnitCell. This one reads through the _symmetry_pos_as_xyz
> lines and evals them, whereas OBUnitCell reads the unit cell dimensions and
> fills in voids.
They are not really different, the command-line option "--fillUC
strict" should give the same result as FillUnitCell(), they are just separated
in the code.
> Thanks for your time! I think I'm going to roll out my own code to fix this
> for now, but I would still be interested to see if this is an open babel bug,
> or just something I'm doing wrong.
Nothing wrong on your part, though normally calling ConnectTheDots()
and PerceiveBondOrder() should be the way to go, but the code is not optimized
enough for your number of atoms.
I have made changes to FillUnitCell (both portions of code), which can
be tested from my open babel fork at :
git://github.com/vincefn/openbabel.git
Changes @:
https://github.com/vincefn/openbabel/commit/358f207e9fe8190c6c56cf6ae1ad294ac6541ec1
In this version the symmetry operations are also applied to existing
bonds, checking that the bond lengths are unchanged. It will not create bonds
which are not symmetrical from existing bonds - so it is not as thorough as
ConnectTheDots(). It should be adequate for structures where all bonds are
described in the asymmetric unit cell.
Could you give it a try ? If it works, I'll make a pull request so that
it is included in the may open babel repository.
Vincent
--
Vincent Favre-Nicolin http://inac.cea.fr
CEA/Grenoble Institut Nanosciences & Cryogénie
Laboratoire SP2M/Nano-structures et Rayonnement Synchrotron
17, rue des Martyrs
38054 Grenoble Cedex 9 - France
Université Joseph Fourier http://www.ujf-grenoble.fr
tél: (+33) 4 38 78 95 40 fax: (+33) 4 38 78 51 38
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