Le 3 mai 2013 à 21:26, Patrick Fuller a écrit :
> I think open babel wants me to do something like
> `mol.unitcell.FillUnitCell(mol.OBMol)`, where `mol` is an instance of
> `pybel.Molecule`. Doing so results in
>
> I think that the unit-cell-filling operation is skipping bonds entirely, and
> these bonds are residual from the pre-filled structure.
>
> Is this a legitimate bug, or am I just using the functions improperly?
Yes it looks like a bug, FillUnitCell skips the bonds altogether - in
this case it looks like the original atomic positions are at least in part
outside the UC, so they are moved around when FillUnitCell is called, so that
even old bonds can end up wrong (because 1 atom of a bond has been wrapped and
not the other..).
FillUnitCell should either discard the bonds (keep only atoms), or redo
ConnectTheDots & PerceiveBondOrder(), or do its best to generate symmetric
bonds (but it is tricky as it depends on whether both atoms of any given bond
are wrapped or not).
After mol.unitcell.FillUnitCell, can you try:
mol.OBMol.ConnectTheDots()
mol.OBMol.PerceiveBondOrders()
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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