Le 6 mai 2013 à 18:12, Patrick Fuller a écrit :
>
> After mol.unitcell.FillUnitCell, can you try:
> mol.OBMol.ConnectTheDots()
> mol.OBMol.PerceiveBondOrders()
>
> I've tried this, but it's way too slow. I'm guessing ConnectTheDots is
> O(N^2), and N is big in crystal structures.
What N are you talking about - the time should be negligible even for
1000s of atoms, unless you are doing this in a loop ? Could you supply an
example /test case ?
> Is there a way to better control the unit cell? Say, returning a 2x2x2-cell
> structure or recentering the coordinates so the organic molecules don't get
> split up?
There are actually several FillUnitCell functions in open babel:
1) in https://github.com/openbabel/openbabel/blob/master/src/generic.cpp (line
578)
2) in https://github.com/openbabel/openbabel/blob/master/src/ops/fillUC.cpp
The latter (which is used from the command line) has two options,
'keepconnect' and 'strict' - the first option should keep the atoms connected.
Can you try it (I don't know if it can be used from python, from the command
line it would be --fillUC keepconnect ) ?
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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