Le 10 mai 2013 à 22:20, Patrick Fuller a écrit :
> Bond inference isn't perfect (I think it's treating metal atoms covalently,
> where they should probably just be ignored here), but that's independent of
> this fix.
In the code the bonds are simply cloned - they should have the same
order and flags as the original ones. For a MOF the bond type will likely not
be guessed correctly.
> Also irrelevant to your commit, the bonds show that filling the unit cell
> results in duplicate atoms in the output. I'm guessing cleaning those will
> result in the same O(N^2) problem as bond inference did.
That is not normal - the algorithm checks for duplicate, so something
is wrong here. By assuming original atoms are really unique, the complexity is
not N^2, we just need to check all the symmetrical atoms from a given one are
not duplicated. I'll look into this.
> One thing to note, however, I keep getting this (nonfatal) error printing
>
> ==============================
> *** Open Babel Error in RegisterOptionParam
> The number of parameters needed by option "t" in The LPMD file format.
> differs from an earlier registration.
> ==============================
> *** Open Babel Error in SMARTSError
> SMARTS Error:
> [#6+:1](~N:2)(~N:3)*
> ^
>
> I don't think your commit touched SMARTS, but I don't get this error from
> master?
I have the same, and absolutely no idea where this comes from.
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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