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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