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 ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss