Hi all, I agree about the impractical task of fixing the task in more than a handful of files. Besides, there's an intrinsic problem with fully supported file formats that do not have such information.
@David Koes: A week ago I posted about this issue: if you try reading a perfectly valid XYZ file (which has no charges) of ammonium with this command, you end up with a nitrogen with 5 bonds: obabel ammonium.xyz -ph 7 -O ammonium_xyz.mol2 @David van der Spoel: one thing I've noticed is that charged systems get properly recognized if you perform an intermediate conversion before manipulating the molecule. For the above issue, for example, it generates the proper protonated nitrogen:obabel ammonium.xyz -O ammonium_xyz_step1.mol2
obabel ammonium_xyz_step1.mol2 -ph 7 -O ammonium_xyz_step2.mol2 I've tried to figure out where the formal charge perception happens, but without success. Possibly doing so before the bond perception might help fixing your problem without having to extend the bondtyp.txt file? (but definitely not if the SMARTS pattern is missing). S On 5/13/21 12:52 PM, Ghahremanpour, Mohammad wrote:
Hi David, Thanks for your reply. It is practical to manually specify the formal charge of the atoms in the input file for a few compounds, the problem arises when you work with many compounds in different file formats. In this case, it would be good to have a backup plan. It seems that if the bond order of bonds and the formal charge of atoms are specified correctly, Kekulization works fine in most cases, if I am not mistaken. It would definitely help to see what other people suggest before changing the source code or the format of data files. Any suggestion is highly appreciated. Cheers, MohammadOn May 13, 2021, at 3:33 PM, David Koes <dk...@pitt.edu> wrote: Hi Mohammad, bondtyper.txt does not have any ability to set formal charges. If you need to do something more sophisticated than matching with SMARTS to set bond orders you need to modify the C++ code. Whether what you are proposing is the right thing to do, I leave to others to decide. I would typically assume that the formal charge should be specified in the input file. Also, I'm not sure bondtyping is the right place for Kekulization fixes. David Koes Associate Professor Computational & Systems Biology University of Pittsburgh On 5/13/21 10:50 AM, Ghahremanpour, Mohammad wrote:Hi David, In order to make kekulization work on imidazolium rings, I hard coded SMARTS in bondtyper.cpp, where I explicitly set the formal charge of one of the nitrogens to 1 and also set the bond order to 2 for two of the bonds in the ring. Doing this, kekulization works fine. As pointed out by you, the SMARTS for bond typing should be defined in bondtyp.txt data file not hardcoded in the source file. I did it but kelulizataion fails again, as the result of which the imidazolium ring is considered as AL instead of AR. I think the problem is the formal charge which is set to 0 for all atoms by default. While, for rings like imidazolium, the formal charge of the nitrogen with four bonds is 1. In bondtyper.cpp, there are other examples were the formal charges are set explicitly, oxido-n+ (e.g., pyridine-N-oxide). I was wondering if there is some data file to tabulate formal charge for specific cases like this. I checked atomtyp.txt, not formal charge is stored there. Thanks, Mohammad_______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
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ammonium.xyz
Description: Xmol XYZ data
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