Hello, I would like to share another example that illustrates that OB does not seem to take charges into account when assigning bonds. Processing azete (neutral) using a Gaussian output file with OB, I obtain the following charged azete analog. [cid:37A33AC3-1985-4A7C-8CD0-AF16300D318D] Is there any part in the code that should take care of charges when assigning bonds?
With kind regards, Madeleine On 28 May 2021, at 11:41, Marie-Madeleine Walz <marie-madeleine.w...@icm.uu.se<mailto:marie-madeleine.w...@icm.uu.se>> wrote: Hello, I’m working on processing Gaussian output files (g09) with OB to set bond orders. I noticed that the compound's charge information does not seem to be taken into account when setting bond orders. For example, I obtain for neutral compounds structures that are charged, e.g. carbon atoms with only three single bonds, or nitrogens with only two bonds. One of the most obvious examples is sulfite (SO_3^(2-)) vs. sulfur trioxide (SO_3). Both have their bond orders coded in bondtyp.txt. # Sulfite [#16D3]([#8D1])([#8D1-])([#8D1-]) 0 1 2 0 2 1 0 3 1 # Sulfur trioxide [#16D3]([#8D1])([#8D1])([#8D1]) 0 1 2 0 2 2 0 3 2 However, OB does not recognise sulfite as charged, and instead it assigns three double bonds (i.e. it uses the sulfur trioxide definition). If I remove the charge information from the sulfite SMARTS structure, it assigns the correct bond order. However, obviously, sulfur trioxide is also assigned this bond order as now the SMARTS structures are identical. # Sulfite [#16D3]([#8D1])([#8D1])([#8D1]) 0 1 2 0 2 1 0 3 1 Any ideas on how to solve this issue are highly appreciated. With kind regards, Madeleine När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
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