Hi Zheng, I get the following atom types when generation mol2. Note the actual file can’t be read… but not sure why as I don’t use mol2.
> @<TRIPOS>MOLECULE > CDKMolecule > 9 9 > SMALL > NO CHARGES > @<TRIPOS>ATOM > 1 Cl1 0.002 -0.004 0.002 Cl > 2 C2 -0.022 1.732 0.012 C.ar > 3 C3 1.167 2.44 0.004 C.ar > 4 C4 1.149 3.822 0.012 C.ar > 5 C5 -0.057 4.498 0.027 C.ar > 6 C6 -1.248 3.79 0.035 C.ar > 7 C7 -1.229 2.407 0.021 C.ar > 8 Cl8 -0.08 6.234 0.038 Cl > 9 Cl9 -2.762 4.638 0.055 Cl > @<TRIPOS>BOND > 1 1 2 1 > 2 2 3 ar > 3 2 7 ar > 4 3 4 ar > 5 4 5 ar > 6 5 6 ar > 7 5 8 1 > 8 6 7 ar On Aug 12, 2014, at 9:27 PM, Zheng Shi <zs...@ualberta.ca> wrote: > For this kind of data, it represents benzene ring as single/double bond > pairs. So when I want to perceive its aromaticity, the bond order is either > single or double, the SYBYL atom type for the carbon atoms on the ring are > "C.2", not "C.ar", and the aromaticity flag is false. So I just wonder how to > use aromaticity class to perceive this property. Thanks, > > > On Tue, Aug 12, 2014 at 2:18 PM, Zheng Shi <zs...@ualberta.ca> wrote: > Here it is. > > > On Tue, Aug 12, 2014 at 2:16 PM, John May <john...@ebi.ac.uk> wrote: > Do you for .mol file rather than a screen shot? > > Cheers, > J > > On Aug 12, 2014, at 9:13 PM, Zheng Shi <zs...@ualberta.ca> wrote: > > > Hi, John, > > > > I just want to perceive aromaticity for the molecules in a data. The data > > represents the benzene ring as sing/double bond pairs like below. So I just > > wonder how I can perceive the aromaticity in such representation. I use the > > aromaticity class like below, and keeps getting the exceptions. I don't > > know why. Then how to use the aromaticity class to get the aromaticity > > property for data like this. Thanks. > > <example data.JPG><exception error.JPG> > > >
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