Hi Zheng,
That second molecule looks 2D rather than just the off change of having perfect
planar conformation. You need to add/generate 3D coordinates for the molecule,
the CDK can not reliable do this.
Thanks,
J
On Dec 21, 2014, at 5:25 PM, Zheng Shi <zs...@ualberta.ca> wrote:
> It's a standard sdf file. The molecules have 3D coordinates indeed. But
> some's z coordinates are all zero. So I just wonder how I can calculate TPSA
> for this kind of molecule. Below is an example file. One molecule is OK, but
> for the other will get a NullPointerException. You can look at it. I hope
> someone could help me out. Thanks.
>
> On Sun, Dec 21, 2014 at 3:33 AM, Egon Willighagen
> <egon.willigha...@gmail.com> wrote:
> On Fri, Dec 19, 2014 at 11:42 PM, Zheng Shi <zs...@ualberta.ca> wrote:
> > When I look at these molecules which report exception, I find their z
> > coordinates are all 0. I just wonder whether this does effect on
> > calculating TPSA. If so, how can I calculate TPSA for these? Thanks.
>
> Is your input perhaps from a MDL molfile? Those files do not
> explicitly say if the coordinates are 2D or 3D and the heuristics have
> the side effect that planar molecules in the XY plane are
> misinterpreted as 2D.
>
> However, you can force them to be read as 3D with this:
>
> InputStream ins =
> this.getClass().getClassLoader().getResourceAsStream(filename);
> MDLV2000Reader reader = new MDLV2000Reader(ins);
> Properties prop = new Properties();
> prop.setProperty("ForceReadAs3DCoordinates", "true");
> PropertiesListener listener = new PropertiesListener(prop);
> reader.addChemObjectIOListener(listener);
> reader.customizeJob();
>
> IAtomContainer mol = reader.read(new AtomContainer());
>
> Does that help?
>
> Egon
>
>
> --
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: 0000-0001-7542-0286
> ImpactStory: https://impactstory.org/EgonWillighagen
>
>
> <example.sdf>------------------------------------------------------------------------------
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