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
Description: Binary data
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