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
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