On Fri, May 8, 2009 at 5:36 PM, Loren Lenzen <[email protected]> wrote:
> My fault, I did not mean ID tags. I was referring to the data fields that
> come after the structural information. For example:
>
>> <Vendor>
> Sigma
>
> I know I can get them by looking for the regex, but I assumed that the
> MDLReaders would already have a method to do that.
Ah, ic.
Well, those property fields are part of the MDL SD file format, not of
the MDL molfile format.
So, you should read a IChemFile, and not a IMolecule (1.2.0 introduced
the SDFWriter, and I think I will have to introduce a SDFReader too...
would make things easier to understand...)
Here is a relevent unit test:
String filename = "data/mdl/emptyStructure.sdf";
logger.info("Testing: " + filename);
InputStream ins =
this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins);
ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
Assert.assertNotNull(chemFile);
List<IAtomContainer> containersList =
ChemFileManipulator.getAllAtomContainers(chemFile);
Assert.assertEquals(1, containersList.size());
IAtomContainer container = containersList.get(0);
Assert.assertNotNull(container);
Assert.assertEquals(0, container.getAtomCount());
Assert.assertEquals(0, container.getBondCount());
Map<Object,Object> props = container.getProperties();
Set<Object> keys = props.keySet();
Assert.assertTrue(keys.contains("SubstanceType"));
Assert.assertTrue(keys.contains("TD50 Rat"));
Assert.assertTrue(keys.contains("ChemCount"));
Where the SD file property sections looks like:
> <SubstanceType>
mixture or unknown
> <ChemNote>
unknown composition
> <ChemCount>
1
> <StudyType>
carcinogenicity
> <Species>
rat
> <Endpoint>
TD50, Tumor Target Sites
> <TD50 Rat>
NP
I hope this helps.
Egon
--
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
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