Thanks, that's got all the properties.
I was wondering about automatic format recognition.
I found the FormatFactory and its guessFormat() methods, but this
doesn't seem to recognise files of smiles strings (even though the
SMILESReader can read the file), and it doesn't seem to recognise
gzipped sdf files, even though the javadocs suggest it should.
Is this the right way to do this?
Tim
On 07/01/2015 20:50, John May wrote:
> Hi Tim,
>
> You want MDLV2000Reader instead of MDLReader.
>
> J
>
> On Jan 6, 2015, at 6:27 PM, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
>
>> I'm just starting to use CDK, so may not be doing things right, but it
>> seems to me like the first property in a SD file is missing.
>> I have code like this:
>>
>> InputStream ins = new FileInputStream(filename);
>> MDLReader reader = new MDLReader(ins);
>> ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
>> List<IAtomContainer> containersList =
>> ChemFileManipulator.getAllAtomContainers(chemFile);
>> IMolecularDescriptor descriptor = new WienerNumbersDescriptor();
>> for (IAtomContainer mol : containersList) {
>> System.out.println(mol.getProperties());
>> }
>>
>> The SD file properties bit of my file looks like this:
>>
>> M END
>>> <mr_id>
>> 4358263
>>
>>> <SMI>
>> Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2
>>
>> $$$$
>>
>>
>> But what gets written out by CDK is this:
>>
>> {SMI=OC(=O)c1ccc(Nc2ncc3CN=C(c4c(F)cccc4F)c5cc(Cl)ccc5-c3n2)cc1}
>>
>> The first property (mr_id) is missing.
>> This happens with 2 different files.
>>
>> Tim
>>
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