Hi John,
You say that by using DescriptorEngine you first define which descriptors
you want. Do you then process them individually using their constructors or
the two lines (descriptors.process(container) and
container.getProperties()) calculate those descriptors automatically?
Please advice
Regards,
Anurag
On Thu, Jan 30, 2014 at 10:09 PM, John May <john...@ebi.ac.uk> wrote:
> Hi Anurag,
>
> I'm not sure what, CDKDesc.jar is - It's not currently release by us.
> Perhaps someone on list knows? The jar you need can be downloaded from
> here: https://sourceforge.net/projects/cdk/files/. Look for
> 'cdk-1.5.5.jar' or 'cdk-1.4.19.jar'.
>
> The CDK does divide descriptors as 1D, 2D etc but rather atomic, bond or
> molecular. It sounds like you're interested
> in molecular descriptors 'cdk-qsar' module. Fingerprints are not considered
> descriptors in the cdk (available in 'cdk-fingerprint' module) but should
> be easy to figure out. Here is the current list of molecular descriptors -
> https://github.com/cdk/cdk/blob/master/src/main/META-INF/services/org.openscience.cdk.qsar.IMolecularDescriptor
>
> I've attached an example (below) of using the DescriptorEngine in 1.5.-.
> We define which molecular qsar-descriptors we want and then process each
> entry. Results are stored on the properties of each molecule.
>
> If you just want the descriptors there are several user interfaces that
> will provide this functionality.
> - http://padel.nus.edu.sg/software/padeldescriptor/ (CDK 1.4.-) - also
> available in Knime
> - http://tech.knime.org/community/cdk (CDK 1.5.-)
> - https://github.com/johnmay/cdk/tree/master/src/main/org/openscience/cdk/
>
> Thanks,
> John
>
> String fname = "/Users/johnmay/Desktop/input.sdf";
>
> IChemObjectBuilder bldr =
> SilentChemObjectBuilder.getInstance();
> DescriptorEngine descriptors = new
> DescriptorEngine(Arrays.asList(XLogPDescriptor.class.getName(),
>
> ALOGPDescriptor.class.getName(),
>
> RuleOfFiveDescriptor.class.getName()),
> bldr);
>
>
> IteratingSDFReader sdf = new IteratingSDFReader(new
> FileReader(fname), bldr, true);
> while (sdf.hasNext()) {
> IAtomContainer container = sdf.next();
> descriptors.process(container);
>
> // atomic/bond properties are set on atoms and bonds
> for (Map.Entry<Object,Object> e :
> container.getProperties().entrySet()) {
> if (e.getKey() instanceof DescriptorSpecification) {
> System.out.print(((DescriptorSpecification)
> e.getKey()).getImplementationTitle() + ": ");
> System.out.println(((DescriptorValue)
> e.getValue()).getValue());
> }
> }
> }
> sdf.close();
>
> On 30 Jan 2014, at 16:06, Anurag Passi <anuragpassibioi...@gmail.com>
> wrote:
>
> Sorry to bother you again. Could you provide me with all the descriptors
> (hybrid,constitutional,topological,electronic and geometrical) present in
> the CDKDesc.jar?
>
>
> On Thu, Jan 30, 2014 at 9:26 PM, Anurag Passi <
> anuragpassibioi...@gmail.com> wrote:
>
>> Sorry, sent the message by mistake.
>>
>> I am looking for the primary 1D, 2D and 3D descriptor (eg: lipinski
>> descriptors, pharmacophore descriptors, topological descriptors and a
>> couple of good fingerprints like PubChem fingerprints, MACCS keys, or any
>> other.)
>>
>> Does that answer your question?
>>
>> I do not know if there are any more important and basic descriptors that
>> are usually used.
>>
>> I am writing one script as well but if you could provide me yours it can
>> help me do my work quickly.
>>
>> Regards,
>> Anurag
>>
>>
>> On Thu, Jan 30, 2014 at 9:22 PM, Anurag Passi <
>> anuragpassibioi...@gmail.com> wrote:
>>
>>> Hi John,
>>>
>>> I am looking for the primary 1d
>>> On 30 Jan 2014 20:42, "John May" <john...@ebi.ac.uk> wrote:
>>>
>>>> Hi Anurag,
>>>>
>>>> Sure - I can provide an example. Which version of CDK are you using?
>>>> Also what type of descriptors, atomic, bond or molecular?
>>>>
>>>> Thanks,
>>>> J
>>>>
>>>> On 30 Jan 2014, at 09:21, Anurag Passi <anuragpassibioi...@gmail.com>
>>>> wrote:
>>>>
>>>> > Hello,
>>>> >
>>>> > I have just started with writing Java program using CDK and I am
>>>> having a little problem in claculating descriptors. I was wondering if
>>>> there is a simple code or snippet that uses DescriptorEngine() to calculate
>>>> all the molecular descriptors for a list of molecules in sdf file.
>>>> >
>>>> > Please advice,
>>>> > Anurag
>>>> >
>>>> > --
>>>> > Anurag Passi
>>>> > Sr. Project Fellow
>>>> > OSDD, CSIR
>>>> > 00-91-9899767938
>>>> > skype: anurag.passi
>>>> >
>>>> ------------------------------------------------------------------------------
>>>> > WatchGuard Dimension instantly turns raw network data into actionable
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>>>> import
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>>>> >
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>>>>
>>>>
>>
>>
>> --
>> Anurag Passi
>> Sr. Project Fellow
>> OSDD, CSIR
>> 00-91-9899767938
>> skype: anurag.passi
>>
>
>
>
> --
> Anurag Passi
> Sr. Project Fellow
> OSDD, CSIR
> 00-91-9899767938
> skype: anurag.passi
>
>
>
--
Anurag Passi
Sr. Project Fellow
OSDD, CSIR
00-91-9899767938
skype: anurag.passi
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