HI,
I have imported the following classes relative to bonds:
import 'org.openscience.cdk.Bond'
import 'org.openscience.cdk.interfaces.IBond'
import 'org.openscience.cdk.interfaces.IBond$Order'
import 'org.openscience.cdk.interfaces.IBond$Stereo'
When using the command you just mentioned, I still get the following error:
NoMethodError: undefined method `Order' for
Java::OrgOpenscienceCdkInterfaces::IBond:Module
Cheers,
Yannick
On Mon, Feb 24, 2014 at 2:15 PM, John May <john...@ebi.ac.uk> wrote:
> Sorry, I was going on what you had and presumed ruby was loading Order
> directly. The full name is IBond.Order.SINGLE.
>
> Bond.new(mol.getAtom(0), mol.getAtom(1), IBond.Order.SINGLE)
>
>
> - John
>
> On 24 Feb 2014, at 21:10, Yannick .Djoumbou <y.djoum...@gmail.com> wrote:
>
> Thanks for the very quick reply.
>
> I actually use the Bond class.
> I've tried the following options:
> - bond = Bond.new(mol.getAtom(0), mol.getAtom(1), Order.SINGLE)
>
> NoMethodError: undefined method `SINGLE' for
> Java::OrgOpenscienceCdkInterfaces::Order:Class
> from (irb):37:in `evaluate'
> from org/jruby/RubyKernel.java:1121:in `eval'
> from org/jruby/RubyKernel.java:1517:in `loop'
> from org/jruby/RubyKernel.java:1282:in `catch'
> from org/jruby/RubyKernel.java:1282:in `catch'
>
> - mol.addBond(0,1,Order.Single)
>
> NoMethodError: undefined method `Single' for
> Java::OrgOpenscienceCdkInterfaces::Order:Class
> from (irb):38:in `evaluate'
> from org/jruby/RubyKernel.java:1121:in `eval'
> from org/jruby/RubyKernel.java:1517:in `loop'
> from org/jruby/RubyKernel.java:1282:in `catch'
> from org/jruby/RubyKernel.java:1282:in `catch'
>
> I guess it comes from the fact that I am using Jruby. I should normally
> not have a problem with this. It's kind of confusing. Do you have a hint?
>
> Cheers,
>
> Yannick
>
>
> On Mon, Feb 24, 2014 at 1:21 PM, John May <john...@ebi.ac.uk> wrote:
>
>> Hi Yannick,
>>
>> I don't now about ruby wrappers but can answer 2 and 3. Also looks like
>> rcdk is used for ruby and R bindings which is a little confusing.
>>
>> 2) IBond is an
>> interface<http://docs.oracle.com/javase/tutorial/java/concepts/interface.html>
>> you
>> need to use the concrete class. There are a couple of way to do this, you
>> can use Bond concrete class (silent package is best)
>>
>> Bond.new(mol.getAtom(0), mol.getAtom(1), Order.SINGLE)
>>
>>
>> use a builder -
>>
>> SilentChemObjectBuilder.getInstance().newInstance(IBond.class,
>> mol.getAtom(0),
>> mol.getAtom(1), Order.SINGLE)
>>
>>
>> or use the convince method on the molecule -
>>
>> molcule.addBond(0,1, Order.Single);
>>
>>
>> 3-1) CDKHydrogenAdder is only for implicit hydrogens - you only need this
>> if you have null hydrogen values. For explicit hydrogens use the
>> manipulator<http://pele.farmbio.uu.se/nightly/api/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.html#convertImplicitToExplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer)>
>> .
>>
>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol)
>>
>>
>> 3-2) You have a SMARTS pattern and so need to use the SMARTSQueryTool. I
>> don't think that will be available in the version you are using. Here's the
>> java code anyways.
>>
>> SMARTSQueryTool sqt = new SMARTSQueryTool("[#8]=[#6]");
>> sqt.matches(mol);
>> for (List<Integer> mapping : sqt.getAllMappings()) {
>> for (int i = 0; i < mapping.size(); i++) {
>> System.out.println(mapping.get(i) + 1);
>> }
>> }
>>
>> Hope that helps,
>> John
>>
>
>
>
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