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 <[email protected]> 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 <[email protected]> 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 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.
>
>> 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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