Eaxctly, I understand the relationship between IBond and Order.
I tried both options but they do not work. Ruby seems to just represent
Order as a method of the IBond class.
I also tried this:
- I deleted line >> import 'org.openscience.cdk.interfaces.IBond::Order'
- I ran Bond.new(0, 1, IBond::Order.SINGLE), but got the following message:
NoMethodError: undefined method `SINGLE' for
Java::OrgOpenscienceCdkInterfaces::Order:Class
With this call, jruby seems to recognize Order as a class, but SINGLE as a
method for the class Order.
Yannick
On Mon, Feb 24, 2014 at 3:08 PM, John May <[email protected]> wrote:
> The Order is a not method of IBond it is an nested class - perhaps the
> wrappers can't represent it but it's pretty common so I doubt that's the
> case.
>
> I'm flying blind having only spent about 5 mins in Ruby but either try
>
> import 'org.openscience.cdk.interfaces.IBond.Order'
>
>
> or
>
> import 'org.openscience.cdk.interfaces.IBond'
>
>
> with IBond.Order.SINGLE
>
> J
>
> On 24 Feb 2014, at 21:53, Yannick .Djoumbou <[email protected]> wrote:
>
> 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 <[email protected]> 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 <[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<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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