However, this seems to work
Bond.newI(mol.getAtom(0),mol.getAtom(1),Bond::Order::SINGLE).
And by the way, Bond.new does not work with (FixNum, FixNum, IBond.Order,
IBond.Stereo) but with arguments (IAtom, IAtom, IBond.Order, IBond.Stereo).
Thanks,
Yannick
On Mon, Feb 24, 2014 at 3:35 PM, Yannick .Djoumbou <y.djoum...@gmail.com>wrote:
> 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 <john...@ebi.ac.uk> 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 <y.djoum...@gmail.com> 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 <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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