Yes - that would not make sense, the bond holds atom references and knows
nothing about the molecule. Giving it indices (FixNum) only makes sense in the
context of a molecule which is where the addBond method is. The method may be
missing on this version (1.2.2 i believe) which is nearly 5 years old.
John
On 24 Feb 2014, at 22:42, Yannick .Djoumbou <[email protected]> wrote:
> 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 <[email protected]>
> 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 <[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 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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