Exactly.
Having added a new atom and linked it to an already existing atom, I
realize that specific properties of the atom have not been set
automatically. For example, the AtomTypeName of the newly added atom is
still nil. How do I get these to be set?
In the current example, mol.getAtom(2).getAtomTypeName() and
mol.getAtom(2).getCharge() both return nil.
Cheers,
Yannick
On Mon, Feb 24, 2014 at 3:46 PM, John May <john...@ebi.ac.uk> wrote:
> 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 <y.djoum...@gmail.com> 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
> <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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