AtomContainerManipulator and CDKHydrogenAdder again - you had the method in
your SMARTS example. You need to perceive atom types and add hydrogens.
Also remember these are indices so atom 1 = 0, atom 2 = 1 and not how one would
number atoms in an editor.
J
On 24 Feb 2014, at 23:07, Yannick .Djoumbou <[email protected]> wrote:
> 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 <[email protected]> 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 <[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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