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 <y.djoumbou@gmail.com> 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 <johnmay@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.djoumbou@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.djoumbou@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 <johnmay@ebi.ac.uk> wrote:
The Order is a not method of IBond it is an nested class - perhaps the wrappers canít represent it but it's pretty common so I doubt thatís the case.

Iím flying blind having only spent about 5 mins in Ruby but either try

import Ďorg.openscience.cdk.interfaces.IBond.Order'

or

import Ďorg.openscience.cdk.interfaces.IBondí 

with IBond.Order.SINGLE

J

On 24 Feb 2014, at 21:53, Yannick .Djoumbou <y.djoumbou@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 <johnmay@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.djoumbou@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 <johnmay@ebi.ac.uk> wrote:
Hi Yannick,

I donít 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 donít think that will be available in the version you are using. Hereís the java code anyways.

SMARTSQueryTool sqt = new SMARTSQueryTool(ď[#8]=[#6]Ē);
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