Hello,
I have the following questions regarding CDK.
1) - Is there a recent version of a ruby wrapper to cdk?
The older versions, on rubyforge or rcdk-ng are really out to date. Sofar,
I am using jruby to work with CDK. It could be easier with a wrapper.
2)- I try to create a bond and assign a bond order. I have used the
following
mol : a molecule with the formula 'O.CN'
I want to create a single bond between "O" and "C".
I used this syntax to create a bond before adding it to the molecule
- bond = IBond.new(mol.getAtom(0), mol.getAtom(1), Order.SINGLE).
However, I got the following error:
NoMethodError: undefined method `SINGLE' for
Java::OrgOpenscienceCdkInterfaces::Order:Class
3)- I would like to solve this little problem:
target: O=CCC(=O)C
query: [#8]=[#6]
I would like to:
3-1) add explicit hydrogens to my target.
According to the Efficient Bits article from December
18<http://efficientbits.blogspot.ca/2013/12/new-smiles-behaviour-parsing-cdk-154.html>,
I should use the CDKHydrogenAdder class. I have tried it using the CDK
version 1.4.19
a) builder = SilentChemObjectBuilder.getInstance()
b) sg = SmilesGenerator.new
c)
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol)
d) CDKHydrogenAdder.getInstance(builder).addImplicitHydrogens(mol)
e) sg.createSMILES(mol)
However, sg.createSMILES(mol) returns a smiles without explicit
hydrogen atoms: "O=CCC(=O)C". How to I get CDK to return a smiles/molecule
with explicit atoms.
3-2) Get the results of the superstructure search with the atom indexes
of the two matches.
the mol atom's types are: ["O.sp2", "C.sp2", "C.sp3", "C.sp2",
"O.sp2", "C.sp3"]
Assuming the atom indexing begins at 1 and not 0
match 1 [2,1]
match 2 [5,6]
Could you please give me some hints?
Cheers,
Yannick
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