Molecule 2 CDK


I am trying to use the node "Molecule to CDK" of community nodes of CDK section. In the transformaton I need to add the hydrogens, and for this reason I tick the checkbox: "Add explicit hydrogens". My problem is that the node _always_ raises the following ERROR:

ERROR     Molecule to CDK     Execute failed: Error while writing to buffer, failed to write to file "knime_container_20111109_6202373782423599593.bin.gz": org.openscience.cdk.stereo.TetrahedralChirality

Anybody has experienced a similar behavior ? Any clue/hint of the root of the problem ?

Thanks in advance

PS: the node works fine if I do not select the option "Add explicit hydrogens"



Hi Oscar,

thanks for your message. I assume the node always fails for the same molecule?

I am not sure about the root of the problem but if you send me the molecule(s), I will look into it.

Implicit hydrogens are automatically added to the molecule when you convert it to a CDK molecule via the "Molecule to CDK" node. The option "Add explicit hydrogens" simply converts the implicit hydrogens to explicit hydrogens  using AtomContainerManipulator.convertImplicitToExplicitHydrogens(myCdkMolecule). 

Following the molecule gets serialized via the CMLWriter and that's where the problem might occur. I can tell you more once I get the molecule in question.

What happens if you try to convert the hydrogens via the the "Hydrogen Manipulator" node?

With regards,


Hi Stephan, 

thanks for your help. First of all, an SMILES example of a molecule which creates this problem:

N[C@](C)(F)C(=O)O    chiral
NC(C)(F)C(=O)O         nochiral

Please, notice that I experience the problem with the molecule which brings chirality information (the first one). The second one (nochiral) works fine. Maybe, I not sure (just an educated guess), the poblem could be related with the chiral centers.

As you say, my following step was to use the node Hydrogen Manipulator, but I discarded it because it does not generate 2D coordinaates for the added H (please correct me if I'm wrong).

thanks again



Hi Oscar,

the CDK smiles parser (v 1.4.x) does not support chiral smiles. The default behaviour is to ignore stereo information.

In the special case of chiral smiles in the CDK KNIME integration, the CMLWriter used for serialization crashes because it cannot process the chiral atom configuration.

I have fixed the node method for smiles parsing. Every time the method encounters a chiral smiles, it will process the molecule without chiral information (nightly build).

Stereochemistry is supported for other input formats such as SDF or Mol.

The "Hydrogen Manipulator" does not calculate 2D coordinates. However, you can use the "2D Coordinates" node subsequent to the "Hydrogen Manipulator" as remedy.

I hope that helps.


Hi Stephan,

thanks for your comment, I'll follow your advice.


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