knime-rdkit

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We have discovered that rooted fingerprints in KNIME have are different from Python and pure Java. The reason we found is that there is a bug how the atom list...

manuelschwarze

RDKit From Molecule node can't render molecule with wedged bond

1

Dear developper, Thanks for developping really useful node for drug discovery, I found that RDKit From Molecule node can't render chiral modelcule with wedged bond. I think it's better to...

iwatobipen

What fingerprint settings does the RDKit Molecule Substructure Filter use?

1

I'm trying to figure out what fingerprint settings the RDKit Molecule Substructure Filter node uses when it pre-calculates fingerprints. I looked at the documentation of the node on KNIME Hub...

TraceLD

Trying to understand the RDKit Aromatizer node and the comparison to 0 to determine success

4

I'm trying to understand an existing RDKit-based KNIME workflow and having used RDKit in Python previously I can't understand the RDKit Aromatizer node. It calls `.setAromaticity(temp)` where `temp` is a...

TraceLD

I like having rdkit as rendering option in preferred renders. However the render settings used by default and I can't seem to change them are pretty bad in my opinion....

kienerj

I can set RDKit 2D depictions as preferred renderer for smiles and sdf but not for molfile or inchi. For molfile columns in the table view I can switch to...

kienerj

Pre-condition Violation Number of atom mismatch Violation occurred on line 564 in file Code\GraphMol\ROMol.cpp Failed Expression: conf->getNumAtoms() == this->getNumAtoms() RDKIT: 2017.09.1 BOOST: 1_56

2

Hi, When using Python Script node in Knime after the RDKit R-group Decomposition node, I am getting the following error message. ERROR Python Script 0:54 Execute failed: Pre-condition Violation Number...

ssalaniwal

Log4j Security Vulnerability

1

The RDKit nodes plugin makes use of the OPSIN library, which has a dependency to log4j 2.14.1 in our current RDKit nodes version. It is kind of hidden, because we...

manuelschwarze

Add RDKit renderer for SMILES, MOL, and SDF cells

1

This would make numerous tasks easier. Could also think about adding it for SMARTS cells

greglandrum

Provide better error messages when RDKit nodes fail completely or by row

1

Steve Roughley, Vernalis, has suggested the following interesting idea as it was successfully implemented already in the Vernalis nodes: In the spirit of OSS/sharing etc I thought that this latest...

manuelschwarze