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RDKit Molecule Extractor Node Cannot Handle Single Molecule #18

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manuelschwarze opened this issue Apr 24, 2017 · 0 comments
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RDKit Molecule Extractor Node Cannot Handle Single Molecule #18

manuelschwarze opened this issue Apr 24, 2017 · 0 comments
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The RDKit Molecule Extractor Node splits a set of molecules into individual structures, but this only works if the SDF or SMILES contains two or more structures. If there's only one structure in the SDF or SMILES the RDKit Molecule Extractor generates no output structure at all resulting for instance in a blank table. This is a bug. It should in that case output the only structure that was found.

This was reported in the RDKit forum: http://tech.knime.org/forum/rdkit/rdkit-molecule-extractor-returns-empty-field-if-only-one-structure-present
manuelschwarze added a commit to manuelschwarze/knime-rdkit that referenced this issue Apr 26, 2017
@manuelschwarze
Bugfix for handling a single fragment in input data of RDKit Molecule
4c50efe 
Extractor node (Fixes rdkit#18).

Single fragments are treated as expected, resulting in a single output
row. If the sanitization option is on, it will be sanitized as multiple
fragments would.
Updated documentation and regression tests.
Additionally, added JRebel startup parameter for test preparation launch
file.
@manuelschwarze manuelschwarze mentioned this issue Apr 26, 2017
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@manuelschwarze manuelschwarze self-assigned this Apr 26, 2017
greglandrum pushed a commit that referenced this issue Apr 27, 2017
@manuelschwarze @greglandrum
Bugfix for handling single fragment in Mol Extractor input data (#19)
f445971 
* Bugfix for handling a single fragment in input data of RDKit Molecule
Extractor node (Fixes #18).

Single fragments are treated as expected, resulting in a single output
row. If the sanitization option is on, it will be sanitized as multiple
fragments would.
Updated documentation and regression tests.
Additionally, added JRebel startup parameter for test preparation launch
file.

* Updated copyright information
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