This node uses OpenBabel for converting molecules between many different formats. You can either use the bundled version or specify the path to a local installation. Bundled OpenBabel not available for Mac
Options
Popular Predecessors
- CSV Reader3 %
- Column Filter3 %
XLS Reader3 %- SDF Reader3 %
- Excel Reader3 %
Excel Reader (XLS)3 %- Molecule Type Cast2 %
Row Filter (deprecated)2 %- RDKit Canon SMILES1 %
- String Manipulation1 %
- OpenBabel1 %
Excel Reader (XLS)1 %- RDKit From Molecule1 %
- RowID< 1 %
File Reader< 1 %- Partitioning< 1 %
- CDK to Molecule< 1 %
- RDKit To Molecule< 1 %
CSV Reader< 1 %Database Reader< 1 %Variable to Table Row< 1 %- Concatenate< 1 %
- GroupBy< 1 %
- String Replacer< 1 %
- Canonical SMILES< 1 %
- Column Splitter< 1 %
- SDF Extractor< 1 %
- SDF Stripper< 1 %
- Mol2 Reader< 1 %
XML Reader< 1 %- Cell Splitter< 1 %
- Standardizer< 1 %
- PDB Loader< 1 %
Table Row To Variable Loop Start< 1 %Line Reader< 1 %- Table Creator< 1 %
- Column Rename (Regex)< 1 %
Column Rename< 1 %Excel Reader (XLS)< 1 %- RDKit Molecule Fragmenter< 1 %
- Binary Objects to Strings< 1 %
- File Reader< 1 %
- MolConverter< 1 %
- Chunk Loop Start< 1 %
Joiner< 1 %- Sorter< 1 %
- SDF Inserter< 1 %
- Rxn/RD Reader< 1 %
- Math Formula< 1 %
- Substructure Search< 1 %
- RDKit Interactive Table< 1 %
- RDKit Molecule Substructure Filter< 1 %
- RDKit Salt Stripper< 1 %
- Duplicate Row Filter< 1 %
- File Reader (Complex Format)< 1 %
- Generate 2D Coordinates< 1 %
- Murcko Scaffold< 1 %
- Load Local PDB Files< 1 %
- Standardizer< 1 %
- MarvinSketch< 1 %
- Strings to Binary Objects< 1 %
- Try (Data Ports)< 1 %
Database Looping< 1 %- Column Merger< 1 %
- Constant Value Column< 1 %
Row Splitter (deprecated)< 1 %- Reference Row Filter< 1 %
- Row Sampling< 1 %
- Value Counter< 1 %
- Rule-based Row Filter< 1 %
- Rule Engine< 1 %
- Molfile Reader< 1 %
- Smiles Directory Reader< 1 %
- Molecule to CDK< 1 %
- RDKit Generate Coords< 1 %
- RDKit From InChI< 1 %
- RDKit Optimize Geometry< 1 %
- RDKit To InChI< 1 %
- CIR< 1 %
- PDB Reader< 1 %
- Load Local Mol2 Files< 1 %
- Load SD-Files (SDF)< 1 %
- Table Column to Variable< 1 %
- Joiner< 1 %
- Python Script (legacy)< 1 %
- Structure Sketcher< 1 %
- Loop End< 1 %
- DB Query Reader< 1 %
- Speedy SMILES De-salt< 1 %
Database Connection Table Reader< 1 %- Column Resorter< 1 %
- Rule-based Row Filter (Dictionary)< 1 %
- RDKit Add Hs< 1 %
- RDKit Remove Hs< 1 %
- Text Extractor< 1 %
- XPath< 1 %
- RDKit MCS< 1 %
- Molecule Properties< 1 %
- Load Local Mol Files< 1 %
- Java Snippet< 1 %
Concatenate (Optional in)< 1 %- Column Combiner< 1 %
Column Appender< 1 %- RDKit Chemical Transformation< 1 %
RDKit Structure Normalizer< 1 %- Aromatizer< 1 %
- SMILES Reader< 1 %
- Nominal Value Row Filter< 1 %
- Empty Table Creator< 1 %
- RDKit Substructure Filter< 1 %
Read MDB< 1 %- PDB Downloader (Source)< 1 %
Variable to Table Column< 1 %Loop End (2 ports)< 1 %- HiLite Row Splitter< 1 %
- Reference Row Splitter< 1 %
- Number Rounder< 1 %
- Parallel Chunk Start< 1 %
- Java Snippet Row Filter< 1 %
- File Chooser (legacy)< 1 %
- Score Erosion< 1 %
- RDKit Fingerprint< 1 %
- Tautomer Generator< 1 %
- Hydrogen Remover< 1 %
- Reaction Builder< 1 %
- Reaction Splitter< 1 %
- Tautomer Generator< 1 %
- Load Local CDXML Files< 1 %
Recursive Loop End< 1 %- MoSS< 1 %
- Value Filter (legacy)< 1 %
- Container Input (Table)< 1 %
- GET Request< 1 %
- Duplicate Filter< 1 %
- Mol Reader< 1 %
- PDB Sequence Extractor< 1 %
- MolImporter< 1 %
- PNGs to Binary Objects< 1 %
- Table Row to Variable< 1 %
- Variable Loop End< 1 %
- Number to String< 1 %
- Table Validator< 1 %
- Pivot< 1 %
- RDKit Molecule Catalog Filter< 1 %
IF Switch (Flow Variable Value)< 1 %Loop End (3 ports)< 1 %- Load Text Files< 1 %
- Load text-based files< 1 %
- PDB Property Extractor< 1 %
- ChemSpider< 1 %
- Fingerprint Similarity< 1 %
- URL to File Path< 1 %
- Breakpoint< 1 %
- Image to Table< 1 %
Table Reader< 1 %- Java Edit Variable< 1 %
Loop End< 1 %- Cell Splitter By Position< 1 %
String To Number< 1 %- Renderer to Image< 1 %
- Rule-based Row Splitter< 1 %
Merge Variables< 1 %- Molfile Writer< 1 %
- Tags to String< 1 %
- External Tool (Labs)< 1 %
Python Script (1⇒1)< 1 %String Radio Buttons (legacy)< 1 %- Column to XML< 1 %
- 2D Coordinates< 1 %
- Lipinski's Rule-of-Five< 1 %
- RDKit Add Conformers< 1 %
- RDKit Descriptor Calculation< 1 %
- RDKit Kekulizer< 1 %
- Feature Remover< 1 %
- Hydrogen Adder< 1 %
- Isomer Enumerator< 1 %
- R-Group Decomposer< 1 %
- Molecule Transformation (beta)< 1 %
- AutoDock Vina< 1 %
- Mol2 Reader< 1 %
- SDF Reader< 1 %
- Bundle Generator< 1 %
- Force Field Conformer Energies< 1 %
- Speedy SMILES Possible Stereoisomer Count< 1 %
- Speedy SMILES Enumerate Stereoisomers< 1 %
- Speedy SMILES Strip Stereochemistry< 1 %
- Fingerprint to String< 1 %
MMP Molecule Fragment (3rd Gen)< 1 %- List Folders< 1 %
- R Snippet< 1 %
- Structure Checker< 1 %
Binary Objects to Files< 1 %- Files to Binary Objects< 1 %
- URI Port to Variable< 1 %
Variable to Table Column< 1 %Table Row to Variable< 1 %Variable to Table Row< 1 %- Read Images< 1 %
- ARFF Reader< 1 %
Line Reader< 1 %- Fixed Width File Reader< 1 %
List Files< 1 %- Loop End (Column Append)< 1 %
Generic Loop Start< 1 %PCA< 1 %- Linear Regression Learner< 1 %
- PCA< 1 %
Cell Replacer< 1 %- Column Auto Type Cast< 1 %
- Column Aggregator< 1 %
- Column Renamer (Dictionary)< 1 %
- Column to Grid< 1 %
- Nominal Value Row Splitter< 1 %
- Missing Value< 1 %
- Numeric Row Splitter< 1 %
- Shuffle< 1 %
- Table Transposer< 1 %
- Unpivot< 1 %
- Parallel Chunk End< 1 %
- Parameterized DB Query Reader< 1 %
- MoSS MCSS Molecule Similarity< 1 %
- External Tool< 1 %
Read Excel Sheet Names (XLS)< 1 %- Java Snippet (simple)< 1 %
- Flat File Document Parser< 1 %
- PDF Parser< 1 %
- Google Sheets Reader< 1 %
- Column Filter (legacy)< 1 %
- Table View (JavaScript)< 1 %
- Table Editor (JavaScript)< 1 %
- JSON to Table< 1 %
- Triple File Reader< 1 %
- 3D Coordinates< 1 %
- Molecular Properties< 1 %
- Fingerprint Similarity< 1 %
- RDKit Aromatizer< 1 %
- RDKit Calculate Charges< 1 %
- RDKit Diversity Picker< 1 %
RDKit Fingerprint Reader< 1 %RDKit Functional Group Filter< 1 %- RDKit From IUPAC< 1 %
- RDKit Two Component Reaction< 1 %
- Sequence Convert< 1 %
- InChi< 1 %
- Templated Conformer Generation (RDKit)< 1 %
- Speedy SMILES Invert Stereochemistry< 1 %
- Collection to String< 1 %
- PDB Downloader< 1 %
- pKa< 1 %
- Stereoisomers< 1 %
- Variable to Table Row< 1 %
Simple File Reader< 1 %- Table Reader< 1 %
- Group Loop Start< 1 %
Table Row To Variable Loop Start< 1 %- Table Row to Variable Loop Start< 1 %
- Random Forest Predictor< 1 %
- Normalizer< 1 %
- String Manipulation (Variable)< 1 %
- Ungroup< 1 %
- Fingerprint Bayesian Learner< 1 %
- DB Reader< 1 %
- List Files/Folders< 1 %
- Column Selection Configuration< 1 %
- Element Filter< 1 %
- RDKit Molecule Extractor< 1 %
- RDKit RMSD Filter< 1 %
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Workflows
05_DrugBank_Network_analysisKNIME Hub- 4D-QSAR Docking of ChEMBL LigandsKNIME Hub
- 4D-QSAR Docking Selected COVID-19 DrugsKNIME Hub
- 4D-QSAR ML Both Binding and 2D FeaturesKNIME Hub
- 4D-QSAR ML Both Binding and 2D FeaturesKNIME Hub
- Show all 17 workflows
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