Converts the elements in one of the input table's columns into an internal format (CDKCell), which can then be rendered as molecule or used for further computations. The target column must contain string representations of molecules (SDF, Mol2, SMILES [no stereo information], CML, InChI).
For on untyped InChI or SMILES string, the line notation is inferred. If the string starts with "InChI=", the InChI parser is used, the SMILES parser otherwise. The option's dialog will not automatically select an input column as a string cell may not contain the right input, in contrast to typed SDF, Mol2, or SMILES cells.
This node uses CDK classes to parse and display structures.
Options
Popular Predecessors
Excel Reader (XLS)11 %- SDF Reader4 %
- Molecule Type Cast3 %
- Excel Reader3 %
- CSV Reader2 %
- Sorter2 %
- RDKit Descriptor Calculation2 %
XLS Reader1 %Excel Reader (XLS)1 %Row Filter (deprecated)1 %- Chunk Loop Start1 %
- CIR1 %
Column Rename1 %Table Reader1 %- MolConverter< 1 %
- Column Resorter< 1 %
- Missing Value< 1 %
- Rule-based Row Filter< 1 %
- Molecule to CDK< 1 %
- 3D D-Similarity< 1 %
CSV Reader< 1 %Row Splitter (deprecated)< 1 %- GroupBy< 1 %
- Smiles Directory Reader< 1 %
- RDKit Add Conformers< 1 %
- Substructure Search< 1 %
File Reader< 1 %Joiner< 1 %- OpenBabel< 1 %
- CDK to Molecule< 1 %
- Loop End< 1 %
- Concatenate< 1 %
- RowID< 1 %
- Unpivot< 1 %
- Rule-based Row Splitter< 1 %
Excel Reader (XLS)< 1 %- SMARTS Query< 1 %
- RDKit Add Hs< 1 %
- RDKit From Molecule< 1 %
RDKit Structure Normalizer< 1 %- Hydrogen Remover< 1 %
- Cell Splitter< 1 %
- File Reader< 1 %
- Joiner< 1 %
- RDKit Molecule Catalog Filter< 1 %
- Strings to Binary Objects< 1 %
- Advanced MolConverter< 1 %
- MarvinSketch< 1 %
- ChemSpider< 1 %
- Table Creator< 1 %
- Bootstrap Sampling< 1 %
- Column Aggregator< 1 %
Column Appender< 1 %- Column Filter< 1 %
- Reference Row Filter< 1 %
- String Manipulation< 1 %
- SDF Extractor< 1 %
- Molfile Reader< 1 %
- Mol2 Reader< 1 %
- Math Formula< 1 %
- Structure Sketcher< 1 %
- RDKit Canon SMILES< 1 %
- RDKit To Molecule< 1 %
- Constant Value Column< 1 %
- Duplicate Row Filter< 1 %
- Filter Apply< 1 %
- String Replacer< 1 %
- Table Manipulator< 1 %
- RDKit Molecule Fragmenter< 1 %
- Column Appender< 1 %
- Line Plot (JavaScript)< 1 %
- Group Loop Start< 1 %
- Column Combiner< 1 %
- Column Splitter< 1 %
- Fingerprints< 1 %
- Numeric Row Splitter< 1 %
- Load SD-Files (SDF)< 1 %
Database Reader< 1 %- HiLite Row Splitter< 1 %
- Counter Generation< 1 %
- Hydrogen Manipulator< 1 %
- RDKit Interactive Table< 1 %
- RDKit To InChI< 1 %
- RDKit Substructure Filter< 1 %
- Tautomer Generator< 1 %
- Column Merger< 1 %
- SDF Inserter< 1 %
- Java Snippet (simple)< 1 %
- JSON to Table< 1 %
- Lipinski's Rule-of-Five< 1 %
- Mass Calculator< 1 %
- RDKit Generate Coords< 1 %
- RDKit From IUPAC< 1 %
- RDKit Open 3D Alignment< 1 %
- Canonical SMILES< 1 %
- Component Separator< 1 %
- InChi< 1 %
- Load Local Mol Files< 1 %
Loop End< 1 %- Missing Value Column Filter< 1 %
- Table Transposer< 1 %
- Molecular Properties< 1 %
- XLogP< 1 %
- RDKit Fingerprint< 1 %
- Murcko Scaffold< 1 %
- Reaction Automapper< 1 %
- Substructure Matcher< 1 %
- Load Local Mol2 Files< 1 %
Variable to Table Row< 1 %Concatenate (Optional in)< 1 %Read Excel Sheet Names (XLS)< 1 %- GET Request< 1 %
- Connectivity< 1 %
- 3D Coordinates< 1 %
- Sum Formula< 1 %
- RDKit Chemical Transformation< 1 %
- Atom Replacer< 1 %
Simple File Reader< 1 %- Cross Joiner< 1 %
- XML to JSON< 1 %
- Hydrogen Adder< 1 %
- Load Text Files< 1 %
- PDB Loader< 1 %
Database Connection Table Reader< 1 %Database Looping< 1 %- k-Means< 1 %
- Column Auto Type Cast< 1 %
- Reference Row Splitter< 1 %
- Partitioning< 1 %
- Pivot< 1 %
- Number Rounder< 1 %
- IF Switch< 1 %
- Similarity Search< 1 %
- MoSS< 1 %
- Term to String< 1 %
- Column Filter (legacy)< 1 %
- Table Editor (JavaScript)< 1 %
- R Snippet< 1 %
- Element Filter< 1 %
- Feature Remover< 1 %
- Molecule Properties< 1 %
- Standardizer< 1 %
- Molecule Transformation (beta)< 1 %
- ICon< 1 %
- SDF Reader< 1 %
- Speedy SMILES Remove Broken Bonds Filter< 1 %
- Speedy SMILES Remove Multicomponent Molecules Filter< 1 %
- Speedy SMILES Organic Subset Molecules Filter< 1 %
- Speedy SMILES De-salt< 1 %
- Speedy SMILES Strip Double Bond Geometry< 1 %
- Fingerprint From String< 1 %
- PDB Downloader< 1 %
- Create Collection Column< 1 %
- Auto-Binner< 1 %
Cell Replacer< 1 %- Double to Integer< 1 %
- Reference Column Filter< 1 %
- Nominal Value Row Splitter< 1 %
- Value Counter< 1 %
- Rule Engine< 1 %
- Parallel Chunk Start< 1 %
- Empty Table Creator< 1 %
- TimeDelay Loop Start< 1 %
Python Script (2⇒1)< 1 %String Input (legacy)< 1 %- XPath< 1 %
- RDKit Aromatizer< 1 %
- RDKit Calculate Charges< 1 %
- RDKit Optimize Geometry< 1 %
- RDKit R-Group Decomposition< 1 %
- RDKit R-Group Decomposition (deprecated)< 1 %
- RDKit Salt Stripper< 1 %
- Fingerprint Similarity< 1 %
- MCS Scaffold Finder< 1 %
- SMARTSViewer< 1 %
Table Row to Variable< 1 %- Create Bit Vector< 1 %
- Normalizer (Apply)< 1 %
- Renderer to Image< 1 %
- SDF Stripper< 1 %
- Fingerprint Bayesian Learner< 1 %
- DB Query Reader< 1 %
- List Files/Folders< 1 %
- Fingerprint Similarity< 1 %
- OPSIN< 1 %
Views
- This node has no views
Workflows
_01_ChemicalLibraryEnumerationKNIME Hub- 03_Example_for_a_Chemical_ReportKNIME Hub
- 03_Example_for_a_Chemical_Report_EditedKNIME Forum
- BDBBuilderKNIME Hub
- BindingDB_FMCT-5-AveragedKNIME Hub
- Show all 14 workflows
Links
- No links available
Developers
You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.