This node is currently not available in KNIME v5.3 — instead we’re showing this page for KNIME v5.2. You can use the version menu in the title bar to permanently switch your preferred version. This will also show the link to the update site.
Read molecules in Maestro, SD, Mol, Mol2, SMILES, CIF or PDB format. All molecules are converted to Maestro format by default.
The default loading mechanism loads each molecule individually into a table row/cell.
To remove files from the list select the file and press the 'Delete' key.
To select all files in the list press Ctrl-A.
To add all files that match a pattern, using an asterisk (*) into the dialog "File Name" field. Press return, and the file filter will show up in the "Files of Type" drop down, then press Ctrl-A to select all of the files that show up with that filter. The list of files will then show up in the "File Name:" field, space delimited with double quotes around each file name. Then press "Open" to load all of those files.
Backend implementation
$SCHRODINGER/utilities/structconvert
Options
Popular Successors
- Extract Properties13 %
- LigPrep3 %
- MAE-to-SD3 %
- MAE-to-Smiles2 %
- Glide Ligand Docking2 %
Ionizer2 %- Similarity Matrix (from Molecules)2 %
- Table Viewer1 %
- Reference Row Filter1 %
- Row Filter1 %
- Joiner1 %
- Molecule Writer (from MAE)1 %
- MacroModel Conformational Search1 %
- QikProp1 %
- Align Binding Sites1 %
- Lookup and Add Columns1 %
- Phase DB Creation1 %
- DeepAutoQSAR Build1 %
Column Appender1 %- Ungroup MAE< 1 %
- Reaction Based Enumeration< 1 %
- Chunk Loop Start< 1 %
- Parallel Chunk Start< 1 %
- RDKit From Molecule< 1 %
- Canvas Fingerprint Generation< 1 %
- Fragment Joiner< 1 %
- Set MAE Properties< 1 %
- Prime MM-GBSA< 1 %
- Canvas Molecular Descriptors< 1 %
- Molecule-to-MAE< 1 %
- Python Script 1:0< 1 %
- Protein Preparation Workflow< 1 %
- Generate Unique Smiles< 1 %
- Loop End< 1 %
- Column Appender< 1 %
- SD-to-Smiles< 1 %
- Desmond System Builder< 1 %
- Run Maestro< 1 %
- Pose Filter< 1 %
- Property Filter (Propfilter)< 1 %
- PoseViewer-to-Complexes< 1 %
- Residue Scanning< 1 %
- Concatenate< 1 %
- Row Splitter< 1 %
- String Manipulation< 1 %
- RDKit Canon SMILES< 1 %
- Add Hydrogens< 1 %
- AutoQSAR Build Model< 1 %
- Maestro Molecular Properties< 1 %
- Substructure Search< 1 %
- Chemistry External Tool< 1 %
- Delete Atoms< 1 %
- Convert Fingerprint to Table< 1 %
- Glide Sort Results< 1 %
- Glide Grid Generation< 1 %
- Induced Fit Docking< 1 %
- KNIME-Maestro Connector< 1 %
- Export to LiveDesign< 1 %
- Ligfilter< 1 %
- MAE-to-Mol2< 1 %
- MAE-to-Pdb< 1 %
- Group MAE< 1 %
- Run Maestro Command< 1 %
- Volume Overlap Matrix< 1 %
Protein Preparation Wizard< 1 %- REOS Filter< 1 %
- RMSD< 1 %
- Shape Screening< 1 %
- Split by Structure< 1 %
- Ligand Alignment< 1 %
- Java Snippet< 1 %
Cell Splitter< 1 %- CASE Switch End< 1 %
- SDF Writer< 1 %
- RDKit Descriptor Calculation< 1 %
- RDKit Molecule Substructure Filter< 1 %
- Compare Ligand Sets< 1 %
- Epik Classic< 1 %
- Glide Ensemble Merge< 1 %
- Hierarchical Clustering< 1 %
- Set PDB Name< 1 %
- Protein Structure Alignment< 1 %
Joiner< 1 %- Rule-based Row Filter< 1 %
- Standard Properties< 1 %
Desalter< 1 %- Assign Bond Orders< 1 %
- Fragments from Molecules< 1 %
- Strain Rescore< 1 %
Table Row To Variable Loop Start< 1 %CSV Writer< 1 %Loop End< 1 %- Column Name Extractor< 1 %
- Constant Value Column< 1 %
- GroupBy< 1 %
- Row Sampling< 1 %
- Column Expressions< 1 %
- OpenBabel< 1 %
- Substructure Matcher< 1 %
- AutoQSAR Predict< 1 %
- Maximum Common Substructure Search< 1 %
- ConfGen< 1 %
- Covalent Docking< 1 %
- Jaguar Minimization< 1 %
- Jaguar Single Point Energy< 1 %
- MacroModel Single Point Energy< 1 %
Neutralizer< 1 %- Phase Screening< 1 %
- Prime Refine Loops< 1 %
- SD Format Checker< 1 %
Table Row to Variable< 1 %Generic Loop Start< 1 %Concatenate (Optional in)< 1 %- Table Manipulator< 1 %
- Numeric Row Splitter< 1 %
- Sorter< 1 %
- RDKit Generate Coords< 1 %
- RDKit To Molecule< 1 %
- CIR< 1 %
- Similarity Calculator (FTrees)< 1 %
- AutoDock 4< 1 %
Run Canvas< 1 %CombiGlide Library Enumeration< 1 %- Complexes-to-PoseViewers< 1 %
- Conformer Cluster< 1 %
- Delete MAE Properties< 1 %
- Desmond Molecular Dynamics< 1 %
- Embrace Minimization< 1 %
- Generate Pairwise Matrix< 1 %
- Glide Grid Writer< 1 %
Glide Ligand Docking< 1 %Glide Ensemble Docking< 1 %- Glide Merge< 1 %
- Impref< 1 %
- Extract Atom/bond Properties< 1 %
- MacroModel Coordinate Scan< 1 %
- MacroModel Minimization< 1 %
- Multiple Sequence Viewer< 1 %
- Prime Side Chain Sampling< 1 %
- Prime Minimization< 1 %
- Rotate All< 1 %
- Run PyMOL< 1 %
- Python Script 1:1< 1 %
- BLAST< 1 %
- Set Molecule Title< 1 %
- SiteMap< 1 %
- String-to-Type< 1 %
Desmond System Builder< 1 %- Desmond Trajectory Extract Frames< 1 %
- Unique Title Check< 1 %
- Run Spreadsheet Viewer< 1 %
- MarvinView< 1 %
- Interaction Fingerprint Retriever< 1 %
- Catch Errors (Data Ports)< 1 %
Table Row to Variable< 1 %Table Writer< 1 %- Table Creator< 1 %
- Java Edit Variable< 1 %
Random Forest Learner< 1 %- Cell Splitter< 1 %
- Duplicate Row Filter< 1 %
- Column Filter< 1 %
- Filter Apply< 1 %
- Missing Value< 1 %
- Regex Split< 1 %
- Column Splitter< 1 %
- Rule-based Row Filter (Dictionary)< 1 %
- Extract Table Dimension< 1 %
- Timer Info< 1 %
- Molecule Type Cast< 1 %
- SDF Stripper< 1 %
- Fingerprint Bayesian Learner< 1 %
- MoSS MCSS Molecule Similarity< 1 %
- Java Snippet (simple)< 1 %
- Credentials Input (legacy)< 1 %
- Table View (JavaScript)< 1 %
Python Script (1⇒1)< 1 %- RDKit Add Hs< 1 %
- RDKit Find Murcko Scaffolds< 1 %
Views
- StdErr View
- StdErr View
Workflows
01_Chemistry external toolKNIME Hub- 01_Chemistry external toolKNIME Hub
- Add structures as Generic EntityKNIME Hub
- AutoQSARKNIME Hub
- AutoQSARKNIME Hub
- Show all 194 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.