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Write molecules in Maestro, SD, Mol2, SMILES or PDB format. There are two ways to specify the output file, either
by text field (i.e., one file) or by selecting a column which has an output file specified for each row. When
specifying one file, it is possible to write a file for each row (i.e., using the checkbox option): in this
case an additional suffix consisting of the row number is added to the original specified file name for each row.
Backend implementation
$SCHRODINGER/utilities/structconvert
Options
Popular Predecessors
- Molecule-to-MAE4 %
- Reaction Based Enumeration4 %
- GroupBy3 %
- LigPrep2 %
- Row Filter2 %
Glide Ensemble Docking2 %- MAE-to-Pdb2 %
- Group MAE2 %
- Shape Screening2 %
- Missing Value2 %
- Table Row to Variable2 %
- Molecule Reader (to MAE)1 %
- Chunk Loop Start1 %
- Java Snippet (simple)1 %
- Glide Ligand Docking1 %
Protein Preparation Wizard1 %- Concatenate1 %
- Prime Minimization1 %
- CSV Writer1 %
- String Configuration1 %
- Complexes-to-PoseViewers1 %
- Glide Sort Results1 %
- Extract Properties1 %
- Set Molecule Title1 %
- String Manipulation1 %
- MAE-to-SD1 %
- Duplicate Row Filter1 %
- Run PyMOL1 %
- Joiner1 %
- Maestro Molecular Properties< 1 %
- MAE-to-Mol2< 1 %
- Set MAE Properties< 1 %
- Pose Filter< 1 %
- SiteMap< 1 %
- Split by Structure< 1 %
Loop End< 1 %- Column Filter< 1 %
- Reference Row Filter< 1 %
- String Manipulation (Variable)< 1 %
- Delete MAE Properties< 1 %
- Fragments from Molecules< 1 %
- Ligfilter< 1 %
- Ungroup MAE< 1 %
- MacroModel Conformational Search< 1 %
- PoseViewer-to-Complexes< 1 %
- String-to-Type< 1 %
- Desmond Trajectory Extract Frames< 1 %
Variable to Table Column< 1 %Table Column to Variable< 1 %- Row Splitter< 1 %
- Column Splitter< 1 %
- Rule-based Row Filter< 1 %
- Parallel Chunk End< 1 %
- Property Filter (Propfilter)< 1 %
- Table Column to Variable< 1 %
- Loop End< 1 %
- Ligand Alignment< 1 %
- Protein Preparation Workflow< 1 %
Glide Ligand Docking< 1 %- MAE-to-Smiles< 1 %
- PDB Reader< 1 %
Column Appender< 1 %- Row Sampling< 1 %
Desalter< 1 %- Canvas Molecular Descriptors< 1 %
Table Row to Variable< 1 %- Column Combiner< 1 %
- Column Merger< 1 %
- Fragment Joiner< 1 %
- Sorter< 1 %
- Align Binding Sites< 1 %
- SD-to-Smiles< 1 %
- Python Script 1:1< 1 %
- Smiles Reader< 1 %
- Generate Unique Smiles< 1 %
Variable to Table Column< 1 %CSV Reader< 1 %- Rule Engine< 1 %
Ionizer< 1 %- KNIME-Maestro Connector< 1 %
- RDKit To Molecule< 1 %
- Compare Ligand Sets< 1 %
Table Row To Variable Loop Start< 1 %- Add Hydrogens< 1 %
- Epik Classic< 1 %
- Assign Bond Orders< 1 %
- Import from LiveDesign< 1 %
- Run Maestro Command< 1 %
- Phase Screening< 1 %
- Protein Structure Alignment< 1 %
- QikProp< 1 %
- RMSD< 1 %
Tautomerizer< 1 %- Unique Title Check< 1 %
Table Column to Variable< 1 %- Glide Ensemble Merge< 1 %
- Similarity Calculator (FTrees)< 1 %
- Chemistry External Tool< 1 %
- Induced Fit Docking< 1 %
- Jaguar Single Point Energy< 1 %
- Python Script 0:1< 1 %
- PDB Saver< 1 %
- Create File Name (legacy)< 1 %
Table Row to Variable< 1 %Concatenate (Optional in)< 1 %- Column Resorter< 1 %
Joiner< 1 %- Partitioning< 1 %
- RowID< 1 %
- SDF Reader< 1 %
- RDKit Canon SMILES< 1 %
- Molecule Properties< 1 %
- Boltzmann Population< 1 %
- ConfGen< 1 %
- Conformer Cluster< 1 %
- Delete Atoms< 1 %
- Desmond Trajectory Reader< 1 %
- Embrace Minimization< 1 %
- Canvas Fingerprint Reader< 1 %
- Get PDB< 1 %
- Glide Merge< 1 %
- Glide Grid Generation< 1 %
- Phase Hypothesis Reader< 1 %
- Impref< 1 %
- Jaguar Minimization< 1 %
- Lookup and Add Columns< 1 %
- MacroModel Coordinate Scan< 1 %
- Prime MM-GBSA< 1 %
- MacroModel Minimization< 1 %
- Pose Entropy< 1 %
- Prime Refine Loops< 1 %
- Protein Assignment< 1 %
- Residue Scanning< 1 %
- QSAR Model Reader< 1 %
Stereoizer< 1 %- Strain Rescore< 1 %
- Benchmark End< 1 %
- Fingerprint Similarity< 1 %
- Create Directory (legacy)< 1 %
- Try (Variable Ports)< 1 %
Table Reader< 1 %- Column Aggregator< 1 %
Column Rename< 1 %- Numeric Row Splitter< 1 %
- Rule-based Row Splitter< 1 %
- Create Temp Dir (legacy)< 1 %
- SDF Inserter< 1 %
- Smiles Directory Reader< 1 %
- Column Expressions< 1 %
- Math Formula< 1 %
- String Input (legacy)< 1 %
- RDKit Molecule Fragmenter< 1 %
- AutoQSAR Predict< 1 %
- Covalent Docking< 1 %
- Generate Pairwise Matrix< 1 %
- Set MAE Index< 1 %
Neutralizer< 1 %File Reader< 1 %- Row Filter (Labs)< 1 %
- Top k Row Filter< 1 %
Views
- Molecule Writer StdOutErr View
- Std out/err of Molecule Writer
Workflows
Add structures as Generic EntityKNIME Hub- Binding Poses and Energies CalculationKNIME Hub
- Binding site 1KNIME Hub
- Binding site shape clusteringKNIME Hub
- Binding site shape clusteringKNIME Hub
- Show all 107 workflows
Links
- No links available
Developers
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