Molfile Writer
KNIME Chemistry Base nodes version 4.1.1.v202001312017 by KNIME AG, Zurich, Switzerland
This nodes writes molecules from a Mol column into separate files into a local directory or a remote
location denoted by a URL. The files may optionally be compressed with gzip.
Note that if the destination location is a remote URL not all options are available because in general it's
not possible to determine whether the remote location exists. In this case it will always be overwritten.
Options
- Directory
- The directory into which the Molfiles should be written. The directory must already exist. You can also specify remote URLs, in this case the final destination URLs are built by directly appending the file name to this base URL.
- Use molecule title as file name
- If selected, the molecules' titles are used as file names. You have to make sure, that the titles are unique. Otherwise files may be overwritten or the node fails, depending on the "Overwrite existing files" option. If unselected, the row ID is used as file name.
- Structure column
- Select the column containing the Mol structures here.
- Overwrite existing files
- If selected, existing files are overwritten, if unselected, the node fails if a file already exists.
- Compress files
- If selected, the output files will be compressed with gzip.
Input Ports
Best Friends (Incoming)
- MolConverter (18 %) Streamable
- Molecule Type Cast (9 %) Streamable
- OpenBabel (8 %)
- Concatenate (5 %) Streamable
- Column Filter (5 %) Streamable
- RowID (5 %) Streamable
- SDF Reader (5 %)
- Column Rename (3 %) Streamable
- Molfile Reader (3 %)
- Load Local Rxn Files (2 %) Streamable
- MarvinSketch (2 %)
- ChemSpider (2 %)
- Chemical File Writer (2 %)
Table Column to Variable(2 %) DeprecatedTable Row to Variable(2 %) Deprecated- CSV Reader (2 %)
- File Reader (2 %) Streamable
- Loop End (2 %)
- Column Combiner (2 %) Streamable
- Row Filter (2 %) Streamable
- SDF Extractor (2 %)
- Mol2 Reader (2 %)
- MoSS (2 %)
XLS Reader(2 %) DeprecatedExcel Reader (XLS)(2 %) StreamableDeprecated- String Input (2 %)
- Structure Converter (2 %)
- Ceres Draw (2 %)
- CDK to Molecule (2 %)
- Fingerprints (2 %)
- RDKit Generate Coords (2 %) Streamable
- RDKit Diversity Picker (2 %)
- RDKit From Molecule (2 %)
- RDKit Optimize Geometry (2 %) Streamable
- RDKit To Molecule (2 %) Streamable
- Show all 35 recommendations
Best Friends (Outgoing)
- OpenBabel (30 %)
- Loop End (20 %)
- Variable Loop End (20 %)
- MarvinSketch (10 %)
- Database Writer (legacy) (10 %) Streamable
- Concatenate (10 %) Streamable
- Show all 6 recommendations
Workflows
Installation
To use this node in KNIME, install KNIME Base Chemistry Types & Nodes from the following update site:
A zipped version of the software site can be downloaded here. Read our FAQs to get instructions about how to install nodes from a zipped update site.
Developers
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