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Node Readers and Writers

Readers and Writers

Read and write structure files. Read a list of PDB files from a directory.

[Requires: Maestro]

See also:
- Docking - Grid generation: Glide grid reader node

Readers and Writers: Read and write structure files. Read a list of PDB files from a directory.[Requires: Maestro]See also:- Docking - Grid generation: Glide grid reader nodeRead a file embedded in the workflowknime://knime.workflow/<directory in the workspace workflow folder>/<filenameknime://LOCAL/<workflow group(s)>/<filename>eg when drag/dropping a file stored in the workspace(see input files in our workflow examples)file:/tmp/input.maeWrite structuresin the temporary directoryfiles named after the PDB ID using the column containing output file name optionProtein structure in a specified directory[configure] PDB IDas mol2Some structures from the fileOrigin directory and file name As .maeAs .maegzAs smiles Molecule Reader(to MAE) Molecule Reader(to MAE) Molecule Reader(to MAE) Molecule Writer(from MAE) Get PDB Molecule Reader(to MAE) Loop End Table Row ToVariable Loop Start PDB file list Extract Properties Molecule-to-MAE Molecule Writer(from MAE) Molecule Reader(to MAE) Table Viewer Smiles Reader Sequence Writer Alignment Writer Molecule Writer(from MAE) Molecule Writer(from MAE) Molecule Writer(from MAE) Sequence Reader Alignment Reader Readers and Writers: Read and write structure files. Read a list of PDB files from a directory.[Requires: Maestro]See also:- Docking - Grid generation: Glide grid reader nodeRead a file embedded in the workflowknime://knime.workflow/<directory in the workspace workflow folder>/<filenameknime://LOCAL/<workflow group(s)>/<filename>eg when drag/dropping a file stored in the workspace(see input files in our workflow examples)file:/tmp/input.maeWrite structuresin the temporary directoryfiles named after the PDB ID using the column containing output file name optionProtein structure in a specified directory[configure] PDB IDas mol2Some structures from the fileOrigin directory and file name As .maeAs .maegzAs smiles Molecule Reader(to MAE) Molecule Reader(to MAE) Molecule Reader(to MAE) Molecule Writer(from MAE) Get PDB Molecule Reader(to MAE) Loop End Table Row ToVariable Loop Start PDB file list Extract Properties Molecule-to-MAE Molecule Writer(from MAE) Molecule Reader(to MAE) Table Viewer Smiles Reader Sequence Writer Alignment Writer Molecule Writer(from MAE) Molecule Writer(from MAE) Molecule Writer(from MAE) Sequence Reader Alignment Reader

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: jcmozzic
Created at: 2015-03-25
On NodePit since: 2020-02-06
Last update: 2020-02-26
Created with KNIME version: v4.0.1
Tags: NodesMaestro

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