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Molecule Reader (to MAE)

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

Load files into cell: Select from the 3 options to set how the files are loaded into the table cells
Load each structure in one cell
Load each file in one cell
Load all files in one cell
Add additional columns: If checked ON, the origin directory, origin filename and origin hostname of the files will be added as separate columns in the output table. This option will be disabled if "Load all files in one cell" is selected.
File Name: The name of the file to be loaded
File can be an URL like:
knime://LOCAL/path/to/file - knime://LOCAL refers to the current workspace
knime://knime.workflow/path/to/file - knime://knime.workspace refers to the current workflow
Import all structures: Whether the entire file should be loaded
Start: If not all structures are loaded, which number structure should loader start at (disabled if Import all structures is set)
End: Should the file be loaded until to end (disabled if Import all structures is set)
Total: If not all structures are imported and not loaded until the end, how many total structures should be loaded (disabled if Import all structures or End is set)
Parameter flow variables: Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: MoleculeReader
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through the flow variable.

To add a new option without a value, specify the option_name and the value as _on_ through the flow variable.

To override an existing option's value, specify the option_name and the new value through the flow variable.

To remove an existing option without a value, specify the option_name and the value as _off_ through the flow variable.

To remove an existing option with a value, specify the option_name and the value as _rm_ through the flow variable.

Note: This node adds a new flow variable 'backend' so that downstream node can access the backend used by this node.

Input Ports

This node has no input ports

Output Ports

: Molecules (in Maestro format)

Views

StdErr View: StdErr View

Workflows

Developers

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Installation

To use this node in KNIME, install the extension Schrödinger Extensions for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Schrödinger

Plugin version: 24.3.138.v202407300410

On NodePit since: 2023-12-06

Last update: 2024-11-20

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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