LigPrep

LigPrep generates high quality, all-atom 3D structures for large numbers of drug-like molecules, starting with 1D, 2D or 3D structures in SMILES, SD, Mol2 or Maestro format. The simplest use of LigPrep produces a single, low-energy, 3D structure with correct chiralities for each successfully processed input structure. LigPrep can also produce a number of structures from each input structure with various ionization states, tautomers, stereochemistries, and ring conformations.

For additional documentation on the available options see the Ligprep documentation.

Backend implementation

$SCHRODINGER/ligprep

Options

Column containing input
Choose the input column for LigPrep
Output Column Structure
Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaces Input - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Allow implicit conversion
If selected, the node will accept Mol2 as input type and converts it into Maestro implicitly. By default this is OFF.
Group output
Ligprep generates a molecule (or list of molecules) for each input molecule. Since each Maestro/SD/Mol2 type cell can either hold one or more structures, this option determines whether output from one row is grouped. If the Group output is not selected, and the output columns have input columns, then the matching input row data is duplicated for each output molecule.
Settings...
On clicking "Settings" button, this node brings up the "LigPrep" Python panel for configuration.
Read Maestro Settings...
On clicking "Read Maestro Settings" button, this node brings up a file browser. Browse to a LigPrep job diretcory written by Maestro and select the jobname.inp file. The LigPrep Python panel will now be opened by loading the settings read from the selected jobfile.
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: LigPrep
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 flow variable.

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

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

To remove an existing option from command line, just specify the option_name and the value as _off_ 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

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Input data table containing molecules in Maestro, Sdf or SMILESformat

Output Ports

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Molecules in Maestro or Sdf format
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Structures that did not pass a particular stage of the process

Popular Predecessors

Popular Successors

Views

Log output of LigPrep
Log output of LigPrep

Workflows

Links

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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