Split by Structure

Split structures by chain, molecule, or residue.

Backend implementation

$SCHRODINGER/run split_structure.py

Options

Column containing input

Choose the input column

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

Group output

Structures resulting from the same molecule will be grouped into one cell.

Split by

Split input structures by chain, molecule, residue, ligand or pdb.

Keep Properties

All MAE properties from Input molecules are included in split output molecules.

Group Waters

Water molecules extracted from the same structure are grouped together into one entry, instead of generating individual molecule entries for each water molecule.

Split All

Split cofactors and metals into different structures. (Default is to keep with nearest protein structure)

Ligand ASL

ASL used to define ligand structures.

Cofactor ASL

ASL used to define cofactor structures.

Positive Ion ASL

ASL used to define non-metal positive ions.

Negative Ion ASL

ASL used to define negative ions.

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: SplitStruct
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.

Input Ports

: Molecules in Maestro, Sd, Mol2 or Pdb format

Output Ports

: Molecules in Maestro, Sd, Mol2 or SMILES format

Popular Predecessors

Popular Successors

Views

Std output/error of Split by Structure: Std output/error of Split by Structure

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: 24.1.135.v202402072122

On NodePit since: 2023-12-06

Last update: 2024-04-18

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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