Extract Atom/bond Properties

This node takes in structures in Maestro, Sdf and Mol2 formats and outputs the properties for the CTs, Atoms, and Bonds into three different output tables. This node also adds output properties to provide the relationships between CTs and its atoms and bonds. The CT has a property in the first column "ct-id" which starts at 1 and is incremented for every CT. The atoms and bonds also have a column "ct-id" that refers to the CT each item belongs. Since the atom and bond index in the Maestro format has no name, we simply set these properties to "atom-id" and "bond-id" respectively. By default, this node outputs all information from the CTs, Atoms, and Bonds.

Backend implementation

$SCHRODINGER/run proplister.py

Options

Column containing structure: Select column in the data input table containing the structures
Include input: Include all input columns in each of the output tables
Short Column Names in output: Display user-friendly column names in output tables
Output CT properties only: Outputs only the CT properties
Output CT and atom properties: Outputs the CT and atom properties
Output CT, atom, and bond properties: Outputs the CT, atom, and bond properties (default)
Parameter flow variables: Any valid option for proplister.py can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: Proplister
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 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.

Input Ports

: Molecules in Maestro, Sdf or Mol2 format

Output Ports

: All CT properties of the input molecules
: All atom properties of the input molecules
: All bond properties of the input molecules

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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: 2024-04-19

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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