KNIME User's Manual - ISP

Schrödinger KNIME Extensions User Manual
Chapter 3
Chapter 3:
Schrödinger KNIME Extensions Tutorial
This chapter provides a tutorial introduction to KNIME and the Schrödinger KNIME Extensions.
In this tutorial, you will build a workflow that calculates molecular properties for a set of
compounds provided as SMILES strings. The general outline of the workflow is as follows:
• Read a SMILES string from a file
• Carry out 1D to 3D conversion using LigPrep
• Calculate molecular properties using QikProp
• Extract a subset of properties for analysis
• View the molecular properties
3.1 Starting KNIME
1. Start KNIME with the following command:
$SCHRODINGER/knime
While KNIME is starting, the following message is displayed in the terminal window:
starting KNIME workbench with workspace directory: /home/username/knime_workspace
This message indicates that the workflows will be stored in the directory shown. You can
change the directory by using the -data directory option to the knime command.
A splash screen is also displayed, as shown in Figure 3.1. The splash screen should
include the Schrödinger logo under Installed Extensions. If this logo is missing, the version
of KNIME you are running does not have the Schrödinger KNIME Extensions, and
you must either add them, or run a version that does.
Figure 3.1. The KNIME splash screen.
Schrödinger KNIME Extensions 1.2 User Manual 9