KNIME User's Manual - ISP

Contents
Document Conventions ...................................................................................................... v
Chapter 1: Introduction ....................................................................................................... 1
1.1 About KNIME.............................................................................................................. 1
1.2 About Schrödinger KNIME Extensions ................................................................. 1
Chapter 2: KNIME Overview .......................................................................................... 3
2.1 The KNIME Panel ....................................................................................................... 3
2.2 Nodes........................................................................................................................... 4
2.3 Workflows ................................................................................................................... 5
2.4 Running KNIME from the Schrödinger Installation............................................. 6
2.5 Common Tasks .......................................................................................................... 7
Chapter 3: Schrödinger KNIME Extensions Tutorial ...................................... 9
3.1 Starting KNIME .......................................................................................................... 9
3.2 Creating a New KNIME Project.............................................................................. 11
3.3 Adding a Smiles Reader......................................................................................... 13
3.4 Adding the LigPrep and QikProp Nodes............................................................. 15
3.5 Running the Workflow ............................................................................................ 18
3.6 Extracting Properties.............................................................................................. 19
3.7 Writing the Results to Disk in Excel Format ...................................................... 21
3.8 Visualization of the Results.................................................................................. 22
3.8.1 Analyzing the Distribution of Violations of Lipinski’s Rules via a Histogram ..... 22
3.8.2 Plotting the Solvent Accessible Surface Area (SASA) Against the Molecular
Weight.......................................................................................................... 24
3.9 Workflow Samples................................................................................................... 26
Chapter 4: Running Workflows from the Command Line ......................... 27
4.1 The knime Command.............................................................................................. 27
Schrödinger KNIME Extensions 1.2 User Manual
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