ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2020, Molsoft LLC
Jun 20 2021

Contents
 
Introduction
Reference Guide
 ICM options
 Editing
 Graph.Controls
 Alignment Editor
 Constants
 Subsets
 Molecules
 Selections
 Fingerprints
 Regexp
 Cgi programming with icm
 Xml drugbank example
 Tree cluster
 Arithmetics
 Flow control
 MolObjects
 Energy Terms
 Integers
 Reals
 Logicals
 Strings
 Preferences
 Tables
 Other
 Chemical
 Smiles
 Chemical Functions
 MolLogP
 MolLogS
 MolSynth
 Soap
 Gui programming
 Commands
 Functions
 Icm shell functions
 Macros
 Files
Command Line User's Guide
References
Glossary
 
Index
PrevICM Language Reference
Chemical Synthetic Accessibility
Next

Statistical model based on analysis of frequencies of ECFP-4 fragments in available chemical libraries from different vendors

The Synthesizability score is derived as follows Each ECFP-4 fragments with frequency less than 10000 gives P[i] = 4-Log10(frequency) The total penalty is calculated as Penalty = Sqrt( Sum( P[i]*P[i] ) ) The penalty is transformed to score as Score = 3./(3.+Penalty)

  • Training set: ~20M compounds available from vendors
  • Descriptors: ECFP4
Example: add column t Chemical("CC(C)Cc1ccc(cc1)[C@@H](C)C(=O)O") name="mol" add column t function="MolSynth(mol)" name="molSynth"

Chemical Functions


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