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 Functions
Next

The list of functions is expanding. The current list of the functions is the following:

  • MolWeight(mol) :
  • Nof_Molecules(mol) : the number of individual molecules,including ions and salts
  • Nof_Chirals(mol [{0|1|2|3}]) : the total number of racemic or chiral centers
  • Nof_RotB(mol): rotatable bonds
  • Nof_HBA(mol): hydrogen bonding acceptors
  • Nof_HBD(mol): hydrogen bonding donors
  • Nof_Atoms(mol [s_atomSmarts]): the total number of non-hydrogen atoms (default) or number of atoms matching the smarts argument
  • Nof_Frags( mol, s_smarts ) : counts the number of fragments
  • MolLogP(mol) : Octanol water partition, Log10(C_oct/C_w) from .mol prediction
  • MolLogD(mol) : LogD is a log of partition of a chemical compound between the lipid and aqueous phases
  • Volume(mol) : 3D molecule volume prediction in cubic Angstroms
  • MolPSA(mol) : polar surface area in squared Angstoms
  • MoldHf(mol) : heats of formation
  • MolLogS(mol) : Water solubility, Log10([C]): 10-based logarithm of the solubility in mol/l or M units predicted from .mol
  • pKa_ma(mol) : Calculate pKa the Most Acidic Group
  • pKa_mb(mol) : Calculate pKa the Most Basic Group
  • MolSynth(mol) : Chemical Synthetic Accessibility [0-1]. 1-all fragments are very common, 0.-many unknown fragments
  • bbbScore(mol) : Calculate the Blood-Brain Barries (BBB) Score


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