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

Reference Guide
 ICM options
 Alignment Editor
 Cgi programming with icm
 Xml drugbank example
 Tree cluster
 Flow control
 Energy Terms
 Chemical Functions
 Gui programming
 Icm shell functions
Command Line User's Guide
PrevICM Language Reference
Chemical Functions

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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