The list of functions is expanding. See add column function section for the syntax to use the in a command line. See the GUI/Chemistry menu in ICM-graphics version for different properties that are added through some of these functions. The current list of the functions is the following: E.g. add column t function="MolPSA(mol)" name="PLSA"

• MolWeight(mol ["monoiso"|"aveiso"]) : molecular mass in Dalton, default is "monoiso"
• MolFormula(mol) : chemical composition formula, eg {"C2H6O",..}
• IupacName(mol) : IUPAC names of chemicals from .mol, e.g. {"ethanol",..}
• 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
• MolLogS(mol) : predicted water solubility, Log10([C]): logarithm of the solubility in moles/liter
• MolPSA(mol) : polar surface area in squared Angstoms
• MolArea(mol) : rarray of predicted total surface areas in square angstroms
• MolVolume(mol) : rarray of predicted volume in cubic angstroms
• MoldHf(mol) : predicted heats of formation in kJ/mol
• pKa_ma(mol) : Calculate pKa the Most Acidic Group
• pKa_mb(mol) : Calculate pKa the Most Basic Group
• DrugLikeness(mol) : predicted drug-likeness values, approx.normal distribution N(0,1.), positive values are more drug-like.
• MolSynth(mol) : chemical synthetic accessibility values [0-1]; values of 1. mean that all fragments are very common, zero value - too many rare or unknown fragments
• Smiles(mol,['unique'|'unique_cistrans'|'asis'|'topology'|'unique_topology']) : SMILES/SMARTS strings. Default - 'unique'.
• Nof_Atoms(mol,[]) : n.of atoms of specified type, e.g. '*'|'H'|'[!H]'|'[#6]'|'[!#6]'|..
• Nof_Molecules(mol) : Number of individual molecules in .mol drawings
• Nof_Fragments(mol,) n.of specified fragments, e.g. Nof_Fragments(mol,'CCC')
• Nof_Chirals(mol,['any'|'left'|'right'|'racemic']) : n.of chiral centers, R,S,or (RS) from .mol
• Max_Ring_Size(mol) : Largest independent ring size from .mol
• Min_Ring_Size(mol) : Smallest independent ring size from .mol
• Max_Fused_Rings(mol,[(no)]) : n.of elementary rings in the largest fused ring
• Nof_RotB(mol) : n.of freely rotatable bonds
• Nof_HBA(mol,[(yes)] ) : n.of hydrogen bond acceptors
• Nof_HBD(mol) : n.of hydrogen bond donors
• ToxScore(mol,,) : bad score is ≥ 1.5
• predCovfunc(mol) : predicts covalent function and adds two columns: MolCovalent, and MolProdrug

add column t Chemical({"CCO","CCCCO","CO"}) {"ethanol","propanol","methanol"} name={"mol","name"} #make (or read) a chemical table.
add column t function="MolLogD(mol)" name="cLogD"

Direct Icm built-in-functions, e.g.:

• Descriptor(,number,atom) : Atom counts
• Descriptor(,number,bond) : Bond counts
• Descriptor(,number,topology) : Topological, connectivity and shape indices
• Find(,problem) : unwanted or reactive chemical functionality from .mol

Functions using Molscreen models in $ICMHOME/models/ folder (alternatively, the full path to the model-file location needs to be specified).

• predictModelsCol(mol,'mcpCACO2') (MolCACO2 column) : Predict CACO-2 Permeability LogPapp in cm/sec, a value >-5. indicates high permeability, <-6. indicates low permeability
• predictModelsCol(mol,'mcphERGclass') MolHERG : Predict hERG inhibition, a value >0.5 indicates high probability of being a hERG inhibitor
• predictModelsCol(mol,'mcpLD50') MolLD50 : Predict Log LD50 in mg/kg, a value of <0 indicates 1mg/kg high toxicity, 2 indicates 100mg/kg low toxicity
• predictModelsCol(mol,'mcpLogHALFLIFE') MolLogHALFLIFE : Predict Log10 Half Life in Human Plasma in hour, a value >1. indicates half life > 10 hours; Also output half life in plasma and microsome in hours
• predictModelsCol(mol,'mcpLogPERME') MolLogPERME : Predict Log Permeability of PAMPA, CACO2 in cm/sec, a value >-5. indicates high permeability, <-6. indicates low permeability; Efflux Ratio of CACO2 >2. indicates active efflux
• predictModelsCol(mol,'mcpPAINS') MolPAINS : Predict Pan Assay Interference Compound (PAINS), a value >0.5 indicates high probability of being a PAINS Compound
• predictModelsCol(mol,'mcpPAMPA') MolPAMPA : Predict PAMPA Permeability LogPapp in cm/sec, a value >-5. indicates high permeability, <-6. indicates low permeability
• predictModelsCol(mol,'mcpPGP') MolPGP : Predict P-Glycoprotein inhibitor/substrate, a value >0.5 indicates high probability of being a P-Glycoprotein inhibitor/substrate

add colummn t function="predictModelsCol(mol,'mcpPGP')" name="PGP"