ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov Copyright © 2020, Molsoft LLC Nov 14 2024
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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
Example of how to use the functions:
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
Direct Icm shell-script-functions, e.g. predCovfunc( X ):
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
To run this function from a command line one needs to do the following (assuming a table 't' with a column 'mol':
add colummn t function="predictModelsCol(mol,'mcpPGP')" name="PGP"
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