AtomList

AtomList[mol]

gives the list of atoms in the molecule mol.

AtomList[mol,patt]

gives the list of atoms in the molecule mol matching the atom pattern patt.

AtomList[mol,patt,"prop"]

gives the value for the specified property of the atoms matching patt.

Details

  • Possible values for patt are:
  • "sym"an atom with atomic symbol "sym"
    Atom["sym",rules]an atom with properties described by rules
    MoleculePattern["patt"]an atom pattern defined by the SMARTS string "patt"
    patt1|patt2|an atom matching any of the patti
  • Possible values for "prop" include:
  • "AromaticAtomQ"aromatic atom
    "AtomChirality"absolute atomic chirality as determined using the Cahn-Ingold-Prelog priority rules
    "AtomicNumber"atomic number
    "AtomicSymbol"standard atomic symbol
    "AtomIndex"atom index
    "CIPRank"atom rank computed using the Cahn-Ingold-Prelog priority rules
    "CoordinationNumber"number of explicit bonds for an atom
    "Element"element entity
    "FormalCharge"formal charge
    "GasteigerPartialCharge"Gasteiger partial charge
    "GeometricStericEffectIndex"geometric steric index
    "HeavyAtomCoordinationNumber"number of bonds to heavy atoms
    "HydrogenCount"hydrogen count
    "ImplicitHydrogenCount"implicit hydrogen count
    "Isotope"isotope entity
    "MassNumber"mass number
    "MMFFPartialCharge"MMFF partial charge
    "MostAbundantMassNumber"mass number for the most commonly occurring isotope
    "OrbitalHybridization"orbital hybridization
    "PiElectronCount" electron count
    "RingAtomQ"ring membership
    "TopologicalStericEffectIndex"topological steric index
    "UnpairedElectronCount"unpaired electron count
    "UnsaturatedAtomQ"unsaturated atom
    "Valence"atomic valence

Examples

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Basic Examples  (4)

Get all the atoms from a molecule:

Get only the carbon atoms:

Get only the non-carbon atoms:

Get property values for atoms matching a pattern:

Feed the results to MoleculePlot to highlight them:

Find unsaturated atoms with partial negative charge:

Retrieve multiple properties for atoms matching a pattern:

Scope  (1)

Use AtomList to find the hybridization of all non-hydrogen atoms:

Use GroupBy to group the atom indices by their corresponding hybridization:

Introduced in 2019
 (12.0)