Package CHEM :: Package CombiCDB :: Module OrbitalScore

Module OrbitalScore

Score or rank orbitals by reactivity

Classes

OrbitalEnergyComparator
Comparator object for Orbitals.

Functions

occupiedMolecularOrbitals(mol, resonanceWeightFunction=molBoltzmannWeight)
Return a list of all of the occupied molecular orbitals in the molecule, ordered (ascending) by their relative energies.

unoccupiedMolecularOrbitals(mol, resonanceWeightFunction=molBoltzmannWeight)
Return a list of all of the UNoccupied molecular orbitals in the molecule, ordered (ascending) by their relative energies.

molecularOrbitals(mol, occupied, resonanceWeightFunction=molBoltzmannWeight)
Return all of the occupied or unoccupied molecular orbitals for the molecular, ordered by their relative energies

homo(mol, resonanceWeightFunction=molBoltzmannWeight)
Return a reference to the Highest Occupied Molecular Orbital, essentially the most nucleophilic electron orbital.

lumo(mol, resonanceWeightFunction=molBoltzmannWeight)
Return a reference to the Lowest Unoccupied Molecular Orbital, essentially the most electrophilic electron orbital.

scoredOrbitalsByAtomIndex(mol, orbitalComparator, resonanceWeightFunction)
Return a dictionary keyed by the molecule's atom indexes.

Variables

[hide private]

energyCalc = FreeEnergyNoResonance()

molBoltzmannWeight = MolBoltzmannProbabilityWeight(energyCalc,...

Function Details

[hide private]

occupiedMolecularOrbitals(mol, resonanceWeightFunction=molBoltzmannWeight)

Return a list of all of the occupied molecular orbitals in the molecule,
ordered (ascending) by their relative energies.  The highest occupied MO
should be the last one in the list.

resonanceWeightFunction - If not None, will average (weighted by 
    the supplied function) across all resonance structures to find the HOMO.
    If None, will only consider the input structure, without considering resonance structures

unoccupiedMolecularOrbitals(mol, resonanceWeightFunction=molBoltzmannWeight)

Return a list of all of the UNoccupied molecular orbitals in the molecule,
ordered (ascending) by their relative energies.  The lowest unoccupied MO
should be the first one in the list.

resonanceWeightFunction - If not None, will average (weighted by 
    the supplied function) across all resonance structures to find the HOMO.
    If None, will only consider the input structure, without considering resonance structures

lumo(mol, resonanceWeightFunction=molBoltzmannWeight)

Return a reference to the Lowest Unoccupied Molecular Orbital,
essentially the most electrophilic electron orbital.

resonanceWeightFunction - If not None, will average (weighted by 
    the supplied function) across all resonance structures to find the LUMO.
    If None, will only consider the input structure, without considering resonance structures

scoredOrbitalsByAtomIndex(mol, orbitalComparator, resonanceWeightFunction)

Return a dictionary keyed by the molecule's atom indexes.
Each item is a list of orbitals matching the respective atom.
Each orbital should have its score value set based on the ranking
established by the orbitalComparator.  Includes enumeration
of the different resonance structures of the molecule and average
the ranking score across all.

resonanceWeightFunction - If not None, will average (weighted by 
    the supplied function) across all resonance structures to find the LUMO.
    If None, will only consider the input structure, without considering resonance structures

Variables Details

[hide private]

molBoltzmannWeight

Value:

MolBoltzmannProbabilityWeight(energyCalc, ROOM_TEMPERATURE)