Package CHEM :: Package CombiCDB :: Module ReactionScore :: Class BondDissociationEnergyScore

Class BondDissociationEnergyScore

MolScore --+
           |
          BondDissociationEnergyScore

Just by looking up and summing standard values from a bond energy table.

Known Limitations: (1) Bond energy table has listings for most common organic molecule bonds, but is non-comprehensive.

Instance Methods

[hide private]

__init__(self)
Default constructor.

score(self, mol)
Given a molecule object, calculate / predict the enthalpy to completely dissociate it into component atoms.

bondEnergy(self, bond)
Given an individual bond, return the bond dissociation energy.

__bondTableKey(self, bond)
Given a bond object, translate it into a key for rapid lookup into the bond energy table.

Inherited from MolScore: __call__

Class Variables

[hide private]

BOND_ENERGY_TABLE = "P-O", 599, ("P=O", 599* 1.5), ("P-H", 297...

Method Details

[hide private]

init(self)
(Constructor)

Default constructor. Regenerates an instance of the bond energy table, but keyed by atomic numbers and numerical bond orders for faster lookup when doing actual calculations.

Overrides: MolScore.__init__

score(self, mol)

Given a molecule object, calculate / predict the enthalpy to completely dissociate it into component atoms.

Overrides: MolScore.score

bondEnergy(self, bond)

Given an individual bond, return the bond dissociation energy. If the bond type is unrecognized, log a warning and just return 0.

If either end atom type has an atomic number of 0, this is a sentinel value that indicates a dummy atom, representing some "R" group. This is normal, just return 0, don't even log a warning.

Class Variable Details

[hide private]

BOND_ENERGY_TABLE

Value:

"P-O", 599, ("P=O", 599* 1.5), ("P-H", 297), ("P-P", 489), ("P-C", 513
), ("P-Cl", 289), ("P-F", 439), ("P-P", 489), ("P-S", 444), ("H-H", 10
4.2), ("C-C", 83), ("N-N", 38.4), ("O-O", 35), ("F-F", 36.6), ("[Si]-[
Si]", 52), ("P-P", 50), ("S-S", 54), ("Cl-Cl", 58), ("Br-Br", 46), ("I
-I", 36.), ("H-C", 99), ("H-N", 93), ("H-O", 111), ("H-F", 135), ("H-C
l", 103), ("H-Br", 87.5), ("H-I", 71), ("H-B", 90), ("H-S", 81), ("H-[
Si]", 75), ("H-P", 77), ("B-F", 150), ("B-O", 125), ("C-N", 73), ("C-O
", 85.5), ("C-S", 65), ("C-F", 116), ("C-Cl", 81), ("C=[Cl+]", 81* 1.5
...

Class BondDissociationEnergyScore

__init__(self) (Constructor)

score(self, mol)

bondEnergy(self, bond)

BOND_ENERGY_TABLE

init(self)
(Constructor)