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Package CHEM :: Package CombiCDB :: Module ReactionScore :: Class FreeEnergy
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Class FreeEnergy



MolScore --+
           |
          FreeEnergy

General energy calculator. Defers to FreeEnergyNoResonance, but does so for every resonance structure that can be enumerated for the molecule, then generates a score for the total hybrid.

Present idea: Start with the minimum energy, and then apply a bonus to that for each other resonance structure, weighted by the relative Boltzmann probability of that resonance structures' energy and the number of atoms involved (proportional to amount of delocalization). Thus, other resonance structures of equal weight will confer the most bonus, while structures that are much less stable (such as charge separated) will confer to little to no bonus.

Instance Methods [hide private]
 
__init__(self, temperature=ROOM_TEMPERATURE, minimizeResonance=True, singleEnergy=None)
Initialization constructor.
 
score(self, mol)
Overide this method to return numerical score of this mol

Inherited from MolScore: __call__

Class Variables [hide private]
  minimizeResonance = <CHEM.DB.rdb.search.NameRxnPatternMatching...
  singleEnergy = <CHEM.DB.rdb.search.NameRxnPatternMatchingModel...
  energyWeight = <CHEM.DB.rdb.search.NameRxnPatternMatchingModel...
  RESONANCE_BONUS = -6.0
Method Details [hide private]

__init__(self, temperature=ROOM_TEMPERATURE, minimizeResonance=True, singleEnergy=None)
(Constructor)

  
Initialization constructor.

temperature - Absolute temperature (Kelvin) to evaluate at.  Becomes relevant
                when using Boltzmann equation to weight different structure energies.
minimizeResonance - If true, when called on a molecule object,
                    will rearrange the electrons into a minimum energy configuration
singleEnergy - Function to provide energy score for an individual resonance structure
                contributor.  If not provided, will just default to FreeEnergyNoResonance
Overrides: MolScore.__init__

score(self, mol)

 
Overide this method to return numerical score of this mol
Overrides: MolScore.score
(inherited documentation)

Class Variable Details [hide private]

minimizeResonance

Value:
None

singleEnergy

Value:
None

energyWeight

Value:
None

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