Package PyAutoDock :: Module desolvation :: Class NewDesolvationRefImpl

Class NewDesolvationRefImpl

scorer.ScoringStrategy --+        
                         |        
     scorer.PairwiseScorer --+    
                             |    
  scorer.DistDepPairwiseScorer --+
                                 |
                                NewDesolvationRefImpl

Known Subclasses:: NewDesolvationAtomMapRefImpl, NewDesolvationDesolvMapRefImpl, NewDesolvationLigOnlyRefImpl

Instance Methods

[hide private]

__init__(self, ms=None, solpar_q=0.01097)
constructor

get_ddsol(self, distance)
return distance dependent solvation parameter

_f(self, at_a, at_b, dist)
Return desolvation energy in kcal/mole.

Inherited from scorer.DistDepPairwiseScorer: get_score_array

Inherited from scorer.PairwiseScorer: get_score, post_process, set_molecular_system

Class Variables

[hide private]

Vols = {'ZN': 1.7, 'HS': 0.0, 'Mg': 1.5600000000000001, 'L'...

Solpars = {'A': -0.00051999999999999995, 'C': -0.0014300000000...

Inherited from scorer.DistDepPairwiseScorer: non_bonded_cutoff

Method Details

[hide private]

init(self, ms=None, solpar_q=0.01097)
(Constructor)

source code

constructor

Overrides: scorer.DistDepPairwiseScorer.__init__: (inherited documentation)

get_ddsol(self, distance)

source code

return distance dependent solvation parameter

WHERE DID THIS COME FROM?? ===========================

Stouten @@ Document this @@

_f(self, at_a, at_b, dist)

source code

Return desolvation energy in kcal/mole.

Atom Volumes are in units of kcal/mol*Ang**3
NB: pdbqs volumes are cal/mol*Ang**3 and must be converted!!
    This is done by MolecularSystem.py for now.

In Autodock3.0.5, this term is valid only for C atoms
in the ligand and is used to discriminate aromatic carbons
from aliphatic carbons

Overrides: scorer.DistDepPairwiseScorer._f

Class Variable Details

[hide private]

Vols

None

Value:

{'A': 33.510300000000001,
 'BR': 42.566099999999999,
 'Br': 42.566099999999999,
 'C': 33.510300000000001,
 'CA': 2.77,
 'CL': 35.823500000000003,
 'Ca': 2.77,
 'Cl': 35.823500000000003,
...

Solpars

None

Value:

{'A': -0.00051999999999999995,
 'C': -0.0014300000000000001,
 'H': 0.00051000000000000004,
 'HD': 0.00051000000000000004,
 'N': -0.0016199999999999999,
 'NA': -0.0016199999999999999,
 'O': -0.0025100000000000001,
 'OA': -0.0025100000000000001,
...

Class NewDesolvationRefImpl

__init__(self, ms=None, solpar_q=0.01097) (Constructor)

get_ddsol(self, distance)

_f(self, at_a, at_b, dist)

Vols

Solpars

init(self, ms=None, solpar_q=0.01097)
(Constructor)