Package MolKit :: Module APBSParameters :: Class APBSParams

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Class APBSParams

source code

Class to represent APBS parameters. The list of attributes that can be set is found in self.keywords.

Instance Methods

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__init__(self, name='Default', **kw)
Constructor for class APBSParams

Set(self, check=1, **kw)
Sets APBSParams member variable(s)

apbsWriteCalculationParams(self, fp, molname)
None <--- apbsWriteCalculationParams(fp)

apbsWriteGridParams(self, fp)
None <--- apbsWriteGridParams(fp)

apbsWritePhysicsParams(self, fp)
None <--- apbsWritePhysicsParams(fp)

apbsWriteSolvationEnergy(self, fp)
None <--- apbsWriteSolvationEnergy(fp)

apbsWriteBindingEnergy(self, fp)
None <--- apbsWriteBindingEnergy(fp)

apbsWriteElectrostaticPotential(self, fp)
None <--- apbsWriteElectrostaticPotential(fp)

SaveAPBSInput(self, filename)
None <--- apbsWriteElectrostaticPotential(filename)

Class Variables

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GAMMA = 0.105

CFAC = 1.5

MEGABYTES_PER_GRID_POINT = 0.00016000000000000001

GRID_VALUES = [9, 17, 33, 49, 65, 81, 97, 113, 129, 145, 161, 177,...

FILETYPES = ('', 'OpenDX', 'AVS UCD', 'UHBD')

CALCULATIONTYPES = ('Solvation energy', 'Binding energy', 'Electrostati...

PBETYPES = ('Linearized', 'Nonlinear')

BOUNDARYTYPES = ('Zero E', 'Single Debye-Huckel', 'Multiple Debye-Hu...

CHARGEDISCRETIZATIONTYPES = ('Trilinear hat-function', 'Cubic B-spline', 'Quinti...

SURFACECALCULATIONTYPES = ('No smoothing', 'Harmonic Average', 'Cubic B-spline...

ENERGYOUTPUTTYPES = ('', 'Total', 'Total and Individual')

FORCEOUTPUTTYPES = ('', 'Total', 'Total and Individual')

keywords = ['APBS_Path', 'pdb2pqr_Path', 'pdb2pqr_ForceField', ...

Method Details

[hide private]

init(self, name='Default', **kw)
(Constructor)

source code

Constructor for class APBSParams

Set(self, check=1, **kw)

source code

Sets APBSParams member variable(s)

apbsWriteCalculationParams(self, fp, molname)

source code

None <--- apbsWriteCalculationParams(fp)

Writes APBS Calculation Parameters into fp

apbsWriteGridParams(self, fp)

source code

None <--- apbsWriteGridParams(fp)

Writes APBS Grid Parameters into fp

apbsWritePhysicsParams(self, fp)

source code

None <--- apbsWritePhysicsParams(fp)

Writes APBS Physics Parameters into fp

apbsWriteSolvationEnergy(self, fp)

source code

None <--- apbsWriteSolvationEnergy(fp)

Writes APBS Solvation Energy Parameters into fp

apbsWriteBindingEnergy(self, fp)

source code

None <--- apbsWriteBindingEnergy(fp)

Writes APBS Binding Energy Parameters into fp

apbsWriteElectrostaticPotential(self, fp)

source code

None <--- apbsWriteElectrostaticPotential(fp)

Writes APBS Electrostatic Potential Parameters into fp

SaveAPBSInput(self, filename)

source code

None <--- apbsWriteElectrostaticPotential(filename)

Saves APBS Input Parameters in a file named filename

Class Variable Details

[hide private]

GAMMA

None

Value:

0.105

CFAC

None

Value:

1.5

MEGABYTES_PER_GRID_POINT

None

Value:

0.00016000000000000001

GRID_VALUES

None

Value:

[9, 17, 33, 49, 65, 81, 97, 113, 129]

FILETYPES

None

Value:

('', 'OpenDX', 'AVS UCD', 'UHBD')

CALCULATIONTYPES

None

Value:

('Solvation energy', 'Binding energy', 'Electrostatic potential')

PBETYPES

None

Value:

('Linearized', 'Nonlinear')

BOUNDARYTYPES

None

Value:

('Zero E', 'Single Debye-Huckel', 'Multiple Debye-Huckel')

CHARGEDISCRETIZATIONTYPES

None

Value:

('Trilinear hat-function', 'Cubic B-spline', 'Quintic B-spline')

SURFACECALCULATIONTYPES

None

Value:

('No smoothing', 'Harmonic Average', 'Cubic B-spline', '7th Order Poly
nomial')

ENERGYOUTPUTTYPES

None

Value:

('', 'Total', 'Total and Individual')

FORCEOUTPUTTYPES

None

Value:

('', 'Total', 'Total and Individual')

keywords

None

Value:

['APBS_Path',
 'pdb2pqr_Path',
 'pdb2pqr_ForceField',
 'name',
 'calculationType',
 'pbeType',
 'boundaryConditions',
 'chargeDiscretization',
...

Class APBSParams

__init__(self, name='Default', **kw) (Constructor)

Set(self, check=1, **kw)

apbsWriteCalculationParams(self, fp, molname)

apbsWriteGridParams(self, fp)

apbsWritePhysicsParams(self, fp)

apbsWriteSolvationEnergy(self, fp)

apbsWriteBindingEnergy(self, fp)

apbsWriteElectrostaticPotential(self, fp)

SaveAPBSInput(self, filename)

GAMMA

CFAC

MEGABYTES_PER_GRID_POINT

GRID_VALUES

FILETYPES

CALCULATIONTYPES

PBETYPES

BOUNDARYTYPES

CHARGEDISCRETIZATIONTYPES

SURFACECALCULATIONTYPES

ENERGYOUTPUTTYPES

FORCEOUTPUTTYPES

keywords

init(self, name='Default', **kw)
(Constructor)