Class StructureGenome

pyevolve.GenomeBase.GenomeBase --+
                                 |
                                StructureGenome

Manage a genome. The genome, aka chromosome, is the solution to the problem trying to be solved via genetic optimization. It is referred to as being composed of genes that are manipulated by the crossover and mutation operators. In our genetic optimization module this genome is basically just a schrodinger.structure.Structure object.

Instance Methods

[hide private]

__init__(self)
Create an instance.

copy(self, genome)
Copy the current genome to the provided genome.

StructureGenome

clone(self)
Clone the current genome.

updateStructureProperties(self, index, generation)
Update some structure properties.

resetParentProperties(self)
Reset the crossover and mutation parent structure properties.

removeProperties(self)
Remove some structure properties.

optimizeGeometry(self)
Optimize the geometry of this genome's structure using OPLS.

addPreviousFreezerFile(self, freezer_file)
Add the given file to the list of previous freezer files.

evaluate(self, **args)
Evaluate the score of this individual.

Inherited from pyevolve.GenomeBase.GenomeBase: __repr__, getFitnessScore, getParam, getRawScore, initialize, mutate, resetStats, setParams

Class Variables

[hide private]

Inherited from pyevolve.GenomeBase.GenomeBase: crossover, evaluator, initializator, mutator

Method Details

[hide private]

init(self)
(Constructor)

Create an instance.

Overrides: pyevolve.GenomeBase.GenomeBase.__init__

copy(self, genome)

Copy the current genome to the provided genome.

Parameters:

genome (StructureGenome) - a new genome instance to which to copy the current genome

Overrides: pyevolve.GenomeBase.GenomeBase.copy

clone(self)

Clone the current genome.

Returns: StructureGenome: genome
Overrides: pyevolve.GenomeBase.GenomeBase.clone

updateStructureProperties(self, index, generation)

Update some structure properties.

Parameters:

index (int) - the index of this individual
generation (int) - this generation

addPreviousFreezerFile(self, freezer_file)

Add the given file to the list of previous freezer files.

Parameters:

freezer_file (str) - the name of the file to be added

evaluate(self, **args)

Evaluate the score of this individual.

Parameters:

args (dict) - dictionary of genetic optimization parameters created and used by pyevolve

Overrides: pyevolve.GenomeBase.GenomeBase.evaluate

Class StructureGenome

__init__(self) (Constructor)

copy(self, genome)

clone(self)

updateStructureProperties(self, index, generation)

addPreviousFreezerFile(self, freezer_file)

evaluate(self, **args)

init(self)
(Constructor)