Biskit :: Dock :: HexParser :: HexParser :: Class HexParser

Class HexParser

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Parse hex result file and extract Complex objects into a dictionary indexed by the hex solution number. The hex file is only closed when this object is discarded. The HexParser is created with a dictionary containing PCRModel objects for ligand and receptor indexed by hex model number.

Instance Methods

[hide private]

__init__(self, hexFile, rec_dic, lig_dic, forceModel=None)

__del__(self)

Complex nextComplex(self)
Take list of lines, extract all Hex info about one complex (Solution number, hex energy,..) also extract 16 numbers of the transformation matrix and put them into 4 by 4 numeric array.

[str] _nextBlock(self)
return all lines describing next complex in the Hex output file.

ComplexList parseHex(self)
Create one Complex Object for each paragraph in hex output file.

Method Details

[hide private]

init(self, hexFile, rec_dic, lig_dic, forceModel=None)
(Constructor)

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Parameters:

hexFile (string) - name of hex output file
rec_dic ({int:model}) - { int : PCRModel}
lig_dic ({int:model}) - same as rec_dic but for ligand PCRModels
forceModel (int, int) - force parser to accept model numbers

del(self)
(Destructor)

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nextComplex(self)

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Take list of lines, extract all Hex info about one complex (Solution number, hex energy,..) also extract 16 numbers of the transformation matrix and put them into 4 by 4 numeric array.

Returns: Complex: Complex created from the output from Hex

_nextBlock(self)

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return all lines describing next complex in the Hex output file.

Returns: [str]: list of information strings

parseHex(self)

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Create one Complex Object for each paragraph in hex output file.

Returns: ComplexList: ComplexList with all complexes from the Hex output

Class HexParser

__init__(self, hexFile, rec_dic, lig_dic, forceModel=None) (Constructor)

__del__(self) (Destructor)

nextComplex(self)

_nextBlock(self)

parseHex(self)

init(self, hexFile, rec_dic, lig_dic, forceModel=None)
(Constructor)

del(self)
(Destructor)