Package schrodinger :: Package application :: Package bioluminate :: Package patch_utils :: Module patch_finder :: Class ProteinProperties

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Class ProteinProperties

object --+
         |
        ProteinProperties

Calculates protein properties for display on the Properties tab

Instance Methods

[hide private]

__init__(self, struc, asa_by_atom)
x.__init__(...) initializes x; see help(type(x)) for signature

float

_calcHydrophobicMoment(self, struc)
Calculate the hydrophobic moment

tuple

_calcPosNegSurfaceArea(self, struc, asa_by_atom)
Calculate the surface area for positively and negatively charged atoms

tuple

_calcHBondSurfaceArea(self, struc, asa_by_atom)
Calculate the surface area for hydrogen bond acceptors and donors

__getstate__(self)

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

dict KYTE_DOOLITTLE_SCALE = {u'ALA': 1.8, u'ARG': -4.5, u'ASN': -3....
A hydrophobicity scale taken from A simple method for displaying the hydropathic character of a protein.

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, struc, asa_by_atom)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

struc (schrodinger.structure.Structure) - The structure to calculate the properties of
asa_by_atom (OneIndexedList) - The accessible surface area of each atom

Overrides: object.__init__

_calcHydrophobicMoment(self, struc)

Calculate the hydrophobic moment

Parameters:

struc (schrodinger.structure.Structure) - The structure to calculate the hydrophobic moment of

Returns: float

The hydrophobic moment

Note: This implementation is based on calc_protein_descriptors in psp-src/python.modules/pro_descriptors.py.

_calcPosNegSurfaceArea(self, struc, asa_by_atom)

Calculate the surface area for positively and negatively charged atoms

Parameters:

struc (schrodinger.structure.Structure) - The structure to calculate the surface areas of
asa_by_atom (OneIndexedList) - The accessible surface area of each atom

Returns: tuple

A tuple of

The surface area for positively charged atoms (float)
The surface area for negatively charged atoms (float)

_calcHBondSurfaceArea(self, struc, asa_by_atom)

Calculate the surface area for hydrogen bond acceptors and donors

Parameters:

struc (schrodinger.structure.Structure) - The structure to calculate the surface areas of
asa_by_atom (OneIndexedList) - The accessible surface area of each atom

Returns: tuple

A tuple of

The surface area for hydrogen bond acceptors (float)
The surface area for hydrogren bond donors (float)

Class Variable Details

[hide private]

KYTE_DOOLITTLE_SCALE

A hydrophobicity scale taken from A simple method for displaying the hydropathic character of a protein. J. Kyte, R.F. Doolittle, J Mol Biol. 1982 May 5;157(1):105-32.

Type:: dict

Value:

{u'ALA': 1.8,
 u'ARG': -4.5,
 u'ASN': -3.5,
 u'ASP': -3.5,
 u'CYS': 2.5,
 u'GLN': -3.5,
 u'GLU': -3.5,
 u'GLY': -0.4,
...

Class ProteinProperties

__init__(self, struc, asa_by_atom) (Constructor)

_calcHydrophobicMoment(self, struc)

_calcPosNegSurfaceArea(self, struc, asa_by_atom)

_calcHBondSurfaceArea(self, struc, asa_by_atom)

KYTE_DOOLITTLE_SCALE

init(self, struc, asa_by_atom)
(Constructor)