schrodinger.application.bioluminate.asp_max module

Calculate the ASP max for a given structure.

This script uses hydrophobicity values from Kyte-Doolittle and Hopp-Woods scales

Hopp, T.P. and Woods, K.R. (1983) A computer program for predicting protein antigenic determinants. Mol. Immunol., 20(4):483-489.

Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157(1):105-132.

Salgado JC, Rapaport I, and Asenjo JA. (2005) Predicting the behaviour of proteins in hydrophobic interaction chromatography. 2. Using a statistical description of their surface amino acid distribution. J Chromatogr A., 1107(1-2):120-9.

class schrodinger.application.bioluminate.asp_max.SurfaceRes(hydrophobicity)

Bases: object

Data about a single residue. Includes the accessible surface area, and hydrophobicity.

__init__(hydrophobicity)
schrodinger.application.bioluminate.asp_max.get_hydrophobicity_values(scale: int) → dict[slice(<class 'str'>, <class 'float'>, None)]

Get the hydrophobicity values for a given scale.

Parameters:

scale – The scale to use. 0 for Kyte-Doolittle, 1 for Hopp-Woods, up to 7 for Salgado-Rapaport-Asenjo 2006.

Returns:

A dictionary mapping residue types to their hydrophobicity values.

schrodinger.application.bioluminate.asp_max.get_hydrophobicity(residue: ~schrodinger.structure._structure.Residue, hydrophobicity_by_aa: dict[slice(<class 'str'>, <class 'float'>, None)]) → float | None

Get the hydrophobicity of a residue.

Parameters:

  • residue – The residue to analyze.

  • hydrophobicity_by_aa – The hydrophobicity for each amino acid. The dictionary maps the amino acid three-letter code to its hydrophobicity value.

Returns:

The hydrophobicity value of the residue.

schrodinger.application.bioluminate.asp_max.get_asp_values_for_surface_residues(st: ~schrodinger.structure._structure.Structure, surface_residues: dict[slice(<class 'str'>, <class 'schrodinger.application.bioluminate.asp_max.SurfaceRes'>, None)], radius: int) → Generator[float, None, None]

Calculate the ASP values for each residue in the structure.

Parameters:

  • st – The structure to analyze.

  • surface_residues – A dictionary mapping residue ASL to SurfaceRes

  • radius – The distance threshold for ASP calculation.

Returns:

A generator yielding the ASP values for each residue.

schrodinger.application.bioluminate.asp_max.get_asa_by_atom(st: Structure) → list[float]

For a given structure, get the accessible surface area for each atom.

Parameters:

st – The structure to analyze.

Returns:

A list of accessible surface area for each atom where the index is the atom number.

schrodinger.application.bioluminate.asp_max.get_surface_name(st_title: str) → str

From the structure title, return a surface name to describe the surface formed to calculate the asp max.

Parameters:

st_title – The title of the structure

Returns:

The surface name.

schrodinger.application.bioluminate.asp_max.get_surface_residues(st: ~schrodinger.structure._structure.Structure, asa_by_atom: list[float], hydrophobicity_by_aa: dict[slice(<class 'str'>, <class 'float'>, None)]) → dict[slice(<class 'str'>, <class 'schrodinger.application.bioluminate.asp_max.SurfaceRes'>, None)]

For a given structure, get the SurfaceRes object for each residue.

Parameters:

  • st – structure

  • asa_by_atom – list of accessible surface area for each atom where the index is the atom number

  • hydrophobicity_by_aa – The hydrophobicity for each amino acid.

Retrun:

A dictionary mapping residue ASL to SurfaceRes objects.

schrodinger.application.bioluminate.asp_max.get_asp_values(st: ~schrodinger.structure._structure.Structure, radius: int, hydrophobicity_by_aa: dict[slice(<class 'str'>, <class 'float'>, None)]) → list[float]

For a given structure, get the asp values.

Parameters:

  • st – The structure to analyze.

  • radius – The distance threshold for ASP calculation in Angstroms.

  • hydrophobicity_by_aa – The hydrophobicity for each amino acid.

Returns:

A list of ASP values for each residue.

schrodinger.application.bioluminate.asp_max.get_asp_max(st: ~schrodinger.structure._structure.Structure, radius: int, hydrophobicity_by_aa: dict[slice(<class 'str'>, <class 'float'>, None)]) → float

For a given structure, get the asp max value. An asp value is obtained for each patch on the surface of the structure. A patch is created for each residue on the surface of the structure with a radius described by the radius parameter. The ASP value for a given patch is the weighted average of the hydrophobicity of the residues in the patch, weighted by their accessible surface area. The maximum ASP value is returned.

Parameters:

  • st – The structure to analyze.

  • radius – The distance threshold for ASP calculation in Angstroms.

  • hydrophobicity_by_aa – The hydrophobicity for each amino acid.

Returns:

The maximum ASP value.