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Definition

The hydrophobic energy is the fraction of atoms belonging to hydrophobic residues within the selected group. Ehydrophobic=NhydrophobicNGE_{\mathrm{hydrophobic}} = \frac{N_{\mathrm{hydrophobic}}}{N_{G}}
  • NhydrophobicN_{\mathrm{hydrophobic}} is the count of atoms belonging to hydrophobic residues (V, I, L, F, M, W) in the group
  • NGN_G is the total atom count in the group
When mode is set to 'surface' or 'core', this fraction is additionally weighted by the mean normalized SASA of the hydrophobic atoms.

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Parameters

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FoldingOracle
required
The oracle to use for the energy term.
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bool
default:"True"
If a new residue is added next to a residue included in this energy term, this dictates whether that new residue could then be added to this energy term.
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list[Residue] | None
default:"None"
Which residues to include in the calculation. If not set, simply considers all residues by default.
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Literal['surface', 'core', 'all']
default:"'all'"
Selection of which atoms contribute to the hydrophobicity score: - ‘surface’: counts hydrophobic residues at the surface, weighted by normalised SASA - ‘core’: counts hydrophobic residues in the core, weighted by 1 - normalised SASA - ‘all’: counts all hydrophobic residues, no SASA weighting Normalisation uses max_sasa_values['S'] and the probe radius probe_radius_water.
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bool
default:"False"
Deprecated. Use mode='surface' instead.
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bool
default:"False"
Deprecated. Use mode='core' instead.
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float
default:"1.0"
The weight of the energy term.
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str | None
default:"None"
Optional name to append to the energy term name.

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Methods

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compute

Parameters
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OraclesResultDict
required

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Example