hydrophobicity module
Code author: Niklaus Johner <niklaus.johner@a3.epfl.ch>
This module contains function to calculate hydrophobicity and hydrophobic
moments from different hydrophobic scales.
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CalculateCharge(sequence)[source]
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CalculateChargeWithSlidingWindow(sequence, w=11)[source]
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GetResidueHydrophobicity(res, hydrophobicity_dict={'A': 0.62, 'C': 0.29, 'E': -0.74, 'D': -0.9, 'G': 0.48, 'F': 1.19, 'I': 1.38, 'H': -0.4, 'K': -1.5, 'M': 0.64, 'L': 1.06, 'N': -0.78, 'Q': -0.85, 'P': 0.12, 'S': -0.18, 'R': -2.53, 'T': -0.05, 'W': 0.81, 'V': 1.08, 'Y': 0.26})[source]
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CalculateHydrophobicMoment(sequence, angle=1.7453292519943295, hydrophobicity_dict={'A': 0.62, 'C': 0.29, 'E': -0.74, 'D': -0.9, 'G': 0.48, 'F': 1.19, 'I': 1.38, 'H': -0.4, 'K': -1.5, 'M': 0.64, 'L': 1.06, 'N': -0.78, 'Q': -0.85, 'P': 0.12, 'S': -0.18, 'R': -2.53, 'T': -0.05, 'W': 0.81, 'V': 1.08, 'Y': 0.26})[source]
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CalculateHydrophobicMoment2(sequence, angle=1.7453292519943295, hydrophobicity_dict={'A': 0.62, 'C': 0.29, 'E': -0.74, 'D': -0.9, 'G': 0.48, 'F': 1.19, 'I': 1.38, 'H': -0.4, 'K': -1.5, 'M': 0.64, 'L': 1.06, 'N': -0.78, 'Q': -0.85, 'P': 0.12, 'S': -0.18, 'R': -2.53, 'T': -0.05, 'W': 0.81, 'V': 1.08, 'Y': 0.26})[source]
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CalculateHydrophobicMoment3(sequence, angle=1.7453292519943295, hydrophobicity_dict={'A': 0.62, 'C': 0.29, 'E': -0.74, 'D': -0.9, 'G': 0.48, 'F': 1.19, 'I': 1.38, 'H': -0.4, 'K': -1.5, 'M': 0.64, 'L': 1.06, 'N': -0.78, 'Q': -0.85, 'P': 0.12, 'S': -0.18, 'R': -2.53, 'T': -0.05, 'W': 0.81, 'V': 1.08, 'Y': 0.26})[source]
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CalculateHydrophobicMomentWithSlidingWindow(sequence, w=11, angle=1.7453292519943295, hydrophobicity_dict={'A': 0.62, 'C': 0.29, 'E': -0.74, 'D': -0.9, 'G': 0.48, 'F': 1.19, 'I': 1.38, 'H': -0.4, 'K': -1.5, 'M': 0.64, 'L': 1.06, 'N': -0.78, 'Q': -0.85, 'P': 0.12, 'S': -0.18, 'R': -2.53, 'T': -0.05, 'W': 0.81, 'V': 1.08, 'Y': 0.26})[source]
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CalculateHydrophobicity(sequence, hydrophobicity_dict={'A': 0.62, 'C': 0.29, 'E': -0.74, 'D': -0.9, 'G': 0.48, 'F': 1.19, 'I': 1.38, 'H': -0.4, 'K': -1.5, 'M': 0.64, 'L': 1.06, 'N': -0.78, 'Q': -0.85, 'P': 0.12, 'S': -0.18, 'R': -2.53, 'T': -0.05, 'W': 0.81, 'V': 1.08, 'Y': 0.26})[source]
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CalculateHydrophobicityWithSlidingWindow(sequence, w=11, hydrophobicity_dict={'A': 0.62, 'C': 0.29, 'E': -0.74, 'D': -0.9, 'G': 0.48, 'F': 1.19, 'I': 1.38, 'H': -0.4, 'K': -1.5, 'M': 0.64, 'L': 1.06, 'N': -0.78, 'Q': -0.85, 'P': 0.12, 'S': -0.18, 'R': -2.53, 'T': -0.05, 'W': 0.81, 'V': 1.08, 'Y': 0.26})[source]
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DetermineAmphipathicity(sequence, w=11, angle=1.7453292519943295)[source]
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AnalyzeHydrophobicMoment(sequence, w=11, angle_min=1.39, angle_max=3.14, step=0.1, hydrophobicity_dict={'A': 0.62, 'C': 0.29, 'E': -0.74, 'D': -0.9, 'G': 0.48, 'F': 1.19, 'I': 1.38, 'H': -0.4, 'K': -1.5, 'M': 0.64, 'L': 1.06, 'N': -0.78, 'Q': -0.85, 'P': 0.12, 'S': -0.18, 'R': -2.53, 'T': -0.05, 'W': 0.81, 'V': 1.08, 'Y': 0.26})[source]