Hydrophobicity scales and profiling

[NoraHeese]

Description

Added hydrophobicity scale data by adding the function getHydrophobicity() to the Residue which returns the hydrophobocity value for an amino acid in a given scale.
Added the new class HydrophobicityProfile which is used for calculation hydrophobicity profiles for peptides.
It has functions for calculating GRAVY score, hydrophobicity profiles, windowed hydrophobicity profiles and hydrophobic moments of a peptide.

for Issue OpenMS#9005

Checklist

• Make sure that you are listed in the AUTHORS file
• Add relevant changes and new features to the CHANGELOG file
• I have commented my code, particularly in hard-to-understand areas
• New and existing unit tests pass locally with my changes
• Updated or added python bindings for changed or new classes (Tick if no updates were necessary.)

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[TheClaervoyant]

Coding Convention

[TheClaervoyant]

In the exception, the empty String part is kind of irritating. Replacement with the scale, since it caused the exception. Or - if needed - cast to string?

[TheClaervoyant]

See comment above. One letter Code caused the exception here

[TheClaervoyant]

Why not SIXSEVEN?

[TheClaervoyant]

SICKSEVEN

[TheClaervoyant]

Hey Chris ;D

[cbielow]

Suggested change

	throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Unknown hydrophobicity scale", "");
	throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Unknown hydrophobicity scale", String(scale_idx));

[cbielow]

Suggested change

	Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol. 1984 Oct 15;179(1):125-42. doi: 10.1016/0022-2836(84)90309-7. PMID: 6502707.
	Eisenberg D, Weiss RM, Terwilliger TC. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci U S A. 1984 Jan;81(1):140-4. doi: 10.1073/pnas.81.1.140. PMID: 6582470; PMCID: PMC344626.
	- Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol. 1984 Oct 15;179(1):125-42. doi: 10.1016/0022-2836(84)90309-7. PMID: 6502707.
	- Eisenberg D, Weiss RM, Terwilliger TC. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci U S A. 1984 Jan;81(1):140-4. doi: 10.1073/pnas.81.1.140. PMID: 6582470; PMCID: PMC344626.

[cbielow]

Suggested change

	Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105-32. doi: 10.1016/0022-2836(82)90515-0. PMID: 7108955.
	Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol. 1984 Oct 15;179(1):125-42. doi: 10.1016/0022-2836(84)90309-7. PMID: 6502707.
	T.P. Hopp, & K.R. Woods, Prediction of protein antigenic determinants from amino acid sequences., Proc. Natl. Acad. Sci. U.S.A. 78 (6) 3824-3828, https://doi.org/10.1073/pnas.78.6.3824 (1981).
	- Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105-32. doi: 10.1016/0022-2836(82)90515-0. PMID: 7108955.
	- Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol. 1984 Oct 15;179(1):125-42. doi: 10.1016/0022-2836(84)90309-7. PMID: 6502707.
	- T.P. Hopp, & K.R. Woods, Prediction of protein antigenic determinants from amino acid sequences., Proc. Natl. Acad. Sci. U.S.A. 78 (6) 3824-3828, https://doi.org/10.1073/pnas.78.6.3824 (1981).

[cbielow]

Suggested change

	Henry B. Bull, Keith Breese, Surface tension of amino acid solutions: A hydrophobicity scale of the amino acid residues, Archives of Biochemistry and Biophysics, Volume 161, Issue 2, 1974, Pages 665-670, ISSN 0003-9861, https://doi.org/10.1016/0003-9861(74)90352-X. (https://www.sciencedirect.com/science/article/pii/000398617490352X)
	Black SD, Mould DR. Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications. Anal Biochem. 1991 Feb 15;193(1):72-82. doi: 10.1016/0003-2697(91)90045-u. PMID: 2042744.
	Guy, H. R. (1985). Amino acid side-chain partition energies and distribution of residues in soluble proteins. Biophysical journal, 47(1), 61-70.
	- Henry B. Bull, Keith Breese, Surface tension of amino acid solutions: A hydrophobicity scale of the amino acid residues, Archives of Biochemistry and Biophysics, Volume 161, Issue 2, 1974, Pages 665-670, ISSN 0003-9861, https://doi.org/10.1016/0003-9861(74)90352-X. (https://www.sciencedirect.com/science/article/pii/000398617490352X)
	- Black SD, Mould DR. Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications. Anal Biochem. 1991 Feb 15;193(1):72-82. doi: 10.1016/0003-2697(91)90045-u. PMID: 2042744.
	- Guy, H. R. (1985). Amino acid side-chain partition energies and distribution of residues in soluble proteins. Biophysical journal, 47(1), 61-70.

[cbielow]

Suggested change

	Size window_size = 7,
	const Size window_size = 7,

[cbielow]

Suggested change

	/// @brief returns the hydrophobicity value of the residue
	/// The sources for the hydrophobicity scales are here: @ref HydrophobicityProfile
	/// @param scale which scale to use for the hydrophobicity value
	/// @return hydrophobicity value of the residue
	/// @throw Exception::InvalidValue Throws an exception if the residue is not one of the 20 common amino acids or when an unknown scale is used
	/**
	@brief returns the hydrophobicity value of the residue
	The sources for the hydrophobicity scales are here: @ref HydrophobicityProfile
	@param scale which scale to use for the hydrophobicity value
	@return hydrophobicity value of the residue
	@throw Exception::InvalidValue Throws an exception if the residue is not one of the 20 common amino acids or when an unknown scale is used
	*/

[cbielow]

Suggested change

	/// @brief Enum for different hydrophobicity scales
	/// If a new scale is introduced, append it to the list below and assign it an enum value equal to the current maximum enum value plus one.
	/// Add the data for this scale here: @ref Residue::getHydrophobicity
	/**
	@brief Enum for different hydrophobicity scales
	If a new scale is introduced, append it to the list below and assign it an enum value equal to the current maximum enum value plus one.
	Add the data for this scale here: @ref Residue::getHydrophobicity
	*/

[cbielow]

Suggested change

	Size window_size,
	const Size window_size,

[cbielow]

Suggested change

	if (window_size > seq.size())
	{
	OPENMS_LOG_WARN << "Warning: window size (" << window_size << ") is larger than sequence length. Window size clamped to sequence length: " << seq.size() << "\n";
	}
	std::vector<double> profile;
	Size effective_window = std::min(window_size, seq.size()); // size of the window
	const Size effective_window = [&](){
	if (window_size > seq.size())
	{
	OPENMS_LOG_WARN << "Warning: window size (" << window_size << ") is larger than sequence length. Window size clamped to sequence length: " << seq.size() << "\n";
	return seq.size();
	}
	return window_size;
	};
	std::vector<double> profile;

[cbielow]

Suggested change

	Size window_size,
	double angle
	const Size window_size,
	const double angle

[cbielow]

Suggested change

	sum_sin = std::pow(sum_sin,2);
	sum_cos = std::pow(sum_cos,2);
	sum_sin *= sum_sin; // square
	sum_cos *= sum_cos; // square

[cbielow]

Suggested change

	profile.push_back(std::sqrt(sum_sin+sum_cos) / std::min(window_size, seq.size()));
	profile.push_back(std::sqrt(sum_sin+sum_cos) / effective_window);

[cbielow]

Suggested change

	if (amino_acid < 65 || amino_acid > 90)
	if (amino_acid < 'A' || amino_acid > 'Z')