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Support ES modules #2

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76289a7
Create protparam.es.js
omaraltayyan Oct 30, 2020
3dba459
Update package.json
omaraltayyan Oct 30, 2020
8d9149a
minor code style fixes
omaraltayyan Oct 30, 2020
bb125bc
fix styling in protparam.js
omaraltayyan Oct 30, 2020
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2 changes: 1 addition & 1 deletion package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"name": "protparamjs",
"version": "1.0.1",
"description": "ProtParam module for javascript",
"main": "protparam.js",
"main": "protparam.es.js",
"scripts": {
"test": "echo \"Error: no test specified\" && exit 1"
},
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375 changes: 375 additions & 0 deletions protparam.es.js
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@@ -0,0 +1,375 @@
// A part of the code below fetched from https://github.com/biopython/biopython

let protein_weights = {
"A": 89.0932,
"C": 121.1582,
"D": 133.1027,
"E": 147.1293,
"F": 165.1891,
"G": 75.0666,
"H": 155.1546,
"I": 131.1729,
"K": 146.1876,
"L": 131.1729,
"M": 149.2113,
"N": 132.1179,
"O": 255.3134,
"P": 115.1305,
"Q": 146.1445,
"R": 174.201,
"S": 105.0926,
"T": 119.1192,
"U": 168.0532,
"V": 117.1463,
"W": 204.2252,
"Y": 181.1885,
};

let monoisotopic_protein_weights = {
"A": 89.047678,
"C": 121.019749,
"D": 133.037508,
"E": 147.053158,
"F": 165.078979,
"G": 75.032028,
"H": 155.069477,
"I": 131.094629,
"K": 146.105528,
"L": 131.094629,
"M": 149.051049,
"N": 132.053492,
"O": 255.158292,
"P": 115.063329,
"Q": 146.069142,
"R": 174.111676,
"S": 105.042593,
"T": 119.058243,
"U": 168.964203,
"V": 117.078979,
"W": 204.089878,
"Y": 181.073893,
};


// Copyright 2003 Yair Benita. All rights reserved.
// This file is part of the Biopython distribution and governed by your
// choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
// Please see the LICENSE file that should have been included as part of this
// package.
// Indices to be used with ProtParam.


// Kyte & Doolittle index of hydrophobicity
// J. Mol. Biol. 157:105-132(1982).
let kd = {
'A': 1.8, 'R': -4.5, 'N': -3.5, 'D': -3.5, 'C': 2.5,
'Q': -3.5, 'E': -3.5, 'G': -0.4, 'H': -3.2, 'I': 4.5,
'L': 3.8, 'K': -3.9, 'M': 1.9, 'F': 2.8, 'P': -1.6,
'S': -0.8, 'T': -0.7, 'W': -0.9, 'Y': -1.3, 'V': 4.2,
};

// Flexibility
// Normalized flexibility parameters (B-values), average
// Vihinen M., Torkkila E., Riikonen P. Proteins. 19(2):141-9(1994).
let Flex = {
'A': 0.984, 'C': 0.906, 'E': 1.094, 'D': 1.068,
'G': 1.031, 'F': 0.915, 'I': 0.927, 'H': 0.950,
'K': 1.102, 'M': 0.952, 'L': 0.935, 'N': 1.048,
'Q': 1.037, 'P': 1.049, 'S': 1.046, 'R': 1.008,
'T': 0.997, 'W': 0.904, 'V': 0.931, 'Y': 0.929,
};

// Hydrophilicity
// 1 Hopp & Wood
// Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981).
let hw = {
'A': -0.5, 'R': 3.0, 'N': 0.2, 'D': 3.0, 'C': -1.0,
'Q': 0.2, 'E': 3.0, 'G': 0.0, 'H': -0.5, 'I': -1.8,
'L': -1.8, 'K': 3.0, 'M': -1.3, 'F': -2.5, 'P': 0.0,
'S': 0.3, 'T': -0.4, 'W': -3.4, 'Y': -2.3, 'V': -1.5,
};

// Surface accessibility
// Vergoten G & Theophanides T, Biomolecular Structure and Dynamics,
// pg.138 (1997).
// 1 Emini Surface fractional probability
let em = {
'A': 0.815, 'R': 1.475, 'N': 1.296, 'D': 1.283, 'C': 0.394,
'Q': 1.348, 'E': 1.445, 'G': 0.714, 'H': 1.180, 'I': 0.603,
'L': 0.603, 'K': 1.545, 'M': 0.714, 'F': 0.695, 'P': 1.236,
'S': 1.115, 'T': 1.184, 'W': 0.808, 'Y': 1.089, 'V': 0.606,
};

// 2 Janin Interior to surface transfer energy scale
let ja = {
'A': 0.28, 'R': -1.14, 'N': -0.55, 'D': -0.52, 'C': 0.97,
'Q': -0.69, 'E': -1.01, 'G': 0.43, 'H': -0.31, 'I': 0.60,
'L': 0.60, 'K': -1.62, 'M': 0.43, 'F': 0.46, 'P': -0.42,
'S': -0.19, 'T': -0.32, 'W': 0.29, 'Y': -0.15, 'V': 0.60,
};


// A two dimensional dictionary for calculating the instability index.
// Guruprasad K., Reddy B.V.B., Pandit M.W. Protein Engineering 4:155-161(1990).
// It is based on dipeptide values; therefore, the value for the dipeptide DG
// is DIWV['D']['G'].
let DIWV = {
'A': {
'A': 1.0, 'C': 44.94, 'E': 1.0, 'D': -7.49,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': -7.49,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0,
},
'C': {
'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 20.26,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 33.60,
'K': 1.0, 'M': 33.60, 'L': 20.26, 'N': 1.0,
'Q': -6.54, 'P': 20.26, 'S': 1.0, 'R': 1.0,
'T': 33.60, 'W': 24.68, 'V': -6.54, 'Y': 1.0,
},
'E': {
'A': 1.0, 'C': 44.94, 'E': 33.60, 'D': 20.26,
'G': 1.0, 'F': 1.0, 'I': 20.26, 'H': -6.54,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': 1.0,
'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0,
},
'D': {
'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0,
'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 1.0, 'P': 1.0, 'S': 20.26, 'R': -6.54,
'T': -14.03, 'W': 1.0, 'V': 1.0, 'Y': 1.0,
},
'G': {
'A': -7.49, 'C': 1.0, 'E': -6.54, 'D': 1.0,
'G': 13.34, 'F': 1.0, 'I': -7.49, 'H': 1.0,
'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': -7.49,
'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0,
'T': -7.49, 'W': 13.34, 'V': 1.0, 'Y': -7.49,
},
'F': {
'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 13.34,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
'K': -14.03, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 33.601,
},
'I': {
'A': 1.0, 'C': 1.0, 'E': 44.94, 'D': 1.0,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 13.34,
'K': -7.49, 'M': 1.0, 'L': 20.26, 'N': 1.0,
'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0,
'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0,
},
'H': {
'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': -9.37, 'F': -9.37, 'I': 44.94, 'H': 1.0,
'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 24.68,
'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0,
'T': -6.54, 'W': -1.88, 'V': 1.0, 'Y': 44.94,
},
'K': {
'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': -7.49, 'F': 1.0, 'I': -7.49, 'H': 1.0,
'K': 1.0, 'M': 33.60, 'L': -7.49, 'N': 1.0,
'Q': 24.64, 'P': -6.54, 'S': 1.0, 'R': 33.60,
'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0,
},
'M': {
'A': 13.34, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 58.28,
'K': 1.0, 'M': -1.88, 'L': 1.0, 'N': 1.0,
'Q': -6.54, 'P': 44.94, 'S': 44.94, 'R': -6.54,
'T': -1.88, 'W': 1.0, 'V': 1.0, 'Y': 24.68,
},
'L': {
'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 33.60, 'P': 20.26, 'S': 1.0, 'R': 20.26,
'T': 1.0, 'W': 24.68, 'V': 1.0, 'Y': 1.0,
},
'N': {
'A': 1.0, 'C': -1.88, 'E': 1.0, 'D': 1.0,
'G': -14.03, 'F': -14.03, 'I': 44.94, 'H': 1.0,
'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': -6.54, 'P': -1.88, 'S': 1.0, 'R': 1.0,
'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 1.0,
},
'Q': {
'A': 1.0, 'C': -6.54, 'E': 20.26, 'D': 20.26,
'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 1.0,
'T': 1.0, 'W': 1.0, 'V': -6.54, 'Y': -6.54,
},
'P': {
'A': 20.26, 'C': -6.54, 'E': 18.38, 'D': -6.54,
'G': 1.0, 'F': 20.26, 'I': 1.0, 'H': 1.0,
'K': 1.0, 'M': -6.54, 'L': 1.0, 'N': 1.0,
'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': -6.54,
'T': 1.0, 'W': -1.88, 'V': 20.26, 'Y': 1.0,
},
'S': {
'A': 1.0, 'C': 33.60, 'E': 20.26, 'D': 1.0,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 20.26, 'P': 44.94, 'S': 20.26, 'R': 20.26,
'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0,
},
'R': {
'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 20.26,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 13.34,
'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 58.28,
'T': 1.0, 'W': 58.28, 'V': 1.0, 'Y': -6.54,
},
'T': {
'A': 1.0, 'C': 1.0, 'E': 20.26, 'D': 1.0,
'G': -7.49, 'F': 13.34, 'I': 1.0, 'H': 1.0,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': -14.03,
'Q': -6.54, 'P': 1.0, 'S': 1.0, 'R': 1.0,
'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0,
},
'W': {
'A': -14.03, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': -9.37, 'F': 1.0, 'I': 1.0, 'H': 24.68,
'K': 1.0, 'M': 24.68, 'L': 13.34, 'N': 13.34,
'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0,
'T': -14.03, 'W': 1.0, 'V': -7.49, 'Y': 1.0,
},
'V': {
'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': -14.03,
'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 1.0,
'K': -1.88, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
'T': -7.49, 'W': 1.0, 'V': 1.0, 'Y': -6.54,
},
'Y': {
'A': 24.68, 'C': 1.0, 'E': -6.54, 'D': 24.68,
'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 13.34,
'K': 1.0, 'M': 44.94, 'L': 1.0, 'N': 1.0,
'Q': 1.0, 'P': 13.34, 'S': 1.0, 'R': -15.91,
'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 13.34,
},
};

let protein_letters = "ACDEFGHIKLMNPQRSTVWY";

let sum = function (arr) {
return arr.reduce(function (prev, current, i, arr) {
return prev + current;
});
};

export default class ProtParam {

/**
*
* @param protein {string}
* @param id
* @param description
*/
constructor(protein, id = '', description = '') {
this.protein = protein.toUpperCase();
this.amino_acids = Array.from(this.protein);
this.id = id;
this.description = description;
}

count_amino_acids() {
let count_dict = {};
for (let aa in this.amino_acids) {
if (count_dict[aa]) {
count_dict[aa] += 1;
} else {
count_dict[aa] = 1;
}
}
for (let aa in this.amino_acids) {
if (!count_dict[aa]) {
count_dict[aa] = 0;
}
}
return count_dict;
}

get_amino_acids_percent() {
let count_dict = this.count_amino_acids();
for (let aa in count_dict) {
if (this.protein.length !== 0) {
count_dict[aa] = count_dict[aa] / this.protein.length;
}
}
return count_dict;
}

molecular_weight(circular = false, monoisotopic = false) {
if (this.protein.length === 0) {
return null;
}
// circular: Is the molecule circular (has no ends)?
// monoisotopic: Use the monoisotopic mass tables?
let water = 18.0153;
let weight_table = protein_weights;

if (monoisotopic) {
water = 18.010565;
weight_table = monoisotopic_protein_weights;
}
let weight = sum(this.amino_acids.map(function (aa) {
return weight_table[aa];
}));
weight -= (this.protein.length - 1) * water;
if (circular) {
weight -= water;
}
return weight;
}

gravy() {
if (this.protein.length === 0) {
return null;
}
let total_gravy = sum(this.kd_hydrophobicity());
return total_gravy / this.protein.length;
}

absorbance() {
if (this.protein.length === 0) {
return null;
}
// Tyr Y , Thr T, Trp W, Cys C
let ext_Y = 1490;
let ext_W = 5500;
let ext_C = 125;
let count_dict = this.count_amino_acids();
let extinction_coefficients = count_dict["Y"] * ext_Y + count_dict["W"] * ext_W + count_dict["C"] * ext_C;
return extinction_coefficients / this.molecular_weight();
}

instability_index() {
if (this.protein.length === 0) {
return null;
}
let score = 0.0;
for (let i = 0; i < this.amino_acids.length; i++ ) {
if (i >= this.protein.length - 1) {
return (10.0 / this.protein.length) * score;
}
let this_aa = this.protein[i];
let next_aa = this.protein[i + 1];
let dipeptide_value = DIWV[this_aa][next_aa];
score += dipeptide_value;
}
}

kd_hydrophobicity() {
return this.amino_acids.map(function (aa) {
return kd[aa];
});
}

}
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