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protparam.js
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// A part of the code below fetched from https://github.com/biopython/biopython
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
}
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).
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).
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).
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
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
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'].
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},
}
protein_letters = "ACDEFGHIKLMNPQRSTVWY"
var sum = function(arr) {
return arr.reduce(function(prev, current, i, arr) {
return prev+current;
});
};
class ProtParam {
constructor (protein, id = '', description = '') {
this.protein = protein.toUpperCase();
this.amino_acids = Array.from(this.protein)
this.id = id
this.description = description
}
count_amino_acids (){
var count_dict = {}
for (var i in this.protein) {
var aa = this.protein[i]
if (count_dict[aa]) {
count_dict[aa] += 1
} else {
count_dict[aa] = 1
}
}
for (var i in protein_letters) {
var aa = protein_letters[i]
if(!count_dict[aa]){
count_dict[aa] = 0
}
}
return count_dict
}
get_amino_acids_percent (){
var count_dict = this.count_amino_acids()
for (var aa in count_dict) {
if(this.protein.length==0){
continue
} else{
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?
if(monoisotopic){
var water = 18.010565
var weight_table = monoisotopic_protein_weights
} else {
var water = 18.0153
var weight_table = protein_weights
}
var 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
}
var 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
var ext_Y = 1490
var ext_W = 5500
var ext_C = 125
var count_dict = this.count_amino_acids()
var 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
}
var score = 0.0
for (var i in this.amino_acids){
i = parseInt(i)
if(i >= this.protein.length - 1){
return (10.0 / this.protein.length) * score
}
var this_aa = this.protein[i]
var next_aa = this.protein[i+1]
var dipeptide_value = DIWV[this_aa][next_aa]
score += dipeptide_value
}
}
kd_hydrophobicity(){
return this.amino_acids.map(function(aa){ return kd[aa] })
}
}