peptide-score 2.3.14

package/lib/src/generatePeptideFragments.js

@@ -0,0 +1,89 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.generatePeptideFragments = generatePeptideFragments;
+function generatePeptideFragments(mf, options) {
+    if (options === undefined) {
+        options = {
+            a: false,
+            b: true,
+            c: false,
+            x: false,
+            y: true,
+            z: false,
+            i: false,
+            ya: false,
+            yb: false,
+            yc: false,
+            zc: false,
+        };
+    }
+    options.maxInternal = options.maxInternal || Number.MAX_VALUE;
+    options.minInternal = options.minInternal || 0;
+    let mfs = [];
+    // need to allow 0-9 to deal with neutral loss
+    let mfparts = mf
+        .replaceAll(/([\d)a-z])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
+        .split(/ /);
+    let nTerm = '';
+    let cTerm = '';
+    if (mfparts[0].startsWith('(')) {
+        nTerm += mfparts[0];
+        mfparts = mfparts.splice(1);
+    }
+    if (mfparts.at(-1).includes('(')) {
+        cTerm += mfparts.at(-1).replace(/^[^()]*/, '');
+        mfparts[mfparts.length - 1] = mfparts.at(-1).replace(/\(.*/, '');
+    }
+    for (let i = 1; i < mfparts.length; i++) {
+        nTerm += mfparts[i - 1];
+        cTerm = mfparts[mfparts.length - i] + cTerm;
+        addNTerm(mfs, nTerm, i, options);
+        addCTerm(mfs, cTerm, i, options);
+        if (options.i)
+            mfs.push(`${mfparts[i]}HC-1O-1(+1)$i:${mfparts[i]}`);
+        if (options.ya || options.yb || options.yc || options.zc) {
+            // we have double fragmentations
+            for (let j = i + 1; j < Math.min(mfparts.length, options.maxInternal + i + 1); j++) {
+                let iTerm = '';
+                if (j - i >= options.minInternal) {
+                    for (let k = i; k < j; k++) {
+                        iTerm += mfparts[k];
+                    }
+                    addITerm(mfs, iTerm, mfparts.length - i, j, options);
+                }
+            }
+        }
+    }
+    // todo does this make sense ??? I think we should remote those 3 lines
+    if (mfs.length === 0) {
+        mfs = mfs.concat([mf]);
+    }
+    return mfs;
+}
+function addNTerm(mfs, nTerm, i, options) {
+    if (options.a)
+        mfs.push(`${nTerm}C-1O-1(+1)$a${i}`);
+    if (options.b)
+        mfs.push(`${nTerm}(+1)$b${i}`);
+    if (options.c)
+        mfs.push(`${nTerm}NH3(+1)$c${i}`);
+}
+function addITerm(mfs, iTerm, i, j, options) {
+    if (options.ya)
+        mfs.push(`H${iTerm}C-1O-1(+1)$a${j}y${i}`);
+    if (options.yb)
+        mfs.push(`H${iTerm}(+1)$b${j}y${i}`);
+    if (options.yc)
+        mfs.push(`H${iTerm}NH3(+1)$c${j}y${i}`);
+    if (options.zc)
+        mfs.push(`N-1${iTerm}NH3(+1)$c${j}z${i}`);
+}
+function addCTerm(mfs, cTerm, i, options) {
+    if (options.x)
+        mfs.push(`CO(+1)${cTerm}$x${i}`);
+    if (options.y)
+        mfs.push(`H2(+1)${cTerm}$y${i}`);
+    if (options.z)
+        mfs.push(`N-1H-1(+1)${cTerm}$z${i}`);
+}
+//# sourceMappingURL=generatePeptideFragments.js.map

package/lib/src/generatePeptideFragments.js.map

@@ -0,0 +1 @@
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package/lib/src/getAA.d.ts

@@ -0,0 +1,29 @@
+export function getAA(code: any): {
+    name: string;
+    aa3: string;
+    aa1: string;
+    sc: {
+        type: string;
+        pKa?: undefined;
+    };
+    pKaC: number;
+    pKaN: number;
+} | {
+    name: string;
+    aa3: string;
+    aa1: string;
+    sc: {
+        type: string;
+        pKa: number;
+    };
+    pKaC: number;
+    pKaN: number;
+} | {
+    name: string;
+    aa3: string;
+    aa1: string;
+    sc?: undefined;
+    pKaC?: undefined;
+    pKaN?: undefined;
+} | undefined;
+//# sourceMappingURL=getAA.d.ts.map

package/lib/src/getAA.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"getAA.d.ts","sourceRoot":"","sources":["../../src/getAA.js"],"names":[],"mappings":"AAEA;;;;;;;;;;;;;;;;;;;;;;;;;;;cAeC"}

package/lib/src/getAA.js

@@ -0,0 +1,21 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getAA = getAA;
+const aminoAcids_1 = require("./aminoAcids");
+function getAA(code) {
+    if (code.length === 1) {
+        for (let i = 0; i < aminoAcids_1.aminoAcids.length; i++) {
+            if (aminoAcids_1.aminoAcids[i].aa1 === code) {
+                return aminoAcids_1.aminoAcids[i];
+            }
+        }
+    }
+    if (code.length === 3) {
+        for (let i = 0; i < aminoAcids_1.aminoAcids.length; i++) {
+            if (aminoAcids_1.aminoAcids[i].aa3 === code) {
+                return aminoAcids_1.aminoAcids[i];
+            }
+        }
+    }
+}
+//# sourceMappingURL=getAA.js.map

package/lib/src/getAA.js.map

@@ -0,0 +1 @@
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package/lib/src/index.d.ts

@@ -0,0 +1,44 @@
+export function getInfo(): ({
+    name: string;
+    aa3: string;
+    aa1: string;
+    sc: {
+        type: string;
+        pKa?: undefined;
+    };
+    pKaC: number;
+    pKaN: number;
+} | {
+    name: string;
+    aa3: string;
+    aa1: string;
+    sc: {
+        type: string;
+        pKa: number;
+    };
+    pKaC: number;
+    pKaN: number;
+} | {
+    name: string;
+    aa3: string;
+    aa1: string;
+    sc?: undefined;
+    pKaC?: undefined;
+    pKaN?: undefined;
+})[];
+export function calculateIEP(sequence: any): number | undefined;
+export function calculateIEPChart(sequence: any): {
+    first: any;
+    last: any;
+    basic: {};
+    acid: {};
+} | undefined;
+export function getColorForIEP(iep: any): string;
+export function calculateCharge(sequence: any, ph: any): number | undefined;
+export * from "./allowNeutralLoss.js";
+export * from "./chargePeptide.js";
+export * from "./sequenceToMF.js";
+export * from "./generatePeptideFragments.js";
+export * from "./digestPeptide.js";
+export * from "./splitPeptide.js";
+//# sourceMappingURL=index.d.ts.map

package/lib/src/index.d.ts.map

@@ -0,0 +1 @@
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package/lib/src/index.js

@@ -0,0 +1,74 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getInfo = getInfo;
+exports.calculateIEP = calculateIEP;
+exports.calculateIEPChart = calculateIEPChart;
+exports.getColorForIEP = getColorForIEP;
+exports.calculateCharge = calculateCharge;
+const aminoAcids_1 = require("./aminoAcids");
+const IEP = __importStar(require("./isoElectricPoint"));
+const splitPeptide_js_1 = require("./splitPeptide.js");
+__exportStar(require("./allowNeutralLoss.js"), exports);
+__exportStar(require("./chargePeptide.js"), exports);
+__exportStar(require("./sequenceToMF.js"), exports);
+__exportStar(require("./generatePeptideFragments.js"), exports);
+__exportStar(require("./digestPeptide.js"), exports);
+__exportStar(require("./splitPeptide.js"), exports);
+function getInfo() {
+    return aminoAcids_1.aminoAcids;
+}
+// sequence should be in the "right" format like HAlaGlyProOH
+function calculateIEP(sequence) {
+    let aas = (0, splitPeptide_js_1.splitPeptide)(sequence);
+    let result = IEP.calculateIEP(aas);
+    return result;
+}
+function calculateIEPChart(sequence) {
+    let aas = (0, splitPeptide_js_1.splitPeptide)(sequence);
+    let result = IEP.calculateChart(aas);
+    return result;
+}
+function getColorForIEP(iep) {
+    return IEP.getColor(iep);
+}
+function calculateCharge(sequence, ph) {
+    let aas = (0, splitPeptide_js_1.splitPeptide)(sequence);
+    return IEP.calculateCharge(aas, ph);
+}
+//# sourceMappingURL=index.js.map

package/lib/src/index.js.map

@@ -0,0 +1 @@
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package/lib/src/isoElectricPoint.d.ts

@@ -0,0 +1,10 @@
+export function calculateCharge(aas: any, pH?: number): number | undefined;
+export function calculateIEP(aas: any): number | undefined;
+export function calculateChart(aas: any): {
+    first: any;
+    last: any;
+    basic: {};
+    acid: {};
+} | undefined;
+export function getColor(iep: any): string;
+//# sourceMappingURL=isoElectricPoint.d.ts.map

package/lib/src/isoElectricPoint.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"isoElectricPoint.d.ts","sourceRoot":"","sources":["../../src/isoElectricPoint.js"],"names":[],"mappings":"AAQA,2EAKC;AAID,2DAqBC;AAED;;;;;cAiBC;AAuDD,2CAWC"}

package/lib/src/isoElectricPoint.js

@@ -0,0 +1,134 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.calculateCharge = calculateCharge;
+exports.calculateIEP = calculateIEP;
+exports.calculateChart = calculateChart;
+exports.getColor = getColor;
+const aminoAcids_1 = require("./aminoAcids");
+// we will convert the data to an object to be much faster
+let aaObject = {};
+for (let i = 0; i < aminoAcids_1.aminoAcids.length; i++) {
+    aaObject[aminoAcids_1.aminoAcids[i].aa3] = aminoAcids_1.aminoAcids[i];
+}
+function calculateCharge(aas, pH = 7) {
+    let combined = combine(aas);
+    if (!combined)
+        return;
+    let charge = calculateForPh(combined, pH);
+    return Math.round(charge * 1000) / 1000;
+}
+// this methods required an array of aas
+function calculateIEP(aas) {
+    let combined = combine(aas);
+    if (!combined)
+        return;
+    let first = 0;
+    let last = 14;
+    let current = 14;
+    let previous = 0;
+    let currentCharge;
+    while (Math.abs(current - previous) > 0.0001) {
+        previous = current;
+        current = (last + first) / 2;
+        currentCharge = calculateForPh(combined, current);
+        if (currentCharge > 0) {
+            first = current;
+        }
+        else if (currentCharge < 0) {
+            last = current;
+        }
+        else {
+            previous = current;
+        }
+    }
+    return Math.round(current * 1000) / 1000;
+}
+function calculateChart(aas) {
+    let combined = combine(aas);
+    if (!combined)
+        return;
+    let y = [];
+    let x = [];
+    let yAbs = [];
+    for (let i = 0; i <= 14; i = i + 0.01) {
+        let charge = calculateForPh(combined, i);
+        x.push(i);
+        y.push(charge);
+        yAbs.push(Math.abs(charge));
+    }
+    combined.x = x;
+    combined.y = y;
+    combined.yAbs = yAbs;
+    return combined;
+}
+function calculateForPh(combined, pH) {
+    let total = 0;
+    total += 1 / (1 + 10 ** (pH - combined.first));
+    total += -1 / (1 + 10 ** (combined.last - pH));
+    for (let key in combined.acid) {
+        total += -combined.acid[key] / (1 + 10 ** (aaObject[key].sc.pKa - pH));
+    }
+    for (let key in combined.basic) {
+        total += combined.basic[key] / (1 + 10 ** (pH - aaObject[key].sc.pKa));
+    }
+    return total;
+}
+// we will combine the amino acids
+function combine(aas) {
+    let combined = {};
+    if (aaObject[aas[0]]) {
+        combined.first = aaObject[aas[0]].pKaN;
+    }
+    else {
+        return;
+    }
+    if (aaObject[aas.at(-1)]) {
+        combined.last = aaObject[aas.at(-1)].pKaC;
+    }
+    else {
+        return;
+    }
+    combined.basic = {};
+    combined.acid = {};
+    for (let i = 0; i < aas.length; i++) {
+        let currentAA = aas[i];
+        if (!aaObject[currentAA])
+            return;
+        if (aaObject[currentAA].sc && aaObject[currentAA].sc.type) {
+            if (aaObject[currentAA].sc.type === 'positive') {
+                if (!combined.basic[currentAA]) {
+                    combined.basic[currentAA] = 0;
+                }
+                combined.basic[currentAA]++;
+            }
+            else if (aaObject[currentAA].sc.type === 'negative') {
+                if (!combined.acid[currentAA]) {
+                    combined.acid[currentAA] = 0;
+                }
+                combined.acid[currentAA]++;
+            }
+        }
+    }
+    return combined;
+}
+/*
+ We can generate a color based on iep
+ 0 -> 7 means that at pH 7 it is charged negatively (blue)
+ 7 -> 14 means that at pH7 it is charged positively (red)
+ */
+function getColor(iep) {
+    if (iep < 7) {
+        if (iep < 3)
+            iep = 3;
+        let white = Math.round(255 - (7 - iep) * (200 / 4));
+        return `rgb(${white},${white},255)`;
+    }
+    else if (iep > 7) {
+        if (iep > 11)
+            iep = 11;
+        let white = Math.round(255 - (iep - 7) * (200 / 4));
+        return `rgb(255,${white},${white})`;
+    }
+    return 'rgb(255,255,255)';
+}
+//# sourceMappingURL=isoElectricPoint.js.map

package/lib/src/isoElectricPoint.js.map

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package/lib/src/sequenceToMF.d.ts

@@ -0,0 +1,2 @@
+export function sequenceToMF(mf: any): any;
+//# sourceMappingURL=sequenceToMF.d.ts.map

package/lib/src/sequenceToMF.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"sequenceToMF.d.ts","sourceRoot":"","sources":["../../src/sequenceToMF.js"],"names":[],"mappings":"AAIA,2CA+DC"}

package/lib/src/sequenceToMF.js

@@ -0,0 +1,99 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.sequenceToMF = sequenceToMF;
+const mf_utilities_1 = require("mf-utilities");
+const aminoAcids_1 = require("./aminoAcids");
+function sequenceToMF(mf) {
+    if (mf === '')
+        return '';
+    mf = (0, mf_utilities_1.ensureUppercaseSequence)(mf);
+    // this function will check if it is a sequence of aa in 1 letter or 3 letters and convert them if it is the case
+    // it could be a multiline mf !
+    // if it is a multiline we could make some "tricks" ...
+    let newMF = mf;
+    // SEQRES   1 B  256  MET PRO VAL GLU ILE THR VAL LYS GLU LEU LEU GLU ALA
+    // SEQRES   2 B  256  GLY VAL HIS PHE GLY HIS GLU ARG LYS ARG TRP ASN PRO
+    // or
+    // MET PRO VAL GLU ILE THR VAL LYS GLU LEU LEU GLU ALA
+    // GLY VAL HIS PHE GLY HIS GLU ARG LYS ARG TRP ASN PRO
+    if (mf.search(/(?:[A-Z]{3} ){2}[A-Z]{3}/) > -1) {
+        // this is a PDB !
+        let tmpmf = mf.replaceAll(/[\n\r]+/g, ' ');
+        tmpmf = tmpmf.replaceAll(/(SEQRES|\d+| [A-Z] | [\dA-Z]{4-50})/g, '');
+        // we need to correct the uppercase / lowercase
+        let parts = tmpmf.split(' ');
+        newMF = 'H';
+        for (let i = 0; i < parts.length; i++) {
+            newMF += parts[i].slice(0, 1) + parts[i].slice(1).toLowerCase();
+        }
+        newMF += 'OH';
+    }
+    else if (mf.includes('(') && isOneLetterCode(mf)) {
+        // we expect one-letter code with modification
+        newMF = '';
+        let nTerminal = 'H';
+        let cTerminal = 'OH';
+        let parenthesisCounter = 0;
+        for (let i = 0; i < mf.length; i++) {
+            let currentSymbol = mf[i];
+            if (currentSymbol === '(' ||
+                currentSymbol === ')' ||
+                parenthesisCounter > 0) {
+                if (currentSymbol === '(') {
+                    parenthesisCounter++;
+                    if (i === 0)
+                        nTerminal = '';
+                }
+                if (currentSymbol === ')') {
+                    parenthesisCounter--;
+                    if (i === mf.length - 1)
+                        cTerminal = '';
+                }
+                newMF += currentSymbol;
+                continue;
+            }
+            newMF += convertAA1To3(currentSymbol);
+        }
+        newMF = nTerminal + newMF + cTerminal;
+    }
+    else if (mf.search(/[A-Za-z][\da-z]/) === -1) {
+        // UNIPROT
+        //   370        380        390        400        410        420
+        //GFKPNLRKTF VSGLFRESCG AHFYRGVDVK PFYIKKPVDN LFALMLILNR LRGWGVVGGM
+        //
+        //    430        440        450        460        470        480
+        //SDPRLYKVWV RLSSQVPSMF FGGTDLAADY YVVSPPTAVS VYTKTPYGRL LADTRTSGFR
+        // We remove all the number, all the spaces, etc
+        newMF = `H${convertAA1To3(newMF.replaceAll(/[^A-Z]/g, ''))}OH`;
+    }
+    return newMF;
+}
+function convertAA1To3(mf) {
+    let newmf = '';
+    for (let i = 0; i < mf.length; i++) {
+        newmf += aa1To3(mf.charAt(i));
+    }
+    return newmf;
+}
+function aa1To3(code) {
+    for (let i = 0; i < aminoAcids_1.aminoAcids.length; i++) {
+        if (aminoAcids_1.aminoAcids[i].aa1 === code) {
+            return aminoAcids_1.aminoAcids[i].aa3;
+        }
+    }
+    throw new Error(`Invalid 1 letter code: ${code}`);
+}
+// mf can contain as well parenthesis. We need to check if it is not yet a correct molecular formula
+function isOneLetterCode(mf) {
+    let parenthesisLevel = 0;
+    for (let char of mf) {
+        if (parenthesisLevel === 0 && char.match(/[a-z]/))
+            return false;
+        if (char === '(')
+            parenthesisLevel++;
+        if (char === ')')
+            parenthesisLevel--;
+    }
+    return true;
+}
+//# sourceMappingURL=sequenceToMF.js.map

package/lib/src/sequenceToMF.js.map

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package/lib/src/splitPeptide.d.ts

@@ -0,0 +1,2 @@
+export function splitPeptide(sequence: any): any;
+//# sourceMappingURL=splitPeptide.d.ts.map

package/lib/src/splitPeptide.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"splitPeptide.d.ts","sourceRoot":"","sources":["../../src/splitPeptide.js"],"names":[],"mappings":"AAAA,iDAYC"}

package/lib/src/splitPeptide.js

@@ -0,0 +1,17 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.splitPeptide = splitPeptide;
+function splitPeptide(sequence) {
+    let aas = sequence.replaceAll(/([A-Z])/g, ' $1').split(/ /);
+    let begin = 0;
+    while (aas[begin] === '' || aas[begin] === 'H') {
+        begin++;
+    }
+    let end = aas.length - 1;
+    while (aas[end] === 'O' || aas[end] === 'H') {
+        end--;
+    }
+    aas = aas.slice(begin, end + 1);
+    return aas;
+}
+//# sourceMappingURL=splitPeptide.js.map

package/lib/src/splitPeptide.js.map

@@ -0,0 +1 @@
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