peptide-score 2.3.14

package/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2015 cheminfo
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

package/README.md

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+# peptide
+
+[![NPM version][npm-image]][npm-url]
+[![build status][travis-image]][travis-url]
+[![David deps][david-image]][david-url]
+[![npm download][download-image]][download-url]
+
+Peptide
+
+## Amino acids
+
+#### getInfo()
+
+Returns an array of information about amino acids
+
+## Amino acids sequence
+
+#### sequenceToMF(sequence)
+
+Previously convertAASequence(sequence) (deprecated)
+
+Returns a peptidic sequence from a PDB or one letter code to the internal molecular formula format
+
+**Arguments**
+
+- `sequence` - string with the amino acids sequence
+
+#### chargePeptide(mf, options)
+
+Charge the peptide at a specific pH. 'mf' is either a 3 letter peptide sequence or an array of peptide sequences.
+
+**Arguments**
+
+- `mf` - string with a molecular formula to charge
+- options:
+- pH : you may specify the pH to calculate the protonation state. By default: 0,
+  it has the consequence to add a positive charge on Arg, His and Lys.
+
+#### allowNeutralLoss(mf, options)
+
+Allow neutral loss :
+
+- H2O for S, T, E, D residues
+- NH3 for R, K, Q, N residues
+
+The residues may not be modified.
+
+**Arguments**
+
+- `mf` - string with a molecular formula to charge
+
+#### generatePeptideFragments(mf, [options])
+
+Generate [peptide fragmentation](http://en.wikipedia.org/wiki/Peptide_sequence_tag).
+Returns an array of molecular formulas with the different fragments.
+
+**Arguments**
+
+- `mf` - string with the molecular formula
+- `options` - object with requested fragments. Default: `{a:false, b:true, c:false, x:false, y:true, z:false, i:false}`
+
+You can also specify internal fragments using the options 'ya', 'yb', 'yc' and 'zc' as well as the minimal length of internal fragments 'minInternal'
+and the maximal length of internal fragments 'maxInternal'
+
+## Isoelectric Point
+
+pKa of amino acids is based on https://en.wikipedia.org/wiki/Amino_acid.
+
+#### calculateCharge(sequence, ph)
+
+Calculate the charge for a specific amino acid sequence. The sequence should be entered in the form "HAlaGlyOH".
+Please take care about the N and C terminal end. You may use the methods "convertAASequence" to create such a sequence
+from other format.
+
+**Arguments**
+
+- `sequence` - string with the amino acids sequence
+- `ph` - ph for which to calculate the charge. Default: 7.0
+
+#### splitPeptide(sequence)
+
+Split a 3 letter code sequence respecting uppercase, lowercase in an array of residu.
+
+**Arguments**
+
+- `sequence` - string with the amino acids sequence
+
+#### digestPeptide(sequence, options)
+
+Allows to digest virtually a peptide
+
+**Arguments**
+
+- `sequence` - string with the amino acids sequence
+- `options`
+  - `minMissed` - minimal missed cleavage (default: 0)
+  - `maxMissed` - maximal missed cleavage (default: 0)
+  - `minResidue` - minimal number of residues (default: 0)
+  - `maxResidue` - maximal number of residues (default: infinity)
+  - `enzyme` - enzyme used for digestion
+    - chymotrypsin : (Phe|Tyr|Trp)(?!Pro)
+    - trypsin : (Lys|Arg)(?!Pro)
+    - lysc : (Lys)(?!Pro)
+    - glucph4 : (Glu)(?!Pro|Glu)
+    - glucph8 : (Asp|Glu)(?!Pro|Glu)
+    - thermolysin : (Leu|Ile|Met|Phe|Trp)
+    - cyanogenbromide : (Met)
+
+#### calculateIEP(sequence)
+
+Calculate the isoelectric point for a specific amino acid sequence. The sequence should be entered in the form "HAlaGlyOH".
+Please take care about the N and C terminal end. You may use the methods "convertAASequence" to create such a sequence
+from other format.
+
+**Arguments**
+
+- `sequence` - string with the amino acids sequence
+
+#### calculateIEPChart(sequence)
+
+Returns an object containing the y and yAbs array of the charge of the peptide for a pH that goes from 0 to 14.
+
+**Arguments**
+
+- `sequence` - string with the amino acids sequence
+
+#### getColorForIEP(iep)
+
+Returns a color based on the isoelectric point :
+
+- 0 -> 7 means that at pH 7 it is charged negatively (blue)
+- 7 -> 14 means that at pH7 it is charged positively (red)
+
+**Arguments**
+
+- `iep` - the value of the isoelectric point
+
+## License
+
+[MIT](./LICENSE)
+
+[npm-image]: https://img.shields.io/npm/v/peptide.svg?style=flat-square
+[npm-url]: https://www.npmjs.com/package/peptide
+[travis-image]: https://img.shields.io/travis/cheminfo-js/peptide/main.svg?style=flat-square
+[travis-url]: https://travis-ci.org/cheminfo-js/peptide
+[david-image]: https://img.shields.io/david/cheminfo-js/peptide.svg?style=flat-square
+[david-url]: https://david-dm.org/cheminfo-js/peptide
+[download-image]: https://img.shields.io/npm/dm/peptide.svg?style=flat-square
+[download-url]: https://www.npmjs.com/package/peptide

package/lib/src/allowNeutralLoss.d.ts

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+/**
+ * Add neutral loss on natural amino acids
+ * @param {*} mf
+ * @returns
+ */
+export function allowNeutralLoss(mf: any): any;
+//# sourceMappingURL=allowNeutralLoss.d.ts.map

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

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+{"version":3,"file":"allowNeutralLoss.d.ts","sourceRoot":"","sources":["../../src/allowNeutralLoss.js"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,qCAHW,GAAC,OAYX"}

package/lib/src/allowNeutralLoss.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.allowNeutralLoss = allowNeutralLoss;
+/**
+ * Add neutral loss on natural amino acids
+ * @param {*} mf
+ * @returns
+ */
+function allowNeutralLoss(mf) {
+    if (Array.isArray(mf)) {
+        for (let i = 0; i < mf.length; i++) {
+            mf[i] = allowOneNeutralLoss(mf[i]);
+        }
+        return mf;
+    }
+    else {
+        return allowOneNeutralLoss(mf);
+    }
+}
+function allowOneNeutralLoss(mf) {
+    mf = mf.replaceAll(/(Ser|Thr|Asp|Glu)(?!\()/g, '$1(H-2O-1)0-1');
+    mf = mf.replaceAll(/(Arg|Lys|Asn|Gln)(?!\()/g, '$1(N-1H-3)0-1');
+    return mf;
+}
+//# sourceMappingURL=allowNeutralLoss.js.map

package/lib/src/allowNeutralLoss.js.map

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+{"version":3,"file":"allowNeutralLoss.js","sourceRoot":"","sources":["../../src/allowNeutralLoss.js"],"names":[],"mappings":";;AAKA,4CASC;AAdD;;;;GAIG;AACH,SAAgB,gBAAgB,CAAC,EAAE;IACjC,IAAI,KAAK,CAAC,OAAO,CAAC,EAAE,CAAC,EAAE,CAAC;QACtB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YACnC,EAAE,CAAC,CAAC,CAAC,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;QACrC,CAAC;QACD,OAAO,EAAE,CAAC;IACZ,CAAC;SAAM,CAAC;QACN,OAAO,mBAAmB,CAAC,EAAE,CAAC,CAAC;IACjC,CAAC;AACH,CAAC;AAED,SAAS,mBAAmB,CAAC,EAAE;IAC7B,EAAE,GAAG,EAAE,CAAC,UAAU,CAAC,0BAA0B,EAAE,eAAe,CAAC,CAAC;IAChE,EAAE,GAAG,EAAE,CAAC,UAAU,CAAC,0BAA0B,EAAE,eAAe,CAAC,CAAC;IAEhE,OAAO,EAAE,CAAC;AACZ,CAAC"}

package/lib/src/aminoAcids.d.ts

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+export const aminoAcids: ({
+    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;
+})[];
+//# sourceMappingURL=aminoAcids.d.ts.map

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

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+{"version":3,"file":"aminoAcids.d.ts","sourceRoot":"","sources":["../../src/aminoAcids.js"],"names":[],"mappings":"AAEA;;;;;;;;;;;;;;;;;;;;;;;;;;;KAgPE"}

package/lib/src/aminoAcids.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.aminoAcids = void 0;
+// SOURCE: https://en.wikipedia.org/wiki/Amino_acid
+// Link for UTF8 code for modified: https://codepoints.net/search?sc=Grek
+exports.aminoAcids = [
+    // Standard amino acids
+    {
+        name: 'Alanine',
+        aa3: 'Ala',
+        aa1: 'A',
+        sc: {
+            type: 'hydrophobic',
+        },
+        pKaC: 2.33,
+        pKaN: 9.71,
+    },
+    {
+        name: 'Arginine',
+        aa3: 'Arg',
+        aa1: 'R',
+        sc: {
+            type: 'positive',
+            pKa: 12.1,
+        },
+        pKaC: 2.03,
+        pKaN: 9,
+    },
+    {
+        name: 'Asparagine',
+        aa3: 'Asn',
+        aa1: 'N',
+        sc: {
+            type: 'polar',
+        },
+        pKaC: 2.13,
+        pKaN: 9.05,
+    },
+    {
+        name: 'Aspartic acid',
+        aa3: 'Asp',
+        aa1: 'D',
+        sc: {
+            type: 'negative',
+            pKa: 3.71,
+        },
+        pKaC: 1.95,
+        pKaN: 9.66,
+    },
+    {
+        name: 'Cysteine',
+        aa3: 'Cys',
+        aa1: 'C',
+        sc: {
+            type: 'special',
+            pKa: 8.14,
+        },
+        pKaC: 1.91,
+        pKaN: 10.28,
+    },
+    {
+        name: 'Glutamic acid',
+        aa3: 'Glu',
+        aa1: 'E',
+        sc: {
+            type: 'negative',
+            pKa: 4.15,
+        },
+        pKaC: 2.16,
+        pKaN: 9.58,
+    },
+    {
+        name: 'Glutamine',
+        aa3: 'Gln',
+        aa1: 'Q',
+        sc: {
+            type: 'polar',
+        },
+        pKaC: 2.18,
+        pKaN: 9,
+    },
+    {
+        name: 'Glycine',
+        aa3: 'Gly',
+        aa1: 'G',
+        sc: {
+            type: 'special',
+        },
+        pKaC: 2.34,
+        pKaN: 9.58,
+    },
+    {
+        name: 'Histidine',
+        aa3: 'His',
+        aa1: 'H',
+        sc: {
+            type: 'positive',
+            pKa: 6.04,
+        },
+        pKaC: 1.7,
+        pKaN: 9.09,
+    },
+    {
+        name: 'Isoleucine',
+        aa3: 'Ile',
+        aa1: 'I',
+        sc: {
+            type: 'hydrophobic',
+        },
+        pKaC: 2.26,
+        pKaN: 9.6,
+    },
+    {
+        name: 'Leucine',
+        aa3: 'Leu',
+        aa1: 'L',
+        sc: {
+            type: 'hydrophobic',
+        },
+        pKaC: 2.32,
+        pKaN: 9.58,
+    },
+    {
+        name: 'Lysine',
+        aa3: 'Lys',
+        aa1: 'K',
+        sc: {
+            type: 'positive',
+            pKa: 10.67,
+        },
+        pKaC: 2.15,
+        pKaN: 9.16,
+    },
+    {
+        name: 'Methionine',
+        aa3: 'Met',
+        aa1: 'M',
+        sc: {
+            type: 'hydrophobic',
+        },
+        pKaC: 2.16,
+        pKaN: 9.08,
+    },
+    {
+        name: 'Phenylalanine',
+        aa3: 'Phe',
+        aa1: 'F',
+        sc: {
+            type: 'hydrophobic',
+        },
+        pKaC: 2.18,
+        pKaN: 9.09,
+    },
+    {
+        name: 'Proline',
+        aa3: 'Pro',
+        aa1: 'P',
+        sc: {
+            type: 'special',
+        },
+        pKaC: 1.95,
+        pKaN: 10.47,
+    },
+    {
+        name: 'Serine',
+        aa3: 'Ser',
+        aa1: 'S',
+        sc: {
+            type: 'polar',
+        },
+        pKaC: 2.13,
+        pKaN: 9.05,
+    },
+    {
+        name: 'Threonine',
+        aa3: 'Thr',
+        aa1: 'T',
+        sc: {
+            type: 'polar',
+        },
+        pKaC: 2.2,
+        pKaN: 8.96,
+    },
+    {
+        name: 'Tryptophan',
+        aa3: 'Trp',
+        aa1: 'W',
+        sc: {
+            type: 'hydrophobic',
+        },
+        pKaC: 2.38,
+        pKaN: 9.34,
+    },
+    {
+        name: 'Tyrosine',
+        aa3: 'Tyr',
+        aa1: 'Y',
+        sc: {
+            type: 'hydrophobic',
+        },
+        pKaC: 2.24,
+        pKaN: 9.04,
+    },
+    {
+        name: 'Valine',
+        aa3: 'Val',
+        aa1: 'V',
+        sc: {
+            type: 'hydrophobic',
+        },
+        pKaC: 2.27,
+        pKaN: 9.52,
+    },
+    // Additional
+    {
+        name: 'Selenocysteine',
+        aa3: 'Sec',
+        aa1: 'U',
+    },
+    {
+        name: 'Pyrrolysine',
+        aa3: 'Pyl',
+        aa1: 'O',
+    },
+    // Ambiguous
+    {
+        name: 'Asparagine or aspartic acid',
+        aa3: 'Asx',
+        aa1: 'B',
+    },
+    {
+        name: 'Glutamine or glutamic acid',
+        aa3: 'Glx',
+        aa1: 'Z',
+    },
+    {
+        name: 'Leucine or isoleucine',
+        aa3: 'Xle',
+        aa1: 'J',
+    },
+    {
+        name: 'Unspecified or unknown',
+        aa3: 'Xaa',
+        aa1: 'X',
+    },
+];
+//# sourceMappingURL=aminoAcids.js.map

package/lib/src/aminoAcids.js.map

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

@@ -0,0 +1,2 @@
+export function chargePeptide(mf: any, options?: {}): any;
+//# sourceMappingURL=chargePeptide.d.ts.map

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

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

package/lib/src/chargePeptide.js

@@ -0,0 +1,50 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.chargePeptide = chargePeptide;
+const getAA_1 = require("./getAA");
+// SOURCE: https://en.wikipedia.org/wiki/Amino_acid
+function chargePeptide(mf, options = {}) {
+    if (Array.isArray(mf)) {
+        for (let i = 0; i < mf.length; i++) {
+            mf[i] = chargeOnePeptide(mf[i], options);
+        }
+        return mf;
+    }
+    else {
+        return chargeOnePeptide(mf, options);
+    }
+}
+function chargeOnePeptide(mf, options) {
+    const { pH = 0 } = options;
+    // we will allow to charge the peptide at a specific pH
+    // first amino acids (N-terminal)
+    if (mf.match(/^H[A-Z][a-z]{2}/)) {
+        let firstAA = mf.replace(/^H([A-Z][a-z]{2}).*/, '$1');
+        if ((0, getAA_1.getAA)(firstAA) && pH < (0, getAA_1.getAA)(firstAA).pKaN) {
+            mf = mf.replace(/^H([^+])/, 'H+H$1');
+        }
+    }
+    // last amino acids (C-terminal)
+    if (mf.match(/[A-Z][a-z]{2}OH$/)) {
+        let lastAA = mf.replace(/.*([A-Z][a-z]{2})OH$/, '$1');
+        if ((0, getAA_1.getAA)(lastAA) && pH > (0, getAA_1.getAA)(lastAA).pKaC) {
+            mf = mf.replace(/OH$/, 'O-');
+        }
+    }
+    // basic AA
+    if (pH < (0, getAA_1.getAA)('Arg').sc.pKa)
+        mf = mf.replaceAll(/(Arg)(?!\()/g, '$1(H+)');
+    if (pH < (0, getAA_1.getAA)('His').sc.pKa)
+        mf = mf.replaceAll(/(His)(?!\()/g, '$1(H+)');
+    if (pH < (0, getAA_1.getAA)('Lys').sc.pKa)
+        mf = mf.replaceAll(/(Lys)(?!\()/g, '$1(H+)');
+    // acid AA
+    if (pH > (0, getAA_1.getAA)('Asp').sc.pKa)
+        mf = mf.replaceAll(/(Asp)(?!\()/g, '$1(H-1-)');
+    if (pH > (0, getAA_1.getAA)('Glu').sc.pKa)
+        mf = mf.replaceAll(/(Glu)(?!\()/g, '$1(H-1-)');
+    if (pH > (0, getAA_1.getAA)('Cys').sc.pKa)
+        mf = mf.replaceAll(/(Cys)(?!\()/g, '$1(H-1-)');
+    return mf;
+}
+//# sourceMappingURL=chargePeptide.js.map

package/lib/src/chargePeptide.js.map

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

@@ -0,0 +1,2 @@
+export function digestPeptide(sequence: any, options?: {}): string[];
+//# sourceMappingURL=digestPeptide.d.ts.map

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

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

package/lib/src/digestPeptide.js

@@ -0,0 +1,83 @@
+"use strict";
+/*
+Iotuibs:
+* minMissed (default: 0)
+* maxMissed (default: 0)
+* minResidue: 0;
+* maxResidue: infinity
+* enzyme: chymotrypsin, trypsin, glucph4, glucph8, thermolysin, cyanogenbromide : Mandatory, no default value !
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.digestPeptide = digestPeptide;
+function digestPeptide(sequence, options = {}) {
+    sequence = sequence.replace(/^H([^a-z])/, '$1').replace(/OH$/, '');
+    options.enzyme = options.enzyme || 'trypsin';
+    if (options.minMissed === undefined)
+        options.minMissed = 0;
+    if (options.maxMissed === undefined)
+        options.maxMissed = 0;
+    if (options.minResidue === undefined)
+        options.minResidue = 0;
+    if (options.maxResidue === undefined)
+        options.maxResidue = Number.MAX_VALUE;
+    let regexp = getRegexp(options.enzyme);
+    let fragments = sequence.replace(regexp, '$1 ').split(/ /).filter(Boolean);
+    {
+        let from = 0;
+        for (let i = 0; i < fragments.length; i++) {
+            let nbResidue = fragments[i]
+                .replaceAll(/([A-Z][a-z]{2})/g, ' $1')
+                .split(/ /)
+                .filter(Boolean).length;
+            fragments[i] = {
+                sequence: fragments[i],
+                nbResidue,
+                from,
+                to: from + nbResidue - 1,
+            };
+            from += nbResidue;
+        }
+    }
+    let results = [];
+    for (let i = 0; i < fragments.length - options.minMissed; i++) {
+        for (let j = options.minMissed; j <= Math.min(options.maxMissed, fragments.length - i - 1); j++) {
+            let fragment = '';
+            let nbResidue = 0;
+            for (let k = i; k <= i + j; k++) {
+                fragment += fragments[k].sequence;
+                nbResidue += fragments[k].nbResidue;
+            }
+            let from = fragments[i].from + 1;
+            let to = fragments[i + j].to + 1;
+            if (fragment &&
+                nbResidue >= options.minResidue &&
+                nbResidue <= options.maxResidue) {
+                results.push(`H${fragment}OH$D${from}>${to}`);
+            }
+        }
+    }
+    return results;
+}
+function getRegexp(enzyme) {
+    switch (enzyme.toLowerCase().replaceAll(/[^\da-z]/g, '')) {
+        case 'chymotrypsin':
+            return /(Phe|Tyr|Trp)(?!Pro)/g;
+        case 'trypsin':
+            return /(Lys|Arg)(?!Pro)/g;
+        case 'lysc':
+            return /(Lys)(?!Pro)/g;
+        case 'glucph4':
+            return /(Glu)(?!Pro|Glu)/g;
+        case 'glucph8':
+            return /(Asp|Glu)(?!Pro|Glu)/g;
+        case 'thermolysin': // N-term of  Leu, Phe, Val, Ile, Ala, Met
+            return /()(?=Ile|Leu|Val|Ala|Met|Phe)/g;
+        case 'cyanogenbromide':
+            return /(Met)/g;
+        case 'any':
+            return /()(?=[A-Z][a-z]{2})/g;
+        default:
+            throw new Error(`Digestion enzyme: ${enzyme} is unknown`);
+    }
+}
+//# sourceMappingURL=digestPeptide.js.map

package/lib/src/digestPeptide.js.map

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

@@ -0,0 +1,2 @@
+export function generatePeptideFragments(mf: any, options: any): string[];
+//# sourceMappingURL=generatePeptideFragments.d.ts.map

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

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