@datagrok/bio 1.7.7 → 1.7.8
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- package/detectors.js +5 -5
- package/dist/package-test.js +57 -13
- package/dist/package.js +35 -11
- package/files/tests/testActivityCliffs.csv +311 -0
- package/package.json +1 -1
- package/src/tests/detectors-test.ts +8 -2
- package/src/tests/splitters-test.ts +19 -0
- package/src/utils/convert.ts +15 -3
- package/src/utils/multiple-sequence-alignment.ts +2 -1
- package/src/utils/utils.ts +10 -8
- package/{test-Bio-34f75e5127b8-7c42ea4b.html → test-Bio-34f75e5127b8-cdc230d8.html} +6 -2
package/detectors.js
CHANGED
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@@ -23,8 +23,8 @@ class BioPackageDetectors extends DG.Package {
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static RnaFastaAlphabet = new Set(['A', 'C', 'G', 'U']);
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static SmilesRawAlphabet = new Set([
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-
'
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-
'1', '2', '3', '4', '5', '6', '7',
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+
'B', 'C', 'c', 'E', 'H', 'L', 'M', 'N', 'O', 'S', 'F', '(', ')',
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+
'0', '1', '2', '3', '4', '5', '6', '7', '8', '9',
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'+', '-', '@', '[', ']', '/', '\\', '#', '=']);
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/** @param s {String} - string to check
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@@ -58,7 +58,7 @@ class BioPackageDetectors extends DG.Package {
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// TODO: Lazy calculations could be helpful for performance and convenient for expressing classification logic.
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const statsAsChars = BioPackageDetectors.getStats(col, 5, BioPackageDetectors.splitterAsChars);
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-
const decoy = BioPackageDetectors.detectAlphabet(statsAsChars.freq, decoyAlphabets, null, 0.
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+
const decoy = BioPackageDetectors.detectAlphabet(statsAsChars.freq, decoyAlphabets, null, 0.35);
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if (decoy != 'UN') return null;
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if (statsAsChars.sameLength) {
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@@ -110,10 +110,10 @@ class BioPackageDetectors extends DG.Package {
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// !!! What is the difference between the gap symbol and separator symbol in stats terms?
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// const noSeparatorRe = /[a-z\d]+$/i;
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const noSeparatorChemRe = /[HBCNOFPSKVYI]/i; // Mendeleev's periodic table single char elements
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-
const noSeparatorAlphaDigitRe = /[\dA-Z]/i;
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+
const noSeparatorAlphaDigitRe = /[\dA-Z,& _]/i; // ..., comma, ampersand, space, underscore
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const noSeparatorBracketsRe = /[\[\]()<>{}]/i;
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const cleanFreq = Object.assign({}, ...Object.entries(freq)
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-
.filter(([m, f]) =>
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+
.filter(([m, f]) =>
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!noSeparatorChemRe.test(m) && !noSeparatorAlphaDigitRe.test(m) && !noSeparatorBracketsRe.test(m) &&
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!BioPackageDetectors.PeptideFastaAlphabet.has(m) &&
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!BioPackageDetectors.DnaFastaAlphabet.has(m))
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