@datagrok/bio 1.7.21 → 1.7.24

package/detectors.js

@@ -26,6 +26,15 @@ class BioPackageDetectors extends DG.Package {
     '0', '1', '2', '3', '4', '5', '6', '7', '8', '9',
     '+', '-', '.', , '/', '\\', '@', '[', ']', '(', ')', '#', '%', '=']);
 
+  static SmartsRawAlphabet = new Set([
+    '0', '1', '2', '3', '4', '5', '6', '7', '8', '9',
+    '!', '#', '$', '&', '(', ')', '*', '+', ',', '-', '.', ':', ';', '=', '@', '~', '[', ']',
+    'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M',
+    'N', 'O', 'P', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z',
+    'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm',
+    'n', 'o', 'p', 'r', 's', 't', 'u', 'v', 'y',
+  ]);
+
   /** @param s {String} - string to check
    * @returns {boolean} */
   static isHelm(s) {
@@ -48,13 +57,14 @@ class BioPackageDetectors extends DG.Package {
     }
 
     const decoyAlphabets = [
-      ['SMILES', BioPackageDetectors.SmilesRawAlphabet],
+      ['SMILES', BioPackageDetectors.SmilesRawAlphabet, 0.30],
+      ['SMARTS', BioPackageDetectors.SmartsRawAlphabet, 0.45],
     ];
 
     const candidateAlphabets = [
-      ['PT', BioPackageDetectors.PeptideFastaAlphabet],
-      ['DNA', BioPackageDetectors.DnaFastaAlphabet],
-      ['RNA', BioPackageDetectors.RnaFastaAlphabet],
+      ['PT', BioPackageDetectors.PeptideFastaAlphabet, 0.55],
+      ['DNA', BioPackageDetectors.DnaFastaAlphabet, 0.55],
+      ['RNA', BioPackageDetectors.RnaFastaAlphabet, 0.55],
     ];
 
     // Check for url column, maybe it is too heavy check
@@ -76,7 +86,7 @@ class BioPackageDetectors extends DG.Package {
     const statsAsChars = BioPackageDetectors.getStats(col, 5, BioPackageDetectors.splitterAsChars);
     // if (Object.keys(statsAsChars.freq).length === 0) return;
 
-    const decoy = BioPackageDetectors.detectAlphabet(statsAsChars.freq, decoyAlphabets, null, 0.30);
+    const decoy = BioPackageDetectors.detectAlphabet(statsAsChars.freq, decoyAlphabets, null);
     if (decoy != 'UN') return null;
 
     if (statsAsChars.sameLength) {
@@ -148,9 +158,11 @@ class BioPackageDetectors extends DG.Package {
     return sepFreq / otherSumFreq > freqThreshold ? sep : null;
   }
 
-  /** With a separator, spaces are nor allowed in monomer names. */
+  /** With a separator, spaces are nor allowed in monomer names.
+   * The monomer name/label cannot contain digits only.
+   */
   static checkForbiddenWithSeparators(freq) {
-    const forbiddenRe = /[ ]/i;
+    const forbiddenRe = /[ ]|^\d+$/i;
     return Object.keys(freq).filter((m) => forbiddenRe.test(m)).length > 0;
   }
 
@@ -191,16 +203,16 @@ class BioPackageDetectors extends DG.Package {
    * @param freq       frequencies of monomers in sequence set
    * @param candidates  an array of pairs [name, monomer set]
    * */
-  static detectAlphabet(freq, candidates, gapSymbol, cut = 0.55) {
+  static detectAlphabet(freq, candidates, gapSymbol) {
     const candidatesSims = candidates.map((c) => {
       const sim = BioPackageDetectors.getAlphabetSimilarity(freq, c[1], gapSymbol);
-      return [c[0], c[1], freq, sim];
+      return [c[0], c[1], c[2], freq, sim];
     });
 
     let alphabetName;
-    const maxSim = Math.max(...candidatesSims.map((cs) => cs[3]));
-    if (maxSim > cut) {
-      const sim = candidatesSims.find((cs) => cs[3] == maxSim);
+    const maxSim = Math.max(...candidatesSims.map((cs) => cs[4] > cs[2] ? cs[4] : -1));
+    if (maxSim > 0) {
+      const sim = candidatesSims.find((cs) => cs[4] == maxSim);
       alphabetName = sim[0];
     } else {
       alphabetName = 'UN';