nmr-learning/src/preprocess/cheminfo.js

Learn a database of chemical shift and coupling constants assignments

const FS = require('fs');

const SD = require('spectra-data');

function loadFile(filename) {
  return FS.readFileSync(filename).toString();
}

function createSpectraData(filename) {
  var spectrum = SD.NMR.fromJcamp(
    FS.readFileSync(filename).toString()
  );
  return spectrum;
}

function load(path, datasetName, options) {
  let OCLE = options.OCLE;
  // var keepMolfile = false || options.keepMolfile;
  // var keepMolecule = false || options.keepMolecule;
  var filter = { filter: '.mol' };
  if (typeof options.filter === 'object') {
    filter = options.filter;
  }

  // var datasetName = "learningDataSet";
  // var path = "/Research/NMR/AutoAssign/data/"+datasetName;
  var molFiles = FS.readdirSync(path).filter((line) => {
    return line.endsWith(filter.filter);
  });

  var max = molFiles.length;
  var result = [];// new Array(max);
  // we could now loop on the sdf to add the int index
  for (var i = 0; i < max; i++) {
    try {
      var molfile = loadFile(path + molFiles[i]);
      var molecule = OCLE.Molecule.fromMolfile(molfile);
      molecule.addImplicitHydrogens();
      var nH = molecule.getMolecularFormula().formula.replace(/.*H([0-9]+).*/, '$1') * 1;
      var diaIDs = molecule.getGroupedDiastereotopicAtomIDs();
      diaIDs.sort(function (a, b) {
        if (a.atomLabel === b.atomLabel) {
          return b.counter - a.counter;
        }
        return a.atomLabel < b.atomLabel ? 1 : -1;
      });


      // const diaIdsH = molecule.getGroupedDiastereotopicAtomIDs("H");
      const linksOH = molecule.getAllPaths({
        fromLabel: 'H',
        toLabel: 'O',
        minLength: 1,
        maxLength: 1
      });
      const linksNH = molecule.getAllPaths({
        fromLabel: 'H',
        toLabel: 'N',
        minLength: 1,
        maxLength: 1
      });
      const linksClH = molecule.getAllPaths({
        fromLabel: 'H',
        toLabel: 'Cl',
        minLength: 1,
        maxLength: 1
      });
      const atoms = {};
      const levels = [6, 5, 4, 3];
      let hasLabile = false;
      for (const diaId of diaIDs) {
        delete diaId._highlight;
        diaId.hose = OCLE.Util.getHoseCodesFromDiastereotopicID(diaId.oclID, {
          maxSphereSize: levels[0],
          type: 0
        });

        for (const atomID of diaId.atoms) {
          atoms[atomID] = diaId.oclID;
        }

        diaId.isLabile = false;

        for (const linkOH of linksOH) {
          if (diaId.oclID === linkOH.fromDiaID) {
            diaId.isLabile = true;
            break;
          }
        }
        for (const linkNH of linksNH) {
          if (diaId.oclID === linkNH.fromDiaID) {
            diaId.isLabile = true;
            break;
          }
        }
        for (const linkClH of linksClH) {
          if (diaId.oclID === linkClH.fromDiaID) {
            diaId.isLabile = true;
            hasLabile = true;
            break;
          }
        }
      }
      // let ocl = {value: molecule};
      // ocl.diaIDs = diaIDs;
      // ocl.diaID = molecule.getIDCode();
      // ocl.nH = nH;

      // Simulate and process the 1H-NMR spectrum at 400MHz
      var jcampFile = molFiles[i].replace('mol_', 'h1_').replace('.mol', '.jdx');
      var spectraData1H = createSpectraData(path + jcampFile);

      var signals = spectraData1H.getRanges(
        {
          nH: nH,
          realTop: true,
          thresholdFactor: 1,
          // minMaxRatio:0.001,
          clean: true,
          compile: true,
          format: 'new'
        }
      );

      let sum = 0;
      for (var j = signals.length - 1; j >= 0; j--) {
        if (signals[j].from < 0 || signals[j].from > 11.8) {
          signals.splice(j, 1);
        } else {
          if (signals[j].from > 2.48 && signals[j].to < 2.59 && signals[j].signal[0].multiplicity === 'quint') {
            signals.splice(j, 1);
          } else
          if (signals[j].from > 7.10 && signals[j].to < 7.30 && signals[j].signal[0].multiplicity === 's') {
            signals.splice(j, 1);
          } else {
            sum += signals[j].integral;
          }
        }
      }
      // Restore the integral to nH
      /* for (var j = signals.length - 1; j >= 0; j--) {
                signals[j].integral *= nH / sum;
            }*/
      // It seems that the compiler makes crazy things some times. We need to join the signals in the same range
      for (var j = signals.length - 2; j >= 0; j--) {
        if (Math.abs((signals[j].to + signals[j].from) - (signals[j + 1].to + signals[j + 1].from)) <
                    (Math.abs(signals[j].to - signals[j].from) + Math.abs(signals[j + 1].to - signals[j + 1].from))) {
          signals[j].from = Math.min(signals[j].from, signals[j + 1].from);
          signals[j].to = Math.max(signals[j].to, signals[j + 1].to);
          signals[j].integral += signals[j + 1].integral;
          signals[j].signal[0].multiplicity = 'm';
          signals[j].signal[0].delta = (signals[j].from + signals[j].to) / 2;
          signals.splice(j + 1, 1);
        }
      }

      signals.forEach((range, index) => {
        range.signalID = `1H_${index}`;
      });

      // console.log(JSON.stringify(signals));
      let sample = { general: { ocl: { id: molecule.getIDCode(), atom: atoms, diaId: diaIDs, nH: nH, hasLabile } }, // {ocl: ocl, molfile: molecule.toMolfileV3()},
        spectra: { nmr: [{ nucleus: 'H', experiment: '1d', range: signals, solvent: spectraData1H.getParamString('.SOLVENT NAME', 'unknown') }] } };
      // {nucleus: ["H", "H"],  experiment: "cosy", region: cosyZones, solvent: cosy.getParamString(".SOLVENT NAME", "unknown")}
      result.push(sample);
    } catch (e) {
      // console.log('Could not load the entry ' + i + ' ' + e);
    }
  }
  return result;
}
module.exports = { load };