@datagrok/bio 2.12.12 → 2.12.13

package/src/utils/atomic-works.ts

@@ -1,367 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-
-export async function getMacroMol(monomers: any[][]): Promise<string[]> {
-  const result: string[] = [];
-  const moduleRdkit = await grok.functions.call('Chem:getRdKitModule');
-  for (let i = 0; i < monomers.length; i++) {
-    for (let j = 0; j < monomers[i].length; j++) {
-      const mol = moduleRdkit.get_mol(monomers[i][j]['molfile']);
-      const a = mol.get_v3Kmolblock();
-      const indices = getIndices(monomers[i][j], a);
-      monomers[i][j]['indices'] = indices;
-
-      monomers[i][j]['molfile'] = await rotateBackboneV3000(a, indices);
-      mol?.delete();
-    }
-    result.push(linkV3000(monomers[i]));
-  }
-
-  return result;
-}
-
-function getIndices(monomer: any, molV3000: string): {first: number, last: number,
-                                    remFirst: number, remLast: number,
-                                    remBondFirst: number, remBondLast: Number} {
-  const molfile = monomer['molfile'];
-  let indexStart = molfile.indexOf('M  RGP', 0) + 8;
-  let indexEnd = molfile.indexOf('\n', indexStart);
-  const indicesData = molfile.substring(indexStart, indexEnd).replaceAll('  ', ' ').replaceAll('  ', ' ');
-  let parsedData = indicesData.split(' ');
-  const remFirst = parsedData[2] == '1' ? parseInt(parsedData[1]) : parseInt(parsedData[3]);
-  const remLast = parsedData[2] == '2' ? parseInt(parsedData[1]) : parseInt(parsedData[3]);
-
-  const numbers = extractAtomsBondsNumbersV3000(molV3000);
-  let indexBonds = molV3000.indexOf('M  V30 BEGIN BOND'); // V3000 index for bonds
-  indexBonds = molV3000.indexOf('\n', indexBonds);
-  indexStart = indexBonds;
-  indexEnd = indexBonds;
-
-  let first = 0;
-  let last = 0;
-  let remBondFirst = 0;
-  let remBondLast = 0;
-
-  for (let j = 0; j < numbers.nbond; j++) {
-    if (first == 0 || last == 0) {
-      indexStart = molV3000.indexOf('V30', indexStart) + 4;
-      indexEnd = molV3000.indexOf('\n', indexStart);
-      const bondData = molV3000.substring(indexStart, indexEnd).replaceAll('  ', ' ').replaceAll('  ', ' ');
-      parsedData = bondData.split(' ');
-
-      if (parseInt(parsedData[2]) == remFirst) {
-        first = parseInt(parsedData[3]);
-        remBondFirst = parseInt(parsedData[0]);
-      } else if (parseInt(parsedData[3]) == remFirst) {
-        first = parseInt(parsedData[2]);
-        remBondFirst = parseInt(parsedData[0]);
-      } else if (parseInt(parsedData[2]) == remLast) {
-        last = parseInt(parsedData[3]);
-        remBondLast = parseInt(parsedData[0]);
-      } else if (parseInt(parsedData[3]) == remLast) {
-        last = parseInt(parsedData[2]);
-        remBondLast = parseInt(parsedData[0]);
-      }
-    }
-  }
-
-  return {first, last, remFirst, remLast, remBondFirst, remBondLast};
-}
-
-async function rotateBackboneV3000(molBlock: string, indices:any): Promise<string> {
-  const coordinates = extractAtomDataV3000(molBlock);
-  const natom = coordinates.atomIndex.length;
-  const first = indices['first'];
-  const last = indices['last'];
-
-  const xCenter = (coordinates.x[last] + coordinates.x[first]) / 2;
-  const yCenter = (coordinates.y[last] + coordinates.y[first]) / 2;
-
-  //place to center
-  for (let i = 0; i < natom; i++) {
-    coordinates.x[i] -= xCenter;
-    coordinates.y[i] -= yCenter;
-  }
-
-  let angle = 0;
-  if (coordinates.x[first] == 0) {
-    angle = coordinates.y[first] > coordinates.y[last] ? Math.PI / 2 : 3 * Math.PI / 2;
-  } else if (coordinates.y[first] == 0) {
-    angle = coordinates.x[first] > coordinates.x[last] ? Math.PI : 0;
-  } else {
-    const derivative = coordinates.y[first] / coordinates.x[first];
-    if (coordinates.x[first] < coordinates.x[last])
-      angle = derivative > 0 ? Math.PI - Math.atan(derivative) : Math.atan(derivative);
-    else
-      angle = derivative > 0 ? Math.atan(derivative) : Math.PI - Math.atan(derivative);
-  }
-
-  const cos = Math.cos(angle);
-  const sin = Math.sin(angle);
-
-  for (let i = 0; i < natom; i++) {
-    const xAdd = coordinates.x[i];
-    coordinates.x[i] = xAdd * cos - coordinates.y[i] * sin;
-    coordinates.y[i] = xAdd * sin + coordinates.y[i] * cos;
-  }
-
-  //place to right
-  const xShift = coordinates.x[first];
-  for (let i = 0; i < natom; i++)
-    coordinates.x[i] -= xShift;
-
-  //rewrite molBlock
-  let index = molBlock.indexOf('M  V30 BEGIN ATOM'); // V3000 index for atoms coordinates
-  index = molBlock.indexOf('\n', index);
-  let indexEnd = index;
-  for (let i = 0; i < natom; i++) {
-    index = molBlock.indexOf('V30', index) + 4;
-    index = molBlock.indexOf(' ', index) + 1;
-    index = molBlock.indexOf(' ', index) + 1;
-    indexEnd = molBlock.indexOf(' ', index) + 1;
-    indexEnd = molBlock.indexOf(' ', indexEnd);
-
-    molBlock = molBlock.slice(0, index) +
-      coordinates.x[i] + ' ' + coordinates.y[i] +
-      molBlock.slice(indexEnd);
-
-    index = molBlock.indexOf('\n', index) + 1;
-  }
-
-  return molBlock;
-}
-
-function extractAtomDataV3000(molBlock: string) {
-  const numbers = extractAtomsBondsNumbersV3000(molBlock);
-  let index = molBlock.indexOf('M  V30 BEGIN ATOM'); // V3000 index for atoms coordinates
-  index = molBlock.indexOf('\n', index);
-  let indexEnd = index;
-
-  const indexes: number[] = Array(numbers.natom);
-  const types: string[] = Array(numbers.natom);
-  const x: number[] = Array(numbers.natom);
-  const y: number[] = Array(numbers.natom);
-
-  for (let i = 0; i < numbers.natom; i++) {
-    index = molBlock.indexOf('V30', index) + 4;
-    indexEnd = molBlock.indexOf(' ', index);
-    indexes[i] = parseInt(molBlock.substring(index, indexEnd));
-
-    index = indexEnd + 1;
-    indexEnd = molBlock.indexOf(' ', index);
-    types[i] = molBlock.substring(index, indexEnd);
-
-    index = indexEnd + 1;
-    indexEnd = molBlock.indexOf(' ', index);
-    x[i] = parseFloat(molBlock.substring(index, indexEnd));
-
-    index = indexEnd + 1;
-    indexEnd = molBlock.indexOf(' ', index);
-    y[i] = parseFloat(molBlock.substring(index, indexEnd));
-
-    index = molBlock.indexOf('\n', index) + 1;
-  }
-
-  return {atomIndex: indexes, atomType: types, x: x, y: y};
-}
-
-function linkV3000(monomers: any[]): string {
-  let macroMolBlock = '\nDatagrok macromolecule handler\n\n';
-  macroMolBlock += '  0  0  0  0  0  0            999 V3000\n';
-  macroMolBlock += 'M  V30 BEGIN CTAB\n';
-  let atomBlock = '';
-  let bondBlock = '';
-  let natom = 0;
-  let nbond = 0;
-  let xShift = 0;
-
-  for (let i = 0; i < monomers.length; i++) {
-    let molfile = monomers[i]['molfile'];
-    const first = monomers[i]['indices']['first'];
-    const last = monomers[i]['indices']['last'];
-    const remFirst = monomers[i]['indices']['remFirst'];
-    const remLast = monomers[i]['indices']['remLast'];
-    const remBondFirst = monomers[i]['indices']['remBondFirst'];
-    const remBondLast = monomers[i]['indices']['remBondLast'];
-    molfile = molfile.replaceAll('(-\nM  V30 ', '(')
-      .replaceAll('-\nM  V30 ', '').replaceAll(' )', ')');
-    const numbers = extractAtomsBondsNumbersV3000(molfile);
-    const coordinates = extractAtomDataV3000(molfile);
-
-    let indexAtoms = molfile.indexOf('M  V30 BEGIN ATOM'); // V3000 index for atoms coordinates
-    indexAtoms = molfile.indexOf('\n', indexAtoms);
-    let index = indexAtoms;
-    let indexEnd = indexAtoms;
-    const totalShift = xShift - coordinates.x[first - 1];
-
-    for (let j = 0; j < numbers.natom; j++) {
-      if (coordinates.atomIndex[j] != remFirst && coordinates.atomIndex[j] != remLast) { //|| i == 0) {
-        //rewrite atom number
-        index = molfile.indexOf('V30', index) + 4;
-        indexEnd = molfile.indexOf(' ', index);
-
-        let atomNumber = parseInt(molfile.substring(index, indexEnd));
-        atomNumber = (atomNumber > remFirst && atomNumber > remLast) ? atomNumber - 2 :
-          (atomNumber > remFirst || atomNumber > remLast) ? atomNumber - 1 : atomNumber;
-        atomNumber += natom;
-        molfile = molfile.slice(0, index) + atomNumber + molfile.slice(indexEnd);
-
-        //rewrite coordinates
-        index = molfile.indexOf(' ', index) + 1;
-        index = molfile.indexOf(' ', index) + 1;
-        indexEnd = molfile.indexOf(' ', index);
-
-        let coordinate = Math.round(10000 * (parseFloat(molfile.substring(index, indexEnd)) + totalShift)) / 10000;
-        molfile = molfile.slice(0, index) + coordinate + molfile.slice(indexEnd);
-
-        index = molfile.indexOf(' ', index) + 1;
-        indexEnd = molfile.indexOf(' ', index);
-        coordinate = Math.round(10000 * (parseFloat(molfile.substring(index, indexEnd)))) / 10000;
-        molfile = molfile.slice(0, index) + coordinate + molfile.slice(indexEnd);
-
-        index = molfile.indexOf('\n', index) + 1;
-      } else {
-        index = molfile.indexOf('M  V30', index) - 1;
-        indexEnd = molfile.indexOf('\n', index + 1);
-        molfile = molfile.slice(0, index) + molfile.slice(indexEnd);
-      }
-    }
-
-    const indexAtomsEnd = molfile.indexOf('M  V30 END ATOM');
-    atomBlock += molfile.substring(indexAtoms + 1, indexAtomsEnd);
-
-    let indexBonds = molfile.indexOf('M  V30 BEGIN BOND'); // V3000 index for bonds
-    indexBonds = molfile.indexOf('\n', indexBonds);
-    index = indexBonds;
-    indexEnd = indexBonds;
-    let bondNumber = 0;
-
-    for (let j = 0; j < numbers.nbond; j++) {
-      //rewrite bond number
-      index = molfile.indexOf('V30', index) + 4;
-      indexEnd = molfile.indexOf(' ', index);
-      bondNumber = parseInt(molfile.substring(index, indexEnd));
-
-      if (bondNumber == remBondFirst || bondNumber == remBondLast) {
-        indexEnd = molfile.indexOf('\n', index) + 1;
-        index -= 7;
-        molfile = molfile.slice(0, index) + molfile.slice(indexEnd);
-        continue;
-      }
-
-      bondNumber = (bondNumber > remBondFirst && bondNumber > remBondLast) ? bondNumber - 2 :
-        (bondNumber > remBondFirst || bondNumber > remBondLast) ? bondNumber - 1 : bondNumber;
-      bondNumber += nbond;
-
-      molfile = molfile.slice(0, index) + bondNumber + molfile.slice(indexEnd);
-
-      //rewrite atom pair in bond
-      index = molfile.indexOf(' ', index) + 1;
-      index = molfile.indexOf(' ', index) + 1;
-      indexEnd = molfile.indexOf(' ', index);
-      let atomNumber = parseInt(molfile.substring(index, indexEnd));
-      atomNumber = (atomNumber > remFirst && atomNumber > remLast) ? atomNumber - 2 :
-        (atomNumber > remFirst || atomNumber > remLast) ? atomNumber - 1 : atomNumber;
-      atomNumber += natom;
-      molfile = molfile.slice(0, index) + atomNumber + molfile.slice(indexEnd);
-      index = molfile.indexOf(' ', index) + 1;
-      indexEnd = Math.min(molfile.indexOf('\n', index), molfile.indexOf(' ', index));
-      atomNumber = parseInt(molfile.substring(index, indexEnd));
-      atomNumber = (atomNumber > remFirst && atomNumber > remLast) ? atomNumber - 2 :
-        (atomNumber > remFirst || atomNumber > remLast) ? atomNumber - 1 : atomNumber;
-      atomNumber += natom;
-      molfile = molfile.slice(0, index) + atomNumber + molfile.slice(indexEnd);
-
-      index = molfile.indexOf('\n', index) + 1;
-    }
-
-    const indexBondEnd = molfile.indexOf('M  V30 END BOND');
-    bondBlock += molfile.substring(indexBonds + 1, indexBondEnd);
-    //let indexCollection = molfile.indexOf('M  V30 MDLV30/STEABS ATOMS=('); // V3000 index for collections
-
-    // while (indexCollection != -1) {
-    //   indexCollection += 28;
-    //   const collectionEnd = molfile.indexOf(')', indexCollection);
-    //   const collectionEntries = molfile.substring(indexCollection, collectionEnd).split(' ').slice(1);
-    //   collectionEntries.forEach((e: string) => {
-    //     collection.push(parseInt(e) + natom);
-    //   });
-    //   indexCollection = collectionEnd;
-    //   indexCollection = molfile.indexOf('M  V30 MDLV30/STEABS ATOMS=(', indexCollection);
-    // }
-
-    natom += numbers.natom - 2;
-    nbond += numbers.nbond - 2;
-    xShift += coordinates.x[last] - coordinates.x[first] + 1;
-
-    if (i == monomers.length - 1) {
-      natom++;
-      const shift = xShift + 0.2;
-      atomBlock += 'M  V30 ' + natom + ' O ' + shift + ' 0 0.000000 0\n';
-    }
-    nbond++;
-    if (i == monomers.length - 1) {
-      const rightTerminal = (last > remFirst && last > remLast) ? last + natom - (numbers.natom - 2) - 3 :
-        (last > remFirst || last > remLast) ? last + natom - (numbers.natom - 2) - 2 :
-          last + natom - (numbers.natom - 2) - 1;
-      bondBlock += 'M  V30 ' + nbond + ' 1 ' + rightTerminal + ' ' + natom + '\n';
-    } else {
-      const rightTerminal = (last > remFirst && last > remLast) ? last + natom - (numbers.natom - 2) - 2 :
-        (last > remFirst || last > remLast) ? last + natom - (numbers.natom - 2) - 1 :
-          last + natom - (numbers.natom - 2);
-
-      const next = monomers[i + 1]['indices'];
-      const nextFirst = next['first'];
-      const nextRemFirst = next['remFirst'];
-      const nextRemLast = next['remLast'];
-
-      const leftTerminal = (nextFirst > nextRemFirst && nextFirst > nextRemLast) ? nextFirst + natom - 2 :
-        (nextFirst > nextRemFirst || nextFirst > nextRemLast) ? nextFirst + natom - 1 :
-          nextFirst + natom;
-
-      bondBlock += 'M  V30 ' + nbond + ' 1 ' + rightTerminal + ' ' + leftTerminal + '\n';
-    }
-  }
-
-  // const entries = 4;
-  // const collNumber = Math.ceil(collection.length / entries);
-  // collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length + ' -\n';
-  // for (let i = 0; i < collNumber; i++) {
-  //   collectionBlock += 'M  V30 ';
-  //   const entriesCurrent = i + 1 == collNumber ? collection.length - (collNumber - 1)*entries : entries;
-  //   for (let j = 0; j < entriesCurrent; j++) {
-  //     collectionBlock += (j + 1 == entriesCurrent) ?
-  //       (i == collNumber - 1 ? collection[entries*i + j] + ')\n' : collection[entries*i + j] + ' -\n') :
-  //       collection[entries*i + j] + ' ';
-  //   }
-  // }
-
-  //generate file
-  macroMolBlock += 'M  V30 COUNTS ' + natom + ' ' + nbond + ' 0 0 0\n';
-  macroMolBlock += 'M  V30 BEGIN ATOM\n';
-  macroMolBlock += atomBlock;
-  macroMolBlock += 'M  V30 END ATOM\n';
-  macroMolBlock += 'M  V30 BEGIN BOND\n';
-  macroMolBlock += bondBlock;
-  macroMolBlock += 'M  V30 END BOND\n';
-  //macroMolBlock += 'M  V30 BEGIN COLLECTION\n';
-  //macroMolBlock += collectionBlock;
-  //macroMolBlock += 'M  V30 END COLLECTION\n';
-  macroMolBlock += 'M  V30 END CTAB\n';
-  macroMolBlock += 'M  END\n';
-
-  return macroMolBlock;
-}
-
-function extractAtomsBondsNumbersV3000(molBlock: string): {natom: number, nbond: number} {
-  molBlock = molBlock.replaceAll('\r', ''); //equalize old and new sdf standards
-  let index = molBlock.indexOf('COUNTS') + 7; // V3000 index for atoms and bonds number
-  let indexEnd = molBlock.indexOf(' ', index);
-
-  const atomsNumber = parseInt(molBlock.substring(index, indexEnd));
-  index = indexEnd + 1;
-  indexEnd = molBlock.indexOf(' ', index);
-  const bondsNumber = parseInt(molBlock.substring(index, indexEnd));
-
-  return {natom: atomsNumber, nbond: bondsNumber};
-}
-