{"version":3,"file":"openchemlib-utils.min.js","sources":["../src/util/tagAtom.js","../src/diastereotopic/addDiastereotopicMissingChirality.js","../src/util/makeRacemic.js","../src/diastereotopic/getDiastereotopicAtomIDs.js","../src/diastereotopic/getDiastereotopicAtomIDsAndH.js","../src/diastereotopic/groupDiastereotopicAtomIDs.js","../src/diastereotopic/getGroupedDiastereotopicAtomIDs.js","../src/util/isCsp3.js","../src/hose/getHoseCodesForAtoms.js","../src/hose/getHoseCodesForAtom.js","../src/hose/getHoseCodesFromDiastereotopicID.js","../src/hose/getHoseCodesForPath.js","../src/util/combineSmiles.js","../src/util/getAtomsInfo.js","../node_modules/is-any-array/lib-esm/index.js","../node_modules/ml-array-rescale/lib-es6/index.js","../node_modules/ml-array-min/lib-es6/index.js","../node_modules/ml-array-max/lib-es6/index.js","../node_modules/ml-matrix/src/inspect.js","../node_modules/ml-matrix/src/util.js","../node_modules/ml-matrix/src/matrix.js","../node_modules/ml-matrix/src/stat.js","../src/util/getConnectivityMatrix.js","../node_modules/ml-floyd-warshall/src/index.js","../node_modules/atom-sorter/src/index.js","../src/util/getMF.js","../src/path/getPathAndTorsion.js","../src/path/getPathsInfo.js","../node_modules/ensure-string/lib-esm/index.js","../node_modules/isutf8/dist/index.esm.js","../node_modules/ml-matrix/src/mathOperations.js","../node_modules/papaparse/papaparse.min.js","../src/db/utils/getMoleculeCreators.js","../src/db/utils/appendCSV.js","../node_modules/sdf-parser/src/util/getMolecule.js","../src/db/utils/appendSDF.js","../node_modules/sdf-parser/src/parse.js","../node_modules/sdf-parser/src/getEntriesBoundaries.js","../src/util/noWait.js","../src/db/utils/search.js","../src/misc/dwar/utils/parseColumnbProperties.js","../src/misc/dwar/utils/parseData.js","../src/misc/dwar/parseDwar.js","../src/reaction/utils/getReactantInfo.js","../src/reaction/utils/applyOneReactantReaction.js","../src/db/MoleculesDB.js","../src/db/utils/appendSmilesList.js","../src/db/utils/pushEntry.js","../src/db/utils/pushMoleculeInfo.js","../src/db/utils/appendColor.js","../src/reaction/applyReactions.js","../src/fragment/fragmentAcyclicSingleBonds.js","../src/features/getAtomFeatures.js","../src/diastereotopic/getDiastereotopicAtomIDsFromMolfile.js","../src/hose/getHoseCodesAndDiastereotopicIDs.js","../src/path/getShortestPaths.js","../src/util/nbCHO.js","../src/util/nbCN.js","../src/util/nbCOOH.js","../src/util/nbNH2.js","../src/util/nbOH.js","../src/misc/dwar/utils/getParts.js","../src/diastereotopic/toDiastereotopicSVG.js","../src/misc/toVisualizerMolfile.js"],"sourcesContent":["let xAtomicNumber = 0;\n\n/**\n * Tag an atom to be able to visualize it\n * @param {import('openchemlib').Molecule} molecule\n * @param {number} iAtom\n */\nexport function tagAtom(molecule, iAtom) {\n let customLabel = `${molecule.getAtomLabel(iAtom)}*`;\n molecule.setAtomCustomLabel(iAtom, customLabel);\n if (molecule.getAtomicNo(iAtom) === 1) {\n molecule.setAtomicNo(iAtom, getXAtomicNumber(molecule));\n } else {\n // we can not use X because we would have problems with valencies if it is\n // expanded hydrogens or not\n // we can not only use a custom label because it does not count for the canonisation\n molecule.setAtomMass(iAtom, molecule.getAtomMass(iAtom) + 5);\n }\n return customLabel;\n}\n\nfunction getXAtomicNumber(molecule) {\n if (!xAtomicNumber) {\n const OCL = molecule.getOCL();\n xAtomicNumber = OCL.Molecule.getAtomicNoFromLabel(\n 'X',\n OCL.Molecule.cPseudoAtomX,\n );\n }\n return xAtomicNumber;\n}\n","import { tagAtom } from '../util/tagAtom';\n\n/**\n * Add either missing chirality of diastereotopic missing chirality\n * The problem is that sometimes we need to add chiral bond that was not planned because it is the same group\n * This is the case for example for the valine where the 2 C of the methyl groups are diastereotopic\n * @param {import('openchemlib').Molecule} molecule\n * @param {object} [options={}]\n * @param {number} [options.esrType=cESRTypeAnd]\n */\nexport function addDiastereotopicMissingChirality(molecule, options = {}) {\n const { Molecule } = molecule.getOCL();\n const { esrType = Molecule.cESRTypeAnd } = options;\n\n for (let iAtom = 0; iAtom < molecule.getAllAtoms(); iAtom++) {\n let tempMolecule = molecule.getCompactCopy();\n tagAtom(tempMolecule, iAtom);\n // After copy, helpers must be recalculated\n tempMolecule.ensureHelperArrays(Molecule.cHelperBitsStereo);\n // We need to have >0 and not >1 because there could be unspecified chirality in racemate\n\n for (let i = 0; i < tempMolecule.getAtoms(); i++) {\n // changed from from handling below; TLS 9.Nov.2015\n if (\n tempMolecule.isAtomStereoCenter(i) &&\n tempMolecule.getStereoBond(i) === -1\n ) {\n let stereoBond = tempMolecule.getAtomPreferredStereoBond(i);\n if (stereoBond !== -1) {\n molecule.setBondType(stereoBond, Molecule.cBondTypeUp);\n if (molecule.getBondAtom(1, stereoBond) === i) {\n let connAtom = molecule.getBondAtom(0, stereoBond);\n molecule.setBondAtom(0, stereoBond, i);\n molecule.setBondAtom(1, stereoBond, connAtom);\n }\n // To me it seems that we have to add all stereo centers into AND group 0. TLS 9.Nov.2015\n molecule.setAtomESR(i, esrType, 0);\n }\n }\n }\n }\n}\n","/**\n *\n * @param {import('openchemlib').Molecule} [molecule] An instance of a molecule\n * @param {object} [options={}]\n * @param {object} [options.OCL] openchemlib library\n */\nexport function makeRacemic(molecule) {\n const { Molecule } = molecule.getOCL();\n\n // if we don't calculate this we have 2 epimers\n molecule.ensureHelperArrays(Molecule.cHelperCIP);\n\n // we need to make one group \"AND\" for chiral (to force to racemic, this means diastereotopic and not enantiotopic)\n for (let i = 0; i < molecule.getAllAtoms(); i++) {\n if (molecule.getAtomParity(i) !== Molecule.cAtomParityNone) {\n molecule.setAtomESR(i, Molecule.cESRTypeAnd, 0); // changed to group 0; TLS 9.Nov.2015\n }\n }\n}\n","import { makeRacemic } from '../util/makeRacemic';\nimport { tagAtom } from '../util/tagAtom';\n\nimport { addDiastereotopicMissingChirality } from './addDiastereotopicMissingChirality';\n\n/**\n * Returns an array of diastereotopic ID (as oclCode)\n * @param {import('openchemlib').Molecule} molecule\n */\nexport function getDiastereotopicAtomIDs(molecule) {\n const OCL = molecule.getOCL();\n addDiastereotopicMissingChirality(molecule);\n\n let numberAtoms = molecule.getAllAtoms();\n let ids = [];\n for (let iAtom = 0; iAtom < numberAtoms; iAtom++) {\n let tempMolecule = molecule.getCompactCopy();\n tagAtom(tempMolecule, iAtom);\n makeRacemic(tempMolecule);\n // We need to ensure the helper array in order to get correctly the result of racemisation\n ids[iAtom] = tempMolecule.getCanonizedIDCode(\n OCL.Molecule.CANONIZER_ENCODE_ATOM_CUSTOM_LABELS,\n );\n }\n return ids;\n}\n","import { getDiastereotopicAtomIDs } from './getDiastereotopicAtomIDs';\n\n/**\n *\n * @param {import('openchemlib').Molecule} molecule\n */\nexport function getDiastereotopicAtomIDsAndH(molecule) {\n const OCL = molecule.getOCL();\n molecule = molecule.getCompactCopy();\n molecule.addImplicitHydrogens();\n // TODO Temporary code ???\n molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);\n\n const diaIDs = getDiastereotopicAtomIDs(molecule);\n const newDiaIDs = [];\n\n for (let i = 0; i < diaIDs.length; i++) {\n const diaID = diaIDs[i];\n const newDiaID = {\n oclID: diaID,\n hydrogenOCLIDs: [],\n nbHydrogens: 0,\n };\n if (molecule.getAtomicNo(i) === 1) {\n const atom = molecule.getConnAtom(i, 0);\n newDiaID.heavyAtom = diaIDs[atom];\n }\n for (let j = 0; j < molecule.getAllConnAtoms(i); j++) {\n const atom = molecule.getConnAtom(i, j);\n if (molecule.getAtomicNo(atom) === 1) {\n newDiaID.nbHydrogens++;\n if (newDiaID.hydrogenOCLIDs.indexOf(diaIDs[atom]) === -1) {\n newDiaID.hydrogenOCLIDs.push(diaIDs[atom]);\n }\n }\n }\n\n newDiaIDs.push(newDiaID);\n }\n\n return newDiaIDs;\n}\n","export function groupDiastereotopicAtomIDs(diaIDs, molecule, options = {}) {\n const { atomLabel } = options;\n const diaIDsObject = {};\n for (let i = 0; i < diaIDs.length; i++) {\n if (!atomLabel || molecule.getAtomLabel(i) === atomLabel) {\n let diaID = diaIDs[i];\n if (!diaIDsObject[diaID]) {\n diaIDsObject[diaID] = {\n counter: 0,\n atoms: [],\n oclID: diaID,\n atomLabel: molecule.getAtomLabel(i),\n };\n }\n diaIDsObject[diaID].counter++;\n diaIDsObject[diaID].atoms.push(i);\n }\n }\n\n return Object.keys(diaIDsObject).map((key) => diaIDsObject[key]);\n}\n","import { getDiastereotopicAtomIDs } from './getDiastereotopicAtomIDs';\nimport { groupDiastereotopicAtomIDs } from './groupDiastereotopicAtomIDs';\n/**\n * This function groups the diasterotopic atomIds of the molecule based on equivalence of atoms. The output object contains\n * a set of chemically equivalent atoms(element.atoms) and the groups of magnetically equivalent atoms (element.magneticGroups)\n * @param {import('openchemlib').Molecule} molecule\n * @param {object} [options={}]\n * @param {string} [options.atomLabel] Select atoms of the given atomLabel. By default it returns all the explicit atoms in the molecule\n * @returns {Array}\n */\n\nexport function getGroupedDiastereotopicAtomIDs(molecule, options = {}) {\n let diaIDs = getDiastereotopicAtomIDs(molecule);\n return groupDiastereotopicAtomIDs(diaIDs, molecule, options);\n}\n","/**\n * Check if a specific atom is a sp3 carbon\n * @param {import('openchemlib').Molecule} molecule\n * @param {number} atomID\n */\n\nexport function isCsp3(molecule, atomID) {\n if (molecule.getAtomicNo(atomID) !== 6) return false;\n if (molecule.getAtomCharge(atomID) !== 0) return false;\n if (\n molecule.getImplicitHydrogens(atomID) + molecule.getConnAtoms(atomID) !==\n 4\n ) {\n return false;\n }\n return true;\n}\n","import { isCsp3 } from '../util/isCsp3';\nimport { makeRacemic } from '../util/makeRacemic';\nimport { tagAtom } from '../util/tagAtom';\n\nexport const FULL_HOSE_CODE = 1;\nexport const HOSE_CODE_CUT_C_SP3_SP3 = 2;\n\n/**\n * Returns the hose code for a specific atom number\n * @param {import('openchemlib').Molecule} originalMolecule - The OCL molecule to be fragmented\n * @param {number[]} rootAtoms\n * @param {object} [options={}]\n * @param {boolean} [options.isTagged] Specify is the atoms are already tagged\n * @param {number} [options.minSphereSize=0] Smallest hose code sphere\n * @param {number} [options.maxSphereSize=4] Largest hose code sphere\n * @param {number} [options.kind=FULL_HOSE_CODE] Kind of hose code, default usual sphere\n */\nexport function getHoseCodesForAtoms(\n originalMolecule,\n rootAtoms = [],\n options = {},\n) {\n const OCL = originalMolecule.getOCL();\n const {\n minSphereSize = 0,\n maxSphereSize = 4,\n kind = FULL_HOSE_CODE,\n isTagged = false,\n } = options;\n\n const molecule = originalMolecule.getCompactCopy();\n\n if (!isTagged) {\n const tags = [];\n for (let i = 0; i < rootAtoms.length; i++) {\n let rootAtom = rootAtoms[i];\n tags.push(tagAtom(molecule, rootAtom));\n molecule.addImplicitHydrogens();\n molecule.addMissingChirality();\n molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);\n // because ensuring helper reorder atoms we need to look again for it\n }\n rootAtoms.length = 0;\n for (let j = 0; j < molecule.getAllAtoms(); j++) {\n if (tags.includes(molecule.getAtomCustomLabel(j))) {\n rootAtoms.push(j);\n }\n }\n }\n\n let fragment = new OCL.Molecule(0, 0);\n let results = [];\n let min = 0;\n let max = 0;\n let atomMask = new Array(molecule.getAllAtoms());\n let atomList = new Array(molecule.getAllAtoms());\n\n for (let sphere = 0; sphere <= maxSphereSize; sphere++) {\n if (max === 0) {\n for (let rootAtom of rootAtoms) {\n atomList[max] = rootAtom;\n atomMask[rootAtom] = true;\n max++;\n }\n } else {\n let newMax = max;\n for (let i = min; i < max; i++) {\n let atom = atomList[i];\n for (let j = 0; j < molecule.getAllConnAtoms(atom); j++) {\n let connAtom = molecule.getConnAtom(atom, j);\n if (!atomMask[connAtom]) {\n switch (kind) {\n case FULL_HOSE_CODE:\n atomMask[connAtom] = true;\n atomList[newMax++] = connAtom;\n break;\n case HOSE_CODE_CUT_C_SP3_SP3:\n if (!(isCsp3(molecule, atom) && isCsp3(molecule, connAtom))) {\n atomMask[connAtom] = true;\n atomList[newMax++] = connAtom;\n }\n break;\n default:\n throw new Error('getHoseCoesForAtom unknown kind');\n }\n }\n }\n }\n min = max;\n max = newMax;\n }\n molecule.copyMoleculeByAtoms(fragment, atomMask, true, null);\n if (sphere >= minSphereSize) {\n makeRacemic(fragment);\n results.push(\n fragment.getCanonizedIDCode(\n OCL.Molecule.CANONIZER_ENCODE_ATOM_CUSTOM_LABELS,\n ),\n );\n }\n }\n return results;\n}\n","import { getHoseCodesForAtoms } from './getHoseCodesForAtoms.js';\n\n/**\n * Returns the hose code for a specific atom number\n * @param {import('openchemlib').Molecule} originalMolecule\n * @param {number} rootAtom\n * @param {object} [options={}]\n * @param {boolean} [options.isTagged] Specify is the atom is already tagged\n * @param {number} [options.minSphereSize=0] Smallest hose code sphere\n * @param {number} [options.maxSphereSize=4] Largest hose code sphere\n * @param {number} [options.kind=FULL_HOSE_CODE] Kind of hose code, default usual sphere\n */\nexport function getHoseCodesForAtom(originalMolecule, rootAtom, options = {}) {\n return getHoseCodesForAtoms(originalMolecule, [rootAtom], options);\n}\n","import { getHoseCodesForAtom } from './getHoseCodesForAtom';\n/**\n * Returns the hose code for a specific marked atom\n * @param {import('openchemlib').Molecule} diastereotopicID\n * @param {object} options\n */\n\nexport function getHoseCodesFromDiastereotopicID(molecule, options = {}) {\n molecule.addImplicitHydrogens();\n molecule.addMissingChirality();\n\n // One of the atom has to be marked !\n let atomID = -1;\n for (let i = 0; i < molecule.getAllAtoms(); i++) {\n // we need to find the marked atom\n const atomCustomLabel = molecule.getAtomCustomLabel(i);\n if (atomCustomLabel != null && atomCustomLabel.endsWith('*')) {\n atomID = i;\n break;\n }\n }\n if (atomID >= 0) {\n options.isTagged = true;\n return getHoseCodesForAtom(molecule, atomID, options);\n }\n return undefined;\n}\n","import { makeRacemic } from '../util/makeRacemic';\nimport { tagAtom } from '../util/tagAtom';\n\nlet fragment;\n\n/**\n * Returns the hose code for a specific atom number\n * @param {import('openchemlib').Molecule} molecule\n */\nexport function getHoseCodesForPath(molecule, from, to, maxLength) {\n const OCL = molecule.getOCL();\n const originalFrom = from;\n const originalTo = to;\n molecule = molecule.getCompactCopy();\n\n let originalAtoms = []; // path before renumbering\n molecule.getPath(originalAtoms, from, to, maxLength + 1);\n let torsion;\n if (originalAtoms.length === 4) {\n torsion = molecule.calculateTorsion(originalAtoms);\n }\n\n const tag1 = tagAtom(molecule, from);\n const tag2 = tagAtom(molecule, to);\n\n molecule.addImplicitHydrogens();\n molecule.addMissingChirality();\n\n molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);\n\n from = -1;\n to = -1;\n for (let i = 0; i < molecule.getAllAtoms(); i++) {\n if (tag1 === tag2) {\n if (molecule.getAtomCustomLabel(i) === tag1) {\n if (from === -1) {\n from = i;\n } else {\n to = i;\n }\n }\n } else {\n if (tag1 === molecule.getAtomCustomLabel(i)) {\n from = i;\n }\n if (tag2 === molecule.getAtomCustomLabel(i)) {\n to = i;\n }\n }\n }\n\n if (!fragment) fragment = new OCL.Molecule(0, 0);\n\n let atoms = [];\n molecule.getPath(atoms, from, to, maxLength + 1);\n\n let min = 0;\n let max = 0;\n let atomMask = new Array(molecule.getAllAtoms()).fill(false);\n let atomList = new Array(molecule.getAllAtoms()).fill(-1);\n let hoses = [];\n\n for (let sphere = 0; sphere <= 2; sphere++) {\n if (max === 0) {\n for (let atom of atoms) {\n atomMask[atom] = true;\n atomList[max++] = atom;\n }\n } else {\n let newMax = max;\n for (let i = min; i < max; i++) {\n let atom = atomList[i];\n for (let j = 0; j < molecule.getAllConnAtoms(atom); j++) {\n let connAtom = molecule.getConnAtom(atom, j);\n if (!atomMask[connAtom]) {\n atomMask[connAtom] = true;\n atomList[newMax++] = connAtom;\n }\n }\n }\n min = max;\n max = newMax;\n }\n let atomMap = [];\n\n molecule.copyMoleculeByAtoms(fragment, atomMask, true, atomMap);\n makeRacemic(fragment);\n let oclID = fragment.getCanonizedIDCode(\n OCL.Molecule.CANONIZER_ENCODE_ATOM_CUSTOM_LABELS,\n );\n\n hoses.push({\n sphere,\n oclID,\n });\n }\n\n return {\n atoms: originalAtoms,\n from: originalFrom,\n to: originalTo,\n torsion,\n hoses,\n length: originalAtoms.length - 1,\n };\n}\n","const MAX_R = 10;\n\n/**\n * Generate molecules and calcule predicted properties form a list of smiles and fragments\n * @param {string} [coreSmiles]\n * @param {array} [fragments] Array of {smiles,R1,R2,...}\n * @param {import('openchemlib')} OCL - openchemlib library\n * @param {object} [options={}]\n * @param {function} [options.onStep] method to execute each new molecules\n * @param {boolean} [options.complexity] returns only the number of molecules to evaluate\n * @return {Promise} promise that resolves to molecules or complexity as a number\n */\nexport async function combineSmiles(coreSmiles, fragments, OCL, options = {}) {\n const { complexity = false } = options;\n const core = getCore(coreSmiles);\n const rGroups = getRGroups(core, fragments);\n if (complexity) {\n return getComplexity(rGroups);\n }\n return generate(core, rGroups, OCL, options);\n}\n\nfunction getComplexity(rGroups) {\n let complexity = 1;\n for (let rGroup of rGroups) {\n complexity *= rGroup.smiles.length;\n }\n return complexity;\n}\n\nasync function generate(core, rGroups, OCL, options = {}) {\n const { onStep } = options;\n const molecules = {};\n const sizes = new Array(rGroups.length);\n const currents = new Array(rGroups.length);\n for (let i = 0; i < rGroups.length; i++) {\n sizes[i] = rGroups[i].smiles.length - 1;\n currents[i] = 0;\n }\n let position = 0;\n let counter = 0;\n\n while (true) {\n counter++;\n while (position < currents.length) {\n if (currents[position] < sizes[position]) {\n if (onStep) {\n await onStep(counter);\n }\n appendMolecule(molecules, core, rGroups, currents, OCL);\n currents[position]++;\n for (let i = 0; i < position; i++) {\n currents[i] = 0;\n }\n position = 0;\n } else {\n position++;\n }\n }\n if ((position = currents.length)) {\n if (onStep) {\n await onStep(counter);\n }\n appendMolecule(molecules, core, rGroups, currents, OCL);\n break;\n }\n }\n return Object.keys(molecules)\n .map((key) => molecules[key])\n .sort((m1, m2) => m1.mw - m2.mw);\n}\n\nfunction appendMolecule(molecules, core, rGroups, currents, OCL) {\n let newSmiles = core.smiles;\n for (let i = 0; i < currents.length; i++) {\n newSmiles += `.${rGroups[i].smiles[currents[i]]}`;\n }\n\n const currentMol = OCL.Molecule.fromSmiles(newSmiles);\n const idCode = currentMol.getIDCode();\n\n if (!molecules[idCode]) {\n let molecule = {};\n molecules[idCode] = molecule;\n molecule.smiles = currentMol.toSmiles();\n molecule.combinedSmiles = newSmiles;\n molecule.idCode = idCode;\n molecule.molfile = currentMol.toMolfile();\n\n const props = new OCL.MoleculeProperties(currentMol);\n molecule.nbHAcceptor = props.acceptorCount;\n molecule.nbHDonor = props.donorCount;\n molecule.logP = props.logP;\n molecule.logS = props.logS;\n molecule.PSA = props.polarSurfaceArea;\n molecule.nbRottable = props.rotatableBondCount;\n molecule.nbStereoCenter = props.stereoCenterCount;\n let mf = currentMol.getMolecularFormula();\n molecule.mf = mf.formula;\n molecule.mw = mf.relativeWeight;\n }\n}\n\nfunction getCore(coreSmiles) {\n let core = {\n originalSmiles: coreSmiles,\n smiles: coreSmiles.replace(/\\[R(?[1-4])\\]/g, '%5$'),\n };\n\n for (let i = 0; i < MAX_R; i++) {\n if (core.originalSmiles.indexOf(`[R${i}]`) > -1) core[`R${i}`] = true;\n }\n return core;\n}\n\nfunction getRGroups(core, fragments) {\n let rGroups = {};\n for (const fragment of fragments) {\n if (fragment.smiles) {\n const smiles = updateRPosition(fragment.smiles);\n for (let i = 0; i < MAX_R; i++) {\n if (core[`R${i}`]) {\n // we only consider the R that are in the core\n if (fragment[`R${i}`]) {\n if (!rGroups[`R${i}`]) {\n rGroups[`R${i}`] = {\n group: `R${i}`,\n smiles: [],\n };\n }\n rGroups[`R${i}`].smiles.push(smiles.replace(/\\[R\\]/, `(%5${i})`));\n }\n }\n }\n }\n }\n return Object.keys(rGroups).map((key) => rGroups[key]);\n}\n\nfunction updateRPosition(smiles) {\n // R group should not be at the beginning\n if (smiles.indexOf('[R]') !== 0) return smiles;\n if (smiles.length === 3) return '[H][R]';\n // we are in trouble ... we need to move the R\n let newSmiles = smiles.replace('[R]', '');\n // we need to check where we should put the R group\n let level = 0;\n for (let j = 0; j < newSmiles.length; j++) {\n let currentChar = newSmiles.charAt(j);\n let currentSubstring = newSmiles.substr(j);\n if (currentChar === '(') {\n level++;\n } else if (currentChar === ')') {\n level--;\n } else if (level === 0) {\n if (currentSubstring.match(/^[a-z]/)) {\n return `${newSmiles.substr(0, j + 1)}([R])${newSmiles.substr(j + 1)}`;\n } else if (currentSubstring.match(/^[A-Z][a-z]/)) {\n return `${newSmiles.substr(0, j + 2)}([R])${newSmiles.substr(j + 2)}`;\n } else if (currentSubstring.match(/^[A-Z]/)) {\n return `${newSmiles.substr(0, j + 1)}([R])${newSmiles.substr(j + 1)}`;\n }\n }\n }\n return smiles;\n}\n","import { getDiastereotopicAtomIDs } from '../diastereotopic/getDiastereotopicAtomIDs';\n\n/**\n * Returns various information about atoms in the molecule\n * @param {import('openchemlib').Molecule} [molecule]\n */\nexport function getAtomsInfo(molecule) {\n const OCL = molecule.getOCL();\n molecule.ensureHelperArrays(OCL.Molecule.cHelperRings);\n\n let diaIDs = getDiastereotopicAtomIDs(molecule);\n\n let results = [];\n for (let i = 0; i < diaIDs.length; i++) {\n let result = {\n oclID: diaIDs[i],\n extra: {\n singleBonds: 0,\n doubleBonds: 0,\n tripleBonds: 0,\n aromaticBonds: 0,\n cnoHybridation: 0, // should be 1 (sp), 2 (sp2) or 3 (sp3)\n },\n };\n let extra = result.extra;\n results.push(result);\n result.abnormalValence = molecule.getAtomAbnormalValence(i); // -1 is normal otherwise specified\n result.charge = molecule.getAtomCharge(i);\n result.cipParity = molecule.getAtomCIPParity(i);\n result.color = molecule.getAtomColor(i);\n result.customLabel = molecule.getAtomCustomLabel(i);\n // result.esrGroup=molecule.getAtomESRGroup(i);\n // result.esrType=molecule.getAtomESRType(i);\n result.atomicNo = molecule.getAtomicNo(i);\n result.label = molecule.getAtomLabel(i);\n // result.list=molecule.getAtomList(i);\n // result.listString=molecule.getAtomListString(i);\n // result.mapNo=molecule.getAtomMapNo(i);\n result.mass = molecule.getAtomMass(i);\n // result.parity=molecule.getAtomParity(i);\n // result.pi=molecule.getAtomPi(i);\n // result.preferredStereoBond=molecule.getAtomPreferredStereoBond(i);\n // result.queryFeatures=molecule.getAtomQueryFeatures(i);\n result.radical = molecule.getAtomRadical(i);\n result.ringBondCount = molecule.getAtomRingBondCount(i);\n // result.ringCount=molecule.getAtomRingCount(i);\n result.ringSize = molecule.getAtomRingSize(i);\n result.x = molecule.getAtomX(i);\n result.y = molecule.getAtomY(i);\n result.z = molecule.getAtomZ(i);\n result.allHydrogens = molecule.getAllHydrogens(i);\n result.connAtoms = molecule.getConnAtoms(i);\n result.allConnAtoms = molecule.getAllConnAtoms(i);\n\n result.implicitHydrogens =\n result.allHydrogens + result.connAtoms - result.allConnAtoms;\n\n result.isAromatic = molecule.isAromaticAtom(i);\n result.isAllylic = molecule.isAllylicAtom(i);\n result.isStereoCenter = molecule.isAtomStereoCenter(i);\n result.isRing = molecule.isRingAtom(i);\n result.isSmallRing = molecule.isSmallRingAtom(i);\n result.isStabilized = molecule.isStabilizedAtom(i);\n\n // todo HACK to circumvent bug in OCL that consider than an hydrogen is connected to itself\n result.extra.singleBonds =\n result.atomicNo === 1 ? 0 : result.implicitHydrogens;\n for (let j = 0; j < molecule.getAllConnAtoms(i); j++) {\n let bond = molecule.getConnBond(i, j);\n let bondOrder = molecule.getBondOrder(bond);\n if (molecule.isAromaticBond(bond)) {\n extra.aromaticBonds++;\n } else if (bondOrder === 1) {\n // not an hydrogen\n extra.singleBonds++;\n } else if (bondOrder === 2) {\n extra.doubleBonds++;\n } else if (bondOrder === 3) {\n extra.tripleBonds++;\n }\n }\n result.extra.totalBonds =\n result.extra.singleBonds +\n result.extra.doubleBonds +\n result.extra.tripleBonds +\n result.extra.aromaticBonds;\n\n if (result.atomicNo === 6) {\n result.extra.cnoHybridation = result.extra.totalBonds - 1;\n } else if (result.atomicNo === 7) {\n result.extra.cnoHybridation = result.extra.totalBonds;\n } else if (result.atomicNo === 8) {\n result.extra.cnoHybridation = result.extra.totalBonds + 1;\n } else if (result.atomicNo === 1) {\n let connectedAtom =\n molecule.getAllConnAtoms(i) === 0\n ? 0\n : molecule.getAtomicNo(molecule.getConnAtom(i, 0));\n result.extra.hydrogenOnAtomicNo = connectedAtom;\n if (connectedAtom === 7 || connectedAtom === 8) {\n result.extra.labileHydrogen = true;\n }\n }\n }\n return results;\n}\n","const toString = Object.prototype.toString;\n/**\n * Checks if an object is an instance of an Array (array or typed array).\n *\n * @param {any} value - Object to check.\n * @returns {boolean} True if the object is an array.\n */\nexport function isAnyArray(value) {\n return toString.call(value).endsWith('Array]');\n}\n//# sourceMappingURL=index.js.map","import { isAnyArray } from 'is-any-array';\nimport max from 'ml-array-max';\nimport min from 'ml-array-min';\n\nfunction rescale(input) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};\n\n if (!isAnyArray(input)) {\n throw new TypeError('input must be an array');\n } else if (input.length === 0) {\n throw new TypeError('input must not be empty');\n }\n\n var output;\n\n if (options.output !== undefined) {\n if (!isAnyArray(options.output)) {\n throw new TypeError('output option must be an array if specified');\n }\n\n output = options.output;\n } else {\n output = new Array(input.length);\n }\n\n var currentMin = min(input);\n var currentMax = max(input);\n\n if (currentMin === currentMax) {\n throw new RangeError('minimum and maximum input values are equal. Cannot rescale a constant array');\n }\n\n var _options$min = options.min,\n minValue = _options$min === void 0 ? options.autoMinMax ? currentMin : 0 : _options$min,\n _options$max = options.max,\n maxValue = _options$max === void 0 ? options.autoMinMax ? currentMax : 1 : _options$max;\n\n if (minValue >= maxValue) {\n throw new RangeError('min option must be smaller than max option');\n }\n\n var factor = (maxValue - minValue) / (currentMax - currentMin);\n\n for (var i = 0; i < input.length; i++) {\n output[i] = (input[i] - currentMin) * factor + minValue;\n }\n\n return output;\n}\n\nexport { rescale as default };\n","import { isAnyArray } from 'is-any-array';\n\nfunction min(input) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};\n\n if (!isAnyArray(input)) {\n throw new TypeError('input must be an array');\n }\n\n if (input.length === 0) {\n throw new TypeError('input must not be empty');\n }\n\n var _options$fromIndex = options.fromIndex,\n fromIndex = _options$fromIndex === void 0 ? 0 : _options$fromIndex,\n _options$toIndex = options.toIndex,\n toIndex = _options$toIndex === void 0 ? input.length : _options$toIndex;\n\n if (fromIndex < 0 || fromIndex >= input.length || !Number.isInteger(fromIndex)) {\n throw new Error('fromIndex must be a positive integer smaller than length');\n }\n\n if (toIndex <= fromIndex || toIndex > input.length || !Number.isInteger(toIndex)) {\n throw new Error('toIndex must be an integer greater than fromIndex and at most equal to length');\n }\n\n var minValue = input[fromIndex];\n\n for (var i = fromIndex + 1; i < toIndex; i++) {\n if (input[i] < minValue) minValue = input[i];\n }\n\n return minValue;\n}\n\nexport { min as default };\n","import { isAnyArray } from 'is-any-array';\n\nfunction max(input) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};\n\n if (!isAnyArray(input)) {\n throw new TypeError('input must be an array');\n }\n\n if (input.length === 0) {\n throw new TypeError('input must not be empty');\n }\n\n var _options$fromIndex = options.fromIndex,\n fromIndex = _options$fromIndex === void 0 ? 0 : _options$fromIndex,\n _options$toIndex = options.toIndex,\n toIndex = _options$toIndex === void 0 ? input.length : _options$toIndex;\n\n if (fromIndex < 0 || fromIndex >= input.length || !Number.isInteger(fromIndex)) {\n throw new Error('fromIndex must be a positive integer smaller than length');\n }\n\n if (toIndex <= fromIndex || toIndex > input.length || !Number.isInteger(toIndex)) {\n throw new Error('toIndex must be an integer greater than fromIndex and at most equal to length');\n }\n\n var maxValue = input[fromIndex];\n\n for (var i = fromIndex + 1; i < toIndex; i++) {\n if (input[i] > maxValue) maxValue = input[i];\n }\n\n return maxValue;\n}\n\nexport { max as default };\n","const indent = ' '.repeat(2);\nconst indentData = ' '.repeat(4);\n\nexport function inspectMatrix() {\n return inspectMatrixWithOptions(this);\n}\n\nexport function inspectMatrixWithOptions(matrix, options = {}) {\n const {\n maxRows = 15,\n maxColumns = 10,\n maxNumSize = 8,\n padMinus = 'auto',\n } = options;\n return `${matrix.constructor.name} {\n${indent}[\n${indentData}${inspectData(matrix, maxRows, maxColumns, maxNumSize, padMinus)}\n${indent}]\n${indent}rows: ${matrix.rows}\n${indent}columns: ${matrix.columns}\n}`;\n}\n\nfunction inspectData(matrix, maxRows, maxColumns, maxNumSize, padMinus) {\n const { rows, columns } = matrix;\n const maxI = Math.min(rows, maxRows);\n const maxJ = Math.min(columns, maxColumns);\n const result = [];\n\n if (padMinus === 'auto') {\n padMinus = false;\n loop: for (let i = 0; i < maxI; i++) {\n for (let j = 0; j < maxJ; j++) {\n if (matrix.get(i, j) < 0) {\n padMinus = true;\n break loop;\n }\n }\n }\n }\n\n for (let i = 0; i < maxI; i++) {\n let line = [];\n for (let j = 0; j < maxJ; j++) {\n line.push(formatNumber(matrix.get(i, j), maxNumSize, padMinus));\n }\n result.push(`${line.join(' ')}`);\n }\n if (maxJ !== columns) {\n result[result.length - 1] += ` ... ${columns - maxColumns} more columns`;\n }\n if (maxI !== rows) {\n result.push(`... ${rows - maxRows} more rows`);\n }\n return result.join(`\\n${indentData}`);\n}\n\nfunction formatNumber(num, maxNumSize, padMinus) {\n return (\n num >= 0 && padMinus\n ? ` ${formatNumber2(num, maxNumSize - 1)}`\n : formatNumber2(num, maxNumSize)\n ).padEnd(maxNumSize);\n}\n\nfunction formatNumber2(num, len) {\n // small.length numbers should be as is\n let str = num.toString();\n if (str.length <= len) return str;\n\n // (7)'0.00123' is better then (7)'1.23e-2'\n // (8)'0.000123' is worse then (7)'1.23e-3',\n let fix = num.toFixed(len);\n if (fix.length > len) {\n fix = num.toFixed(Math.max(0, len - (fix.length - len)));\n }\n if (\n fix.length <= len &&\n !fix.startsWith('0.000') &&\n !fix.startsWith('-0.000')\n ) {\n return fix;\n }\n\n // well, if it's still too long the user should've used longer numbers\n let exp = num.toExponential(len);\n if (exp.length > len) {\n exp = num.toExponential(Math.max(0, len - (exp.length - len)));\n }\n return exp.slice(0);\n}\n","import { isAnyArray } from 'is-any-array';\n\n/**\n * @private\n * Check that a row index is not out of bounds\n * @param {Matrix} matrix\n * @param {number} index\n * @param {boolean} [outer]\n */\nexport function checkRowIndex(matrix, index, outer) {\n let max = outer ? matrix.rows : matrix.rows - 1;\n if (index < 0 || index > max) {\n throw new RangeError('Row index out of range');\n }\n}\n\n/**\n * @private\n * Check that a column index is not out of bounds\n * @param {Matrix} matrix\n * @param {number} index\n * @param {boolean} [outer]\n */\nexport function checkColumnIndex(matrix, index, outer) {\n let max = outer ? matrix.columns : matrix.columns - 1;\n if (index < 0 || index > max) {\n throw new RangeError('Column index out of range');\n }\n}\n\n/**\n * @private\n * Check that the provided vector is an array with the right length\n * @param {Matrix} matrix\n * @param {Array|Matrix} vector\n * @return {Array}\n * @throws {RangeError}\n */\nexport function checkRowVector(matrix, vector) {\n if (vector.to1DArray) {\n vector = vector.to1DArray();\n }\n if (vector.length !== matrix.columns) {\n throw new RangeError(\n 'vector size must be the same as the number of columns',\n );\n }\n return vector;\n}\n\n/**\n * @private\n * Check that the provided vector is an array with the right length\n * @param {Matrix} matrix\n * @param {Array|Matrix} vector\n * @return {Array}\n * @throws {RangeError}\n */\nexport function checkColumnVector(matrix, vector) {\n if (vector.to1DArray) {\n vector = vector.to1DArray();\n }\n if (vector.length !== matrix.rows) {\n throw new RangeError('vector size must be the same as the number of rows');\n }\n return vector;\n}\n\nexport function checkRowIndices(matrix, rowIndices) {\n if (!isAnyArray(rowIndices)) {\n throw new TypeError('row indices must be an array');\n }\n\n for (let i = 0; i < rowIndices.length; i++) {\n if (rowIndices[i] < 0 || rowIndices[i] >= matrix.rows) {\n throw new RangeError('row indices are out of range');\n }\n }\n}\n\nexport function checkColumnIndices(matrix, columnIndices) {\n if (!isAnyArray(columnIndices)) {\n throw new TypeError('column indices must be an array');\n }\n\n for (let i = 0; i < columnIndices.length; i++) {\n if (columnIndices[i] < 0 || columnIndices[i] >= matrix.columns) {\n throw new RangeError('column indices are out of range');\n }\n }\n}\n\nexport function checkRange(matrix, startRow, endRow, startColumn, endColumn) {\n if (arguments.length !== 5) {\n throw new RangeError('expected 4 arguments');\n }\n checkNumber('startRow', startRow);\n checkNumber('endRow', endRow);\n checkNumber('startColumn', startColumn);\n checkNumber('endColumn', endColumn);\n if (\n startRow > endRow ||\n startColumn > endColumn ||\n startRow < 0 ||\n startRow >= matrix.rows ||\n endRow < 0 ||\n endRow >= matrix.rows ||\n startColumn < 0 ||\n startColumn >= matrix.columns ||\n endColumn < 0 ||\n endColumn >= matrix.columns\n ) {\n throw new RangeError('Submatrix indices are out of range');\n }\n}\n\nexport function newArray(length, value = 0) {\n let array = [];\n for (let i = 0; i < length; i++) {\n array.push(value);\n }\n return array;\n}\n\nfunction checkNumber(name, value) {\n if (typeof value !== 'number') {\n throw new TypeError(`${name} must be a number`);\n }\n}\n\nexport function checkNonEmpty(matrix) {\n if (matrix.isEmpty()) {\n throw new Error('Empty matrix has no elements to index');\n }\n}\n","import { isAnyArray } from 'is-any-array';\nimport rescale from 'ml-array-rescale';\n\nimport { inspectMatrix, inspectMatrixWithOptions } from './inspect';\nimport { installMathOperations } from './mathOperations';\nimport {\n sumByRow,\n sumByColumn,\n sumAll,\n productByRow,\n productByColumn,\n productAll,\n varianceByRow,\n varianceByColumn,\n varianceAll,\n centerByRow,\n centerByColumn,\n centerAll,\n scaleByRow,\n scaleByColumn,\n scaleAll,\n getScaleByRow,\n getScaleByColumn,\n getScaleAll,\n} from './stat';\nimport {\n checkRowVector,\n checkRowIndex,\n checkColumnIndex,\n checkColumnVector,\n checkRange,\n checkNonEmpty,\n checkRowIndices,\n checkColumnIndices,\n} from './util';\n\nexport class AbstractMatrix {\n static from1DArray(newRows, newColumns, newData) {\n let length = newRows * newColumns;\n if (length !== newData.length) {\n throw new RangeError('data length does not match given dimensions');\n }\n let newMatrix = new Matrix(newRows, newColumns);\n for (let row = 0; row < newRows; row++) {\n for (let column = 0; column < newColumns; column++) {\n newMatrix.set(row, column, newData[row * newColumns + column]);\n }\n }\n return newMatrix;\n }\n\n static rowVector(newData) {\n let vector = new Matrix(1, newData.length);\n for (let i = 0; i < newData.length; i++) {\n vector.set(0, i, newData[i]);\n }\n return vector;\n }\n\n static columnVector(newData) {\n let vector = new Matrix(newData.length, 1);\n for (let i = 0; i < newData.length; i++) {\n vector.set(i, 0, newData[i]);\n }\n return vector;\n }\n\n static zeros(rows, columns) {\n return new Matrix(rows, columns);\n }\n\n static ones(rows, columns) {\n return new Matrix(rows, columns).fill(1);\n }\n\n static rand(rows, columns, options = {}) {\n if (typeof options !== 'object') {\n throw new TypeError('options must be an object');\n }\n const { random = Math.random } = options;\n let matrix = new Matrix(rows, columns);\n for (let i = 0; i < rows; i++) {\n for (let j = 0; j < columns; j++) {\n matrix.set(i, j, random());\n }\n }\n return matrix;\n }\n\n static randInt(rows, columns, options = {}) {\n if (typeof options !== 'object') {\n throw new TypeError('options must be an object');\n }\n const { min = 0, max = 1000, random = Math.random } = options;\n if (!Number.isInteger(min)) throw new TypeError('min must be an integer');\n if (!Number.isInteger(max)) throw new TypeError('max must be an integer');\n if (min >= max) throw new RangeError('min must be smaller than max');\n let interval = max - min;\n let matrix = new Matrix(rows, columns);\n for (let i = 0; i < rows; i++) {\n for (let j = 0; j < columns; j++) {\n let value = min + Math.round(random() * interval);\n matrix.set(i, j, value);\n }\n }\n return matrix;\n }\n\n static eye(rows, columns, value) {\n if (columns === undefined) columns = rows;\n if (value === undefined) value = 1;\n let min = Math.min(rows, columns);\n let matrix = this.zeros(rows, columns);\n for (let i = 0; i < min; i++) {\n matrix.set(i, i, value);\n }\n return matrix;\n }\n\n static diag(data, rows, columns) {\n let l = data.length;\n if (rows === undefined) rows = l;\n if (columns === undefined) columns = rows;\n let min = Math.min(l, rows, columns);\n let matrix = this.zeros(rows, columns);\n for (let i = 0; i < min; i++) {\n matrix.set(i, i, data[i]);\n }\n return matrix;\n }\n\n static min(matrix1, matrix2) {\n matrix1 = this.checkMatrix(matrix1);\n matrix2 = this.checkMatrix(matrix2);\n let rows = matrix1.rows;\n let columns = matrix1.columns;\n let result = new Matrix(rows, columns);\n for (let i = 0; i < rows; i++) {\n for (let j = 0; j < columns; j++) {\n result.set(i, j, Math.min(matrix1.get(i, j), matrix2.get(i, j)));\n }\n }\n return result;\n }\n\n static max(matrix1, matrix2) {\n matrix1 = this.checkMatrix(matrix1);\n matrix2 = this.checkMatrix(matrix2);\n let rows = matrix1.rows;\n let columns = matrix1.columns;\n let result = new this(rows, columns);\n for (let i = 0; i < rows; i++) {\n for (let j = 0; j < columns; j++) {\n result.set(i, j, Math.max(matrix1.get(i, j), matrix2.get(i, j)));\n }\n }\n return result;\n }\n\n static checkMatrix(value) {\n return AbstractMatrix.isMatrix(value) ? value : new Matrix(value);\n }\n\n static isMatrix(value) {\n return value != null && value.klass === 'Matrix';\n }\n\n get size() {\n return this.rows * this.columns;\n }\n\n apply(callback) {\n if (typeof callback !== 'function') {\n throw new TypeError('callback must be a function');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n callback.call(this, i, j);\n }\n }\n return this;\n }\n\n to1DArray() {\n let array = [];\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n array.push(this.get(i, j));\n }\n }\n return array;\n }\n\n to2DArray() {\n let copy = [];\n for (let i = 0; i < this.rows; i++) {\n copy.push([]);\n for (let j = 0; j < this.columns; j++) {\n copy[i].push(this.get(i, j));\n }\n }\n return copy;\n }\n\n toJSON() {\n return this.to2DArray();\n }\n\n isRowVector() {\n return this.rows === 1;\n }\n\n isColumnVector() {\n return this.columns === 1;\n }\n\n isVector() {\n return this.rows === 1 || this.columns === 1;\n }\n\n isSquare() {\n return this.rows === this.columns;\n }\n\n isEmpty() {\n return this.rows === 0 || this.columns === 0;\n }\n\n isSymmetric() {\n if (this.isSquare()) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j <= i; j++) {\n if (this.get(i, j) !== this.get(j, i)) {\n return false;\n }\n }\n }\n return true;\n }\n return false;\n }\n\n isEchelonForm() {\n let i = 0;\n let j = 0;\n let previousColumn = -1;\n let isEchelonForm = true;\n let checked = false;\n while (i < this.rows && isEchelonForm) {\n j = 0;\n checked = false;\n while (j < this.columns && checked === false) {\n if (this.get(i, j) === 0) {\n j++;\n } else if (this.get(i, j) === 1 && j > previousColumn) {\n checked = true;\n previousColumn = j;\n } else {\n isEchelonForm = false;\n checked = true;\n }\n }\n i++;\n }\n return isEchelonForm;\n }\n\n isReducedEchelonForm() {\n let i = 0;\n let j = 0;\n let previousColumn = -1;\n let isReducedEchelonForm = true;\n let checked = false;\n while (i < this.rows && isReducedEchelonForm) {\n j = 0;\n checked = false;\n while (j < this.columns && checked === false) {\n if (this.get(i, j) === 0) {\n j++;\n } else if (this.get(i, j) === 1 && j > previousColumn) {\n checked = true;\n previousColumn = j;\n } else {\n isReducedEchelonForm = false;\n checked = true;\n }\n }\n for (let k = j + 1; k < this.rows; k++) {\n if (this.get(i, k) !== 0) {\n isReducedEchelonForm = false;\n }\n }\n i++;\n }\n return isReducedEchelonForm;\n }\n\n echelonForm() {\n let result = this.clone();\n let h = 0;\n let k = 0;\n while (h < result.rows && k < result.columns) {\n let iMax = h;\n for (let i = h; i < result.rows; i++) {\n if (result.get(i, k) > result.get(iMax, k)) {\n iMax = i;\n }\n }\n if (result.get(iMax, k) === 0) {\n k++;\n } else {\n result.swapRows(h, iMax);\n let tmp = result.get(h, k);\n for (let j = k; j < result.columns; j++) {\n result.set(h, j, result.get(h, j) / tmp);\n }\n for (let i = h + 1; i < result.rows; i++) {\n let factor = result.get(i, k) / result.get(h, k);\n result.set(i, k, 0);\n for (let j = k + 1; j < result.columns; j++) {\n result.set(i, j, result.get(i, j) - result.get(h, j) * factor);\n }\n }\n h++;\n k++;\n }\n }\n return result;\n }\n\n reducedEchelonForm() {\n let result = this.echelonForm();\n let m = result.columns;\n let n = result.rows;\n let h = n - 1;\n while (h >= 0) {\n if (result.maxRow(h) === 0) {\n h--;\n } else {\n let p = 0;\n let pivot = false;\n while (p < n && pivot === false) {\n if (result.get(h, p) === 1) {\n pivot = true;\n } else {\n p++;\n }\n }\n for (let i = 0; i < h; i++) {\n let factor = result.get(i, p);\n for (let j = p; j < m; j++) {\n let tmp = result.get(i, j) - factor * result.get(h, j);\n result.set(i, j, tmp);\n }\n }\n h--;\n }\n }\n return result;\n }\n\n set() {\n throw new Error('set method is unimplemented');\n }\n\n get() {\n throw new Error('get method is unimplemented');\n }\n\n repeat(options = {}) {\n if (typeof options !== 'object') {\n throw new TypeError('options must be an object');\n }\n const { rows = 1, columns = 1 } = options;\n if (!Number.isInteger(rows) || rows <= 0) {\n throw new TypeError('rows must be a positive integer');\n }\n if (!Number.isInteger(columns) || columns <= 0) {\n throw new TypeError('columns must be a positive integer');\n }\n let matrix = new Matrix(this.rows * rows, this.columns * columns);\n for (let i = 0; i < rows; i++) {\n for (let j = 0; j < columns; j++) {\n matrix.setSubMatrix(this, this.rows * i, this.columns * j);\n }\n }\n return matrix;\n }\n\n fill(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, value);\n }\n }\n return this;\n }\n\n neg() {\n return this.mulS(-1);\n }\n\n getRow(index) {\n checkRowIndex(this, index);\n let row = [];\n for (let i = 0; i < this.columns; i++) {\n row.push(this.get(index, i));\n }\n return row;\n }\n\n getRowVector(index) {\n return Matrix.rowVector(this.getRow(index));\n }\n\n setRow(index, array) {\n checkRowIndex(this, index);\n array = checkRowVector(this, array);\n for (let i = 0; i < this.columns; i++) {\n this.set(index, i, array[i]);\n }\n return this;\n }\n\n swapRows(row1, row2) {\n checkRowIndex(this, row1);\n checkRowIndex(this, row2);\n for (let i = 0; i < this.columns; i++) {\n let temp = this.get(row1, i);\n this.set(row1, i, this.get(row2, i));\n this.set(row2, i, temp);\n }\n return this;\n }\n\n getColumn(index) {\n checkColumnIndex(this, index);\n let column = [];\n for (let i = 0; i < this.rows; i++) {\n column.push(this.get(i, index));\n }\n return column;\n }\n\n getColumnVector(index) {\n return Matrix.columnVector(this.getColumn(index));\n }\n\n setColumn(index, array) {\n checkColumnIndex(this, index);\n array = checkColumnVector(this, array);\n for (let i = 0; i < this.rows; i++) {\n this.set(i, index, array[i]);\n }\n return this;\n }\n\n swapColumns(column1, column2) {\n checkColumnIndex(this, column1);\n checkColumnIndex(this, column2);\n for (let i = 0; i < this.rows; i++) {\n let temp = this.get(i, column1);\n this.set(i, column1, this.get(i, column2));\n this.set(i, column2, temp);\n }\n return this;\n }\n\n addRowVector(vector) {\n vector = checkRowVector(this, vector);\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) + vector[j]);\n }\n }\n return this;\n }\n\n subRowVector(vector) {\n vector = checkRowVector(this, vector);\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) - vector[j]);\n }\n }\n return this;\n }\n\n mulRowVector(vector) {\n vector = checkRowVector(this, vector);\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) * vector[j]);\n }\n }\n return this;\n }\n\n divRowVector(vector) {\n vector = checkRowVector(this, vector);\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) / vector[j]);\n }\n }\n return this;\n }\n\n addColumnVector(vector) {\n vector = checkColumnVector(this, vector);\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) + vector[i]);\n }\n }\n return this;\n }\n\n subColumnVector(vector) {\n vector = checkColumnVector(this, vector);\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) - vector[i]);\n }\n }\n return this;\n }\n\n mulColumnVector(vector) {\n vector = checkColumnVector(this, vector);\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) * vector[i]);\n }\n }\n return this;\n }\n\n divColumnVector(vector) {\n vector = checkColumnVector(this, vector);\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) / vector[i]);\n }\n }\n return this;\n }\n\n mulRow(index, value) {\n checkRowIndex(this, index);\n for (let i = 0; i < this.columns; i++) {\n this.set(index, i, this.get(index, i) * value);\n }\n return this;\n }\n\n mulColumn(index, value) {\n checkColumnIndex(this, index);\n for (let i = 0; i < this.rows; i++) {\n this.set(i, index, this.get(i, index) * value);\n }\n return this;\n }\n\n max(by) {\n if (this.isEmpty()) {\n return NaN;\n }\n switch (by) {\n case 'row': {\n const max = new Array(this.rows).fill(Number.NEGATIVE_INFINITY);\n for (let row = 0; row < this.rows; row++) {\n for (let column = 0; column < this.columns; column++) {\n if (this.get(row, column) > max[row]) {\n max[row] = this.get(row, column);\n }\n }\n }\n return max;\n }\n case 'column': {\n const max = new Array(this.columns).fill(Number.NEGATIVE_INFINITY);\n for (let row = 0; row < this.rows; row++) {\n for (let column = 0; column < this.columns; column++) {\n if (this.get(row, column) > max[column]) {\n max[column] = this.get(row, column);\n }\n }\n }\n return max;\n }\n case undefined: {\n let max = this.get(0, 0);\n for (let row = 0; row < this.rows; row++) {\n for (let column = 0; column < this.columns; column++) {\n if (this.get(row, column) > max) {\n max = this.get(row, column);\n }\n }\n }\n return max;\n }\n default:\n throw new Error(`invalid option: ${by}`);\n }\n }\n\n maxIndex() {\n checkNonEmpty(this);\n let v = this.get(0, 0);\n let idx = [0, 0];\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n if (this.get(i, j) > v) {\n v = this.get(i, j);\n idx[0] = i;\n idx[1] = j;\n }\n }\n }\n return idx;\n }\n\n min(by) {\n if (this.isEmpty()) {\n return NaN;\n }\n\n switch (by) {\n case 'row': {\n const min = new Array(this.rows).fill(Number.POSITIVE_INFINITY);\n for (let row = 0; row < this.rows; row++) {\n for (let column = 0; column < this.columns; column++) {\n if (this.get(row, column) < min[row]) {\n min[row] = this.get(row, column);\n }\n }\n }\n return min;\n }\n case 'column': {\n const min = new Array(this.columns).fill(Number.POSITIVE_INFINITY);\n for (let row = 0; row < this.rows; row++) {\n for (let column = 0; column < this.columns; column++) {\n if (this.get(row, column) < min[column]) {\n min[column] = this.get(row, column);\n }\n }\n }\n return min;\n }\n case undefined: {\n let min = this.get(0, 0);\n for (let row = 0; row < this.rows; row++) {\n for (let column = 0; column < this.columns; column++) {\n if (this.get(row, column) < min) {\n min = this.get(row, column);\n }\n }\n }\n return min;\n }\n default:\n throw new Error(`invalid option: ${by}`);\n }\n }\n\n minIndex() {\n checkNonEmpty(this);\n let v = this.get(0, 0);\n let idx = [0, 0];\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n if (this.get(i, j) < v) {\n v = this.get(i, j);\n idx[0] = i;\n idx[1] = j;\n }\n }\n }\n return idx;\n }\n\n maxRow(row) {\n checkRowIndex(this, row);\n if (this.isEmpty()) {\n return NaN;\n }\n let v = this.get(row, 0);\n for (let i = 1; i < this.columns; i++) {\n if (this.get(row, i) > v) {\n v = this.get(row, i);\n }\n }\n return v;\n }\n\n maxRowIndex(row) {\n checkRowIndex(this, row);\n checkNonEmpty(this);\n let v = this.get(row, 0);\n let idx = [row, 0];\n for (let i = 1; i < this.columns; i++) {\n if (this.get(row, i) > v) {\n v = this.get(row, i);\n idx[1] = i;\n }\n }\n return idx;\n }\n\n minRow(row) {\n checkRowIndex(this, row);\n if (this.isEmpty()) {\n return NaN;\n }\n let v = this.get(row, 0);\n for (let i = 1; i < this.columns; i++) {\n if (this.get(row, i) < v) {\n v = this.get(row, i);\n }\n }\n return v;\n }\n\n minRowIndex(row) {\n checkRowIndex(this, row);\n checkNonEmpty(this);\n let v = this.get(row, 0);\n let idx = [row, 0];\n for (let i = 1; i < this.columns; i++) {\n if (this.get(row, i) < v) {\n v = this.get(row, i);\n idx[1] = i;\n }\n }\n return idx;\n }\n\n maxColumn(column) {\n checkColumnIndex(this, column);\n if (this.isEmpty()) {\n return NaN;\n }\n let v = this.get(0, column);\n for (let i = 1; i < this.rows; i++) {\n if (this.get(i, column) > v) {\n v = this.get(i, column);\n }\n }\n return v;\n }\n\n maxColumnIndex(column) {\n checkColumnIndex(this, column);\n checkNonEmpty(this);\n let v = this.get(0, column);\n let idx = [0, column];\n for (let i = 1; i < this.rows; i++) {\n if (this.get(i, column) > v) {\n v = this.get(i, column);\n idx[0] = i;\n }\n }\n return idx;\n }\n\n minColumn(column) {\n checkColumnIndex(this, column);\n if (this.isEmpty()) {\n return NaN;\n }\n let v = this.get(0, column);\n for (let i = 1; i < this.rows; i++) {\n if (this.get(i, column) < v) {\n v = this.get(i, column);\n }\n }\n return v;\n }\n\n minColumnIndex(column) {\n checkColumnIndex(this, column);\n checkNonEmpty(this);\n let v = this.get(0, column);\n let idx = [0, column];\n for (let i = 1; i < this.rows; i++) {\n if (this.get(i, column) < v) {\n v = this.get(i, column);\n idx[0] = i;\n }\n }\n return idx;\n }\n\n diag() {\n let min = Math.min(this.rows, this.columns);\n let diag = [];\n for (let i = 0; i < min; i++) {\n diag.push(this.get(i, i));\n }\n return diag;\n }\n\n norm(type = 'frobenius') {\n let result = 0;\n if (type === 'max') {\n return this.max();\n } else if (type === 'frobenius') {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n result = result + this.get(i, j) * this.get(i, j);\n }\n }\n return Math.sqrt(result);\n } else {\n throw new RangeError(`unknown norm type: ${type}`);\n }\n }\n\n cumulativeSum() {\n let sum = 0;\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n sum += this.get(i, j);\n this.set(i, j, sum);\n }\n }\n return this;\n }\n\n dot(vector2) {\n if (AbstractMatrix.isMatrix(vector2)) vector2 = vector2.to1DArray();\n let vector1 = this.to1DArray();\n if (vector1.length !== vector2.length) {\n throw new RangeError('vectors do not have the same size');\n }\n let dot = 0;\n for (let i = 0; i < vector1.length; i++) {\n dot += vector1[i] * vector2[i];\n }\n return dot;\n }\n\n mmul(other) {\n other = Matrix.checkMatrix(other);\n\n let m = this.rows;\n let n = this.columns;\n let p = other.columns;\n\n let result = new Matrix(m, p);\n\n let Bcolj = new Float64Array(n);\n for (let j = 0; j < p; j++) {\n for (let k = 0; k < n; k++) {\n Bcolj[k] = other.get(k, j);\n }\n\n for (let i = 0; i < m; i++) {\n let s = 0;\n for (let k = 0; k < n; k++) {\n s += this.get(i, k) * Bcolj[k];\n }\n\n result.set(i, j, s);\n }\n }\n return result;\n }\n\n strassen2x2(other) {\n other = Matrix.checkMatrix(other);\n let result = new Matrix(2, 2);\n const a11 = this.get(0, 0);\n const b11 = other.get(0, 0);\n const a12 = this.get(0, 1);\n const b12 = other.get(0, 1);\n const a21 = this.get(1, 0);\n const b21 = other.get(1, 0);\n const a22 = this.get(1, 1);\n const b22 = other.get(1, 1);\n\n // Compute intermediate values.\n const m1 = (a11 + a22) * (b11 + b22);\n const m2 = (a21 + a22) * b11;\n const m3 = a11 * (b12 - b22);\n const m4 = a22 * (b21 - b11);\n const m5 = (a11 + a12) * b22;\n const m6 = (a21 - a11) * (b11 + b12);\n const m7 = (a12 - a22) * (b21 + b22);\n\n // Combine intermediate values into the output.\n const c00 = m1 + m4 - m5 + m7;\n const c01 = m3 + m5;\n const c10 = m2 + m4;\n const c11 = m1 - m2 + m3 + m6;\n\n result.set(0, 0, c00);\n result.set(0, 1, c01);\n result.set(1, 0, c10);\n result.set(1, 1, c11);\n return result;\n }\n\n strassen3x3(other) {\n other = Matrix.checkMatrix(other);\n let result = new Matrix(3, 3);\n\n const a00 = this.get(0, 0);\n const a01 = this.get(0, 1);\n const a02 = this.get(0, 2);\n const a10 = this.get(1, 0);\n const a11 = this.get(1, 1);\n const a12 = this.get(1, 2);\n const a20 = this.get(2, 0);\n const a21 = this.get(2, 1);\n const a22 = this.get(2, 2);\n\n const b00 = other.get(0, 0);\n const b01 = other.get(0, 1);\n const b02 = other.get(0, 2);\n const b10 = other.get(1, 0);\n const b11 = other.get(1, 1);\n const b12 = other.get(1, 2);\n const b20 = other.get(2, 0);\n const b21 = other.get(2, 1);\n const b22 = other.get(2, 2);\n\n const m1 = (a00 + a01 + a02 - a10 - a11 - a21 - a22) * b11;\n const m2 = (a00 - a10) * (-b01 + b11);\n const m3 = a11 * (-b00 + b01 + b10 - b11 - b12 - b20 + b22);\n const m4 = (-a00 + a10 + a11) * (b00 - b01 + b11);\n const m5 = (a10 + a11) * (-b00 + b01);\n const m6 = a00 * b00;\n const m7 = (-a00 + a20 + a21) * (b00 - b02 + b12);\n const m8 = (-a00 + a20) * (b02 - b12);\n const m9 = (a20 + a21) * (-b00 + b02);\n const m10 = (a00 + a01 + a02 - a11 - a12 - a20 - a21) * b12;\n const m11 = a21 * (-b00 + b02 + b10 - b11 - b12 - b20 + b21);\n const m12 = (-a02 + a21 + a22) * (b11 + b20 - b21);\n const m13 = (a02 - a22) * (b11 - b21);\n const m14 = a02 * b20;\n const m15 = (a21 + a22) * (-b20 + b21);\n const m16 = (-a02 + a11 + a12) * (b12 + b20 - b22);\n const m17 = (a02 - a12) * (b12 - b22);\n const m18 = (a11 + a12) * (-b20 + b22);\n const m19 = a01 * b10;\n const m20 = a12 * b21;\n const m21 = a10 * b02;\n const m22 = a20 * b01;\n const m23 = a22 * b22;\n\n const c00 = m6 + m14 + m19;\n const c01 = m1 + m4 + m5 + m6 + m12 + m14 + m15;\n const c02 = m6 + m7 + m9 + m10 + m14 + m16 + m18;\n const c10 = m2 + m3 + m4 + m6 + m14 + m16 + m17;\n const c11 = m2 + m4 + m5 + m6 + m20;\n const c12 = m14 + m16 + m17 + m18 + m21;\n const c20 = m6 + m7 + m8 + m11 + m12 + m13 + m14;\n const c21 = m12 + m13 + m14 + m15 + m22;\n const c22 = m6 + m7 + m8 + m9 + m23;\n\n result.set(0, 0, c00);\n result.set(0, 1, c01);\n result.set(0, 2, c02);\n result.set(1, 0, c10);\n result.set(1, 1, c11);\n result.set(1, 2, c12);\n result.set(2, 0, c20);\n result.set(2, 1, c21);\n result.set(2, 2, c22);\n return result;\n }\n\n mmulStrassen(y) {\n y = Matrix.checkMatrix(y);\n let x = this.clone();\n let r1 = x.rows;\n let c1 = x.columns;\n let r2 = y.rows;\n let c2 = y.columns;\n if (c1 !== r2) {\n // eslint-disable-next-line no-console\n console.warn(\n `Multiplying ${r1} x ${c1} and ${r2} x ${c2} matrix: dimensions do not match.`,\n );\n }\n\n // Put a matrix into the top left of a matrix of zeros.\n // `rows` and `cols` are the dimensions of the output matrix.\n function embed(mat, rows, cols) {\n let r = mat.rows;\n let c = mat.columns;\n if (r === rows && c === cols) {\n return mat;\n } else {\n let resultat = AbstractMatrix.zeros(rows, cols);\n resultat = resultat.setSubMatrix(mat, 0, 0);\n return resultat;\n }\n }\n\n // Make sure both matrices are the same size.\n // This is exclusively for simplicity:\n // this algorithm can be implemented with matrices of different sizes.\n\n let r = Math.max(r1, r2);\n let c = Math.max(c1, c2);\n x = embed(x, r, c);\n y = embed(y, r, c);\n\n // Our recursive multiplication function.\n function blockMult(a, b, rows, cols) {\n // For small matrices, resort to naive multiplication.\n if (rows <= 512 || cols <= 512) {\n return a.mmul(b); // a is equivalent to this\n }\n\n // Apply dynamic padding.\n if (rows % 2 === 1 && cols % 2 === 1) {\n a = embed(a, rows + 1, cols + 1);\n b = embed(b, rows + 1, cols + 1);\n } else if (rows % 2 === 1) {\n a = embed(a, rows + 1, cols);\n b = embed(b, rows + 1, cols);\n } else if (cols % 2 === 1) {\n a = embed(a, rows, cols + 1);\n b = embed(b, rows, cols + 1);\n }\n\n let halfRows = parseInt(a.rows / 2, 10);\n let halfCols = parseInt(a.columns / 2, 10);\n // Subdivide input matrices.\n let a11 = a.subMatrix(0, halfRows - 1, 0, halfCols - 1);\n let b11 = b.subMatrix(0, halfRows - 1, 0, halfCols - 1);\n\n let a12 = a.subMatrix(0, halfRows - 1, halfCols, a.columns - 1);\n let b12 = b.subMatrix(0, halfRows - 1, halfCols, b.columns - 1);\n\n let a21 = a.subMatrix(halfRows, a.rows - 1, 0, halfCols - 1);\n let b21 = b.subMatrix(halfRows, b.rows - 1, 0, halfCols - 1);\n\n let a22 = a.subMatrix(halfRows, a.rows - 1, halfCols, a.columns - 1);\n let b22 = b.subMatrix(halfRows, b.rows - 1, halfCols, b.columns - 1);\n\n // Compute intermediate values.\n let m1 = blockMult(\n AbstractMatrix.add(a11, a22),\n AbstractMatrix.add(b11, b22),\n halfRows,\n halfCols,\n );\n let m2 = blockMult(AbstractMatrix.add(a21, a22), b11, halfRows, halfCols);\n let m3 = blockMult(a11, AbstractMatrix.sub(b12, b22), halfRows, halfCols);\n let m4 = blockMult(a22, AbstractMatrix.sub(b21, b11), halfRows, halfCols);\n let m5 = blockMult(AbstractMatrix.add(a11, a12), b22, halfRows, halfCols);\n let m6 = blockMult(\n AbstractMatrix.sub(a21, a11),\n AbstractMatrix.add(b11, b12),\n halfRows,\n halfCols,\n );\n let m7 = blockMult(\n AbstractMatrix.sub(a12, a22),\n AbstractMatrix.add(b21, b22),\n halfRows,\n halfCols,\n );\n\n // Combine intermediate values into the output.\n let c11 = AbstractMatrix.add(m1, m4);\n c11.sub(m5);\n c11.add(m7);\n let c12 = AbstractMatrix.add(m3, m5);\n let c21 = AbstractMatrix.add(m2, m4);\n let c22 = AbstractMatrix.sub(m1, m2);\n c22.add(m3);\n c22.add(m6);\n\n // Crop output to the desired size (undo dynamic padding).\n let resultat = AbstractMatrix.zeros(2 * c11.rows, 2 * c11.columns);\n resultat = resultat.setSubMatrix(c11, 0, 0);\n resultat = resultat.setSubMatrix(c12, c11.rows, 0);\n resultat = resultat.setSubMatrix(c21, 0, c11.columns);\n resultat = resultat.setSubMatrix(c22, c11.rows, c11.columns);\n return resultat.subMatrix(0, rows - 1, 0, cols - 1);\n }\n\n return blockMult(x, y, r, c);\n }\n\n scaleRows(options = {}) {\n if (typeof options !== 'object') {\n throw new TypeError('options must be an object');\n }\n const { min = 0, max = 1 } = options;\n if (!Number.isFinite(min)) throw new TypeError('min must be a number');\n if (!Number.isFinite(max)) throw new TypeError('max must be a number');\n if (min >= max) throw new RangeError('min must be smaller than max');\n let newMatrix = new Matrix(this.rows, this.columns);\n for (let i = 0; i < this.rows; i++) {\n const row = this.getRow(i);\n if (row.length > 0) {\n rescale(row, { min, max, output: row });\n }\n newMatrix.setRow(i, row);\n }\n return newMatrix;\n }\n\n scaleColumns(options = {}) {\n if (typeof options !== 'object') {\n throw new TypeError('options must be an object');\n }\n const { min = 0, max = 1 } = options;\n if (!Number.isFinite(min)) throw new TypeError('min must be a number');\n if (!Number.isFinite(max)) throw new TypeError('max must be a number');\n if (min >= max) throw new RangeError('min must be smaller than max');\n let newMatrix = new Matrix(this.rows, this.columns);\n for (let i = 0; i < this.columns; i++) {\n const column = this.getColumn(i);\n if (column.length) {\n rescale(column, {\n min: min,\n max: max,\n output: column,\n });\n }\n newMatrix.setColumn(i, column);\n }\n return newMatrix;\n }\n\n flipRows() {\n const middle = Math.ceil(this.columns / 2);\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < middle; j++) {\n let first = this.get(i, j);\n let last = this.get(i, this.columns - 1 - j);\n this.set(i, j, last);\n this.set(i, this.columns - 1 - j, first);\n }\n }\n return this;\n }\n\n flipColumns() {\n const middle = Math.ceil(this.rows / 2);\n for (let j = 0; j < this.columns; j++) {\n for (let i = 0; i < middle; i++) {\n let first = this.get(i, j);\n let last = this.get(this.rows - 1 - i, j);\n this.set(i, j, last);\n this.set(this.rows - 1 - i, j, first);\n }\n }\n return this;\n }\n\n kroneckerProduct(other) {\n other = Matrix.checkMatrix(other);\n\n let m = this.rows;\n let n = this.columns;\n let p = other.rows;\n let q = other.columns;\n\n let result = new Matrix(m * p, n * q);\n for (let i = 0; i < m; i++) {\n for (let j = 0; j < n; j++) {\n for (let k = 0; k < p; k++) {\n for (let l = 0; l < q; l++) {\n result.set(p * i + k, q * j + l, this.get(i, j) * other.get(k, l));\n }\n }\n }\n }\n return result;\n }\n\n kroneckerSum(other) {\n other = Matrix.checkMatrix(other);\n if (!this.isSquare() || !other.isSquare()) {\n throw new Error('Kronecker Sum needs two Square Matrices');\n }\n let m = this.rows;\n let n = other.rows;\n let AxI = this.kroneckerProduct(Matrix.eye(n, n));\n let IxB = Matrix.eye(m, m).kroneckerProduct(other);\n return AxI.add(IxB);\n }\n\n transpose() {\n let result = new Matrix(this.columns, this.rows);\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n result.set(j, i, this.get(i, j));\n }\n }\n return result;\n }\n\n sortRows(compareFunction = compareNumbers) {\n for (let i = 0; i < this.rows; i++) {\n this.setRow(i, this.getRow(i).sort(compareFunction));\n }\n return this;\n }\n\n sortColumns(compareFunction = compareNumbers) {\n for (let i = 0; i < this.columns; i++) {\n this.setColumn(i, this.getColumn(i).sort(compareFunction));\n }\n return this;\n }\n\n subMatrix(startRow, endRow, startColumn, endColumn) {\n checkRange(this, startRow, endRow, startColumn, endColumn);\n let newMatrix = new Matrix(\n endRow - startRow + 1,\n endColumn - startColumn + 1,\n );\n for (let i = startRow; i <= endRow; i++) {\n for (let j = startColumn; j <= endColumn; j++) {\n newMatrix.set(i - startRow, j - startColumn, this.get(i, j));\n }\n }\n return newMatrix;\n }\n\n subMatrixRow(indices, startColumn, endColumn) {\n if (startColumn === undefined) startColumn = 0;\n if (endColumn === undefined) endColumn = this.columns - 1;\n if (\n startColumn > endColumn ||\n startColumn < 0 ||\n startColumn >= this.columns ||\n endColumn < 0 ||\n endColumn >= this.columns\n ) {\n throw new RangeError('Argument out of range');\n }\n\n let newMatrix = new Matrix(indices.length, endColumn - startColumn + 1);\n for (let i = 0; i < indices.length; i++) {\n for (let j = startColumn; j <= endColumn; j++) {\n if (indices[i] < 0 || indices[i] >= this.rows) {\n throw new RangeError(`Row index out of range: ${indices[i]}`);\n }\n newMatrix.set(i, j - startColumn, this.get(indices[i], j));\n }\n }\n return newMatrix;\n }\n\n subMatrixColumn(indices, startRow, endRow) {\n if (startRow === undefined) startRow = 0;\n if (endRow === undefined) endRow = this.rows - 1;\n if (\n startRow > endRow ||\n startRow < 0 ||\n startRow >= this.rows ||\n endRow < 0 ||\n endRow >= this.rows\n ) {\n throw new RangeError('Argument out of range');\n }\n\n let newMatrix = new Matrix(endRow - startRow + 1, indices.length);\n for (let i = 0; i < indices.length; i++) {\n for (let j = startRow; j <= endRow; j++) {\n if (indices[i] < 0 || indices[i] >= this.columns) {\n throw new RangeError(`Column index out of range: ${indices[i]}`);\n }\n newMatrix.set(j - startRow, i, this.get(j, indices[i]));\n }\n }\n return newMatrix;\n }\n\n setSubMatrix(matrix, startRow, startColumn) {\n matrix = Matrix.checkMatrix(matrix);\n if (matrix.isEmpty()) {\n return this;\n }\n let endRow = startRow + matrix.rows - 1;\n let endColumn = startColumn + matrix.columns - 1;\n checkRange(this, startRow, endRow, startColumn, endColumn);\n for (let i = 0; i < matrix.rows; i++) {\n for (let j = 0; j < matrix.columns; j++) {\n this.set(startRow + i, startColumn + j, matrix.get(i, j));\n }\n }\n return this;\n }\n\n selection(rowIndices, columnIndices) {\n checkRowIndices(this, rowIndices);\n checkColumnIndices(this, columnIndices);\n let newMatrix = new Matrix(rowIndices.length, columnIndices.length);\n for (let i = 0; i < rowIndices.length; i++) {\n let rowIndex = rowIndices[i];\n for (let j = 0; j < columnIndices.length; j++) {\n let columnIndex = columnIndices[j];\n newMatrix.set(i, j, this.get(rowIndex, columnIndex));\n }\n }\n return newMatrix;\n }\n\n trace() {\n let min = Math.min(this.rows, this.columns);\n let trace = 0;\n for (let i = 0; i < min; i++) {\n trace += this.get(i, i);\n }\n return trace;\n }\n\n clone() {\n let newMatrix = new Matrix(this.rows, this.columns);\n for (let row = 0; row < this.rows; row++) {\n for (let column = 0; column < this.columns; column++) {\n newMatrix.set(row, column, this.get(row, column));\n }\n }\n return newMatrix;\n }\n\n sum(by) {\n switch (by) {\n case 'row':\n return sumByRow(this);\n case 'column':\n return sumByColumn(this);\n case undefined:\n return sumAll(this);\n default:\n throw new Error(`invalid option: ${by}`);\n }\n }\n\n product(by) {\n switch (by) {\n case 'row':\n return productByRow(this);\n case 'column':\n return productByColumn(this);\n case undefined:\n return productAll(this);\n default:\n throw new Error(`invalid option: ${by}`);\n }\n }\n\n mean(by) {\n const sum = this.sum(by);\n switch (by) {\n case 'row': {\n for (let i = 0; i < this.rows; i++) {\n sum[i] /= this.columns;\n }\n return sum;\n }\n case 'column': {\n for (let i = 0; i < this.columns; i++) {\n sum[i] /= this.rows;\n }\n return sum;\n }\n case undefined:\n return sum / this.size;\n default:\n throw new Error(`invalid option: ${by}`);\n }\n }\n\n variance(by, options = {}) {\n if (typeof by === 'object') {\n options = by;\n by = undefined;\n }\n if (typeof options !== 'object') {\n throw new TypeError('options must be an object');\n }\n const { unbiased = true, mean = this.mean(by) } = options;\n if (typeof unbiased !== 'boolean') {\n throw new TypeError('unbiased must be a boolean');\n }\n switch (by) {\n case 'row': {\n if (!isAnyArray(mean)) {\n throw new TypeError('mean must be an array');\n }\n return varianceByRow(this, unbiased, mean);\n }\n case 'column': {\n if (!isAnyArray(mean)) {\n throw new TypeError('mean must be an array');\n }\n return varianceByColumn(this, unbiased, mean);\n }\n case undefined: {\n if (typeof mean !== 'number') {\n throw new TypeError('mean must be a number');\n }\n return varianceAll(this, unbiased, mean);\n }\n default:\n throw new Error(`invalid option: ${by}`);\n }\n }\n\n standardDeviation(by, options) {\n if (typeof by === 'object') {\n options = by;\n by = undefined;\n }\n const variance = this.variance(by, options);\n if (by === undefined) {\n return Math.sqrt(variance);\n } else {\n for (let i = 0; i < variance.length; i++) {\n variance[i] = Math.sqrt(variance[i]);\n }\n return variance;\n }\n }\n\n center(by, options = {}) {\n if (typeof by === 'object') {\n options = by;\n by = undefined;\n }\n if (typeof options !== 'object') {\n throw new TypeError('options must be an object');\n }\n const { center = this.mean(by) } = options;\n switch (by) {\n case 'row': {\n if (!isAnyArray(center)) {\n throw new TypeError('center must be an array');\n }\n centerByRow(this, center);\n return this;\n }\n case 'column': {\n if (!isAnyArray(center)) {\n throw new TypeError('center must be an array');\n }\n centerByColumn(this, center);\n return this;\n }\n case undefined: {\n if (typeof center !== 'number') {\n throw new TypeError('center must be a number');\n }\n centerAll(this, center);\n return this;\n }\n default:\n throw new Error(`invalid option: ${by}`);\n }\n }\n\n scale(by, options = {}) {\n if (typeof by === 'object') {\n options = by;\n by = undefined;\n }\n if (typeof options !== 'object') {\n throw new TypeError('options must be an object');\n }\n let scale = options.scale;\n switch (by) {\n case 'row': {\n if (scale === undefined) {\n scale = getScaleByRow(this);\n } else if (!isAnyArray(scale)) {\n throw new TypeError('scale must be an array');\n }\n scaleByRow(this, scale);\n return this;\n }\n case 'column': {\n if (scale === undefined) {\n scale = getScaleByColumn(this);\n } else if (!isAnyArray(scale)) {\n throw new TypeError('scale must be an array');\n }\n scaleByColumn(this, scale);\n return this;\n }\n case undefined: {\n if (scale === undefined) {\n scale = getScaleAll(this);\n } else if (typeof scale !== 'number') {\n throw new TypeError('scale must be a number');\n }\n scaleAll(this, scale);\n return this;\n }\n default:\n throw new Error(`invalid option: ${by}`);\n }\n }\n\n toString(options) {\n return inspectMatrixWithOptions(this, options);\n }\n}\n\nAbstractMatrix.prototype.klass = 'Matrix';\nif (typeof Symbol !== 'undefined') {\n AbstractMatrix.prototype[Symbol.for('nodejs.util.inspect.custom')] =\n inspectMatrix;\n}\n\nfunction compareNumbers(a, b) {\n return a - b;\n}\n\nfunction isArrayOfNumbers(array) {\n return array.every((element) => {\n return typeof element === 'number';\n });\n}\n\n// Synonyms\nAbstractMatrix.random = AbstractMatrix.rand;\nAbstractMatrix.randomInt = AbstractMatrix.randInt;\nAbstractMatrix.diagonal = AbstractMatrix.diag;\nAbstractMatrix.prototype.diagonal = AbstractMatrix.prototype.diag;\nAbstractMatrix.identity = AbstractMatrix.eye;\nAbstractMatrix.prototype.negate = AbstractMatrix.prototype.neg;\nAbstractMatrix.prototype.tensorProduct =\n AbstractMatrix.prototype.kroneckerProduct;\n\nexport default class Matrix extends AbstractMatrix {\n constructor(nRows, nColumns) {\n super();\n if (Matrix.isMatrix(nRows)) {\n // eslint-disable-next-line no-constructor-return\n return nRows.clone();\n } else if (Number.isInteger(nRows) && nRows >= 0) {\n // Create an empty matrix\n this.data = [];\n if (Number.isInteger(nColumns) && nColumns >= 0) {\n for (let i = 0; i < nRows; i++) {\n this.data.push(new Float64Array(nColumns));\n }\n } else {\n throw new TypeError('nColumns must be a positive integer');\n }\n } else if (isAnyArray(nRows)) {\n // Copy the values from the 2D array\n const arrayData = nRows;\n nRows = arrayData.length;\n nColumns = nRows ? arrayData[0].length : 0;\n if (typeof nColumns !== 'number') {\n throw new TypeError(\n 'Data must be a 2D array with at least one element',\n );\n }\n this.data = [];\n for (let i = 0; i < nRows; i++) {\n if (arrayData[i].length !== nColumns) {\n throw new RangeError('Inconsistent array dimensions');\n }\n if (!isArrayOfNumbers(arrayData[i])) {\n throw new TypeError('Input data contains non-numeric values');\n }\n this.data.push(Float64Array.from(arrayData[i]));\n }\n } else {\n throw new TypeError(\n 'First argument must be a positive number or an array',\n );\n }\n this.rows = nRows;\n this.columns = nColumns;\n }\n\n set(rowIndex, columnIndex, value) {\n this.data[rowIndex][columnIndex] = value;\n return this;\n }\n\n get(rowIndex, columnIndex) {\n return this.data[rowIndex][columnIndex];\n }\n\n removeRow(index) {\n checkRowIndex(this, index);\n this.data.splice(index, 1);\n this.rows -= 1;\n return this;\n }\n\n addRow(index, array) {\n if (array === undefined) {\n array = index;\n index = this.rows;\n }\n checkRowIndex(this, index, true);\n array = Float64Array.from(checkRowVector(this, array));\n this.data.splice(index, 0, array);\n this.rows += 1;\n return this;\n }\n\n removeColumn(index) {\n checkColumnIndex(this, index);\n for (let i = 0; i < this.rows; i++) {\n const newRow = new Float64Array(this.columns - 1);\n for (let j = 0; j < index; j++) {\n newRow[j] = this.data[i][j];\n }\n for (let j = index + 1; j < this.columns; j++) {\n newRow[j - 1] = this.data[i][j];\n }\n this.data[i] = newRow;\n }\n this.columns -= 1;\n return this;\n }\n\n addColumn(index, array) {\n if (typeof array === 'undefined') {\n array = index;\n index = this.columns;\n }\n checkColumnIndex(this, index, true);\n array = checkColumnVector(this, array);\n for (let i = 0; i < this.rows; i++) {\n const newRow = new Float64Array(this.columns + 1);\n let j = 0;\n for (; j < index; j++) {\n newRow[j] = this.data[i][j];\n }\n newRow[j++] = array[i];\n for (; j < this.columns + 1; j++) {\n newRow[j] = this.data[i][j - 1];\n }\n this.data[i] = newRow;\n }\n this.columns += 1;\n return this;\n }\n}\n\ninstallMathOperations(AbstractMatrix, Matrix);\n","import { newArray } from './util';\n\nexport function sumByRow(matrix) {\n let sum = newArray(matrix.rows);\n for (let i = 0; i < matrix.rows; ++i) {\n for (let j = 0; j < matrix.columns; ++j) {\n sum[i] += matrix.get(i, j);\n }\n }\n return sum;\n}\n\nexport function sumByColumn(matrix) {\n let sum = newArray(matrix.columns);\n for (let i = 0; i < matrix.rows; ++i) {\n for (let j = 0; j < matrix.columns; ++j) {\n sum[j] += matrix.get(i, j);\n }\n }\n return sum;\n}\n\nexport function sumAll(matrix) {\n let v = 0;\n for (let i = 0; i < matrix.rows; i++) {\n for (let j = 0; j < matrix.columns; j++) {\n v += matrix.get(i, j);\n }\n }\n return v;\n}\n\nexport function productByRow(matrix) {\n let sum = newArray(matrix.rows, 1);\n for (let i = 0; i < matrix.rows; ++i) {\n for (let j = 0; j < matrix.columns; ++j) {\n sum[i] *= matrix.get(i, j);\n }\n }\n return sum;\n}\n\nexport function productByColumn(matrix) {\n let sum = newArray(matrix.columns, 1);\n for (let i = 0; i < matrix.rows; ++i) {\n for (let j = 0; j < matrix.columns; ++j) {\n sum[j] *= matrix.get(i, j);\n }\n }\n return sum;\n}\n\nexport function productAll(matrix) {\n let v = 1;\n for (let i = 0; i < matrix.rows; i++) {\n for (let j = 0; j < matrix.columns; j++) {\n v *= matrix.get(i, j);\n }\n }\n return v;\n}\n\nexport function varianceByRow(matrix, unbiased, mean) {\n const rows = matrix.rows;\n const cols = matrix.columns;\n const variance = [];\n\n for (let i = 0; i < rows; i++) {\n let sum1 = 0;\n let sum2 = 0;\n let x = 0;\n for (let j = 0; j < cols; j++) {\n x = matrix.get(i, j) - mean[i];\n sum1 += x;\n sum2 += x * x;\n }\n if (unbiased) {\n variance.push((sum2 - (sum1 * sum1) / cols) / (cols - 1));\n } else {\n variance.push((sum2 - (sum1 * sum1) / cols) / cols);\n }\n }\n return variance;\n}\n\nexport function varianceByColumn(matrix, unbiased, mean) {\n const rows = matrix.rows;\n const cols = matrix.columns;\n const variance = [];\n\n for (let j = 0; j < cols; j++) {\n let sum1 = 0;\n let sum2 = 0;\n let x = 0;\n for (let i = 0; i < rows; i++) {\n x = matrix.get(i, j) - mean[j];\n sum1 += x;\n sum2 += x * x;\n }\n if (unbiased) {\n variance.push((sum2 - (sum1 * sum1) / rows) / (rows - 1));\n } else {\n variance.push((sum2 - (sum1 * sum1) / rows) / rows);\n }\n }\n return variance;\n}\n\nexport function varianceAll(matrix, unbiased, mean) {\n const rows = matrix.rows;\n const cols = matrix.columns;\n const size = rows * cols;\n\n let sum1 = 0;\n let sum2 = 0;\n let x = 0;\n for (let i = 0; i < rows; i++) {\n for (let j = 0; j < cols; j++) {\n x = matrix.get(i, j) - mean;\n sum1 += x;\n sum2 += x * x;\n }\n }\n if (unbiased) {\n return (sum2 - (sum1 * sum1) / size) / (size - 1);\n } else {\n return (sum2 - (sum1 * sum1) / size) / size;\n }\n}\n\nexport function centerByRow(matrix, mean) {\n for (let i = 0; i < matrix.rows; i++) {\n for (let j = 0; j < matrix.columns; j++) {\n matrix.set(i, j, matrix.get(i, j) - mean[i]);\n }\n }\n}\n\nexport function centerByColumn(matrix, mean) {\n for (let i = 0; i < matrix.rows; i++) {\n for (let j = 0; j < matrix.columns; j++) {\n matrix.set(i, j, matrix.get(i, j) - mean[j]);\n }\n }\n}\n\nexport function centerAll(matrix, mean) {\n for (let i = 0; i < matrix.rows; i++) {\n for (let j = 0; j < matrix.columns; j++) {\n matrix.set(i, j, matrix.get(i, j) - mean);\n }\n }\n}\n\nexport function getScaleByRow(matrix) {\n const scale = [];\n for (let i = 0; i < matrix.rows; i++) {\n let sum = 0;\n for (let j = 0; j < matrix.columns; j++) {\n sum += Math.pow(matrix.get(i, j), 2) / (matrix.columns - 1);\n }\n scale.push(Math.sqrt(sum));\n }\n return scale;\n}\n\nexport function scaleByRow(matrix, scale) {\n for (let i = 0; i < matrix.rows; i++) {\n for (let j = 0; j < matrix.columns; j++) {\n matrix.set(i, j, matrix.get(i, j) / scale[i]);\n }\n }\n}\n\nexport function getScaleByColumn(matrix) {\n const scale = [];\n for (let j = 0; j < matrix.columns; j++) {\n let sum = 0;\n for (let i = 0; i < matrix.rows; i++) {\n sum += Math.pow(matrix.get(i, j), 2) / (matrix.rows - 1);\n }\n scale.push(Math.sqrt(sum));\n }\n return scale;\n}\n\nexport function scaleByColumn(matrix, scale) {\n for (let i = 0; i < matrix.rows; i++) {\n for (let j = 0; j < matrix.columns; j++) {\n matrix.set(i, j, matrix.get(i, j) / scale[j]);\n }\n }\n}\n\nexport function getScaleAll(matrix) {\n const divider = matrix.size - 1;\n let sum = 0;\n for (let j = 0; j < matrix.columns; j++) {\n for (let i = 0; i < matrix.rows; i++) {\n sum += Math.pow(matrix.get(i, j), 2) / divider;\n }\n }\n return Math.sqrt(sum);\n}\n\nexport function scaleAll(matrix, scale) {\n for (let i = 0; i < matrix.rows; i++) {\n for (let j = 0; j < matrix.columns; j++) {\n matrix.set(i, j, matrix.get(i, j) / scale);\n }\n }\n}\n","import { floydWarshall } from 'ml-floyd-warshall';\nimport { Matrix } from 'ml-matrix';\n\n/**\n * Returns a connectivity matrix\n * @param {import('openchemlib').Molecule} molecule\n * @param {object} [options={}]\n * @param {boolean} [options.pathLength=false] get the path length between atoms\n * @param {boolean} [options.mass=false] set the nominal mass of the atoms on diagonal\n * @param {boolean} [options.atomicNo=false] set the atomic number of the atom on diagonal\n * @param {boolean} [options.negativeAtomicNo=false] set the atomic number * -1 of the atom on diagonal\n * @param {boolean} [options.sdt=false] set 1, 2 or 3 depending if single, double or triple bond\n * @param {boolean} [options.sdta=false] set 1, 2, 3 or 4 depending if single, double, triple or aromatic bond\n */\nexport function getConnectivityMatrix(molecule, options = {}) {\n const OCL = molecule.getOCL();\n molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);\n let nbAtoms = molecule.getAllAtoms();\n\n let result = new Array(nbAtoms).fill();\n result = result.map(() => new Array(nbAtoms).fill(0));\n\n if (!options.pathLength) {\n if (options.atomicNo) {\n for (let i = 0; i < nbAtoms; i++) {\n result[i][i] = molecule.getAtomicNo(i);\n }\n } else if (options.negativeAtomicNo) {\n for (let i = 0; i < nbAtoms; i++) {\n result[i][i] = -molecule.getAtomicNo(i);\n }\n } else if (options.mass) {\n for (let i = 0; i < nbAtoms; i++) {\n result[i][i] = OCL.Molecule.cRoundedMass[molecule.getAtomicNo(i)];\n }\n } else {\n for (let i = 0; i < nbAtoms; i++) {\n result[i][i] = 1;\n }\n }\n }\n\n if (options.sdt) {\n for (let i = 0; i < nbAtoms; i++) {\n let l = molecule.getAllConnAtoms(i);\n for (let j = 0; j < l; j++) {\n result[i][molecule.getConnAtom(i, j)] = molecule.getConnBondOrder(i, j);\n }\n }\n } else if (options.sdta) {\n for (let i = 0; i < nbAtoms; i++) {\n let l = molecule.getAllConnAtoms(i);\n for (let j = 0; j < l; j++) {\n let bondNumber = molecule.getConnBond(i, j);\n if (molecule.isAromaticBond(bondNumber)) {\n result[i][molecule.getConnAtom(i, j)] = 4;\n } else {\n result[i][molecule.getConnAtom(i, j)] = molecule.getConnBondOrder(\n i,\n j,\n );\n }\n }\n }\n } else {\n for (let i = 0; i < nbAtoms; i++) {\n let l = molecule.getAllConnAtoms(i);\n for (let j = 0; j < l; j++) {\n result[i][molecule.getConnAtom(i, j)] = 1;\n }\n }\n }\n\n if (options.pathLength) {\n result = floydWarshall(new Matrix(result)).to2DArray();\n }\n return result;\n}\n","import { Matrix } from 'ml-matrix';\n\n/**\n * Algorithm that finds the shortest distance from one node to the other\n * @param {Matrix} adjMatrix - A squared adjacency matrix\n * @return {Matrix} - Distance from a node to the other, -1 if the node is unreachable\n */\nexport function floydWarshall(adjMatrix) {\n if (Matrix.isMatrix(adjMatrix) && adjMatrix.columns !== adjMatrix.rows) {\n throw new TypeError('The adjacency matrix should be squared');\n }\n const numVertices = adjMatrix.columns;\n let distMatrix = new Matrix(numVertices, numVertices);\n distMatrix.apply((row, column) => {\n // principal diagonal is 0\n if (row === column) {\n distMatrix.set(row, column, 0);\n } else {\n let val = adjMatrix.get(row, column);\n\n if (val || Object.is(val, -0)) {\n // edges values remain the same\n distMatrix.set(row, column, val);\n } else {\n // 0 values become infinity\n distMatrix.set(row, column, Number.POSITIVE_INFINITY);\n }\n }\n });\n\n for (let k = 0; k < numVertices; ++k) {\n for (let i = 0; i < numVertices; ++i) {\n for (let j = 0; j < numVertices; ++j) {\n let dist = distMatrix.get(i, k) + distMatrix.get(k, j);\n if (distMatrix.get(i, j) > dist) {\n distMatrix.set(i, j, dist);\n }\n }\n }\n }\n\n // When there's no connection the value is -1\n distMatrix.apply((row, column) => {\n if (distMatrix.get(row, column) === Number.POSITIVE_INFINITY) {\n distMatrix.set(row, column, -1);\n }\n });\n return distMatrix;\n}\n","/**\n * Implementation of the Hill system for sorting atoms\n * https://en.wikipedia.org/wiki/Chemical_formula#Hill_system\n * @param {string} a - first atom to compare\n * @param {string} b - second atom to compare\n * @returns\n */\n\nexport function atomSorter(a, b) {\n if (a === b) return 0;\n if (a === 'C') return -1;\n if (b === 'C') return 1;\n if (a === 'H') return -1;\n if (b === 'H') return 1;\n if (a < b) return -1;\n return 1;\n}\n","import { atomSorter } from 'atom-sorter';\n\n/**\n * Calculate the molecular formula in 'chemcalc' notation taking into account fragments, isotopes and charges\n * {OCL.Molecule} [molecule] an instance of OCL.Molecule\n * @returns {object}\n */\n\nexport function getMF(molecule) {\n let entries = molecule.getFragments();\n let result = {};\n let parts = [];\n let allAtoms = [];\n\n entries.forEach((entry) => {\n let mf = getFragmentMF(entry, allAtoms);\n parts.push(mf);\n });\n\n let counts = {};\n for (let part of parts) {\n if (!counts[part]) counts[part] = 0;\n counts[part]++;\n }\n parts = [];\n for (let key of Object.keys(counts).sort()) {\n if (counts[key] > 1) {\n parts.push(counts[key] + key);\n } else {\n parts.push(key);\n }\n }\n\n result.parts = parts;\n result.mf = toMFString(allAtoms);\n return result;\n}\n\nfunction getFragmentMF(molecule, allAtoms) {\n let atoms = [];\n for (let i = 0; i < molecule.getAllAtoms(); i++) {\n let atom = {};\n atom.charge = molecule.getAtomCharge(i);\n atom.label = molecule.getAtomLabel(i);\n atom.mass = molecule.getAtomMass(i);\n atom.implicitHydrogens = molecule.getImplicitHydrogens(i);\n atoms.push(atom);\n allAtoms.push(atom);\n }\n return toMFString(atoms);\n}\n\nfunction toMFString(atoms) {\n let charge = 0;\n let mfs = {};\n for (let atom of atoms) {\n let label = atom.label;\n charge += atom.charge;\n if (atom.mass) {\n label = `[${atom.mass}${label}]`;\n }\n let mfAtom = mfs[label];\n if (!mfAtom) {\n mfs[label] = 0;\n }\n mfs[label] += 1;\n if (atom.implicitHydrogens) {\n if (!mfs.H) mfs.H = 0;\n mfs.H += atom.implicitHydrogens;\n }\n }\n\n let mf = '';\n let keys = Object.keys(mfs).sort(atomSorter);\n for (let key of keys) {\n mf += key;\n if (mfs[key] > 1) mf += mfs[key];\n }\n\n if (charge > 0) {\n mf += `(+${charge > 1 ? charge : ''})`;\n } else if (charge < 0) {\n mf += `(${charge < -1 ? charge : '-'})`;\n }\n return mf;\n}\n","/**\n * Calculates the path between 2 atoms\n * @param {import('openchemlib').Molecule} molecule\n * @param {number} from - index of the first atom\n * @param {number} to - index of the end atom\n * @param {number} maxLength - maximal length of the path\n */\nexport function getPathAndTorsion(molecule, from, to, maxLength) {\n let originalAtoms = []; // path before renumbering\n molecule.getPath(originalAtoms, from, to, maxLength + 1);\n let torsion;\n if (originalAtoms.length === 4) {\n torsion = molecule.calculateTorsion(originalAtoms);\n }\n\n return {\n atoms: originalAtoms,\n from,\n to,\n torsion,\n length: originalAtoms.length - 1,\n };\n}\n","import { getHoseCodesForPath } from '../hose/getHoseCodesForPath';\nimport { getAtomsInfo } from '../util/getAtomsInfo';\nimport { getConnectivityMatrix } from '../util/getConnectivityMatrix';\n\nimport { getPathAndTorsion } from './getPathAndTorsion.js';\n\nlet fragment;\n\n/**\n *\n * @param {import('openchemlib').Molecule} molecule\n * @param {object} [options={}]\n * @param {string} [options.fromLabel='H']\n * @param {string} [options.toLabel='H']\n * @param {number} [options.minLength=1]\n * @param {number} [options.maxLength=4]\n * @param {boolean} [options.withHOSES=false]\n\n */\nexport function getPathsInfo(molecule, options = {}) {\n const {\n fromLabel = 'H',\n toLabel = 'H',\n minLength = 1,\n maxLength = 4,\n withHOSES = false,\n } = options;\n\n const OCL = molecule.getOCL();\n\n if (!fragment) {\n fragment = new OCL.Molecule(0, 0);\n }\n\n let fromAtomicNumber = OCL.Molecule.getAtomicNoFromLabel(fromLabel);\n let toAtomicNumber = OCL.Molecule.getAtomicNoFromLabel(toLabel);\n\n // we need to find all the atoms 'fromLabel' and 'toLabel'\n let atomsInfo = getAtomsInfo(molecule);\n\n let pathLengthMatrix = getConnectivityMatrix(molecule, {\n pathLength: true,\n });\n\n for (let from = 0; from < molecule.getAllAtoms(); from++) {\n atomsInfo[from].paths = [];\n for (let to = 0; to < molecule.getAllAtoms(); to++) {\n if (from !== to) {\n if (molecule.getAtomicNo(from) === fromAtomicNumber) {\n if (molecule.getAtomicNo(to) === toAtomicNumber) {\n let pathLength = pathLengthMatrix[from][to];\n if (pathLength >= minLength && pathLength <= maxLength) {\n if (withHOSES) {\n atomsInfo[from].paths.push(\n getHoseCodesForPath(molecule, from, to, pathLength),\n );\n } else {\n atomsInfo[from].paths.push(\n getPathAndTorsion(molecule, from, to, pathLength),\n );\n }\n }\n }\n }\n }\n }\n }\n\n return atomsInfo;\n}\n","import isutf8 from 'isutf8';\n/**\n * Ensure that the data is string. If it is an ArrayBuffer it will be converted to string using TextDecoder.\n * @param blob\n * @param options\n * @returns\n */\nexport function ensureString(blob, options = {}) {\n if (typeof blob === 'string') {\n return blob;\n }\n if (ArrayBuffer.isView(blob) || blob instanceof ArrayBuffer) {\n const { encoding = guessEncoding(blob) } = options;\n const decoder = new TextDecoder(encoding);\n return decoder.decode(blob);\n }\n throw new TypeError(`blob must be a string, ArrayBuffer or ArrayBufferView`);\n}\nfunction guessEncoding(blob) {\n const uint8 = ArrayBuffer.isView(blob)\n ? new Uint8Array(blob.buffer, blob.byteOffset, blob.byteLength)\n : new Uint8Array(blob);\n if (uint8.length >= 2) {\n if (uint8[0] === 0xfe && uint8[1] === 0xff) {\n return 'utf-16be';\n }\n if (uint8[0] === 0xff && uint8[1] === 0xfe) {\n return 'utf-16le';\n }\n }\n //@ts-expect-error an ArrayBuffer is also ok\n if (!isutf8(blob))\n return 'latin1';\n return 'utf-8';\n}\n//# sourceMappingURL=index.js.map","/*\n https://tools.ietf.org/html/rfc3629\n\n UTF8-char = UTF8-1 / UTF8-2 / UTF8-3 / UTF8-4\n\n UTF8-1 = %x00-7F\n\n UTF8-2 = %xC2-DF UTF8-tail\n\n UTF8-3 = %xE0 %xA0-BF UTF8-tail\n %xE1-EC 2( UTF8-tail )\n %xED %x80-9F UTF8-tail\n %xEE-EF 2( UTF8-tail )\n\n UTF8-4 = %xF0 %x90-BF 2( UTF8-tail )\n %xF1-F3 3( UTF8-tail )\n %xF4 %x80-8F 2( UTF8-tail )\n\n UTF8-tail = %x80-BF\n*/\n/**\n * Check if a Node.js Buffer or Uint8Array is UTF-8.\n */\nfunction isUtf8(buf) {\n if (!buf) {\n return false;\n }\n var i = 0;\n var len = buf.length;\n while (i < len) {\n // UTF8-1 = %x00-7F\n if (buf[i] <= 0x7F) {\n i++;\n continue;\n }\n // UTF8-2 = %xC2-DF UTF8-tail\n if (buf[i] >= 0xC2 && buf[i] <= 0xDF) {\n // if(buf[i + 1] >= 0x80 && buf[i + 1] <= 0xBF) {\n if (buf[i + 1] >> 6 === 2) {\n i += 2;\n continue;\n }\n else {\n return false;\n }\n }\n // UTF8-3 = %xE0 %xA0-BF UTF8-tail\n // UTF8-3 = %xED %x80-9F UTF8-tail\n if (((buf[i] === 0xE0 && buf[i + 1] >= 0xA0 && buf[i + 1] <= 0xBF) ||\n (buf[i] === 0xED && buf[i + 1] >= 0x80 && buf[i + 1] <= 0x9F)) && buf[i + 2] >> 6 === 2) {\n i += 3;\n continue;\n }\n // UTF8-3 = %xE1-EC 2( UTF8-tail )\n // UTF8-3 = %xEE-EF 2( UTF8-tail )\n if (((buf[i] >= 0xE1 && buf[i] <= 0xEC) ||\n (buf[i] >= 0xEE && buf[i] <= 0xEF)) &&\n buf[i + 1] >> 6 === 2 &&\n buf[i + 2] >> 6 === 2) {\n i += 3;\n continue;\n }\n // UTF8-4 = %xF0 %x90-BF 2( UTF8-tail )\n // %xF1-F3 3( UTF8-tail )\n // %xF4 %x80-8F 2( UTF8-tail )\n if (((buf[i] === 0xF0 && buf[i + 1] >= 0x90 && buf[i + 1] <= 0xBF) ||\n (buf[i] >= 0xF1 && buf[i] <= 0xF3 && buf[i + 1] >> 6 === 2) ||\n (buf[i] === 0xF4 && buf[i + 1] >= 0x80 && buf[i + 1] <= 0x8F)) &&\n buf[i + 2] >> 6 === 2 &&\n buf[i + 3] >> 6 === 2) {\n i += 4;\n continue;\n }\n return false;\n }\n return true;\n}\n\nexport { isUtf8 as default };\n","export function installMathOperations(AbstractMatrix, Matrix) {\n AbstractMatrix.prototype.add = function add(value) {\n if (typeof value === 'number') return this.addS(value);\n return this.addM(value);\n };\n\n AbstractMatrix.prototype.addS = function addS(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) + value);\n }\n }\n return this;\n };\n\n AbstractMatrix.prototype.addM = function addM(matrix) {\n matrix = Matrix.checkMatrix(matrix);\n if (this.rows !== matrix.rows ||\n this.columns !== matrix.columns) {\n throw new RangeError('Matrices dimensions must be equal');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) + matrix.get(i, j));\n }\n }\n return this;\n };\n\n AbstractMatrix.add = function add(matrix, value) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.add(value);\n };\n\n AbstractMatrix.prototype.sub = function sub(value) {\n if (typeof value === 'number') return this.subS(value);\n return this.subM(value);\n };\n\n AbstractMatrix.prototype.subS = function subS(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) - value);\n }\n }\n return this;\n };\n\n AbstractMatrix.prototype.subM = function subM(matrix) {\n matrix = Matrix.checkMatrix(matrix);\n if (this.rows !== matrix.rows ||\n this.columns !== matrix.columns) {\n throw new RangeError('Matrices dimensions must be equal');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) - matrix.get(i, j));\n }\n }\n return this;\n };\n\n AbstractMatrix.sub = function sub(matrix, value) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.sub(value);\n };\n AbstractMatrix.prototype.subtract = AbstractMatrix.prototype.sub;\n AbstractMatrix.prototype.subtractS = AbstractMatrix.prototype.subS;\n AbstractMatrix.prototype.subtractM = AbstractMatrix.prototype.subM;\n AbstractMatrix.subtract = AbstractMatrix.sub;\n\n AbstractMatrix.prototype.mul = function mul(value) {\n if (typeof value === 'number') return this.mulS(value);\n return this.mulM(value);\n };\n\n AbstractMatrix.prototype.mulS = function mulS(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) * value);\n }\n }\n return this;\n };\n\n AbstractMatrix.prototype.mulM = function mulM(matrix) {\n matrix = Matrix.checkMatrix(matrix);\n if (this.rows !== matrix.rows ||\n this.columns !== matrix.columns) {\n throw new RangeError('Matrices dimensions must be equal');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) * matrix.get(i, j));\n }\n }\n return this;\n };\n\n AbstractMatrix.mul = function mul(matrix, value) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.mul(value);\n };\n AbstractMatrix.prototype.multiply = AbstractMatrix.prototype.mul;\n AbstractMatrix.prototype.multiplyS = AbstractMatrix.prototype.mulS;\n AbstractMatrix.prototype.multiplyM = AbstractMatrix.prototype.mulM;\n AbstractMatrix.multiply = AbstractMatrix.mul;\n\n AbstractMatrix.prototype.div = function div(value) {\n if (typeof value === 'number') return this.divS(value);\n return this.divM(value);\n };\n\n AbstractMatrix.prototype.divS = function divS(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) / value);\n }\n }\n return this;\n };\n\n AbstractMatrix.prototype.divM = function divM(matrix) {\n matrix = Matrix.checkMatrix(matrix);\n if (this.rows !== matrix.rows ||\n this.columns !== matrix.columns) {\n throw new RangeError('Matrices dimensions must be equal');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) / matrix.get(i, j));\n }\n }\n return this;\n };\n\n AbstractMatrix.div = function div(matrix, value) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.div(value);\n };\n AbstractMatrix.prototype.divide = AbstractMatrix.prototype.div;\n AbstractMatrix.prototype.divideS = AbstractMatrix.prototype.divS;\n AbstractMatrix.prototype.divideM = AbstractMatrix.prototype.divM;\n AbstractMatrix.divide = AbstractMatrix.div;\n\n AbstractMatrix.prototype.mod = function mod(value) {\n if (typeof value === 'number') return this.modS(value);\n return this.modM(value);\n };\n\n AbstractMatrix.prototype.modS = function modS(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) % value);\n }\n }\n return this;\n };\n\n AbstractMatrix.prototype.modM = function modM(matrix) {\n matrix = Matrix.checkMatrix(matrix);\n if (this.rows !== matrix.rows ||\n this.columns !== matrix.columns) {\n throw new RangeError('Matrices dimensions must be equal');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) % matrix.get(i, j));\n }\n }\n return this;\n };\n\n AbstractMatrix.mod = function mod(matrix, value) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.mod(value);\n };\n AbstractMatrix.prototype.modulus = AbstractMatrix.prototype.mod;\n AbstractMatrix.prototype.modulusS = AbstractMatrix.prototype.modS;\n AbstractMatrix.prototype.modulusM = AbstractMatrix.prototype.modM;\n AbstractMatrix.modulus = AbstractMatrix.mod;\n\n AbstractMatrix.prototype.and = function and(value) {\n if (typeof value === 'number') return this.andS(value);\n return this.andM(value);\n };\n\n AbstractMatrix.prototype.andS = function andS(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) & value);\n }\n }\n return this;\n };\n\n AbstractMatrix.prototype.andM = function andM(matrix) {\n matrix = Matrix.checkMatrix(matrix);\n if (this.rows !== matrix.rows ||\n this.columns !== matrix.columns) {\n throw new RangeError('Matrices dimensions must be equal');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) & matrix.get(i, j));\n }\n }\n return this;\n };\n\n AbstractMatrix.and = function and(matrix, value) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.and(value);\n };\n\n AbstractMatrix.prototype.or = function or(value) {\n if (typeof value === 'number') return this.orS(value);\n return this.orM(value);\n };\n\n AbstractMatrix.prototype.orS = function orS(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) | value);\n }\n }\n return this;\n };\n\n AbstractMatrix.prototype.orM = function orM(matrix) {\n matrix = Matrix.checkMatrix(matrix);\n if (this.rows !== matrix.rows ||\n this.columns !== matrix.columns) {\n throw new RangeError('Matrices dimensions must be equal');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) | matrix.get(i, j));\n }\n }\n return this;\n };\n\n AbstractMatrix.or = function or(matrix, value) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.or(value);\n };\n\n AbstractMatrix.prototype.xor = function xor(value) {\n if (typeof value === 'number') return this.xorS(value);\n return this.xorM(value);\n };\n\n AbstractMatrix.prototype.xorS = function xorS(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) ^ value);\n }\n }\n return this;\n };\n\n AbstractMatrix.prototype.xorM = function xorM(matrix) {\n matrix = Matrix.checkMatrix(matrix);\n if (this.rows !== matrix.rows ||\n this.columns !== matrix.columns) {\n throw new RangeError('Matrices dimensions must be equal');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) ^ matrix.get(i, j));\n }\n }\n return this;\n };\n\n AbstractMatrix.xor = function xor(matrix, value) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.xor(value);\n };\n\n AbstractMatrix.prototype.leftShift = function leftShift(value) {\n if (typeof value === 'number') return this.leftShiftS(value);\n return this.leftShiftM(value);\n };\n\n AbstractMatrix.prototype.leftShiftS = function leftShiftS(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) << value);\n }\n }\n return this;\n };\n\n AbstractMatrix.prototype.leftShiftM = function leftShiftM(matrix) {\n matrix = Matrix.checkMatrix(matrix);\n if (this.rows !== matrix.rows ||\n this.columns !== matrix.columns) {\n throw new RangeError('Matrices dimensions must be equal');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) << matrix.get(i, j));\n }\n }\n return this;\n };\n\n AbstractMatrix.leftShift = function leftShift(matrix, value) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.leftShift(value);\n };\n\n AbstractMatrix.prototype.signPropagatingRightShift = function signPropagatingRightShift(value) {\n if (typeof value === 'number') return this.signPropagatingRightShiftS(value);\n return this.signPropagatingRightShiftM(value);\n };\n\n AbstractMatrix.prototype.signPropagatingRightShiftS = function signPropagatingRightShiftS(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) >> value);\n }\n }\n return this;\n };\n\n AbstractMatrix.prototype.signPropagatingRightShiftM = function signPropagatingRightShiftM(matrix) {\n matrix = Matrix.checkMatrix(matrix);\n if (this.rows !== matrix.rows ||\n this.columns !== matrix.columns) {\n throw new RangeError('Matrices dimensions must be equal');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) >> matrix.get(i, j));\n }\n }\n return this;\n };\n\n AbstractMatrix.signPropagatingRightShift = function signPropagatingRightShift(matrix, value) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.signPropagatingRightShift(value);\n };\n\n AbstractMatrix.prototype.rightShift = function rightShift(value) {\n if (typeof value === 'number') return this.rightShiftS(value);\n return this.rightShiftM(value);\n };\n\n AbstractMatrix.prototype.rightShiftS = function rightShiftS(value) {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) >>> value);\n }\n }\n return this;\n };\n\n AbstractMatrix.prototype.rightShiftM = function rightShiftM(matrix) {\n matrix = Matrix.checkMatrix(matrix);\n if (this.rows !== matrix.rows ||\n this.columns !== matrix.columns) {\n throw new RangeError('Matrices dimensions must be equal');\n }\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, this.get(i, j) >>> matrix.get(i, j));\n }\n }\n return this;\n };\n\n AbstractMatrix.rightShift = function rightShift(matrix, value) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.rightShift(value);\n };\n AbstractMatrix.prototype.zeroFillRightShift = AbstractMatrix.prototype.rightShift;\n AbstractMatrix.prototype.zeroFillRightShiftS = AbstractMatrix.prototype.rightShiftS;\n AbstractMatrix.prototype.zeroFillRightShiftM = AbstractMatrix.prototype.rightShiftM;\n AbstractMatrix.zeroFillRightShift = AbstractMatrix.rightShift;\n\n AbstractMatrix.prototype.not = function not() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, ~(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.not = function not(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.not();\n };\n\n AbstractMatrix.prototype.abs = function abs() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.abs(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.abs = function abs(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.abs();\n };\n\n AbstractMatrix.prototype.acos = function acos() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.acos(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.acos = function acos(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.acos();\n };\n\n AbstractMatrix.prototype.acosh = function acosh() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.acosh(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.acosh = function acosh(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.acosh();\n };\n\n AbstractMatrix.prototype.asin = function asin() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.asin(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.asin = function asin(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.asin();\n };\n\n AbstractMatrix.prototype.asinh = function asinh() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.asinh(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.asinh = function asinh(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.asinh();\n };\n\n AbstractMatrix.prototype.atan = function atan() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.atan(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.atan = function atan(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.atan();\n };\n\n AbstractMatrix.prototype.atanh = function atanh() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.atanh(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.atanh = function atanh(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.atanh();\n };\n\n AbstractMatrix.prototype.cbrt = function cbrt() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.cbrt(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.cbrt = function cbrt(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.cbrt();\n };\n\n AbstractMatrix.prototype.ceil = function ceil() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.ceil(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.ceil = function ceil(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.ceil();\n };\n\n AbstractMatrix.prototype.clz32 = function clz32() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.clz32(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.clz32 = function clz32(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.clz32();\n };\n\n AbstractMatrix.prototype.cos = function cos() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.cos(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.cos = function cos(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.cos();\n };\n\n AbstractMatrix.prototype.cosh = function cosh() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.cosh(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.cosh = function cosh(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.cosh();\n };\n\n AbstractMatrix.prototype.exp = function exp() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.exp(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.exp = function exp(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.exp();\n };\n\n AbstractMatrix.prototype.expm1 = function expm1() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.expm1(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.expm1 = function expm1(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.expm1();\n };\n\n AbstractMatrix.prototype.floor = function floor() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.floor(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.floor = function floor(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.floor();\n };\n\n AbstractMatrix.prototype.fround = function fround() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.fround(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.fround = function fround(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.fround();\n };\n\n AbstractMatrix.prototype.log = function log() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.log(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.log = function log(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.log();\n };\n\n AbstractMatrix.prototype.log1p = function log1p() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.log1p(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.log1p = function log1p(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.log1p();\n };\n\n AbstractMatrix.prototype.log10 = function log10() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, 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this.set(i, j, Math.sign(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.sign = function sign(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.sign();\n };\n\n AbstractMatrix.prototype.sin = function sin() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.sin(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.sin = function sin(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.sin();\n };\n\n AbstractMatrix.prototype.sinh = function sinh() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.sinh(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.sinh = function sinh(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.sinh();\n };\n\n AbstractMatrix.prototype.sqrt = function sqrt() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.sqrt(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.sqrt = function sqrt(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.sqrt();\n };\n\n AbstractMatrix.prototype.tan = function tan() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.tan(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.tan = function tan(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.tan();\n };\n\n AbstractMatrix.prototype.tanh = function tanh() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n this.set(i, j, Math.tanh(this.get(i, j)));\n }\n }\n return this;\n };\n\n AbstractMatrix.tanh = function tanh(matrix) {\n const newMatrix = new Matrix(matrix);\n return newMatrix.tanh();\n };\n\n AbstractMatrix.prototype.trunc = function trunc() {\n for (let i = 0; i < this.rows; i++) {\n for (let j = 0; j < this.columns; j++) {\n 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p=m.step;m.step=function(e){if(c=e,_())g();else{if(g(),0===c.data.length)return;i+=e.data.length,m.preview&&i>m.preview?o.abort():(c.data=c.data[0],p(c,t))}}}function y(e){return\"greedy\"===m.skipEmptyLines?\"\"===e.join(\"\").trim():1===e.length&&0===e[0].length}function g(){return c&&h&&(k(\"Delimiter\",\"UndetectableDelimiter\",\"Unable to auto-detect delimiting character; defaulted to '\"+b.DefaultDelimiter+\"'\"),h=!1),m.skipEmptyLines&&(c.data=c.data.filter(function(e){return!y(e)})),_()&&function(){if(!c)return;function e(e,t){M(m.transformHeader)&&(e=m.transformHeader(e,t)),l.push(e)}if(Array.isArray(c.data[0])){for(var t=0;_()&&t=l.length?\"__parsed_extra\":l[i]),m.transform&&(s=m.transform(s,n)),s=v(n,s),\"__parsed_extra\"===n?(r[n]=r[n]||[],r[n].push(s)):r[n]=s}return m.header&&(i>l.length?k(\"FieldMismatch\",\"TooManyFields\",\"Too many fields: expected \"+l.length+\" fields but parsed \"+i,f+t):i=r.length/2?\"\\r\\n\":\"\\r\"}(e,r)),h=!1,m.delimiter)M(m.delimiter)&&(m.delimiter=m.delimiter(e),c.meta.delimiter=m.delimiter);else{var n=function(e,t,i,r,n){var s,a,o,h;n=n||[\",\",\"\\t\",\"|\",\";\",b.RECORD_SEP,b.UNIT_SEP];for(var u=0;u=D)return C(!0)}else for(m=F,F++;;){if(-1===(m=r.indexOf(S,m+1)))return i||u.push({type:\"Quotes\",code:\"MissingQuotes\",message:\"Quoted field unterminated\",row:h.length,index:F}),E();if(m===n-1)return E(r.substring(F,m).replace(_,S));if(S!==L||r[m+1]!==L){if(S===L||0===m||r[m-1]!==L){-1!==p&&p=D)return C(!0);break}u.push({type:\"Quotes\",code:\"InvalidQuotes\",message:\"Trailing quote on quoted field is malformed\",row:h.length,index:F}),m++}}else m++}return E();function k(e){h.push(e),d=F}function b(e){var t=0;if(-1!==e){var i=r.substring(m+1,e);i&&\"\"===i.trim()&&(t=i.length)}return t}function E(e){return i||(void 0===e&&(e=r.substring(F)),f.push(e),F=n,k(f),o&&R()),C()}function w(e){F=e,k(f),f=[],g=r.indexOf(x,F)}function C(e){return{data:h,errors:u,meta:{delimiter:O,linebreak:x,aborted:z,truncated:!!e,cursor:d+(t||0)}}}function R(){T(C()),h=[],u=[]}},this.abort=function(){z=!0},this.getCharIndex=function(){return F}}function _(e){var t=e.data,i=a[t.workerId],r=!1;if(t.error)i.userError(t.error,t.file);else if(t.results&&t.results.data){var n={abort:function(){r=!0,m(t.workerId,{data:[],errors:[],meta:{aborted:!0}})},pause:y,resume:y};if(M(i.userStep)){for(var s=0;s`);\n if (parts.length === 0 || parts[0].length <= 5) return;\n let molecule = {};\n molecule.molfile = parts[0] + options.eol;\n for (let j = 1; j < parts.length; j++) {\n let lines = parts[j].split(options.eol);\n let from = lines[0].indexOf('<');\n let to = lines[0].indexOf('>');\n let label = lines[0].substring(from + 1, to);\n currentLabels.push(label);\n if (!labels[label]) {\n labels[label] = {\n counter: 0,\n isNumeric: options.dynamicTyping,\n keep: false,\n };\n if (\n (!options.exclude || options.exclude.indexOf(label) === -1) &&\n (!options.include || options.include.indexOf(label) > -1)\n ) {\n labels[label].keep = true;\n if (options.modifiers[label]) {\n labels[label].modifier = options.modifiers[label];\n }\n if (options.forEach[label]) {\n labels[label].forEach = options.forEach[label];\n }\n }\n }\n if (labels[label].keep) {\n for (let k = 1; k < lines.length - 1; k++) {\n if (molecule[label]) {\n molecule[label] += options.eol + lines[k];\n } else {\n molecule[label] = lines[k];\n }\n }\n if (labels[label].modifier) {\n let modifiedValue = labels[label].modifier(molecule[label]);\n if (modifiedValue === undefined || modifiedValue === null) {\n delete molecule[label];\n } else {\n molecule[label] = modifiedValue;\n }\n }\n if (labels[label].isNumeric) {\n if (!isFinite(molecule[label]) || molecule[label].match(/^0[0-9]/)) {\n labels[label].isNumeric = false;\n }\n }\n }\n }\n return molecule;\n}\n","import { ensureString } from 'ensure-string';\nimport { parse } from 'sdf-parser';\n\nexport default async function appendSDF(moleculesDB, sdf, options = {}) {\n const { onStep } = options;\n sdf = ensureString(sdf);\n if (typeof sdf !== 'string') {\n throw new TypeError('sdf must be a string');\n }\n const parsed = parse(sdf);\n moleculesDB.statistics = parsed.statistics;\n for (let i = 0; i < parsed.molecules.length; i++) {\n const molecule = parsed.molecules[i];\n moleculesDB.pushEntry(\n moleculesDB.OCL.Molecule.fromMolfile(molecule.molfile),\n molecule,\n );\n if (onStep) {\n await onStep(i + 1, parsed.molecules.length);\n }\n }\n}\n","import { ensureString } from 'ensure-string';\n\nimport { getEntriesBoundaries } from './getEntriesBoundaries';\nimport { getMolecule } from './util/getMolecule';\n/**\n * Parse a SDF file\n * @param {string|ArrayBuffer|Uint8Array} sdf SDF file to parse\n * @param {object} [options={}]\n * @param {string[]} [options.include] List of fields to include\n * @param {string[]} [options.exclude] List of fields to exclude\n * @param {Function} [options.filter] Callback allowing to filter the molecules\n * @param {boolean} [options.dynamicTyping] Dynamically type the data\n * @param {object} [options.modifiers] Object containing callbacks to apply on some specific fields\n * @param {boolean} [options.mixedEOL=false] Set to true if you know there is a mixture between \\r\\n and \\n\n * @param {string} [options.eol] Specify the end of line character. Default will be the one found in the file\n */\nexport function parse(sdf, options = {}) {\n options = { ...options };\n if (options.modifiers === undefined) options.modifiers = {};\n if (options.forEach === undefined) options.forEach = {};\n if (options.dynamicTyping === undefined) options.dynamicTyping = true;\n\n sdf = ensureString(sdf);\n if (typeof sdf !== 'string') {\n throw new TypeError('Parameter \"sdf\" must be a string');\n }\n\n if (options.eol === undefined) {\n options.eol = '\\n';\n if (options.mixedEOL) {\n sdf = sdf.replace(/\\r\\n/g, '\\n');\n sdf = sdf.replace(/\\r/g, '\\n');\n } else {\n // we will find the delimiter in order to be much faster and not use regular expression\n let header = sdf.substr(0, 1000);\n if (header.indexOf('\\r\\n') > -1) {\n options.eol = '\\r\\n';\n } else if (header.indexOf('\\r') > -1) {\n options.eol = '\\r';\n }\n }\n }\n\n let entriesBoundaries = getEntriesBoundaries(\n sdf,\n `${options.eol}$$$$`,\n options.eol,\n );\n let molecules = [];\n let labels = {};\n\n let start = Date.now();\n\n for (let i = 0; i < entriesBoundaries.length; i++) {\n let sdfPart = sdf.substring(...entriesBoundaries[i]);\n\n let currentLabels = [];\n const molecule = getMolecule(sdfPart, labels, currentLabels, options);\n if (!molecule) continue;\n if (!options.filter || options.filter(molecule)) {\n molecules.push(molecule);\n // only now we can increase the counter\n for (let j = 0; j < currentLabels.length; j++) {\n labels[currentLabels[j]].counter++;\n }\n }\n }\n // all numeric fields should be converted to numbers\n for (let label in labels) {\n let currentLabel = labels[label];\n if (currentLabel.isNumeric) {\n currentLabel.minValue = Infinity;\n currentLabel.maxValue = -Infinity;\n for (let j = 0; j < molecules.length; j++) {\n if (molecules[j][label]) {\n let value = parseFloat(molecules[j][label]);\n molecules[j][label] = value;\n if (value > currentLabel.maxValue) {\n currentLabel.maxValue = value;\n }\n if (value < currentLabel.minValue) {\n currentLabel.minValue = value;\n }\n }\n }\n }\n }\n\n // we check that a label is in all the records\n for (let key in labels) {\n if (labels[key].counter === molecules.length) {\n labels[key].always = true;\n } else {\n labels[key].always = false;\n }\n }\n\n let statistics = [];\n for (let key in labels) {\n let statistic = labels[key];\n statistic.label = key;\n statistics.push(statistic);\n }\n\n return {\n time: Date.now() - start,\n molecules,\n labels: Object.keys(labels),\n statistics,\n };\n}\n","export function getEntriesBoundaries(string, substring, eol) {\n const res = [];\n let previous = 0;\n let next = 0;\n while (next !== -1) {\n next = string.indexOf(substring, previous);\n if (next !== -1) {\n res.push([previous, next]);\n const nextMatch = string.indexOf(eol, next + substring.length);\n if (nextMatch === -1) {\n next = -1;\n } else {\n previous = nextMatch + eol.length;\n next = previous;\n }\n } else {\n res.push([previous, string.length]);\n }\n }\n return res;\n}\n","export async function noWait() {\n return new Promise((resolve) => {\n if (typeof setImmediate === 'function') {\n setImmediate(() => resolve());\n } else {\n // didn't find a better way to do it in the browser\n setTimeout(() => resolve(), 0);\n }\n });\n}\n","import { noWait } from '../../util/noWait.js';\n\nimport getMoleculeCreators from './getMoleculeCreators';\n\nclass AbortError extends Error {\n name = 'AbortError';\n code = 20;\n}\n\nfunction getQuery(moleculesDB, query, options) {\n const { format = 'idCode' } = options;\n\n if (typeof query === 'string') {\n const moleculeCreators = getMoleculeCreators(moleculesDB.OCL.Molecule);\n query = moleculeCreators.get(format.toLowerCase())(query);\n } else if (!(query instanceof moleculesDB.OCL.Molecule)) {\n throw new TypeError('toSearch must be a Molecule or string');\n }\n return query;\n}\n\nexport function search(moleculesDB, query = '', options = {}) {\n const { mode = 'substructure' } = options;\n\n query = getQuery(moleculesDB, query, options);\n\n let result;\n switch (mode.toLowerCase()) {\n case 'exact':\n result = exactSearch(moleculesDB, query);\n break;\n case 'substructure':\n result = subStructureSearch(moleculesDB, query);\n break;\n case 'similarity':\n result = similaritySearch(moleculesDB, query);\n break;\n default:\n throw new Error(`unknown search mode: ${options.mode}`);\n }\n return processResult(result, options);\n}\n\nexport async function searchAsync(moleculesDB, query = '', options = {}) {\n const { mode = 'substructure' } = options;\n\n query = getQuery(moleculesDB, query, options);\n\n let result;\n switch (mode.toLowerCase()) {\n case 'exact':\n result = exactSearch(moleculesDB, query);\n break;\n case 'substructure':\n result = await subStructureSearchAsync(moleculesDB, query, options);\n break;\n case 'similarity':\n result = similaritySearch(moleculesDB, query);\n break;\n default:\n throw new Error(`unknown search mode: ${options.mode}`);\n }\n return processResult(result, options);\n}\n\nfunction exactSearch(moleculesDB, query) {\n const queryIDCode = query.getIDCode();\n let searchResult = moleculesDB.db[queryIDCode]\n ? [moleculesDB.db[queryIDCode]]\n : [];\n return searchResult;\n}\n\nfunction substructureSearchBegin(moleculesDB, query) {\n let resetFragment = false;\n if (!query.isFragment()) {\n resetFragment = true;\n query.setFragment(true);\n }\n\n const queryMW = getMW(query);\n const searchResult = [];\n if (query.getAllAtoms() === 0) {\n for (let idCode in moleculesDB.db) {\n searchResult.push(moleculesDB.db[idCode]);\n }\n }\n return { resetFragment, queryMW, searchResult };\n}\n\nfunction substructureSearchEnd(searchResult, queryMW, resetFragment, query) {\n searchResult.sort((a, b) => {\n return (\n Math.abs(queryMW - a.properties.mw) - Math.abs(queryMW - b.properties.mw)\n );\n });\n\n if (resetFragment) {\n query.setFragment(false);\n }\n\n return searchResult;\n}\n\nfunction subStructureSearch(moleculesDB, query) {\n const { resetFragment, queryMW, searchResult } = substructureSearchBegin(\n moleculesDB,\n query,\n );\n\n if (searchResult.length === 0) {\n const queryIndex = query.getIndex();\n const searcher = moleculesDB.searcher;\n searcher.setFragment(query, queryIndex);\n for (let idCode in moleculesDB.db) {\n let entry = moleculesDB.db[idCode];\n searcher.setMolecule(entry.molecule, entry.index);\n if (searcher.isFragmentInMolecule()) {\n searchResult.push(entry);\n }\n }\n }\n\n return substructureSearchEnd(searchResult, queryMW, resetFragment, query);\n}\n\nasync function subStructureSearchAsync(moleculesDB, query, options = {}) {\n const { interval = 100, onStep, controller } = options;\n let shouldAbort = false;\n\n if (controller) {\n const abortEventListener = () => {\n shouldAbort = true;\n };\n controller.signal.addEventListener('abort', abortEventListener);\n }\n\n const { resetFragment, queryMW, searchResult } = substructureSearchBegin(\n moleculesDB,\n query,\n );\n\n let begin = performance.now();\n\n if (searchResult.length === 0) {\n const queryIndex = query.getIndex();\n const searcher = moleculesDB.searcher;\n searcher.setFragment(query, queryIndex);\n let index = 0;\n let length = Object.keys(moleculesDB.db).length;\n for (let idCode in moleculesDB.db) {\n if (shouldAbort) {\n throw new AbortError('Query aborted');\n }\n let entry = moleculesDB.db[idCode];\n searcher.setMolecule(entry.molecule, entry.index);\n if (searcher.isFragmentInMolecule()) {\n searchResult.push(entry);\n }\n if ((onStep || controller) && performance.now() - begin >= interval) {\n begin = performance.now();\n if (onStep) {\n onStep(index, length);\n }\n if (controller && !onStep) {\n await noWait();\n }\n }\n index++;\n }\n }\n return substructureSearchEnd(searchResult, queryMW, resetFragment, query);\n}\n\nfunction similaritySearch(moleculesDB, query) {\n const queryIndex = query.getIndex();\n const queryMW = getMW(query);\n const queryIdCode = query.getIDCode();\n\n const searchResult = [];\n let similarity;\n for (let idCode in moleculesDB.db) {\n let entry = moleculesDB.db[idCode];\n if (entry.idCode === queryIdCode) {\n similarity = Number.MAX_SAFE_INTEGER;\n } else {\n similarity =\n moleculesDB.OCL.SSSearcherWithIndex.getSimilarityTanimoto(\n queryIndex,\n entry.index,\n ) *\n 1000000 -\n Math.abs(queryMW - entry.properties.mw) / 10000;\n }\n searchResult.push({ similarity, entry });\n }\n searchResult.sort((a, b) => {\n return b.similarity - a.similarity;\n });\n return searchResult.map((entry) => entry.entry);\n}\n\nfunction getMW(query) {\n let copy = query.getCompactCopy();\n copy.setFragment(false);\n return copy.getMolecularFormula().relativeWeight;\n}\n\nfunction processResult(entries, options = {}) {\n const {\n flattenResult = true,\n keepMolecule = false,\n limit = Number.MAX_SAFE_INTEGER,\n } = options;\n let results = [];\n\n if (flattenResult) {\n for (let entry of entries) {\n for (let data of entry.data) {\n results.push({\n data,\n idCode: entry.idCode,\n properties: entry.properties,\n molecule: keepMolecule ? entry.molecule : undefined,\n });\n }\n }\n } else {\n for (let entry of entries) {\n results.push({\n data: entry.data,\n idCode: entry.idCode,\n properties: entry.properties,\n molecule: keepMolecule ? entry.molecule : undefined,\n });\n }\n }\n if (limit < results.length) results.length = limit;\n return results;\n}\n","export function parseColumnbProperties(lines) {\n lines = lines.map((line) => {\n const [key, value] = line.slice(1, -1).split('=');\n return { key, value: value.slice(1, -1) };\n });\n const columnProperties = {};\n let currentColumnName = '';\n for (let line of lines) {\n switch (line.key) {\n case 'columnName':\n currentColumnName = line.value;\n columnProperties[currentColumnName] = {};\n break;\n case 'columnProperty':\n {\n if (!currentColumnName) {\n throw new Error('This should not happen');\n }\n const [key, value] = line.value.split('\\t');\n columnProperties[currentColumnName][key] = value;\n }\n break;\n default:\n throw new Error('This should not happen');\n }\n }\n for (let key in columnProperties) {\n const columnPropery = columnProperties[key];\n if (columnProperties[key].parent) {\n const target = columnProperties[columnPropery.parent];\n if (!target) {\n throw new Error('Parent column not found');\n }\n if (!target.related) {\n target.related = {};\n }\n target.related[columnPropery.specialType] = key;\n }\n }\n\n return columnProperties;\n}\n","export function parseData(lines, options = {}) {\n lines = lines.filter((line) => !line.match(/^\\s*$/));\n const { columnProperties = {} } = options;\n const headers = lines\n .shift()\n .split('\\t')\n .map((header) => {\n if (columnProperties[header]) {\n return { label: header, ...columnProperties[header] };\n }\n return { label: header };\n });\n const entries = [];\n const rawEntries = [];\n\n for (let line of lines) {\n const fields = line.split('\\t');\n const rawEntry = {};\n headers.forEach((header, index) => {\n rawEntry[header.label] = fields[index];\n });\n rawEntries.push(rawEntry);\n const entry = {};\n headers.forEach((header) => {\n if (header.parent) return;\n entry[header.label] = valueEhnhancer(header, rawEntry);\n });\n entries.push(entry);\n }\n\n return { entries, rawEntries };\n}\n\nfunction valueEhnhancer(header, rawEntry) {\n if (header?.specialType === 'rxncode') {\n return `${rawEntry[header.label]}#${rawEntry[header.related.atomMapping]}#${\n rawEntry[header.related.idcoordinates2D]\n }`;\n }\n\n return rawEntry[header.label];\n}\n\n/*\nentry.rxnCode =\n*/\n","import { ensureString } from 'ensure-string';\n\nimport { getParts } from './utils/getParts';\nimport { parseColumnbProperties } from './utils/parseColumnbProperties';\nimport { parseData } from './utils/parseData';\n\n/**\n * Convert a DataWarrior database into a JSON object\n * @param {string} text\n * @returns\n */\nexport function parseDwar(text) {\n text = ensureString(text);\n const parts = getParts(text);\n improveParts(parts);\n return parts;\n}\n\nexport function getCamelCase(name) {\n return name.replace(/[ -][a-z]/g, (string) => string[1].toUpperCase());\n}\n\nfunction improveParts(parts) {\n for (let key in parts) {\n switch (key) {\n case 'columnProperties':\n parts[key] = parseColumnbProperties(parts[key]);\n break;\n case 'data':\n break;\n default:\n parts[key] = parseDefault(parts[key]);\n }\n }\n const data = parseData(parts.data, {\n columnProperties: parts.columnProperties,\n });\n parts.data = data.entries;\n parts.rawData = data.rawEntries;\n}\n\nfunction parseDefault(lines) {\n const result = {};\n for (let line of lines) {\n const [key, value] = line.slice(1, -1).split('=');\n result[key] = value.slice(1, -1);\n }\n return result;\n}\n","import { getMF } from '../../util/getMF.js';\n\n/**\n *\n * @param {import('openchemlib').Molecule} molecule\n * @param {Map} moleculesInfo\n * @returns\n */\nexport function getInfo(molecule, moleculesInfo) {\n if (moleculesInfo.has(molecule)) {\n return moleculesInfo.get(molecule);\n }\n const reactantInfo = {\n molfile: molecule.toMolfile(),\n idCode: molecule.getIDCode(),\n mf: getMF(molecule).mf,\n };\n moleculesInfo.set(molecule, reactantInfo);\n return reactantInfo;\n}\n","import { getInfo } from './getReactantInfo.js';\n\nexport function applyOneReactantReaction(reactants, reactions, options) {\n const { currentDepth, maxDepth, moleculesInfo, processedMolecules, results } =\n options;\n const todoNextDepth = [];\n if (currentDepth >= maxDepth) return [];\n if (!Array.isArray(reactants)) {\n reactants = [reactants];\n }\n const { OCL } = options;\n for (const reactant of reactants) {\n const idCode = reactant.getIDCode();\n if (processedMolecules.has(idCode)) {\n continue;\n } else {\n processedMolecules.add(idCode);\n }\n for (const reaction of reactions) {\n const reactor = new OCL.Reactor(reaction.oclReaction);\n const isMatching = Boolean(reactor.setReactant(0, reactant));\n if (isMatching) {\n const oneReactionProducts = reactor.getProducts();\n for (let i = 0; i < oneReactionProducts.length; i++) {\n const products = [];\n for (let j = 0; j < oneReactionProducts[i].length; j++) {\n const moleculeInfo = getInfo(\n oneReactionProducts[i][j],\n moleculesInfo,\n );\n if (!processedMolecules.has(moleculeInfo.idCode)) {\n const product = {\n ...moleculeInfo,\n children: [],\n };\n products.push(product);\n\n todoNextDepth.push(() => {\n return applyOneReactantReaction(\n oneReactionProducts[i][j],\n reactions,\n {\n ...options,\n currentDepth: options.currentDepth + 1,\n results: product.children,\n },\n );\n });\n }\n }\n if (products.length > 0) {\n // eslint-disable-next-line no-unused-vars\n const { oclReaction, ...reactionWithoutOCL } = reaction;\n const oneReaction = {\n reaction: reactionWithoutOCL,\n reactant: getInfo(reactant, moleculesInfo),\n products,\n };\n results.push(oneReaction);\n }\n }\n }\n }\n }\n return todoNextDepth;\n}\n","import appendCSV from './utils/appendCSV';\nimport appendColor from './utils/appendColor';\nimport appendSDF from './utils/appendSDF';\nimport appendSmilesList from './utils/appendSmilesList';\nimport pushEntry from './utils/pushEntry';\nimport pushMoleculeInfo from './utils/pushMoleculeInfo';\nimport { search, searchAsync } from './utils/search';\n/*\n this.db is an object with properties 'oclID' that has as value\n an object that contains the following properties:\n * molecule: an OCL molecule instance\n * index: OCL index used for substructure searching\n * properties: all the calculates properties\n * data: array containing free data associated with this molecule\n */\n\nexport class MoleculesDB {\n /**\n *\n * @param {import('openchemlib')} OCL - openchemlib library\n * @param {object} [options={}]\n * @param {boolean} [options.computeProperties=false]\n */\n constructor(OCL, options = {}) {\n const { computeProperties = false } = options;\n this.OCL = OCL;\n this.db = {};\n this.statistics = null;\n this.computeProperties = computeProperties;\n this.searcher = new OCL.SSSearcherWithIndex();\n }\n\n /**\n * append to the current database a CSV file\n * @param {string|ArrayBuffer} csv - text file containing the comma separated value file\n * @param {object} [options={}]\n * @param {boolean} [options.header=true]\n * @param {boolean} [options.dynamicTyping=true]\n * @param {boolean} [options.skipEmptyLines=true]\n * @param {function} [options.onStep] call back to execute after each molecule\n */\n\n appendCSV(csv, options) {\n return appendCSV(this, csv, {\n computeProperties: this.computeProperties,\n ...options,\n });\n }\n\n /**\n * Append a SDF to the current database\n * @param {string|ArrayBuffer} sdf - text file containing the sdf\n * @param {object} [options={}]\n * @param {function} [options.onStep] call back to execute after each molecule\n * @returns {DB}\n */\n\n appendSDF(sdf, options) {\n return appendSDF(this, sdf, {\n computeProperties: this.computeProperties,\n ...options,\n });\n }\n\n /**\n * Append a SDF to the current database\n * @param {string|ArrayBuffer} smiles - text file containing a list of smiles\n * @param {object} [options={}]\n * @param {function} [options.onStep] call back to execute after each molecule\n * @returns {DB}\n */\n\n appendSmilesList(text, options) {\n return appendSmilesList(this, text, {\n computeProperties: this.computeProperties,\n ...options,\n });\n }\n\n /**\n * Add a molecule to the current database\n * @param {import('openchemlib').Molecule} molecule\n * @param {object} [data={}]\n * @param {object} [moleculeInfo={}] may contain precalculated index and mw\n */\n\n pushEntry(molecule, data, moleculeInfo) {\n pushEntry(this, molecule, data, moleculeInfo);\n }\n\n /**\n * Add an entry in the database\n * @param {object} moleculeInfo - a molecule as a JSON that may contain the following properties: molfile, smiles, idCode, mf, index\n * @param {object} [data={}]\n */\n\n pushMoleculeInfo(moleculeInfo, data) {\n return pushMoleculeInfo(this, moleculeInfo, data);\n }\n\n /**\n * Search in a MoleculesDB\n * Inside the database all the same molecules are group together\n * @param {string|OCL.Molecule} [query] smiles, molfile, oclCode or instance of Molecule to look for\n * @param {object} [options={}]\n * @param {string} [options.format='idCode'] - query is in the format 'smiles', 'oclid' or 'molfile'\n * @param {string} [options.mode='substructure'] - search by 'substructure', 'exact' or 'similarity'\n * @param {boolean} [options.flattenResult=true] - The database group the data for the same product. This allows to flatten the result\n * @param {boolean} [options.keepMolecule=false] - keep the OCL.Molecule object in the result\n * @param {number} [options.limit=Number.MAX_SAFE_INTEGER] - maximal number of result\n * @return {Array} array of object of the type {(molecule), idCode, data, properties}\n */\n search(query, options) {\n return search(this, query, options);\n }\n\n /**\n * Search in a MoleculesDB\n * Inside the database all the same molecules are group together\n * @param {string|OCL.Molecule} [query] smiles, molfile, oclCode or instance of Molecule to look for\n * @param {object} [options={}]\n * @param {string} [options.format='idCode'] - query is in the format 'smiles', 'oclid' or 'molfile'\n * @param {string} [options.mode='substructure'] - search by 'substructure', 'exact' or 'similarity'\n * @param {boolean} [options.flattenResult=true] - The database group the data for the same product. This allows to flatten the result\n * @param {boolean} [options.keepMolecule=false] - keep the OCL.Molecule object in the result\n * @param {number} [options.limit=Number.MAX_SAFE_INTEGER] - maximal number of result\n * @param {number} [options.interval=100] - interval in ms to call the onStep callback\n * @param {function} [options.onStep] - callback to execute after each interval\n * @param {AbortController} [options.controler] - callback to execute to check if the search should be aborted\n * @return {Promise} array of object of the type {(molecule), idCode, data, properties}\n */\n searchAsync(query, options) {\n return searchAsync(this, query, options);\n }\n\n /**\n * Returns an array with the current database\n * @returns\n */\n getDB() {\n return Object.keys(this.db).map((key) => this.db[key]);\n }\n\n /**\n * Append the property `data.color` to each entry based on a data or property label\n * {object} [options={}]\n * {string} [options.dataLabel] name of the property from `data` to use\n * {string} [options.propertyLabel] name of the property from `properties` to use\n * {number} [options.colorLabel='color'] name of the property to add in data that will contain the color\n * {number} [options.minValue]\n * {number} [options.maxValue]\n * {number} [options.minHue=0]\n * {number} [options.maxHue=360]\n * {number} [options.saturation=65] percent of color saturation\n * {number} [options.lightness=65] percent of color lightness\n */\n appendColor(options) {\n appendColor(this, options);\n }\n}\n","import { ensureString } from 'ensure-string';\n\nexport default async function appendSmilesList(\n moleculesDB,\n text,\n options = {},\n) {\n const { onStep } = options;\n text = ensureString(text);\n if (typeof text !== 'string') {\n throw new TypeError('text must be a string');\n }\n const smilesArray = text\n .split(/\\r?\\n/)\n .map((line) => line.trim())\n .filter((line) => line);\n for (let i = 0; i < smilesArray.length; i++) {\n const oneSmiles = smilesArray[i];\n moleculesDB.pushEntry(moleculesDB.OCL.Molecule.fromSmiles(oneSmiles));\n if (onStep) {\n await onStep(i + 1, smilesArray.length);\n }\n }\n}\n","/**\n *\n * @param {MoleculesDB} moleculesDB\n * @param {import('openchemlib').Molecule} molecule\n * @param {object} data\n * @param {object} [moleculeInfo]\n * @param {string} [moleculeInfo.idCode]\n * @param {number[]} [moleculeInfo.index]\n */\n\nexport default function pushEntry(\n moleculesDB,\n molecule,\n data = {},\n moleculeInfo = {},\n) {\n // the following line could be the source of problems if the idCode version\n // changes\n\n let moleculeIDCode = moleculeInfo.idCode\n ? moleculeInfo.idCode\n : molecule.getIDCode();\n let entry = moleculesDB.db[moleculeIDCode];\n if (!entry) {\n // a new molecule\n entry = { molecule, properties: {}, data: [], idCode: moleculeIDCode };\n moleculesDB.db[moleculeIDCode] = entry;\n\n // ensure helper arrays needed for substructure search\n molecule.ensureHelperArrays(moleculesDB.OCL.Molecule.cHelperRings);\n if (!moleculeInfo.index) {\n entry.index = molecule.getIndex();\n } else {\n entry.index = moleculeInfo.index;\n }\n\n let molecularFormula;\n if (!moleculeInfo.mw) {\n molecularFormula = molecule.getMolecularFormula();\n entry.properties.mw = molecularFormula.relativeWeight;\n } else {\n entry.properties.mw = moleculeInfo.mw;\n }\n\n if (moleculesDB.computeProperties) {\n if (!molecularFormula) {\n molecularFormula = molecule.getMolecularFormula();\n }\n const properties = new moleculesDB.OCL.MoleculeProperties(molecule);\n entry.properties.em = molecularFormula.absoluteWeight;\n entry.properties.mf = molecularFormula.formula;\n entry.properties.acceptorCount = properties.acceptorCount;\n entry.properties.donorCount = properties.donorCount;\n entry.properties.logP = properties.logP;\n entry.properties.logS = properties.logS;\n entry.properties.polarSurfaceArea = properties.polarSurfaceArea;\n entry.properties.rotatableBondCount = properties.rotatableBondCount;\n entry.properties.stereoCenterCount = properties.stereoCenterCount;\n }\n }\n entry.data.push(data);\n}\n","export default function pushMoleculeInfo(moleculesDB, moleculeInfo, data = {}) {\n if (typeof moleculeInfo !== 'object') {\n throw new Error('pushMoleculeInfo requires an object as first parameter');\n }\n const Molecule = moleculesDB.OCL.Molecule;\n let molecule;\n if (moleculeInfo.molfile) {\n molecule = Molecule.fromMolfile(moleculeInfo.molfile);\n }\n if (moleculeInfo.smiles) molecule = Molecule.fromSmiles(moleculeInfo.smiles);\n if (moleculeInfo.idCode) {\n if (moleculesDB.db[moleculeInfo.idCode]) {\n molecule = moleculesDB.db[moleculeInfo.idCode].molecule;\n } else {\n molecule = Molecule.fromIDCode(\n moleculeInfo.idCode,\n moleculeInfo.coordinates || false,\n );\n }\n }\n\n if (molecule) {\n moleculesDB.pushEntry(molecule, data, moleculeInfo);\n }\n}\n","export default function appendColor(moleculesDB, options = {}) {\n const {\n dataLabel,\n propertyLabel,\n minValue,\n maxValue,\n minHue = 0,\n maxHue = 360,\n saturation = 65,\n lightness = 65,\n colorLabel = 'color',\n } = options;\n\n const db = moleculesDB.getDB();\n let values;\n if (dataLabel) {\n values = db\n .map((result) =>\n result.data.map((datum) => ({ value: datum[dataLabel], data: datum })),\n )\n .flat();\n } else if (propertyLabel) {\n values = db\n .map((result) =>\n result.data.map((datum) => ({\n value: result.properties[propertyLabel],\n data: datum,\n })),\n )\n .flat();\n } else {\n values = db\n .map((result) =>\n result.data.map((datum) => ({ value: undefined, data: datum })),\n )\n .flat();\n }\n\n if (minValue !== undefined) {\n values = values.forEach((value) => {\n if (value.value !== undefined && value.value < minValue) {\n value.value = minValue;\n }\n });\n }\n\n if (maxValue !== undefined) {\n values = values.forEach((value) => {\n if (value.value !== undefined && value.value > maxValue) {\n value.value = maxValue;\n }\n });\n }\n\n const definedValues = values.filter((value) => value.value !== undefined);\n const min = Math.min(...definedValues.map((value) => value.value));\n const max = Math.max(...definedValues.map((value) => value.value));\n\n for (let value of values) {\n if (value.value !== undefined) {\n value.data[colorLabel] = `hsl(${Math.floor(\n ((value.value - min) / (max - min)) * (maxHue - minHue) + minHue,\n )},${saturation}%,${lightness}%)`;\n } else {\n value.data.color = 'black';\n }\n }\n}\n","import { applyOneReactantReaction } from './utils/applyOneReactantReaction.js';\n\n/**\n * Create a tree of products based on reactions and reactants\n * @param {import('openchemlib').Molecule[]} reactants\n * @param {Array} reactions\n * @param {object} options\n * @param {number} [options.maxDepth=10]\n * @returns\n */\nexport function applyReactions(reactants, reactions, options = {}) {\n const { maxDepth = 10 } = options;\n const moleculesInfo = new Map();\n const processedMolecules = new Set();\n if (!reactants.length) {\n throw new Error('Can not extract OCL because there is no reactants');\n }\n const OCL = reactants[0].getOCL();\n\n reactions = appendOCLReaction(reactions, OCL);\n\n const results = [];\n\n let todoCurrentLevel = applyOneReactantReaction(reactants, reactions, {\n OCL,\n currentDepth: 0,\n moleculesInfo,\n processedMolecules,\n maxDepth,\n results,\n });\n\n do {\n const nexts = [];\n for (const todo of todoCurrentLevel) {\n nexts.push(todo());\n }\n todoCurrentLevel = nexts.flat();\n } while (todoCurrentLevel.length > 0);\n\n return results;\n}\n\nfunction appendOCLReaction(reactions, OCL) {\n reactions = JSON.parse(JSON.stringify(reactions)).filter(\n (reaction) => reaction.rxnCode,\n );\n for (const reaction of reactions) {\n reaction.oclReaction = OCL.ReactionEncoder.decode(reaction.rxnCode);\n }\n return reactions;\n}\n","import { getMF } from '../util/getMF';\n\nexport function fragmentAcyclicSingleBonds(molecule) {\n const OCL = molecule.getOCL();\n let atoms = [];\n for (let i = 0; i < molecule.getAllAtoms(); i++) {\n let atom = {};\n atoms.push(atom);\n atom.i = i;\n atom.links = []; // we will store connected atoms of broken bonds\n }\n\n let bonds = [];\n for (let i = 0; i < molecule.getAllBonds(); i++) {\n let bond = {};\n bonds.push(bond);\n bond.i = i;\n bond.order = molecule.getBondOrder(i);\n bond.atom1 = molecule.getBondAtom(0, i);\n bond.atom2 = molecule.getBondAtom(1, i);\n bond.type = molecule.getBondType(i);\n bond.isAromatic = molecule.isAromaticBond(i);\n bond.isRingBond = molecule.isRingBond(i);\n if (!bond.isAromatic && (bond.type & 0b11) === 1 && !bond.isRingBond) {\n bond.selected = true;\n atoms[bond.atom1].links.push(bond.atom2);\n atoms[bond.atom2].links.push(bond.atom1);\n }\n }\n\n // console.log(bonds);\n\n let brokenMolecule = molecule.getCompactCopy();\n for (let bond of bonds) {\n if (bond.selected) {\n brokenMolecule.markBondForDeletion(bond.i);\n }\n }\n\n brokenMolecule.deleteMarkedAtomsAndBonds();\n let fragmentMap = [];\n let nbFragments = brokenMolecule.getFragmentNumbers(fragmentMap);\n let results = [];\n for (let i = 0; i < nbFragments; i++) {\n let result = {};\n result.atomMap = [];\n let includeAtom = fragmentMap.map((id) => {\n return id === i;\n });\n let fragment = new OCL.Molecule(0, 0);\n let atomMap = [];\n brokenMolecule.copyMoleculeByAtoms(fragment, includeAtom, false, atomMap);\n // we will add some R groups at the level of the broken bonds\n for (let j = 0; j < atomMap.length; j++) {\n if (atomMap[j] > -1) {\n result.atomMap.push(j);\n if (atoms[j].links.length > 0) {\n for (let k = 0; k < atoms[j].links.length; k++) {\n fragment.addBond(atomMap[j], fragment.addAtom(154), 1);\n }\n }\n }\n }\n fragment.setFragment(false);\n result.idCode = fragment.getIDCode();\n result.mf = getMF(fragment).mf.replace(/R[1-9]?/, '');\n results.push(result);\n }\n\n return results;\n}\n","import { makeRacemic } from '../util/makeRacemic';\n\nexport function getAtomFeatures(originalMolecule, options = {}) {\n const OCL = originalMolecule.getOCL();\n\n const { sphere = 1 } = options;\n const fragment = new OCL.Molecule(0, 0);\n const results = [];\n\n for (\n let rootAtom = 0;\n rootAtom < originalMolecule.getAllAtoms();\n rootAtom++\n ) {\n let min = 0;\n let max = 0;\n let atomMask = new Array(originalMolecule.getAtoms());\n let atomList = new Array(originalMolecule.getAtoms());\n\n const molecule = originalMolecule.getCompactCopy();\n for (let currentSphere = 0; currentSphere <= sphere; currentSphere++) {\n if (max === 0) {\n atomList[max] = rootAtom;\n atomMask[rootAtom] = true;\n max++;\n } else {\n let newMax = max;\n for (let i = min; i < max; i++) {\n let atom = atomList[i];\n for (let j = 0; j < molecule.getAllConnAtoms(atom); j++) {\n let connAtom = molecule.getConnAtom(atom, j);\n if (!atomMask[connAtom]) {\n atomMask[connAtom] = true;\n atomList[newMax++] = connAtom;\n }\n }\n }\n min = max;\n max = newMax;\n }\n molecule.copyMoleculeByAtoms(fragment, atomMask, true, null);\n if (currentSphere === sphere) {\n makeRacemic(fragment);\n results.push(fragment.getCanonizedIDCode());\n }\n }\n }\n\n const atoms = {};\n for (let result of results) {\n if (!atoms[result]) {\n atoms[result] = 1;\n } else {\n atoms[result]++;\n }\n }\n\n return atoms;\n}\n","import { getDiastereotopicAtomIDsAndH } from './getDiastereotopicAtomIDsAndH.js';\n\n/**\n * Parse a molfile and returns an object containing the molecule, the map and the diaIDs\n * The map allows to reload properties assigned to the atom molfile\n * Pelase take care than numbering of atoms starts at 0 !\n * @param {import('openchemlib')} OCL - openchemlib library\n * @param {string} molfile\n * @returns\n */\nexport function getDiastereotopicAtomIDsFromMolfile(OCL, molfile) {\n const { map, molecule } = OCL.Molecule.fromMolfileWithAtomMap(molfile);\n\n const diaIDsArray = getDiastereotopicAtomIDsAndH(molecule);\n const diaIDs = {};\n\n for (let i = 0; i < map.length; i++) {\n diaIDs[map[i]] = { source: map[i], destination: i, ...diaIDsArray[i] };\n }\n\n return { map: diaIDs, molecule, diaIDs: diaIDsArray };\n}\n","import { getDiastereotopicAtomIDs } from '../diastereotopic/getDiastereotopicAtomIDs';\n\nimport { getHoseCodesFromDiastereotopicID } from './getHoseCodesFromDiastereotopicID';\n/**\n * Returns an array containing one entry per atom containing\n * diaID and hose code\n * @param {import('openchemlib').Molecule} molecule\n * @param {object} options\n */\n\nexport function getHoseCodesAndDiastereotopicIDs(molecule, options) {\n const diaIDs = getDiastereotopicAtomIDs(molecule).map((oclID) => ({\n oclID,\n }));\n const OCL = molecule.getOCL();\n // TODO: seems like a very slow approach\n diaIDs.forEach((diaID) => {\n const hoses = getHoseCodesFromDiastereotopicID(\n OCL.Molecule.fromIDCode(diaID.oclID),\n options,\n );\n diaID.hoses = [];\n let sphere = 0;\n for (const hose of hoses) {\n diaID.hoses.push({\n sphere: sphere++,\n oclID: hose,\n });\n }\n });\n return diaIDs;\n}\n","/**\n * Get the shortest path between each pair of atoms in the molecule\n * @param {import('openchemlib').Molecule} molecule\n * @param {object} [options={}]\n * @param {string} [opions.fromLabel='H']\n * @param {string} [opions.toLabel='H']\n * @param {string} [opions.maxLength=4]\n * @returns {Array} A matrix containing on each cell (i,j) the shortest path from atom i to atom j\n */\nexport function getShortestPaths(molecule, options = {}) {\n const OCL = molecule.getOCL();\n const { fromLabel = '', toLabel = '', maxLength = 3 } = options;\n\n let fromAtomicNumber = OCL.Molecule.getAtomicNoFromLabel(fromLabel);\n let toAtomicNumber = OCL.Molecule.getAtomicNoFromLabel(toLabel);\n\n const nbAtoms = molecule.getAllAtoms();\n let allShortestPaths = new Array(nbAtoms);\n for (let i = 0; i < nbAtoms; i++) {\n allShortestPaths[i] = new Array(nbAtoms);\n }\n\n for (let from = 0; from < nbAtoms; from++) {\n allShortestPaths[from][from] = [from];\n for (let to = from + 1; to < nbAtoms; to++) {\n if (\n (fromAtomicNumber === 0 ||\n molecule.getAtomicNo(from) === fromAtomicNumber) &&\n (toAtomicNumber === 0 || molecule.getAtomicNo(to) === toAtomicNumber)\n ) {\n let path = [];\n molecule.getPath(path, from, to, maxLength);\n if (path.length) {\n allShortestPaths[from][to] = path.slice();\n allShortestPaths[to][from] = path.reverse();\n } else {\n allShortestPaths[from][to] = null;\n allShortestPaths[to][from] = null;\n }\n } else {\n allShortestPaths[from][to] = null;\n allShortestPaths[to][from] = null;\n }\n }\n }\n\n return allShortestPaths;\n}\n","/**\n * Return the number of Carbonyl groups in a molecule or fragment\n * @param {import('openchemlib').Molecule} molecule\n * @returns {number} 'Number of Carbonyl groups'\n */\n\nexport function nbCHO(molecule) {\n let counter = 0;\n for (let i = 0; i < molecule.getAllAtoms(); i++) {\n // if there is not at least one hydrogen in the carbon atom there can not be a carbonyl group\n if (molecule.getAtomicNo(i) === 6 && molecule.getAllHydrogens(i) > 0) {\n let carbonyl = false;\n let carbonOrHydrogen = true;\n for (\n let neighbour = 0;\n neighbour < molecule.getConnAtoms(i);\n neighbour++\n ) {\n const neighbourAtom = molecule.getConnAtom(i, neighbour);\n\n const neighbourBond = molecule.getConnBond(i, neighbour);\n if (molecule.getAtomicNo(neighbourAtom) === 8) {\n if (molecule.getBondOrder(neighbourBond) === 2) {\n // If there is more than one carbonyl group on the same carbon atom they are not counted as carbonyl groups\n if (carbonyl) {\n carbonyl = false;\n break;\n }\n carbonyl = true;\n }\n } else if (\n // If there is not at least one carbon or hydrogen as neighbour atom it is not counted as Carbonyl group\n molecule.getAtomicNo(neighbourAtom) !== 6 &&\n molecule.getAtomicNo(neighbourAtom) !== 1\n ) {\n carbonOrHydrogen = false;\n }\n }\n if (carbonyl && carbonOrHydrogen) counter++;\n }\n }\n\n return counter;\n}\n","/**\n * Return the number of Nitrile groups in a molecule or fragment\n * @param {import('openchemlib').Molecule} molecule\n * @returns {number} 'Number of Nitrile groups'\n */\n\nexport function nbCN(molecule) {\n let counter = 0;\n for (let i = 0; i < molecule.getAllAtoms(); i++) {\n if (molecule.getAtomicNo(i) === 6) {\n let cn = false;\n let carbonOrHydrogen = true;\n for (\n let neighbour = 0;\n neighbour < molecule.getConnAtoms(i);\n neighbour++\n ) {\n const neighbourAtom = molecule.getConnAtom(i, neighbour);\n\n const neighbourBond = molecule.getConnBond(i, neighbour);\n\n if (\n molecule.getAtomicNo(neighbourAtom) === 7 &&\n molecule.getBondOrder(neighbourBond) === 3\n ) {\n // If there is more than one Nitrile group in the same carbon atome they are not counted as Nitrile groups\n if (cn) {\n cn = false;\n break;\n }\n cn = true;\n } else if (\n // If there is not at least one carbon or hydrogen as neighbour atom it is not counted as Nitrile group\n molecule.getAtomicNo(neighbourAtom) !== 6 &&\n molecule.getAtomicNo(neighbourAtom) !== 1\n ) {\n carbonOrHydrogen = false;\n }\n }\n\n if (cn && carbonOrHydrogen) counter++;\n }\n }\n\n return counter;\n}\n","/**\n * Return the number of Carboxyl groups in a molecule or fragment\n * @param {import('openchemlib').Molecule} molecule\n * @returns {number} 'Number of Carboxyl groups'\n */\n\nexport function nbCOOH(molecule) {\n let counter = 0;\n for (let i = 0; i < molecule.getAllAtoms(); i++) {\n if (molecule.getAtomicNo(i) === 6) {\n let carbonyl = false;\n let hydroxyl = false;\n let carbonOrHydrogen = true;\n for (\n let neighbour = 0;\n neighbour < molecule.getConnAtoms(i);\n neighbour++\n ) {\n const neighbourAtom = molecule.getConnAtom(i, neighbour);\n\n const neighbourBond = molecule.getConnBond(i, neighbour);\n if (molecule.getAtomicNo(neighbourAtom) === 8) {\n if (\n molecule.getBondOrder(neighbourBond) === 1 &&\n molecule.getAllHydrogens(neighbourAtom) > 0\n ) {\n // If there is more than a Hydroxyl in the same carbon atom it is not couted as Carboxyl group\n if (hydroxyl) {\n hydroxyl = false;\n break;\n }\n hydroxyl = true;\n } else if (molecule.getBondOrder(neighbourBond) === 2) {\n // If there is more than one carbonyl in the same carbon atom it is not count as Carboxyl group\n if (carbonyl) {\n carbonyl = false;\n break;\n }\n carbonyl = true;\n }\n } else if (\n // If there is not at least one carbon or hydrogen as neighbour atom it is not counted as Carboxyl group\n molecule.getAtomicNo(neighbourAtom) !== 6 &&\n molecule.getAtomicNo(neighbourAtom) !== 1\n ) {\n carbonOrHydrogen = false;\n }\n }\n if (carbonyl && hydroxyl && carbonOrHydrogen) counter++;\n }\n }\n return counter;\n}\n","/**\n * Return the number of Primary amine groups in a molecule or fragment\n * @param {import('openchemlib').Molecule} molecule\n * @returns {number} 'Number of Primary amine groups'\n */\n\nexport function nbNH2(molecule) {\n let counter = 0;\n for (let i = 0; i < molecule.getAllAtoms(); i++) {\n if (molecule.getAtomicNo(i) === 6) {\n let amine = false;\n let carbonOrHydrogen = true;\n for (\n let neighbour = 0;\n neighbour < molecule.getConnAtoms(i);\n neighbour++\n ) {\n const neighbourAtom = molecule.getConnAtom(i, neighbour);\n\n const neighbourBond = molecule.getConnBond(i, neighbour);\n\n if (\n molecule.getAtomicNo(neighbourAtom) === 7 &&\n molecule.getBondOrder(neighbourBond) === 1 &&\n molecule.getAllHydrogens(neighbourAtom) > 1\n ) {\n // If there is more than a Primary amine in the same carbon atom they are not couted as Primary amines groups\n if (amine) {\n amine = false;\n break;\n }\n amine = true;\n } else if (\n // If there is not at least one carbon or hydrogen as neighbour atom it is not counted as Primary amine group\n molecule.getAtomicNo(neighbourAtom) !== 6 &&\n molecule.getAtomicNo(neighbourAtom) !== 1\n ) {\n carbonOrHydrogen = false;\n }\n }\n if (amine && carbonOrHydrogen) counter++;\n }\n }\n\n return counter;\n}\n","/**\n * Return the number of Hydroxyl groups in a molecule or fragment\n * @param {import('openchemlib').Molecule} molecule\n * @returns {number} 'Number of Hydroxyl groups'\n */\n\nexport function nbOH(molecule) {\n let counter = 0;\n for (let i = 0; i < molecule.getAllAtoms(); i++) {\n if (molecule.getAtomicNo(i) === 6) {\n let carbonyl = false;\n let hydroxyl = false;\n let carbonOrHydrogen = true;\n for (\n let neighbour = 0;\n neighbour < molecule.getConnAtoms(i);\n neighbour++\n ) {\n const neighbourAtom = molecule.getConnAtom(i, neighbour);\n\n const neighbourBond = molecule.getConnBond(i, neighbour);\n if (molecule.getAtomicNo(neighbourAtom) === 8) {\n if (\n molecule.getBondOrder(neighbourBond) === 1 &&\n molecule.getAllHydrogens(neighbourAtom) > 0\n ) {\n // If there is more than a Hydroxyl in the same carbon atome they are not couted as Hydroxyl groups\n if (hydroxyl) {\n hydroxyl = false;\n break;\n }\n hydroxyl = true;\n } else if 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