@morscherlab/mint-sdk 1.3.9 → 1.4.0-beta.2

package/src/composables/useChemicalFormula.ts

@@ -1,301 +0,0 @@
-// Types
-export interface ParsedElement {
-  symbol: string
-  count: number
-}
-
-export interface FormulaParseResult {
-  elements: Record<string, number>
-  valid: boolean
-  error?: string
-}
-
-/** `coefficient` is a full-size multiplier at the start of a hydrate segment (the 5 in CuSO4·5H2O). */
-export type FormulaPartType = 'element' | 'subscript' | 'superscript' | 'paren' | 'dot' | 'charge' | 'coefficient'
-
-export interface FormulaPart {
-  type: FormulaPartType
-  text: string
-}
-
-// Every element with its standard atomic weight (mass number of the most stable isotope when none is defined)
-export const ATOMIC_WEIGHTS: Record<string, number> = {
-  H: 1.008, He: 4.003, Li: 6.941, Be: 9.012, B: 10.81,
-  C: 12.011, N: 14.007, O: 15.999, F: 18.998, Ne: 20.180,
-  Na: 22.990, Mg: 24.305, Al: 26.982, Si: 28.086, P: 30.974,
-  S: 32.065, Cl: 35.453, Ar: 39.948, K: 39.098, Ca: 40.078,
-  Sc: 44.956, Ti: 47.867, V: 50.942, Cr: 51.996,
-  Mn: 54.938, Fe: 55.845, Co: 58.933, Ni: 58.693, Cu: 63.546,
-  Zn: 65.38, Ga: 69.723, Ge: 72.630, As: 74.922, Se: 78.971,
-  Br: 79.904, Kr: 83.798, Rb: 85.468, Sr: 87.62, Y: 88.906,
-  Zr: 91.224, Nb: 92.906, Mo: 95.95, Tc: 98, Ru: 101.07,
-  Rh: 102.906, Pd: 106.42, Ag: 107.868, Cd: 112.414, In: 114.818,
-  Sn: 118.710, Sb: 121.760, Te: 127.60, I: 126.904, Xe: 131.293,
-  Cs: 132.905, Ba: 137.327, La: 138.905, Ce: 140.116, Pr: 140.908,
-  Nd: 144.242, Pm: 145, Sm: 150.36, Eu: 151.964, Gd: 157.25,
-  Tb: 158.925, Dy: 162.500, Ho: 164.930, Er: 167.259, Tm: 168.934,
-  Yb: 173.045, Lu: 174.967, Hf: 178.49, Ta: 180.948, W: 183.84,
-  Re: 186.207, Os: 190.23, Ir: 192.217, Pt: 195.084, Au: 196.967,
-  Hg: 200.592, Tl: 204.38, Pb: 207.2, Bi: 208.980, Po: 209,
-  At: 210, Rn: 222, Fr: 223, Ra: 226, Ac: 227,
-  Th: 232.038, Pa: 231.036, U: 238.029, Np: 237, Pu: 244,
-  Am: 243, Cm: 247, Bk: 247, Cf: 251, Es: 252,
-  Fm: 257, Md: 258, No: 259, Lr: 266, Rf: 267,
-  Db: 268, Sg: 269, Bh: 270, Hs: 277, Mt: 278,
-  Ds: 281, Rg: 282, Cn: 285, Nh: 286, Fl: 289,
-  Mc: 290, Lv: 293, Ts: 294, Og: 294,
-}
-
-function parseFormulaSegment(formula: string): FormulaParseResult {
-  const elements: Record<string, number> = {}
-  const stack: Record<string, number>[] = [{}]
-  let i = 0
-
-  while (i < formula.length) {
-    const ch = formula[i]
-
-    if (ch === '(') {
-      stack.push({})
-      i++
-    } else if (ch === ')') {
-      if (stack.length < 2) {
-        return { elements: {}, valid: false, error: 'Unmatched closing parenthesis' }
-      }
-      i++
-      // Read multiplier after closing paren
-      let numStr = ''
-      while (i < formula.length && /\d/.test(formula[i])) {
-        numStr += formula[i]
-        i++
-      }
-      const multiplier = numStr ? parseInt(numStr, 10) : 1
-      const top = stack.pop()!
-      const current = stack[stack.length - 1]
-      for (const [el, count] of Object.entries(top)) {
-        current[el] = (current[el] || 0) + count * multiplier
-      }
-    } else if (/[A-Z]/.test(ch)) {
-      // Element symbol: uppercase letter optionally followed by lowercase
-      let symbol = ch
-      i++
-      while (i < formula.length && /[a-z]/.test(formula[i])) {
-        symbol += formula[i]
-        i++
-      }
-      // Validate element
-      if (!(symbol in ATOMIC_WEIGHTS)) {
-        return { elements: {}, valid: false, error: `Unknown element: ${symbol}` }
-      }
-      // Read count
-      let numStr = ''
-      while (i < formula.length && /\d/.test(formula[i])) {
-        numStr += formula[i]
-        i++
-      }
-      const count = numStr ? parseInt(numStr, 10) : 1
-      const current = stack[stack.length - 1]
-      current[symbol] = (current[symbol] || 0) + count
-    } else {
-      return { elements: {}, valid: false, error: `Unexpected character: ${ch}` }
-    }
-  }
-
-  if (stack.length !== 1) {
-    return { elements: {}, valid: false, error: 'Unmatched opening parenthesis' }
-  }
-
-  Object.assign(elements, stack[0])
-  return { elements, valid: true }
-}
-
-/** Parses and renders chemical formulas, computes molecular weight, and generates rich-text formula parts. */
-export function useChemicalFormula() {
-  function parseFormula(formula: string): FormulaParseResult {
-    const trimmed = formula.trim()
-    if (!trimmed) {
-      return { elements: {}, valid: false, error: 'Empty formula' }
-    }
-
-    // A trailing charge (SO4^2-, Fe2+, NH4+) does not change the composition. Like renderFormulaParts,
-    // digits before a bare sign are the charge only on a lone element (Fe2+); otherwise they are a
-    // subscript and the sign a unit charge (NH4+). Write Hg2^2+ for any other multiple charge.
-    const body = trimmed.replace(/^([A-Z][a-z]?)\d*[+-]$/, '$1').replace(/(\^\d*)?[+-]$/, '')
-    if (!body) {
-      return { elements: {}, valid: false, error: 'Empty formula' }
-    }
-    // Split on hydrate separator (·, . or *)
-    const parts = body.split(/[·.*]/)
-    const combined: Record<string, number> = {}
-
-    for (const part of parts) {
-      const segment = part.trim()
-      if (!segment) continue
-
-      // Check for leading coefficient (e.g., 5H2O)
-      let coefficient = 1
-      let formulaStr = segment
-      const coeffMatch = segment.match(/^(\d+)([A-Z].*)$/)
-      if (coeffMatch) {
-        coefficient = parseInt(coeffMatch[1], 10)
-        formulaStr = coeffMatch[2]
-      }
-
-      const result = parseFormulaSegment(formulaStr)
-      if (!result.valid) {
-        return result
-      }
-
-      for (const [el, count] of Object.entries(result.elements)) {
-        combined[el] = (combined[el] || 0) + count * coefficient
-      }
-    }
-
-    return { elements: combined, valid: true }
-  }
-
-  function calculateMW(elements: Record<string, number>): number {
-    let mw = 0
-    for (const [el, count] of Object.entries(elements)) {
-      const weight = ATOMIC_WEIGHTS[el]
-      if (weight !== undefined) {
-        mw += weight * count
-      }
-    }
-    return Math.round(mw * 1000) / 1000
-  }
-
-  function renderFormulaParts(formula: string): FormulaPart[] {
-    const parts: FormulaPart[] = []
-    const trimmed = formula.trim()
-    let i = 0
-
-    while (i < trimmed.length) {
-      const ch = trimmed[i]
-
-      // Hydrate dot separator
-      if (ch === '·' || (ch === '.' && i > 0 && /\d/.test(trimmed[i - 1]) && i + 1 < trimmed.length && /\d/.test(trimmed[i + 1]))) {
-        // Disambiguate: '.' as hydrate separator only if followed by a digit then uppercase
-        // For simplicity, treat '·' always as dot
-        if (ch === '·') {
-          parts.push({ type: 'dot', text: '·' })
-          i++
-          continue
-        }
-      }
-
-      // Parentheses
-      if (ch === '(' || ch === ')') {
-        parts.push({ type: 'paren', text: ch })
-        i++
-        // After ')' check for subscript number
-        if (ch === ')' && i < trimmed.length && /\d/.test(trimmed[i])) {
-          let numStr = ''
-          while (i < trimmed.length && /\d/.test(trimmed[i])) {
-            numStr += trimmed[i]
-            i++
-          }
-          parts.push({ type: 'subscript', text: numStr })
-        }
-        continue
-      }
-
-      // Charge notation: ^2+, ^2-, 2+, 2- at end, or +, -
-      if (ch === '^') {
-        i++
-        let chargeStr = ''
-        while (i < trimmed.length && /[\d+\-]/.test(trimmed[i])) {
-          chargeStr += trimmed[i]
-          i++
-        }
-        if (chargeStr) {
-          parts.push({ type: 'charge', text: chargeStr })
-        }
-        continue
-      }
-
-      // Element symbol: uppercase followed by optional lowercase
-      if (/[A-Z]/.test(ch)) {
-        let symbol = ch
-        i++
-        while (i < trimmed.length && /[a-z]/.test(trimmed[i])) {
-          symbol += trimmed[i]
-          i++
-        }
-        parts.push({ type: 'element', text: symbol })
-
-        // Check for subscript number after element
-        if (i < trimmed.length && /\d/.test(trimmed[i])) {
-          let numStr = ''
-          while (i < trimmed.length && /\d/.test(trimmed[i])) {
-            numStr += trimmed[i]
-            i++
-          }
-          parts.push({ type: 'subscript', text: numStr })
-
-          // On a lone element the digits before a trailing sign are the charge (Fe2+);
-          // elsewhere they stay a subscript and the sign renders as a unit charge (NH4+).
-          if (parts.length === 2 && i === trimmed.length - 1 && (trimmed[i] === '+' || trimmed[i] === '-')) {
-            parts.push({ type: 'charge', text: numStr + trimmed[i] })
-            parts.splice(parts.length - 2, 1) // Remove the subscript
-            i++
-            continue
-          }
-        }
-        continue
-      }
-
-      // Leading digit (hydrate coefficient like 5H2O)
-      if (/\d/.test(ch)) {
-        let numStr = ''
-        while (i < trimmed.length && /\d/.test(trimmed[i])) {
-          numStr += trimmed[i]
-          i++
-        }
-        // Could be a subscript or coefficient depending on context
-        // If next char is uppercase, it's a coefficient (render as element-like text)
-        // If at end or followed by +/-, it's a charge component
-        const prev = parts[parts.length - 1]
-        if (i < trimmed.length && (trimmed[i] === '+' || trimmed[i] === '-')) {
-          parts.push({ type: 'charge', text: numStr + trimmed[i] })
-          i++
-        } else if (!prev || prev.type === 'dot') {
-          parts.push({ type: 'coefficient', text: numStr })
-        } else {
-          parts.push({ type: 'subscript', text: numStr })
-        }
-        continue
-      }
-
-      // Standalone + or - (charge)
-      if (ch === '+' || ch === '-') {
-        parts.push({ type: 'charge', text: ch })
-        i++
-        continue
-      }
-
-      // Dot or asterisk as hydrate separator
-      if (ch === '.' || ch === '*') {
-        parts.push({ type: 'dot', text: '·' })
-        i++
-        continue
-      }
-
-      // Skip whitespace
-      if (/\s/.test(ch)) {
-        i++
-        continue
-      }
-
-      // Unknown character, skip
-      i++
-    }
-
-    return parts
-  }
-
-  return {
-    parseFormula,
-    calculateMW,
-    renderFormulaParts,
-  }
-}

package/src/composables/useDoseCalculator.ts

@@ -1,370 +0,0 @@
-import {
-  useConcentrationUnits,
-  type ConcentrationValue,
-  type MolarityUnit,
-  type MassVolumeUnit,
-} from './useConcentrationUnits'
-
-// Volume units
-export type VolumeUnit = 'µL' | 'mL' | 'L'
-
-export interface VolumeValue {
-  value: number
-  unit: VolumeUnit
-}
-
-// Dilution calculation types
-export interface DilutionParams {
-  stockConcentration: ConcentrationValue
-  finalConcentration: ConcentrationValue
-  finalVolume: VolumeValue
-}
-
-export interface DilutionResult {
-  stockVolume: VolumeValue
-  diluentVolume: VolumeValue
-  dilutionFactor: number
-  valid: boolean
-  error?: string
-}
-
-// Serial dilution types
-export interface SerialDilutionParams {
-  startingConcentration: ConcentrationValue
-  dilutionFactor: number
-  numberOfDilutions: number
-  volumePerWell: VolumeValue
-}
-
-export interface SerialDilutionStep {
-  stepNumber: number
-  concentration: ConcentrationValue
-  transferVolume: VolumeValue
-  diluentVolume: VolumeValue
-}
-
-export interface SerialDilutionResult {
-  steps: SerialDilutionStep[]
-  totalStockVolume: VolumeValue
-  valid: boolean
-  error?: string
-}
-
-// Conversion types
-export interface ConversionResult {
-  result: ConcentrationValue
-  valid: boolean
-  error?: string
-}
-
-// Well concentration for plate integration
-export interface WellConcentration {
-  wellId: string
-  concentration: ConcentrationValue
-  volume?: VolumeValue
-}
-
-export interface UseDoseCalculatorReturn {
-  volumeUnits: VolumeUnit[]
-  calculateDilution: (params: DilutionParams) => DilutionResult
-  calculateSerialDilution: (params: SerialDilutionParams) => SerialDilutionResult
-  convertMassToMolar: (
-    mass: number,
-    massUnit: MassVolumeUnit,
-    mw: number
-  ) => ConcentrationValue
-  convertMolarToMass: (
-    molar: number,
-    molarUnit: MolarityUnit,
-    mw: number
-  ) => ConcentrationValue
-  convertVolume: (value: number, from: VolumeUnit, to: VolumeUnit) => number
-  formatVolume: (volume: VolumeValue, precision?: number) => string
-  generateWellConcentrations: (
-    result: SerialDilutionResult,
-    wellIds: string[]
-  ) => WellConcentration[]
-}
-
-const VOLUME_UNITS: VolumeUnit[] = ['µL', 'mL', 'L']
-
-const VOLUME_FACTORS: Record<VolumeUnit, number> = {
-  'µL': 1e-6,
-  'mL': 1e-3,
-  'L': 1,
-}
-
-/** Calculates single dilutions, serial dilution series, and plate-filling volumes for dose-response experiments. */
-export function useDoseCalculator(): UseDoseCalculatorReturn {
-  const { convert } = useConcentrationUnits()
-
-  function convertVolume(value: number, from: VolumeUnit, to: VolumeUnit): number {
-    if (from === to) return value
-    const baseValue = value * VOLUME_FACTORS[from]
-    return baseValue / VOLUME_FACTORS[to]
-  }
-
-  function formatVolume(volume: VolumeValue, precision: number = 3): string {
-    const { value, unit } = volume
-    if (value === 0) return `0 ${unit}`
-
-    let formattedValue: string
-    if (Math.abs(value) >= 1000) {
-      formattedValue = value.toExponential(precision - 1)
-    } else if (Math.abs(value) < 0.001) {
-      formattedValue = value.toExponential(precision - 1)
-    } else {
-      formattedValue = value.toPrecision(precision)
-    }
-
-    // Remove trailing zeros
-    formattedValue = formattedValue.replace(/\.?0+$/, '')
-    formattedValue = formattedValue.replace(/\.?0+e/, 'e')
-
-    return `${formattedValue} ${unit}`
-  }
-
-  function calculateDilution(params: DilutionParams): DilutionResult {
-    const { stockConcentration, finalConcentration, finalVolume } = params
-
-    // Validate inputs
-    if (stockConcentration.value <= 0) {
-      return {
-        stockVolume: { value: 0, unit: 'µL' },
-        diluentVolume: { value: 0, unit: 'µL' },
-        dilutionFactor: 0,
-        valid: false,
-        error: 'Stock concentration must be positive',
-      }
-    }
-
-    if (finalConcentration.value <= 0) {
-      return {
-        stockVolume: { value: 0, unit: 'µL' },
-        diluentVolume: { value: 0, unit: 'µL' },
-        dilutionFactor: 0,
-        valid: false,
-        error: 'Final concentration must be positive',
-      }
-    }
-
-    if (finalVolume.value <= 0) {
-      return {
-        stockVolume: { value: 0, unit: 'µL' },
-        diluentVolume: { value: 0, unit: 'µL' },
-        dilutionFactor: 0,
-        valid: false,
-        error: 'Final volume must be positive',
-      }
-    }
-
-    // Convert concentrations to same unit
-    const convertedFinal = convert(
-      finalConcentration.value,
-      finalConcentration.unit,
-      stockConcentration.unit
-    )
-
-    if (convertedFinal === null) {
-      return {
-        stockVolume: { value: 0, unit: 'µL' },
-        diluentVolume: { value: 0, unit: 'µL' },
-        dilutionFactor: 0,
-        valid: false,
-        error: 'Cannot convert between concentration units. Provide molecular weight for mass↔molarity conversion.',
-      }
-    }
-
-    // Check that stock is more concentrated than final
-    if (convertedFinal >= stockConcentration.value) {
-      return {
-        stockVolume: { value: 0, unit: 'µL' },
-        diluentVolume: { value: 0, unit: 'µL' },
-        dilutionFactor: 0,
-        valid: false,
-        error: 'Stock concentration must be higher than final concentration',
-      }
-    }
-
-    // Calculate using C1V1 = C2V2
-    const dilutionFactor = stockConcentration.value / convertedFinal
-    const finalVolumeInL = convertVolume(finalVolume.value, finalVolume.unit, 'L')
-    const stockVolumeInL = finalVolumeInL / dilutionFactor
-    const diluentVolumeInL = finalVolumeInL - stockVolumeInL
-
-    // Convert to appropriate unit (µL for small volumes, mL for larger)
-    let outputUnit: VolumeUnit = 'µL'
-    if (stockVolumeInL >= 0.001) outputUnit = 'mL'
-    if (stockVolumeInL >= 1) outputUnit = 'L'
-
-    return {
-      stockVolume: {
-        value: convertVolume(stockVolumeInL, 'L', outputUnit),
-        unit: outputUnit,
-      },
-      diluentVolume: {
-        value: convertVolume(diluentVolumeInL, 'L', outputUnit),
-        unit: outputUnit,
-      },
-      dilutionFactor,
-      valid: true,
-    }
-  }
-
-  function calculateSerialDilution(params: SerialDilutionParams): SerialDilutionResult {
-    const { startingConcentration, dilutionFactor, numberOfDilutions, volumePerWell } = params
-
-    // Validate inputs
-    if (startingConcentration.value <= 0) {
-      return {
-        steps: [],
-        totalStockVolume: { value: 0, unit: 'µL' },
-        valid: false,
-        error: 'Starting concentration must be positive',
-      }
-    }
-
-    if (dilutionFactor <= 1) {
-      return {
-        steps: [],
-        totalStockVolume: { value: 0, unit: 'µL' },
-        valid: false,
-        error: 'Dilution factor must be greater than 1',
-      }
-    }
-
-    if (numberOfDilutions < 1) {
-      return {
-        steps: [],
-        totalStockVolume: { value: 0, unit: 'µL' },
-        valid: false,
-        error: 'Number of dilutions must be at least 1',
-      }
-    }
-
-    if (volumePerWell.value <= 0) {
-      return {
-        steps: [],
-        totalStockVolume: { value: 0, unit: 'µL' },
-        valid: false,
-        error: 'Volume per well must be positive',
-      }
-    }
-
-    const steps: SerialDilutionStep[] = []
-    let currentConcentration = startingConcentration.value
-    const transferVolume = volumePerWell.value / (dilutionFactor - 1)
-    const diluentVolume = volumePerWell.value - transferVolume
-
-    for (let i = 0; i < numberOfDilutions; i++) {
-      steps.push({
-        stepNumber: i + 1,
-        concentration: {
-          value: currentConcentration,
-          unit: startingConcentration.unit,
-        },
-        transferVolume: {
-          value: i === 0 ? volumePerWell.value : transferVolume,
-          unit: volumePerWell.unit,
-        },
-        diluentVolume: {
-          value: i === 0 ? 0 : diluentVolume,
-          unit: volumePerWell.unit,
-        },
-      })
-      currentConcentration /= dilutionFactor
-    }
-
-    // Total stock needed for first well
-    const totalStockVolume: VolumeValue = {
-      value: volumePerWell.value + (transferVolume * (numberOfDilutions - 1)),
-      unit: volumePerWell.unit,
-    }
-
-    return {
-      steps,
-      totalStockVolume,
-      valid: true,
-    }
-  }
-
-  function convertMassToMolar(
-    mass: number,
-    massUnit: MassVolumeUnit,
-    mw: number
-  ): ConcentrationValue {
-    // Convert mass to g/mL, then to M using MW
-    const converted = convert(mass, massUnit, 'µM', mw)
-    if (converted !== null) {
-      return { value: converted, unit: 'µM' }
-    }
-    // Fallback to manual calculation
-    // mass (g/mL) / MW (g/mol) = mol/L = M
-    const massInGML = mass * getMassVolumeFactor(massUnit)
-    const molarConc = massInGML / mw
-    return { value: molarConc * 1e6, unit: 'µM' }
-  }
-
-  function convertMolarToMass(
-    molar: number,
-    molarUnit: MolarityUnit,
-    mw: number
-  ): ConcentrationValue {
-    // Convert M to mass using MW
-    const converted = convert(molar, molarUnit, 'µg/mL', mw)
-    if (converted !== null) {
-      return { value: converted, unit: 'µg/mL' }
-    }
-    // Fallback to manual calculation
-    // mol/L * MW (g/mol) = g/L = mg/mL
-    const molarInM = molar * getMolarityFactor(molarUnit)
-    const massConc = molarInM * mw * 1e6 // µg/mL
-    return { value: massConc, unit: 'µg/mL' }
-  }
-
-  function getMassVolumeFactor(unit: MassVolumeUnit): number {
-    const factors: Record<MassVolumeUnit, number> = {
-      'pg/mL': 1e-12,
-      'ng/mL': 1e-9,
-      'µg/mL': 1e-6,
-      'mg/mL': 1e-3,
-      'g/mL': 1,
-    }
-    return factors[unit]
-  }
-
-  function getMolarityFactor(unit: MolarityUnit): number {
-    const factors: Record<MolarityUnit, number> = {
-      'pM': 1e-12,
-      'nM': 1e-9,
-      'µM': 1e-6,
-      'mM': 1e-3,
-      'M': 1,
-    }
-    return factors[unit]
-  }
-
-  function generateWellConcentrations(
-    result: SerialDilutionResult,
-    wellIds: string[]
-  ): WellConcentration[] {
-    if (!result.valid || result.steps.length === 0) return []
-
-    return result.steps.slice(0, wellIds.length).map((step, index) => ({
-      wellId: wellIds[index],
-      concentration: step.concentration,
-      volume: step.transferVolume,
-    }))
-  }
-
-  return {
-    volumeUnits: VOLUME_UNITS,
-    calculateDilution,
-    calculateSerialDilution,
-    convertMassToMolar,
-    convertMolarToMass,
-    convertVolume,
-    formatVolume,
-    generateWellConcentrations,
-  }
-}