A handy notebook to perform molarity conversions using Sympy

molarity.ipynb

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   "source": [
    "from sympy.physics.units import mol, g, L, milli, micro, mg, ug, mL, Quantity, convert_to\n",
    "from sympy import Symbol\n",
    "from sympy.physics.units.systems import SI\n",
    "from sympy.core.numbers import Rational\n",
    "from sympy.physics.units import Dimension\n",
    "import sympy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "41315a46-05f3-4862-80ef-c8c0551a7f73",
   "metadata": {},
   "outputs": [],
   "source": [
    "ul = uL = microliter = microliters = Quantity(\"microliter\", abbrev=\"uL\", latex_repr=r\"\\mu\\text{L}\")\n",
    "ul.set_global_relative_scale_factor(micro, L)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "0c36ead6-11a0-4428-9173-4b4851365995",
   "metadata": {},
   "outputs": [],
   "source": [
    "mmol = millimol = mmole = millimole = Quantity(\"millimole\", abbrev=\"mmol\")\n",
    "mmol.set_global_relative_scale_factor(milli, L)\n",
    "\n",
    "umol = umole = micromol = micromole = Quantity(\"micromole\", abbrev=\"umol\", latex_repr=r\"\\mu\\text{mol}\")\n",
    "umol.set_global_relative_scale_factor(micro, mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "0e5f5df1-e8d0-41ab-9457-9f12459bf5ef",
   "metadata": {},
   "outputs": [],
   "source": [
    "M = molar = Quantity(\"molar\", abbrev=\"M\")\n",
    "molar.set_global_dimension(mol.dimension / L.dimension)\n",
    "SI.set_quantity_dimension(molar, mol.dimension / L.dimension)\n",
    "SI.set_quantity_scale_factor(molar, mol / L)\n",
    "\n",
    "mM = millimolar = Quantity(\"millimolar\", abbrev=\"mM\")\n",
    "millimolar.set_global_relative_scale_factor(milli, molar)\n",
    "\n",
    "uM = micromolar = Quantity(\"millimolar\", abbrev=\"uM\", latex_repr=r\"\\mu\\text{M}\")\n",
    "micromolar.set_global_relative_scale_factor(micro, molar)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "941ae744-5921-4e25-9131-1c5e902f44fd",
   "metadata": {},
   "outputs": [],
   "source": [
    "def molecular_weight(num):\n",
    "    return num * g / mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "12b7ba93-5132-4da9-9821-a8f4ecf60440",
   "metadata": {},
   "outputs": [],
   "source": [
    "def molar_to_gram_per_liter(MW, concentration):\n",
    "    x = MW * concentration\n",
    "    return convert_to(x, [g, L])\n",
    "\n",
    "def gram_per_liter_to_molar(MW, concentration):\n",
    "    x = concentration / MW\n",
    "    return convert_to(x, [M])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "9f171254-3137-4116-8f42-af62b2592112",
   "metadata": {},
   "outputs": [],
   "source": [
    "class Compound(object):\n",
    "\n",
    "    def __init__(self, name, MW, DMSO):\n",
    "        self.name = name\n",
    "        if isinstance(MW, (float, int)):\n",
    "            self.MW = molecular_weight(MW)\n",
    "        else:\n",
    "            assert isinstance(MW, sympy.Expr)\n",
    "            self.MW = MW\n",
    "\n",
    "        self.DMSO = DMSO\n",
    "        return\n",
    "\n",
    "    def __repr__(self):\n",
    "        return f\"Compound({repr(self.name)}, {repr(self.MW)})\"\n",
    "\n",
    "    def molar_to_gram_per_liter(self, concentration):\n",
    "        return molar_to_gram_per_liter(self.MW, concentration)\n",
    "\n",
    "    def gram_per_liter_to_molar(self, concentration):\n",
    "        return gram_per_liter_to_molar(self.MW, concentration)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "9763ce73-19e9-49f9-a832-d2287ecbef2d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Compound('camalexin', 200.26*gram/mole)"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "camalexin = Compound(\n",
    "    \"camalexin\",\n",
    "    MW = 200.26 * g / mol,\n",
    "    DMSO = 20 * mg / mL # 40?\n",
    ")\n",
    "\n",
    "camalexin"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "31533591-20eb-46a1-adfa-d42749609b70",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/latex": [
       "$\\displaystyle 249.675421951463 \\mu\\text{M}$"
      ],
      "text/plain": [
       "249.675421951463*millimolar"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "convert_to(camalexin.gram_per_liter_to_molar(50 * ug / mL), [uM])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "345dc28c-a281-4a5e-9025-c1bf478e7aa4",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/latex": [
       "$\\displaystyle \\frac{50.065 \\mu\\text{g}}{\\text{milliliter}}$"
      ],
      "text/plain": [
       "50.065*microgram/milliliter"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "convert_to(camalexin.molar_to_gram_per_liter(250 * uM), [ug, mL])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "95abf8bd-d1b3-43d7-b6a5-5769a7984494",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Compound('gossypol', 578.6*gram/mole)"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gossypol = Compound(\n",
    "    \"gossypol\",\n",
    "    MW =  578.6 * g / mol,\n",
    "    DMSO = 39.22 * mg / mL\n",
    ")\n",
    "\n",
    "gossypol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "2ee7dd20-b856-4cfb-846f-687dcd606849",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/latex": [
       "$\\displaystyle 34.5661942620118 \\mu\\text{M}$"
      ],
      "text/plain": [
       "34.5661942620118*millimolar"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "convert_to(gossypol.gram_per_liter_to_molar(20 * ug / mL), [uM])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "e656138d-08a2-4101-9e85-96258f4cae93",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/latex": [
       "$\\displaystyle \\frac{14.465 \\mu\\text{g}}{\\text{milliliter}}$"
      ],
      "text/plain": [
       "14.465*microgram/milliliter"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "convert_to(gossypol.molar_to_gram_per_liter(25 * uM), [ug, mL])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "2e239494-dab1-44ea-9b4a-48c055c87cb6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Compound('scopoletin', 192.17*gram/mole)"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "scopoletin = Compound(\n",
    "    \"scopoletin\",\n",
    "    MW = 192.17 * g / mol,\n",
    "    DMSO = 38 * mg/mL\n",
    ")\n",
    "\n",
    "scopoletin"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "ef46652e-9770-4c93-8934-a4ecec11d92a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/latex": [
       "$\\displaystyle 0.520372586772129 \\mu\\text{M}$"
      ],
      "text/plain": [
       "0.520372586772129*millimolar"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "convert_to(scopoletin.gram_per_liter_to_molar(0.1 * ug / mL), [uM])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "522fbcf3-7a40-4de7-8bf6-92d9bdbf8c6e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/latex": [
       "$\\displaystyle \\frac{19.217 \\mu\\text{g}}{\\text{milliliter}}$"
      ],
      "text/plain": [
       "19.217*microgram/milliliter"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "convert_to(scopoletin.molar_to_gram_per_liter(100 * uM), [ug, mL])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "d2d5aadb-fca4-48de-a6eb-c105123dec70",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Compound('resveratrol', 228.24*gram/mole)"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "resveratrol = Compound(\n",
    "    \"resveratrol\",\n",
    "    MW =  228.24 * g / mol,\n",
    "    DMSO = 50 * mg/mL\n",
    ")\n",
    "\n",
    "resveratrol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "1c6e0297-e4fe-42b8-8035-84c4fe35ff6e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/latex": [
       "$\\displaystyle 438.13529617946 \\mu\\text{M}$"
      ],
      "text/plain": [
       "438.13529617946*millimolar"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "convert_to(resveratrol.gram_per_liter_to_molar(100 * ug / mL), [uM])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "09d66367-a4fd-4e20-b536-c5a5853642cf",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/latex": [
       "$\\displaystyle \\frac{13.6944 \\mu\\text{g}}{\\text{milliliter}}$"
      ],
      "text/plain": [
       "13.6944*microgram/milliliter"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "convert_to(resveratrol.molar_to_gram_per_liter(60 * uM), [ug, mL])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "90613377-62a3-4e0c-954d-c749b2b44d63",
   "metadata": {},
   "outputs": [],
   "source": []
  },
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   "cell_type": "code",
   "execution_count": null,
   "id": "cf879e55-a515-4a41-bf65-1cf0309bc954",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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