diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b934d85..4268c05 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,12 +7,12 @@ on: branches: [ main ] jobs: - test: + code-tests: runs-on: ${{ matrix.os }} strategy: matrix: os: [ubuntu-latest, windows-latest, macos-latest] - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.10", "3.12"] steps: - uses: actions/checkout@v4 @@ -28,10 +28,15 @@ jobs: - name: Install dependencies run: uv sync --dev - - name: Run tests with coverage - run: uv run pytest -v --cov=src --cov-report=term --cov-report=xml + - name: Run tests with coverage (as defined in pyproject.toml) + run: uv run pytest - lint: + - name: Upload coverage reports to Codecov + uses: codecov/codecov-action@v5 + with: + token: ${{ secrets.CODECOV_TOKEN }} + + code-quality: runs-on: ubuntu-latest steps: @@ -44,6 +49,9 @@ jobs: - name: Install dependencies run: uv sync --dev - + - name: Run ruff linting run: uv run ruff check src tests + + - name: Run mypy type checking + run: uv run mypy src tests --show-error-codes --show-error-context diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 032042e..9af6341 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -36,7 +36,7 @@ jobs: - name: Smoke test (wheel) run: | WHEEL=$(ls dist/*.whl) - uv run --isolated --no-project -p 3.12 --with "$WHEEL" python -c "from chemformula import ChemFormula; print('Import successful'); water=ChemFormula('H2O'); print('Formula Weight:', water.formula_weight, 'g/mol')" + uv run --isolated --no-project -p 3.13 --with "$WHEEL" python -c "from chemformula import ChemFormula; print('Import successful'); water=ChemFormula('H2O'); print('Formula Weight:', water.formula_weight, 'g/mol')" - name: Publish to PyPI run: uv publish --trusted-publishing always diff --git a/README.md b/README.md index cbdb523..8370cfc 100644 --- a/README.md +++ b/README.md @@ -2,13 +2,14 @@ ![PyPI Version](https://img.shields.io/pypi/v/ChemFormula) ![CI](https://github.com/molshape/ChemFormula/actions/workflows/ci.yml/badge.svg) +[![codecov](https://codecov.io/github/molshape/ChemFormula/graph/badge.svg?token=ARYINWF6KR)](https://codecov.io/github/molshape/ChemFormula) \ ![Python Versions](https://img.shields.io/pypi/pyversions/ChemFormula) ![License](https://img.shields.io/github/license/molshape/ChemFormula) \ ![GitHub stars](https://img.shields.io/github/stars/molshape/ChemFormula)
-Table of Content +Table of Contents 1. [Description](#description) 2. [How to install and uninstall?](#how-to-install-and-uninstall) @@ -24,21 +25,28 @@ **ChemFormula** is a Python class for working with chemical formulas. It allows parsing chemical formulas and generating predefined (LaTeX, HTML) or customized formatted output strings, e. g. [Cu(NH3)4]SO4⋅H2O. **ChemFormula** is also calculating the formula weight and thus enabling stoichiometric calculations with chemical formula objects. Atomic weights are based on IUPAC recommendations (see [Atomic Weight Data](#atomic-weight-data)). -## How to install and uninstall? +## How to install and uninstall **ChemFormula** can be installed from the [Python Package Index (PyPI)](https://pypi.org/) repository by calling - pip install chemformula + pip install chemformula + +or + + uv add chemformula In order to uninstall **ChemFormula** from your local environment use - pip uninstall chemformula + pip uninstall chemformula + +or + uv remove chemformula ## Dependencies **ChemFormula** uses the [casregnum package](https://pypi.org/project/casregnum/) to manage CAS Registry Numbers®. The corresponding properties of the `CAS` class are therefore inherited to the ```ChemFormula``` class. -## How to use? +## How to use **ChemFormula** provides the `ChemFormula` class for creating a chemical formula object: ```Python @@ -67,18 +75,18 @@ theine = ChemFormula("(C5N4H)O2(CH3)3", name = "theine", cas = "58-08-2") The `ChemFormula` class offers the following attributes/functions ```Python -.formula # original chemical formula used to create the chemical formula object +.formula # original chemical formula used to create the chemical formula object -.text_formula # formula including charge as text output +.text_formula # formula including charge as text output -.latex # formats a formula as a string that can be used in LaTeX +.latex # formats a formula as a string that can be used in LaTeX -.html # formats a formula as a string that can be used in HTML +.html # formats a formula as a string that can be used in HTML -.unicode # formats a formula with unicode subscript and superscript numbers +.unicode # formats a formula with unicode subscript and superscript numbers -.format_formula( # custom formatting of the formula, .FormatFormula uses the following optional keyword arguments - formula_prefix = "", # preceeds the complete formula string +.format_formula( # custom formatting of the formula, .FormatFormula uses the following optional keyword arguments + formula_prefix = "", # precedes the complete formula string element_prefix = "", element_suffix = "", # encloses every chemical symbol (Prefix + Symbol + Suffix) freq_prefix = "", freq_suffix = "", # encloses every element frequency (Prefix + Frequency + Suffix) formula_suffix = "", # closes the complete formula string @@ -86,41 +94,43 @@ The `ChemFormula` class offers the following attributes/functions multiply_symbol = "", # replacement for '.' or '*' charge_prefix = "", charge_suffix = "", # encloses every charge information (Prefix + Charge + Suffix) charge_positive = "+", # symbol for a positive charge - charge_negative = "-" # symbol for a negative charge - ) + charge_negative = "-", # symbol for a negative charge + ) -.sum_formula # collapsed sum formula of .OriginalFormula with all bracketed units resolved as a ChemFormula object, - # i.e. use .SumFormula.HTML to retrive an HTML representation of the sum formula +.sum_formula # collapsed sum formula of .OriginalFormula with all bracketed units resolved as a ChemFormula object, + # i.e. use .SumFormula.HTML to retrieve an HTML representation of the sum formula -.hill_formula # sum formula in Hill notation as a ChemFormula object, i.e. use .HillFormula.Unicode to retrive - # a Unicode representation of the Hill formula (first Carbon, then Hydrogen (if carbon is present), - # followed by all other elements in alphabetical order of their chemical symbol) - # Source: Edwin A. Hill, J. Am. Chem. Soc., 1900 (22), 8, 478-494 (https://doi.org/10.1021/ja02046a005) +.hill_formula # sum formula in Hill notation as a ChemFormula object, i.e. use .HillFormula.Unicode to retrieve + # a Unicode representation of the Hill formula (first Carbon, then Hydrogen (if carbon is present), + # followed by all other elements in alphabetical order of their chemical symbol) + # Source: Edwin A. Hill, J. Am. Chem. Soc., 1900 (22), 8, 478-494 (https://doi.org/10.1021/ja02046a005) -.formula_weight # formula weight of the chemical formula in g/mol +.formula_weight # formula weight of the chemical formula in g/mol -.mass_fractions # mass fraction of each element for the chemical formula in the form of - # key, value = chemical symbol, mass fraction +.mass_fractions # mass fraction of each element for the chemical formula in the form of + # key, value = chemical symbol, mass fraction -.name # name of the chemical formula object +.name # name of the chemical formula object -.radioactive # boolean value whether the formula is radioactive (True) or not (False) +.is_radioactive # boolean value whether the formula is radioactive (True) or not (False) -.charged # boolean value whether the formula is charged (True) or not (False) +.contains_isotopes # boolean value whether the formula contains specific isotopes (e.g. D or Tc) -.charge # integer value carrying the charge of the chemical formula object +.charged # boolean value whether the formula is charged (True) or not (False) -.text_charge # formatted string of the charge of the chemical formula object (e. g. 3+, 4-, +, ...) +.charge # integer value carrying the charge of the chemical formula object -.element # is a dictionary representation of the formula composition in the form of - # key, value = chemical symbol, frequency of this element - # e.g.: .element["C"] gives the number of carbon atoms in the corresponding formula object +.text_charge # formatted string of the charge of the chemical formula object (e. g. 3+, 4-, +, ...) -.cas # CAS Registry Number® in a formatted way ('_____00-00-0') - # .cas is a CAS number object from the casregnum package -.cas.cas_string # CAS number as a formatted string, inherited property from casregnum.CAS -.cas.cas_integer # CAS number as an integer value, inherited property from casregnum.CAS -.cas.check_digit # CAS number check digit, inherited property from casregnum.CAS +.element # is a dictionary representation of the formula composition in the form of + # key, value = chemical symbol, frequency of this element + # e.g.: .element["C"] gives the number of carbon atoms in the corresponding formula object + +.cas # CAS Registry Number® in a formatted way ('_____00-00-0') + # .cas is a CAS number object from the casregnum package +.cas.cas_string # CAS number as a formatted string, inherited property from casregnum.CAS +.cas.cas_integer # CAS number as an integer value, inherited property from casregnum.CAS +.cas.check_digit # CAS number check digit, inherited property from casregnum.CAS ``` @@ -156,7 +166,7 @@ print(f" Hill formula: {muscarine.hill_formula.latex}") print(f"\n--- Formula Weights Calculations with {ethylcinnamate.name.title()} ---") print(f" The formula weight of {ethylcinnamate.name} ({ethylcinnamate.sum_formula.unicode}) is {ethylcinnamate.formula_weight:.2f} g/mol.") mole = 1.4 -print(f" {mole:.1f} mol of {ethylcinnamate.name} weight {mole * ethylcinnamate.formula_weight:.1f} g.") +print(f" {mole:.1f} mol of {ethylcinnamate.name} weighs {mole * ethylcinnamate.formula_weight:.1f} g.") mass = 24 print(f" {mass:.1f} g of {ethylcinnamate.name} corresponds to {mass/ethylcinnamate.formula_weight * 1000:.1f} mmol.") print(f" The elemental composition of {ethylcinnamate.name} is as follows:") @@ -164,12 +174,12 @@ for stringElementSymbol, floatElementFraction in ethylcinnamate.mass_fraction.it print(f" {stringElementSymbol:<2}: {floatElementFraction * 100:>5.2f} %") print(f"\n--- {uranophane.name} and {muscarine.name} ---") -print(f" Yes, {uranophane.name} is radioactive.") if uranophane.radioactive else print(f" No, {uranophane.name} is not radioactive.") +print(f" Yes, {uranophane.name} is radioactive.") if uranophane.is_radioactive else print(f" No, {uranophane.name} is not radioactive.") print(f" Yes, {uranophane.name} is charged.") if uranophane.charged else print(f" No, {uranophane.name} is not charged.") -print(f" Yes, {muscarine.name} is radioactive.") if muscarine.radioactive else print(f" No, {muscarine.name} is not radioactive.") +print(f" Yes, {muscarine.name} is radioactive.") if muscarine.is_radioactive else print(f" No, {muscarine.name} is not radioactive.") print(f" Yes, {muscarine.name} is charged.") if muscarine.charged else print(f" No, {muscarine.name} is not charged.") -print("\n--- Accessing Single Elements through FormulaObject.Element[\"Element_Symbol\"] ---") +print("\n--- Accessing Single Elements through FormulaObject.element[\"Element_Symbol\"] ---") print(f" Tetraamminecopper(II)-sulfate contains {tetraamminecoppersulfate.element['N']} nitrogen atoms.") print("\n--- CAS Registry Number ---") @@ -178,43 +188,41 @@ print(f" {caffeine.name.capitalize()} has the CAS RN {caffeine.cas} (or as an in generates the following output -``` ---- Formula Depictions of L-(+)-Muscarine --- - Print instance: ((CH3)3N)(C6H11O2) - Original: ((CH3)3N)(C6H11O2) - Text formula: ((CH3)3N)(C6H11O2) + - HTML: ((CH3)3N)(C6H11O2)+ - LaTeX: \(\(\textnormal{C}\textnormal{H}_{3}\)_{3}\textnormal{N}\)\(\textnormal{C}_{6}\textnormal{H}_{11}\textnormal{O}_{2}\)^{+} - Unicode: ((CH₃)₃N)(C₆H₁₁O₂)⁺ - Charge (int): 1 - Charge (str): + - Sum formula: C9H20NO2 - Sum (HTML): C9H20NO2+ - Sum (Unicode): C₉H₂₀NO₂⁺ - Hill formula: C9H20NO2 - Hill formula: \textnormal{C}_{9}\textnormal{H}_{20}\textnormal{N}\textnormal{O}_{2}^{+} - ---- Formula Weights Calculations with Ethyl Cinnamate --- - The formula weight of ethyl cinnamate (C₁₁H₁₂O₂) is 176.21 g/mol. - 1.4 mol of ethyl cinnamate weight 246.7 g. - 24.0 g of ethyl cinnamate corresponds to 136.2 mmol. - The elemental composition of ethyl cinnamate is as follows: - C : 74.98 % - H : 6.86 % - O : 18.16 % - ---- Uranophane and L-(+)-Muscarine --- - Yes, Uranophane is radioactive. - No, Uranophane is not charged. - No, L-(+)-Muscarine is not radioactive. - Yes, L-(+)-Muscarine is charged. - ---- Accessing Single Elements through FormulaObject.Element["Element_Symbol"] --- - Tetraamminecopper(II)-sulfate contains 4 nitrogen atoms. - ---- CAS Registry Number --- - Caffeine has the CAS RN 58-08-2 (or as an integer: 58082). - ``` + --- Formula Depictions of L-(+)-Muscarine --- + Print instance: ((CH3)3N)(C6H11O2) + Original: ((CH3)3N)(C6H11O2) + Text formula: ((CH3)3N)(C6H11O2) + + HTML: ((CH3)3N)(C6H11O2)+ + LaTeX: \(\(\textnormal{C}\textnormal{H}_{3}\)_{3}\textnormal{N}\)\(\textnormal{C}_{6}\textnormal{H}_{11}\textnormal{O}_{2}\)^{+} + Unicode: ((CH₃)₃N)(C₆H₁₁O₂)⁺ + Charge (int): 1 + Charge (str): + + Sum formula: C9H20NO2 + Sum (HTML): C9H20NO2+ + Sum (Unicode): C₉H₂₀NO₂⁺ + Hill formula: C9H20NO2 + Hill formula: \textnormal{C}_{9}\textnormal{H}_{20}\textnormal{N}\textnormal{O}_{2}^{+} + + --- Formula Weights Calculations with Ethyl Cinnamate --- + The formula weight of ethyl cinnamate (C₁₁H₁₂O₂) is 176.21 g/mol. + 1.4 mol of ethyl cinnamate weight 246.7 g. + 24.0 g of ethyl cinnamate corresponds to 136.2 mmol. + The elemental composition of ethyl cinnamate is as follows: + C : 74.98 % + H : 6.86 % + O : 18.16 % + + --- Uranophane and L-(+)-Muscarine --- + Yes, Uranophane is radioactive. + No, Uranophane is not charged. + No, L-(+)-Muscarine is not radioactive. + Yes, L-(+)-Muscarine is charged. + + --- Accessing Single Elements through FormulaObject.element["Element_Symbol"] --- + Tetraamminecopper(II)-sulfate contains 4 nitrogen atoms. + + --- CAS Registry Number --- + Caffeine has the CAS RN 58-08-2 (or as an integer: 58082). More examples can be found at [/examples/](https://github.com/molshape/ChemFormula/blob/main/examples/). @@ -250,25 +258,57 @@ for position, item in enumerate(sorted(hydrocarbons), start = 1): generates the following output + --- Comparing Caffeine with Theine and Lactic Acid Isomers --- + Caffeine and theine are identical. + L-lactic acid and D-lactic acid are not identical. + + --- Lexical Sorting of Chemical Formulas via Hill Notation --- + 1. C₃H₅ + 2. C₃H₅O + 3. C₄H₅ + 4. C₆H₁₂O₃S₂ + 5. C₆H₁₂O₅S + 6. C₆H₁₂O₆ + 7. C₆H₁₂S₆ + + +## Using Isotopes like Deuterium or Tritium + +If hydrogen isotopes are intended to be used, the global flag `AllowHydrogenIsotopes` must be set to `True`: + +```python +import chemformula.config +from chemformula import ChemFormula +chemformula.config.AllowHydrogenIsotopes = True # Enable usage of hydrogen isotopes like Deuterium ("D") and Tritium ("T") +``` + +The following example + +```python +import chemformula.config +from chemformula import ChemFormula + +chemformula.config.AllowHydrogenIsotopes = True + +water = ChemFormula("H2O") +heavy_water = ChemFormula("D2O") + +print("\n--- Isotopes in ChemFormula Objects ---") +print(f" Yes, {water.unicode} contains specific isotopes.") if water.contains_isotopes else print(f" No, {water.unicode} contains no specific isotopes.") +print(f" Yes, {heavy_water.unicode} contains specific isotopes.\n") if heavy_water.contains_isotopes else print(f" No, {heavy_water.unicode} contains no specific isotopes.\n") ``` ---- Comparing Caffeine with Theine and Lactic Acid Isomers --- - Caffeine and theine are identical. - L-lactic acid and D-lactic acid are not identical. ---- Lexical Sorting of Chemical Formulas via Hill Notation --- - 1. C₃H₅ - 2. C₃H₅O - 3. C₄H₅ - 4. C₆H₁₂O₃S₂ - 5. C₆H₁₂O₅S - 6. C₆H₁₂O₆ - 7. C₆H₁₂S₆ - ``` +creates the following output: + + --- Isotopes in ChemFormula Objects --- + No, H₂O contains no specific isotopes. + Yes, D₂O contains specific isotopes. + ## Atomic Weight Data -All atomic weights are taken from the IUPAC Commission on Isotopic Abundances and Atomic Weights and are based on the following reports and publications: +All atomic weights are taken from the **IUPAC Commission on Isotopic Abundances and Atomic Weights** and are based on the following reports and publications: - [*Pure Appl. Chem.*, **2016**, *88*, 265-291](https://doi.org/10.1515/pac-2015-0305) - [*Chem. Eng. News*, **2015**, *93*(37), 9](https://doi.org/10.1021/cen-09337-notw9) @@ -283,3 +323,7 @@ All atomic weights are taken from the IUPAC Commission on Isotopic Abundances an The current data has been downloaded from https://iupac.qmul.ac.uk/AtWt/ as of August 2nd, 2025. The original data has been mirrored to [AtWt23.html](https://github.com/molshape/ChemFormula/blob/main/misc/AtWt23.html). Quoted atomic weights are those suggested for materials where the origin of the sample is unknown. For most radioactive elements the isotope with the longest half-life is quoted as an integer. + +Data for hydrogen isotopes are taken from the **AME2020 Atomic Mass Evaluation** by Meng Wang *et al.*: + + - [Chinese Phys. C, 2021, (45), 030003](https://doi.org/10.1088/1674-1137/abddaf) diff --git a/examples/example1.py b/examples/example1.py index 9de17a4..755b42c 100644 --- a/examples/example1.py +++ b/examples/example1.py @@ -26,7 +26,7 @@ print(f" {stringElementSymbol:<2}: {floatElementFraction * 100:>5.2f} %") print("\n--- Is Uranophane Radioactive and Charged? ---") -print(f" Yes, {uranophane.name} is radioactive.") if uranophane.radioactive else print(f" No, {uranophane.name} is not radioactive.") # noqa: E501 +print(f" Yes, {uranophane.name} is radioactive.") if uranophane.is_radioactive else print(f" No, {uranophane.name} is not radioactive.") # noqa: E501 print(f" Yes, {uranophane.name} is charged.") if uranophane.charged else print(f" No, {uranophane.name} is not charged.") print("\n--- Accessing Single Elements through FormulaObject.Element['Element_Symbol'] ---") diff --git a/examples/example2.py b/examples/example2.py index 2f430b2..36a6c0a 100644 --- a/examples/example2.py +++ b/examples/example2.py @@ -40,7 +40,7 @@ print(f" {stringElementSymbol:<2}: {floatElementFraction * 100:>5.2f} %") print("\n--- Is L-(+)-Muscarine Radioactive and Charged? ---") -print(f" Yes, {muscarine.name} is radioactive.") if muscarine.radioactive else print(f" No, {muscarine.name} is not radioactive.") # noqa: E501 +print(f" Yes, {muscarine.name} is radioactive.") if muscarine.is_radioactive else print(f" No, {muscarine.name} is not radioactive.") # noqa: E501 print(f" Yes, {muscarine.name} is charged.") if muscarine.charged else print(f" No, {muscarine.name} is not charged.") print("\n--- Accessing Single Elements through FormulaObject.Element['Element_Symbol'] ---") diff --git a/examples/example5.py b/examples/example5.py new file mode 100644 index 0000000..2a927e8 --- /dev/null +++ b/examples/example5.py @@ -0,0 +1,18 @@ +import chemformula.config +from chemformula import ChemFormula + +chemformula.config.AllowHydrogenIsotopes = True # Enable usage of hydrogen isotopes like Deuterium ("D") and Tritium ("T") + +water = ChemFormula("H2O") +heavy_water = ChemFormula("D2O") + +print("\n--- Isotopes in ChemFormula Objects ---") +print(f" Yes, {water.unicode} contains specific isotopes.") if water.contains_isotopes else print(f" No, {water.unicode} contains no specific isotopes.") # noqa: E501 +print(f" Yes, {heavy_water.unicode} contains specific isotopes.\n") if heavy_water.contains_isotopes else print(f" No, {heavy_water.unicode} contains no specific isotopes.\n") # noqa: E501 + +# OUTPUT: +# +# --- Isotopes in ChemFormula Objects --- +# No, H₂O contains no specific isotopes. +# Yes, D₂O contains specific isotopes. +# diff --git a/examples/example_general.py b/examples/example_general.py index fcc7a2b..dff8098 100644 --- a/examples/example_general.py +++ b/examples/example_general.py @@ -34,9 +34,9 @@ print(f" {stringElementSymbol:<2}: {floatElementFraction * 100:>5.2f} %") print(f"\n--- {uranophane.name} and {muscarine.name} ---") -print(f" Yes, {uranophane.name} is radioactive.") if uranophane.radioactive else print(f" No, {uranophane.name} is not radioactive.") # noqa: E501 +print(f" Yes, {uranophane.name} is radioactive.") if uranophane.is_radioactive else print(f" No, {uranophane.name} is not radioactive.") # noqa: E501 print(f" Yes, {uranophane.name} is charged.") if uranophane.charged else print(f" No, {uranophane.name} is not charged.") -print(f" Yes, {muscarine.name} is radioactive.") if muscarine.radioactive else print(f" No, {muscarine.name} is not radioactive.") # noqa: E501 +print(f" Yes, {muscarine.name} is radioactive.") if muscarine.is_radioactive else print(f" No, {muscarine.name} is not radioactive.") # noqa: E501 print(f" Yes, {muscarine.name} is charged.") if muscarine.charged else print(f" No, {muscarine.name} is not charged.") print('\n--- Accessing Single Elements through FormulaObject.Element["Element_Symbol"] ---') diff --git a/pyproject.toml b/pyproject.toml index d034a85..f7bb861 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "chemformula" -version = "1.4.1" +version = "1.5.0" description = "ChemFormula is a Python class for working with chemical formulas. It allows parsing chemical formulas, generating formatted output strings and calculating formula weights." readme = "README.md" authors = [ @@ -9,12 +9,14 @@ authors = [ maintainers = [ {name = "Axel Müller", email = "molshape@gmx.net"}, ] -requires-python = ">=3.9" +requires-python = ">=3.10" dependencies = [ - "casregnum", + "casregnum>=1.1.2", ] classifiers = [ - "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", "Operating System :: OS Independent", "License :: OSI Approved :: MIT License", "Topic :: Scientific/Engineering :: Chemistry", @@ -34,11 +36,12 @@ build-backend = "hatchling.build" [tool.uv] dev-dependencies = [ - "pytest", - "pytest-sugar", - "pytest-cov", - "ruff", - "twine", + "mypy>=1.18.1", + "pytest>=8.4.1", + "pytest-cov>=7.0.0", + "pytest-sugar>=1.1.1", + "ruff>=0.13.0", + "twine>=6.2.0", ] [tool.pytest.ini_options] @@ -50,6 +53,10 @@ addopts = [ "--strict-markers", "--strict-config", "--verbose", + "--cov=src", + "--cov-branch", + "--cov-report=term", + "--cov-report=xml", ] [tool.ruff] diff --git a/src/chemformula/__init__.py b/src/chemformula/__init__.py index 9fbdd0e..c08bb9d 100644 --- a/src/chemformula/__init__.py +++ b/src/chemformula/__init__.py @@ -1,2 +1,8 @@ __all__ = ["ChemFormula"] from .chemformula import ChemFormula + +try: + from importlib.metadata import version + __version__ = version("chemformula") +except ImportError: # pragma: no cover + __version__ = "unknown" # pragma: no cover diff --git a/src/chemformula/chemformula.py b/src/chemformula/chemformula.py index 67edbc9..8cb467f 100644 --- a/src/chemformula/chemformula.py +++ b/src/chemformula/chemformula.py @@ -1,4 +1,11 @@ +""" +ChemFormula: A Python class for working with chemical formulas. It allows parsing chemical formulas, generating formatted output strings and calculating formula weights. +""" + +from __future__ import annotations + import re +import warnings from collections import defaultdict import casregnum @@ -8,37 +15,67 @@ # Class for chemical formula strings class ChemFormulaString: - def __init__(self, formula, charge=0): - self.formula = formula # chemical formula - self.charge = charge # charge of chemical formula - if self.charged: - self.text_formula = self.formula + " " + self.text_charge - else: - self.text_formula = self.formula + """ + ChemFormulaString class for chemical formula strings with charge information + + Attributes: + ----------- + formula : str + Chemical (input) formula as a string + charge : int + Charge of the chemical formula + charged : bool + Boolean property whether the formula object is charged (True) or not (False) + text_charge : str + Text representation of the charge as a text string + text_formula : str + Text representation of the chemical formula including charge information + latex : str + LaTeX representation of the chemical formula including charge information + html : str + HTML representation of the chemical formula including charge information + unicode : str + Unicode representation of the chemical formula including charge information + + Methods: + -------- + format_formula() : str + Formats formula (ChemFormulaString object) as a customized strings + """ + + def __init__(self, formula: str, charge: int = 0) -> None: + self.formula = formula + self.charge = charge # formula as standard string output - def __str__(self): + def __str__(self) -> str: return self.formula + # formula as detailed string output + def __repr__(self) -> str: + return f"{self.__class__.__name__}(formula='{self.formula}', charge={self.charge})" + # Returns original input formula @property - def formula(self): - return self.__formula + def formula(self) -> str: + """Returns the original input formula as a string.""" + return self._formula @formula.setter - def formula(self, input_formula): - self.__formula = str(input_formula) + def formula(self, input_formula: str) -> None: + self._formula = str(input_formula) # Returns the charge of the formula object @property - def charge(self): - return self.__charge + def charge(self) -> int: + """Returns the charge of the formula object as an integer.""" + return self._charge # Checks, whether the charge is valid @charge.setter - def charge(self, charge): + def charge(self, charge: int) -> None: if isinstance(charge, int): - self.__charge = charge + self._charge = charge else: raise TypeError( f"Invalid Charge Value '{charge}' (expected an integer (), but found {type(charge)})" @@ -46,12 +83,14 @@ def charge(self, charge): # Boolean property whether the formula object is charged (True) or not (False) @property - def charged(self): + def charged(self) -> bool: + """Returns whether the formula object is charged (True) or not (False)""" return False if self.charge == 0 else True # Returns the charge of the formula object as a text string @property - def text_charge(self): + def text_charge(self) -> str: + """Returns the charge of the formula object as a text string, without the number "1" for charges of ±1.""" # a charge of "1+" or "1-" is printed without the number "1" charge_output = "" if self.charge == 0: @@ -63,24 +102,39 @@ def text_charge(self): # Returns formula and charge as a text string @property - def text_formula(self): - return self.__text_formula - - @text_formula.setter - def text_formula(self, text_formula_charge): - self.__text_formula = text_formula_charge + def text_formula(self) -> str: + """Returns the chemical formula including charge information as a text string.""" + if self.charged: + return f"{self.formula} {self.text_charge}" + return self.formula # Formats formula (ChemFormulaString object) as a customized strings def format_formula(self, - formula_prefix="", - element_prefix="", element_suffix="", - freq_prefix="", freq_suffix="", - formula_suffix="", - bracket_prefix="", bracket_suffix="", - multiply_symbol="", - charge_prefix="", charge_suffix="", - charge_positive="+", charge_negative="-" - ): + formula_prefix: str = "", + element_prefix: str = "", element_suffix: str = "", + freq_prefix: str = "", freq_suffix: str = "", + formula_suffix: str = "", + bracket_prefix: str = "", bracket_suffix: str = "", + multiply_symbol: str = "", + charge_prefix: str = "", charge_suffix: str = "", + charge_positive: str = "+", charge_negative: str = "-" + ) -> str: + """Formats the chemical formula (ChemFormulaString object) as a customized string with user-defined prefixes and suffixes: + Parameters: + - formula_prefix (str): Prefix for the entire formula + - element_prefix (str): Prefix for each element + - element_suffix (str): Suffix for each element + - freq_prefix (str): Prefix for each frequency + - freq_suffix (str): Suffix for each frequency + - formula_suffix (str): Suffix for the entire formula + - bracket_prefix (str): Prefix for each bracket + - bracket_suffix (str): Suffix for each bracket + - multiply_symbol (str): Symbol for multiplication + - charge_prefix (str): Prefix for the charge + - charge_suffix (str): Suffix for the charge + - charge_positive (str): Symbol for positive charge + - charge_negative (str): Symbol for negative charge + """ formatted_formula = re.sub(r"([\{\[\(\)\]\}]){1}", bracket_prefix + r"\g<1>" + bracket_suffix, self.formula) formatted_formula = re.sub(r"([A-Z]{1}[a-z]{0,1})", element_prefix + r"\g<1>" + element_suffix, formatted_formula) formatted_formula = re.sub(r"(\d+)", freq_prefix + r"\g<1>" + freq_suffix, formatted_formula) @@ -96,7 +150,8 @@ def format_formula(self, # Returns a LaTeX representation of a formula (ChemFormulaString object) @property - def latex(self): + def latex(self) -> str: + """Returns a LaTeX representation of the chemical formula (including charge information) as a string.""" return self.format_formula("", r"\\textnormal{", "}", "_{", "}", @@ -108,7 +163,9 @@ def latex(self): # Returns an HTML representation of a formula (ChemFormulaString object) @property - def html(self): + def html(self) -> str: + """Returns an HTML representation of the chemical formula (including charge information) as a string. + Specifies the class 'ChemFormula' for custom CSS.""" return self.format_formula("", "", "", "", "", @@ -120,7 +177,8 @@ def html(self): # Returns formula with unicode sub- and superscripts (₀₁₂₃₄₅₆₇₈₉⁰¹²³⁴⁵⁶⁷⁸⁹⁺⁻) @property - def unicode(self): + def unicode(self) -> str: + """Returns a Unicode representation of the chemical formula (including charge information) as a string.""" subscript_num = "₀₁₂₃₄₅₆₇₈₉" superscript_num = "⁰¹²³⁴⁵⁶⁷⁸⁹" unicode_formula = self.formula # start with original formula @@ -135,28 +193,109 @@ def unicode(self): return unicode_formula + unicode_charge +# Class for chemical formula dictionaries +class ChemFormulaDict(defaultdict): + """ + ChemFormulaDict class for chemical formula dictionaries with element symbols as keys and element frequencies as values + """ + def __init__(self, *args, **kwargs) -> None: + super().__init__(int, *args, **kwargs) # default value for non-existing elements is 0 + + def __setitem__(self, key_element: str, value_frequency: int | float) -> None: + if key_element not in elements.get_valid_element_symbols(): + raise ValueError( + f"Invalid Element Symbol (unknown element symbol '{key_element}')" + ) + super().__setitem__(key_element, value_frequency) + + # Class for chemical formula objects class ChemFormula(ChemFormulaString): - def __init__(self, formula, charge=0, name=None, cas=None): + """ + ChemFormula class for chemical formula objects with formula, different representations (LaTeX, HTML, Unicode), + formula_weight, charge, name, information on radioactivity and specific isotopes, as well as CAS registry number + information, if provided + + Attributes (inherited from ChemFormulaString): + ---------------------------------------------- + formula : str + Chemical (input) formula as a string + charge : int + Charge of the chemical formula + charged : bool + Boolean property whether the formula object is charged (True) or not (False) + text_charge : str + Text representation of the charge as a text string + text_formula : str + Text representation of the chemical formula including charge information + latex : str + LaTeX representation of the chemical formula including charge information + html : str + HTML representation of the chemical formula including charge information + unicode : str + Unicode representation of the chemical formula including charge information + + Additional Attributes: + ---------------------- + name : str or None + Name of the chemical formula (if provided) + cas : casregnum.CAS or None + CAS registry number as a casregnum.CAS object of the chemical formula (if provided) + element : ChemFormulaDict + Chemical formula as a ChemFormulaDict object with (key : value) = (element symbol : element frequency) + sum_formula : ChemFormulaDict + Chemical formula in Hill notation as a ChemFormulaDict object with (key : value) = (element symbol : element frequency) + hill_formula : ChemFormulaDict + Chemical formula in Hill notation as a ChemFormulaDict object with (key : value) = (element symbol : element frequency) + formula_weight : float + Formula weight of the chemical formula in g/mol + mass_fraction : ChemFormulaDict + Mass fraction of each element as a ChemFormulaDict object with (key : value) = (element symbol : mass fraction) + contains_isotopes : bool + Boolean property whether the formula contains an element symbol that is refering to a specific isotope (e.g. D or Tc) + is_radioactive : bool + Boolean property whether the formula contains at least one radioactive element (True) or not (False) + + Methods (inherited from ChemFormulaString): + ------------------------------------------- + format_formula() : str + Formats formula (ChemFormulaString object) as a customized strings + + Additional Methods: + ------------------- + __eq__() : bool + Tests if two chemical formula objects are identical + __lt__() : bool + Compares two formulas with respect to their lexical sorting according to Hill's notation + """ + + def __init__(self, formula: str, charge: int = 0, name: str | None = None, cas: str | int | None = None) -> None: # Parent information ChemFormulaString.__init__(self, formula, charge) # Additional input information - self.name = None if name is None else name - self.cas = None if cas is None else cas + self.name = name + self.cas = cas # parse chemical formula and test for consistency - self.__clean_formula = self.__clean_up_formula() - self.__check_formula(self.__clean_formula) - self.__resolved_formula = self.__resolve_brackets(self.__clean_formula) + self._clean_formula = self._clean_up_formula() + self._check_formula(self._clean_formula) + self._resolved_formula = self._resolve_brackets(self._clean_formula) + _ = self.mass_fraction # trigger mass_fraction parsing to check for valid element symbols and atomic weights # Test if two chemical formla objects are identical - def __eq__(self, other): + def __eq__(self, other: object) -> bool: + """Tests if two chemical formula objects are identical.""" # two chemical formula objects are considered to be equal if they have # the same chemical composition (in Hill notation), the same charge, # and the same CAS registry number (if provided) + if not isinstance(other, ChemFormula): + raise TypeError("Comparisons can only be made between ChemFormula objects.") return (str(self.hill_formula) == str(other.hill_formula) and self.charge == other.charge and self.cas == other.cas) # Compares two formulas with respect to their lexical sorting according to Hill's notation - def __lt__(self, other): + def __lt__(self, other: object) -> bool: + """Compares two chemical formula objects with respect to their lexical sorting according to Hill's notation.""" + if not isinstance(other, ChemFormula): + raise TypeError("Comparisons can only be made between ChemFormula objects.") elements_self = tuple(self._element_hill_sorted.items()) elements_other = tuple(other._element_hill_sorted.items()) # cycle through the elements in Hill notation @@ -179,7 +318,9 @@ def __lt__(self, other): return False # Clean up chemical formula, i. e. harmonize brackets, add quantifier "1" to bracketed units without quantifier - def __clean_up_formula(self): + def _clean_up_formula(self) -> str: + """Cleans up the input formula by harmonizing brackets, removing whitespaces, dots and asterisks, + and adding a quantifier `1` to bracketed units without a quantifier.""" formula = self.formula # for simplicity reasons: create a (...)1 around the whole formula formula = "(" + formula + ")1" @@ -193,17 +334,19 @@ def __clean_up_formula(self): return formula # Checks whether the formula is valid regarding bracketing - def __check_formula(self, formula): + def _check_formula(self, formula: str) -> bool: + """Checks whether the formula is valid regarding bracketing and general element symbols conventions. + Raises a ValueError if the formula is invalid. Element validation is done in the `ChemFormulaDict` class.""" bracket_counter = 0 for character in formula: if character == "(": bracket_counter += 1 if character == ")": bracket_counter -= 1 - if bracket_counter < 0: # there are more closing brackets than opening brackets during parsing formula - raise ValueError( - "Invalid Bracket Structure in Formula (expecting an opening bracket, but found a closing bracket)" - ) + if bracket_counter < 0: # there are more closing brackets than opening brackets during parsing formula + raise ValueError( + "Invalid Bracket Structure in Formula (expecting an opening bracket, but found a closing bracket)" + ) if not bracket_counter == 0: # number of opening brackets is not identical to the number of closing brackets raise ValueError( "Invalid Bracket Structure in Formula (inconsistent number of opening and closing brackets)" @@ -212,20 +355,17 @@ def __check_formula(self, formula): raise ValueError( "Invalid Element Symbol (two lowercase letters found in sequence)" ) - for element in re.findall("[A-Z]{1}[a-z]{0,1}", formula): - if elements.atomic_weight(element) is False: - raise ValueError( - f"Invalid Element Symbol (unknown element symbol '{element}')" - ) # no error found return True # Recursively resolve all brackets in the provided formula - def __resolve_brackets(self, formula): + def _resolve_brackets(self, formula: str) -> str: + """Recursively resolves all brackets in the provided formula and returns a formula without any brackets as a string.""" # stop recursion if formula contains no more brackets if "(" in formula: # find smallest bracket unit, i. e. a bracketed entity that does not contain any other brackets most_inner_bracket_unit = re.search(r"\(([A-Za-z0-9]*)\)(\d+)", formula) + assert most_inner_bracket_unit is not None # should never be None, as presence of "(" is checked above # remove smallest bracket unit from original formula string using match.span() and string splicing pre_match = formula[0:most_inner_bracket_unit.span()[0]:] # string before the bracketed unit post_match = formula[most_inner_bracket_unit.span()[1]::] # string after the bracketed unit @@ -237,52 +377,57 @@ def __resolve_brackets(self, formula): resolved_match = "" for element_freq_item in element_freq_list: element_freq = re.match(r"(\D+)(\d*)", element_freq_item) + assert element_freq is not None # should never be None, due to the return value of `re.findall()` element = element_freq.group(1) freq = element_freq.group(2) - if not freq: - freq = 1 # if no number is given, use a frequency of 1 + freq = 1 if not freq else freq # if no frequency is given, set frequency to 1 # create a resolved version of the bracketed unit and replace the bracketed unit with this resolved string resolved_match += str(element) + str(int(freq) * multiplier_match) formula = pre_match + resolved_match + post_match # recursively resolve brackets - formula = self.__resolve_brackets(formula) + formula = self._resolve_brackets(formula) return str(formula) # Returns the formula as a dictionary with (key : value) = (element symbol : element frequency) @property - def element(self): + def element(self) -> ChemFormulaDict: + """Returns the chemical formula as a `ChemFormulaDict` object with (key : value) = (element symbol : element frequency).""" # find all occurrences of one capital letter, possibly one lower case letter and some multiplier number # Note: a multiplier number is always present in resolved formulas - dict_formula = defaultdict(lambda: 0) # if element symbol does not exist, set start frequency to 0 - element_freq_list = re.findall(r"[A-Z]{1}[a-z]{0,1}\d+", self.__resolved_formula) + dict_formula = ChemFormulaDict() + element_freq_list = re.findall(r"[A-Z]{1}[a-z]{0,1}\d+", self._resolved_formula) # separate for each occurrence the letter portion from the number portion (if any) for element_freq_item in element_freq_list: # separate element symbol from element frequency element_freq = re.match(r"(\D+)(\d+)", element_freq_item) + assert element_freq is not None # should never be None, due to the return value of `_resolve_brackets()` element = element_freq.group(1) freq = element_freq.group(2) # create a dictionary with element symbols as keys and element frequencies as values dict_formula[element] += int(freq) - return dict(dict_formula) + return ChemFormulaDict(dict_formula) - # Return the formula as a dictionalry with (key : value) = (element symbol : element frequency) in Hill sorting + # Return the formula as a dictionary with (key : value) = (element symbol : element frequency) in Hill sorting @property - def _element_hill_sorted(self): + def _element_hill_sorted(self) -> ChemFormulaDict: + """Returns the chemical formula as a `ChemFormulaDict` object in Hill notation with (key : value) = (element symbol : element frequency).""" dict_sorted_elements = dict(sorted(self.element.items())) dict_hill_sorted_elements = {} # extract "C" and "H" (if "C" is also present) from the original dictionary - if "C" in dict_sorted_elements.keys(): + if "C" in dict_sorted_elements: dict_hill_sorted_elements["C"] = dict_sorted_elements["C"] del dict_sorted_elements["C"] - if "H" in dict_sorted_elements.keys(): + if "H" in dict_sorted_elements: dict_hill_sorted_elements["H"] = dict_sorted_elements["H"] del dict_sorted_elements["H"] # create new Hill dictionary by placing "C" and "H" (if "C" is also present) in front of all other elements dict_hill_sorted_elements = dict_hill_sorted_elements | dict_sorted_elements - return dict(dict_hill_sorted_elements) + return ChemFormulaDict(dict_hill_sorted_elements) # function to contract formula from a given (element symbol : element frequency) dictionary - def _contract_formula(dict_element_freq, charge): + @staticmethod + def _contract_formula(dict_element_freq: ChemFormulaDict, charge: int) -> ChemFormulaString: + """Contracts the formula to a sum formula by generating a `ChemFormulaString` object from a given (element symbol : element frequency) dictionary.""" formula_output = "" for element, freq in dict_element_freq.items(): formula_output += element # element symbol @@ -292,55 +437,81 @@ def _contract_formula(dict_element_freq, charge): # Generate sum formula as a string @property - def sum_formula(self): + def sum_formula(self) -> ChemFormulaString: + """Returns the chemical formula as a `ChemFormulaString` object in sum formula notation.""" return ChemFormula._contract_formula(self.element, self.charge) # Generate sum formula as a string # Source: Edwin A. Hill, J. Am. Chem. Soc., 1900 (22), 8, 478-494 (https://doi.org/10.1021/ja02046a005) @property - def hill_formula(self): + def hill_formula(self) -> ChemFormulaString: + """Returns the chemical formula as a `ChemFormulaString` object in Hill notation.""" return ChemFormula._contract_formula(self._element_hill_sorted, self.charge) # Returns the formula weight of the formula object, atomic weights are taken from elements.py @property - def formula_weight(self): - float_formula_weight = 0.0 + def formula_weight(self) -> float: + """Returns the formula weight of the chemical formula in g/mol as a float.""" + float_formula_weight: float = 0.0 for element, freq in self.element.items(): float_formula_weight += freq * elements.atomic_weight(element) return float(float_formula_weight) # Calculate mass fractions for each element in the formula as a dictionary, atomic weights are taken from elements.py @property - def mass_fraction(self): - dict_mass_fraction = {} + def mass_fraction(self) -> ChemFormulaDict: + """Returns the mass fraction of each element as a `ChemFormulaDict` object with (key : value) = (element symbol : mass fraction).""" + dict_mass_fraction: ChemFormulaDict = ChemFormulaDict() for element, freq in self.element.items(): dict_mass_fraction[element] = float((freq * elements.atomic_weight(element)) / self.formula_weight) - return dict(dict_mass_fraction) + return ChemFormulaDict(dict_mass_fraction) - # Checks, whether an element is classified as radioactive, radioactivitiy data is taken from elements.py + # Checks, whether an element is classified as radioactive, radioactivity data is taken from elements.py @property - def radioactive(self): - for sElement in self.element.keys(): - if elements.radioactive_element(sElement): + def is_radioactive(self) -> bool: + """Returns whether the formula contains at least one radioactive element (True) or not (False) and is therefore classified as radioactive.""" + for element in self.element: + if elements.isradioactive(element): return True # element and therefore the formula is radioactive return False # no radioactive elements found and therefore no radioactive formula + # Deprecated: use is_radioactive instead + @property + def radioactive(self) -> bool: + """Deprecated: use `is_radioactive` instead. Returns whether the formula contains at least one radioactive element (True) or not (False) and is therefore classified as radioactive.""" + warnings.warn( + "The 'radioactive' property is deprecated, use 'is_radioactive' instead.", + DeprecationWarning, + stacklevel=2 + ) + return self.is_radioactive + + # Checks, whether a specific isotop of an element is used, isotop data is taken from elements.py + @property + def contains_isotopes(self) -> bool: + """Returns whether the formula contains an element symbol that is refering to a specific isotope (e.g. D or Tc).""" + for element in self.element: + if elements.isisotope(element): + return True # element is a specific isotope + return False # no isotopes of elements found # Returns the name of the formula @property - def name(self): - return self.__name + def name(self) -> str | None: + """Returns the name of the chemical formula (if provided) as a string or None.""" + return self._name # Makes sure, that the name of the formula is a string @name.setter - def name(self, name): - self.__name = str(name) + def name(self, name: str | None) -> None: + self._name = None if name is None else str(name) # Returns the CAS registry number of the formula object @property - def cas(self): - return None if self.__cas is None else self.__cas + def cas(self) -> casregnum.CAS | None: + """Returns the CAS registry number of the chemical formula as a `casregnum.CAS` object (if provided) or None.""" + return None if self._cas is None else self._cas # Checks, whether the CAS registry number is valid by using the CAS class from CASRegistryNumber.py @cas.setter - def cas(self, cas_rn): - self.__cas = None if cas_rn is None else casregnum.CAS(cas_rn) + def cas(self, cas_rn: int | str | None) -> None: + self._cas = None if cas_rn is None else casregnum.CAS(cas_rn) diff --git a/src/chemformula/chemformula.pyi b/src/chemformula/chemformula.pyi new file mode 100644 index 0000000..9e18ff1 --- /dev/null +++ b/src/chemformula/chemformula.pyi @@ -0,0 +1,62 @@ +from collections import defaultdict + +import casregnum + +from . import elements as elements + +class ChemFormulaString: + def __init__(self, formula: str, charge: int = 0) -> None: ... + @property + def formula(self) -> str: ... + @formula.setter + def formula(self, input_formula: str) -> None: ... + @property + def charge(self) -> int: ... + @charge.setter + def charge(self, charge: int) -> None: ... + @property + def charged(self) -> bool: ... + @property + def text_charge(self) -> str: ... + @property + def text_formula(self) -> str: ... + def format_formula(self, formula_prefix: str = '', element_prefix: str = '', element_suffix: str = '', freq_prefix: str = '', freq_suffix: str = '', formula_suffix: str = '', bracket_prefix: str = '', bracket_suffix: str = '', multiply_symbol: str = '', charge_prefix: str = '', charge_suffix: str = '', charge_positive: str = '+', charge_negative: str = '-') -> str: ... + @property + def latex(self) -> str: ... + @property + def html(self) -> str: ... + @property + def unicode(self) -> str: ... + +class ChemFormulaDict(defaultdict): + def __init__(self, *args, **kwargs) -> None: ... + def __setitem__(self, key_element: str, value_frequency: int | float) -> None: ... + +class ChemFormula(ChemFormulaString): + def __init__(self, formula: str, charge: int = 0, name: str | None = None, cas: str | int | None = None) -> None: ... + def __eq__(self, other: object) -> bool: ... + def __lt__(self, other: object) -> bool: ... + @property + def element(self) -> ChemFormulaDict: ... + @property + def sum_formula(self) -> ChemFormulaString: ... + @property + def hill_formula(self) -> ChemFormulaString: ... + @property + def formula_weight(self) -> float: ... + @property + def mass_fraction(self) -> ChemFormulaDict: ... + @property + def is_radioactive(self) -> bool: ... + @property + def radioactive(self) -> bool: ... + @property + def contains_isotopes(self) -> bool: ... + @property + def name(self) -> str | None: ... + @name.setter + def name(self, name: str | None) -> None: ... + @property + def cas(self) -> casregnum.CAS | None: ... + @cas.setter + def cas(self, cas_rn: int | str | None) -> None: ... diff --git a/src/chemformula/config.py b/src/chemformula/config.py new file mode 100644 index 0000000..e9fdcfe --- /dev/null +++ b/src/chemformula/config.py @@ -0,0 +1,2 @@ +# Hydrogen isotopes like Deuterium ("D") and Tritium ("T") are only allowed if AllowHydrogenIsotopes is set to True, default is False +AllowHydrogenIsotopes = False diff --git a/src/chemformula/config.pyi b/src/chemformula/config.pyi new file mode 100644 index 0000000..46b7a65 --- /dev/null +++ b/src/chemformula/config.pyi @@ -0,0 +1 @@ +AllowHydrogenIsotopes: bool diff --git a/src/chemformula/elements.py b/src/chemformula/elements.py index 0e508e5..5d69fa8 100644 --- a/src/chemformula/elements.py +++ b/src/chemformula/elements.py @@ -1,15 +1,15 @@ -''' +""" ATOMIC WEIGHTS OF THE ELEMENTS (2023) from the IUPAC Commission on Isotopic Abundances and Atomic Weights Based on the following reports: - - Pure Appl. Chem., 2016, 88, 265-291 (https://doi.org/10.1515/pac-2015-0305) - - Chem. Eng. News, 2015, 93(37), 9 (https://doi.org/10.1021/cen-09337-notw9) - - Pure Appl. Chem., 2016, 88, 139-153 (https://doi.org/10.1515/pac-2015-0502) - - Pure Appl. Chem., 2016, 88, 155-160 (https://doi.org/10.1515/pac-2015-0501) - - Pure Appl. Chem., 2016, 88, 1225-1229 (https://doi.org/10.1515/pac-2016-0501) - - Chem. Int., 2018, 40(4), 23-24 (https://doi.org/10.1515/ci-2018-0409) - - Chem. Int., 2020, 42(2), 31 (https://doi.org/10.1515/ci-2020-0222) + - Pure Appl. Chem., 2016, 88, 265-291 (https://doi.org/10.1515/pac-2015-0305) + - Chem. Eng. News, 2015, 93(37), 9 (https://doi.org/10.1021/cen-09337-notw9) + - Pure Appl. Chem., 2016, 88, 139-153 (https://doi.org/10.1515/pac-2015-0502) + - Pure Appl. Chem., 2016, 88, 155-160 (https://doi.org/10.1515/pac-2015-0501) + - Pure Appl. Chem., 2016, 88, 1225-1229 (https://doi.org/10.1515/pac-2016-0501) + - Chem. Int., 2018, 40(4), 23-24 (https://doi.org/10.1515/ci-2018-0409) + - Chem. Int., 2020, 42(2), 31 (https://doi.org/10.1515/ci-2020-0222) - Pure Appl. Chem., 2022, 94(5), 573-600 (https://doi.org/10.1515/pac-2019-0603) - Chem. Int., 2025, 47(1), 20-20 (https://doi.org/10.1515/ci-2025-0105) @@ -17,10 +17,37 @@ Quoted atomic weights are those suggested for materials where the origin of the sample is unknown. For radioactive elements the isotope with the longest half-life is quoted as an integer. -''' +Data for hydrogen isotopes taken from the AME2020 Atomic Mass Evaluation: -def atomic_weight(element): + - Chinese Phys. C, 2021, (45), 030003 (https://doi.org/10.1088/1674-1137/abddaf) + +""" + +# Returns the list of valid element symbols, considering the AllowHydrogenIsotopes flag +def get_valid_element_symbols() -> list[str]: + from .config import AllowHydrogenIsotopes + element_symbols = [ + "H", "He", + "Li", "Be", "B", "C", "N", "O", "F", "Ne", + "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", + "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", + "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe", + "Cs", "Ba", "La", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", + "Fr", "Ra", "Ac", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og", + # Lanthanides + "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", + # Actinides + "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr", + ] + if AllowHydrogenIsotopes: + element_symbols.extend(["D", "T"]) + return element_symbols + + +# Calculates the atomic weight of an element, False if element symbol does not exist +def atomic_weight(element: str) -> float | bool: + from .config import AllowHydrogenIsotopes atomic_weight_table = { "H": 1.008, "He": 4.002602, @@ -141,16 +168,41 @@ def atomic_weight(element): "Ts": 293, "Og": 294 } + if AllowHydrogenIsotopes: + # Data taken from: Chinese Phys. C, 2021, (45), 030003-6, Table I (https://doi.org/10.1088/1674-1137/abddaf) + atomic_weight_table.update({ + "D": 2.01410177784, + "T": 3.01604928132, + }) # return atomic weight of the element symbol passed to the function, False if element symbol does not exist return float(atomic_weight_table[element]) if element in atomic_weight_table else False - -def radioactive_element(element): +# Checks if an element is radioactive +def isradioactive(element: str) -> bool: + from .config import AllowHydrogenIsotopes radioactive_elements = [ "Tc", + "Pm", "Po", "At", "Rn", - "Fr", "Ra", "Pm", "Ac", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og", + "Fr", "Ra", "Ac", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr" ] + if AllowHydrogenIsotopes: + radioactive_elements.extend(["T"]) # element is in the list of radioactive elements => True else False return element in radioactive_elements + +# Checks if an element symbol is only refering to a specific isotope (e.g. D for Deuterium or Tc for Technetium) +def isisotope(element: str) -> bool: + from .config import AllowHydrogenIsotopes + isotope_elements = [ + "Tc", + "Pm", + "Po", "At", "Rn", + "Fr", "Ra", "Ac", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og", + "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr" + ] + if AllowHydrogenIsotopes: + isotope_elements.extend(["D", "T"]) + # element is in the list of elements with only isotopes => True else False + return element in isotope_elements diff --git a/src/chemformula/elements.pyi b/src/chemformula/elements.pyi new file mode 100644 index 0000000..8ea6d34 --- /dev/null +++ b/src/chemformula/elements.pyi @@ -0,0 +1,4 @@ +def get_valid_element_symbols() -> list[str]: ... +def atomic_weight(element: str) -> float | bool: ... +def isradioactive(element: str) -> bool: ... +def isisotope(element: str) -> bool: ... diff --git a/src/chemformula/py.typed b/src/chemformula/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_casregnum.py b/tests/test_casregnum.py index bbc76d6..46e9a0d 100644 --- a/tests/test_casregnum.py +++ b/tests/test_casregnum.py @@ -47,21 +47,21 @@ def test_cas_format_string(caffeine): # Tests for error handling -@pytest.mark.xfail(raises=TypeError) def test_cas_invalid_input(): - ChemFormula("H2O", 0, "Water", cas=6417.5) + with pytest.raises(TypeError): + ChemFormula("H2O", 0, "Water", cas=6417.5) -@pytest.mark.xfail(raises=ValueError) def test_cas_format_unreadable(): - ChemFormula("H2O", 0, "Water", cas="64 - 17 - 5") + with pytest.raises(ValueError): + ChemFormula("H2O", 0, "Water", cas="64 - 17 - 5") -@pytest.mark.xfail(raises=ValueError) def test_cas_range_error(): - ChemFormula("H2O", 0, "Water", cas=100) + with pytest.raises(ValueError): + ChemFormula("H2O", 0, "Water", cas=100) -@pytest.mark.xfail(raises=ValueError) def test_cas_check_digit_error(): - ChemFormula("H2O", 0, "Water", cas="64-17-6") + with pytest.raises(ValueError): + ChemFormula("H2O", 0, "Water", cas="64-17-6") diff --git a/tests/test_general.py b/tests/test_general.py index 395f6d7..c4129b3 100644 --- a/tests/test_general.py +++ b/tests/test_general.py @@ -1,10 +1,9 @@ import pytest -from chemformula import ChemFormula +from chemformula import ChemFormula, elements # pytest fixtures - @pytest.fixture def muscarine(): return ChemFormula( @@ -65,8 +64,25 @@ def test_charged(testinput, expected): (ChemFormula("SO2"), False), ], ) -def test_radioactive(testinput, expected): - assert testinput.radioactive is expected +def test_is_radioactive(testinput, expected): + assert testinput.is_radioactive is expected + assert testinput.radioactive is expected # deprecated property + + +def test_get_valid_element_symbols_without_hydrogen_isotopes(): + allowed_symbols = elements.get_valid_element_symbols() + assert "D" not in allowed_symbols and "T" not in allowed_symbols + + +@pytest.mark.parametrize( + "testinput, expected", + [ + ("NH4ClO4", False), + ("NH4TcO4", True), + ], +) +def test_contains_isotopes(testinput, expected): + assert ChemFormula(testinput).contains_isotopes is expected @pytest.mark.parametrize( @@ -185,26 +201,31 @@ def test_hill_formula_text_formula(testinput, expected): # Tests for error handling -@pytest.mark.xfail(raises=TypeError) +#@pytest.mark.xfail(raises=TypeError) def test_charge_failed(): - ChemFormula("H3O", "+") + with pytest.raises(TypeError): + ChemFormula("H3O", "+") -@pytest.mark.xfail(raises=ValueError) +#@pytest.mark.xfail(raises=ValueError) def test_brackets_closing(): - ChemFormula("H2)O") + with pytest.raises(ValueError): + ChemFormula("H2)O") -@pytest.mark.xfail(raises=ValueError) +#@pytest.mark.xfail(raises=ValueError) def test_brackets(): - ChemFormula("(H2)(O") + with pytest.raises(ValueError): + ChemFormula("(H2)(O") -@pytest.mark.xfail(raises=ValueError) +#@pytest.mark.xfail(raises=ValueError) def test_element(): - ChemFormula("caO") + with pytest.raises(ValueError): + ChemFormula("caO") -@pytest.mark.xfail(raises=ValueError) +#@pytest.mark.xfail(raises=ValueError) def test_unknown_element(): - ChemFormula("XyO") + with pytest.raises(ValueError): + ChemFormula("XyO") diff --git a/tests/test_isotopes.py b/tests/test_isotopes.py new file mode 100644 index 0000000..0c770a6 --- /dev/null +++ b/tests/test_isotopes.py @@ -0,0 +1,52 @@ +import pytest + +import chemformula.config +from chemformula import ChemFormula, elements + +# Tests for functionality + +@pytest.fixture(autouse=True, scope="module") +def enable_hydrogen_isotopes(): + chemformula.config.AllowHydrogenIsotopes = True + + +def test_get_valid_element_symbols_with_hydrogen_isotopes(): + allowed_symbols = elements.get_valid_element_symbols() + assert "D" in allowed_symbols and "T" in allowed_symbols + + +@pytest.mark.parametrize( + "testinput, expected", + [ + ("H2O", False), + ("D2O", True), + ("NH4ClO4", False), + ("NH4TcO4", True), + ], +) +def test_contains_isotopes(testinput, expected): + assert ChemFormula(testinput).contains_isotopes is expected + + +@pytest.mark.parametrize( + "testinput, expected", + [ + ("H2O", 18.02), + ("D2O", 20.03), + ], +) +def test_formula_weight_hydrogen_isotopes(testinput, expected): + assert round(ChemFormula(testinput).formula_weight, 2) == expected + + +@pytest.mark.parametrize( + "testinput, expected", + [ + ("H2O", False), + ("D2O", False), + ("T2O", True), + ], +) +def test_is_radioactive_isotopes(testinput, expected): + assert ChemFormula(testinput).is_radioactive is expected + assert ChemFormula(testinput).radioactive is expected # `radioactive` is deprecated, use `is_radioactive` instead diff --git a/tests/test_sorting.py b/tests/test_sorting.py index fc889c3..8b166d2 100644 --- a/tests/test_sorting.py +++ b/tests/test_sorting.py @@ -79,3 +79,16 @@ def test_for_lesser_than(testinput_left, testinput_right): def test_for_sorting(hydrocarbons, hydrocarbons_sorted): assert sorted(hydrocarbons) == hydrocarbons_sorted + + +# Tests for error handling + + +def test_equal_type_error(caffeine): + with pytest.raises(TypeError): + assert caffeine == "C8H10N4O2" + + +def test_lesser_than_type_error(l_lacticacid): + with pytest.raises(TypeError): + assert l_lacticacid < 10326_41_7 diff --git a/uv.lock b/uv.lock index 80124d3..fc27bb5 100644 --- a/uv.lock +++ b/uv.lock @@ -1,6 +1,6 @@ version = 1 revision = 2 -requires-python = ">=3.9" +requires-python = ">=3.10" [[package]] name = "backports-tarfile" @@ -13,148 +13,142 @@ wheels = [ [[package]] name = "casregnum" -version = "1.0.1" +version = "1.1.2" source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/76/0f/193f6535f82847916cd42d5bf0277028b35564547b53bf2291e5868b09e9/casregnum-1.0.1.tar.gz", hash = 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