Security News
Introducing the Socket Python SDK
The initial version of the Socket Python SDK is now on PyPI, enabling developers to more easily interact with the Socket REST API in Python projects.
This Python module contains a Formula
class for working with chemical formulas, as well as methods for creating, manipulating, and analyzing formulas. It also includes functionality for dealing with adducts and calculating monoisotopic masses.
This Python module provides a Formula
class that allows you to work with chemical formulas. It includes the following features:
To use this module, you'll need Python 3.x and the required dependencies. You can install the dependencies using pip:
pip install rdkit urllib3
## Usage
### Creating Formula Objects
You can create a Formula object using various methods:
- `Formula.formula_from_str_hill(formula_str: str, adduct: str) -> 'Formula'`: Create a Formula object from a chemical formula string in Hill notation.
- `Formula.formula_from_str(formula_str: str, adduct: str, no_api: bool = False) -> 'Formula'`: Create a Formula object from a chemical formula string. You can disable API calls for formula resolution by setting `no_api` to `True`.
- `Formula.formula_from_smiles(smiles: str, adduct: str, no_api: bool = False) -> 'Formula'`: Create a Formula object from a SMILES string representing a molecular structure.
- `Formula.formula_from_inchi(inchi: str, adduct: str, no_api: bool = False) -> 'Formula'`: Create a Formula object from an InChI string representing a molecular structure.
### Basic Operations
You can perform various operations on Formula objects:
- Addition: `formula1 + formula2`
- Subtraction: `formula1 - formula2`
- Multiplication: `formula * num`
### Calculating Mass
You can calculate the monoisotopic mass of a formula and check if it matches an external mass:
- `get_monoisotopic_mass() -> float`: Get the monoisotopic mass of the formula.
- `get_monoisotopic_mass_with_adduct() -> float`: Get the monoisotopic mass of the formula, considering the adduct.
- `check_monoisotopic_mass(external_mass: Union[float, int], mass_tolerance_in_ppm: Union[int, float] = __default_ppm) -> bool`: Check if the monoisotopic mass is within a specified tolerance of an external mass.
- `check_monoisotopic_mass_with_adduct(external_mass: Union[float, int], mass_tolerance_in_ppm: Union[int, float] = __default_ppm) -> bool`: Check if the monoisotopic mass, considering the adduct, is within a specified tolerance of an external mass.
### Fragment Analysis
You can analyze potential fragment masses explained by a formula and adduct:
- `check_possible_fragment_mz(fragment_mz: Union[float, int], ppm: Union[float, int] = __default_ppm) -> bool`: Check if a fragment mass can be explained by the formula and adduct.
- `percentage_intensity_fragments_explained_by_formula(fragments_mz_intensities: Dict[Union[float, int], Union[float, int]], ppm: Union[float, int] = __default_ppm) -> float`: Calculate the percentage of intensity of fragments explained by the formula and adduct.
## Examples
Here are some examples of how to use the Formula class:
```python
# Create Formula objects
formula1 = Formula.formula_from_str_hill("C5H5O4", "[M+H]+")
formula2 = Formula.formula_from_smiles("CCO", "[M+NH4]+")
formula3 = formula1 + formula2
# Calculate monoisotopic mass
mass1 = formula1.get_monoisotopic_mass()
mass2 = formula2.get_monoisotopic_mass_with_adduct()
print(f"Mass of formula1: {mass1}")
print(f"Mass of formula2 with adduct: {mass2}")
# Check mass against an external mass with a tolerance of 5 ppm
check_monoisotopic_mass = formula1.check_monoisotopic_mass(121.05142,5)
check_monoisotopic_mass_with_adduct = formula1.check_monoisotopic_mass_with_adduct(122.05862,5)
FAQs
Package to represent formulas with adducts and process ms data from it.
We found that formula-validation demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
Did you know?
Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.
Security News
The initial version of the Socket Python SDK is now on PyPI, enabling developers to more easily interact with the Socket REST API in Python projects.
Security News
Floating dependency ranges in npm can introduce instability and security risks into your project by allowing unverified or incompatible versions to be installed automatically, leading to unpredictable behavior and potential conflicts.
Security News
A new Rust RFC proposes "Trusted Publishing" for Crates.io, introducing short-lived access tokens via OIDC to improve security and reduce risks associated with long-lived API tokens.