procaliper 0.2.0

Skeleton project created by Python Project Wizard (ppw).

ProCaliper

ProCaliper is an open-source Python library for functional and structural analysis, visualization, and annotation of proteomic data.

ProCaliper enables interfacing with annotation resources such as UniProt, PhosphoSitePlus, AlphaFold, or user-supplied experimental data for computing structural and electromchemical property information, construction and analysis of residue-residue distance networks, and functional site identification at the residue or protein level.

Installation

To install from PyPI:

pip install procaliper

extras

During installation, procaliper will also install openbabel-wheel. If you require specialized features of openbabel that are not available in this precompiled version, please run pip uninstall openbabel-wheel after procaliper is installed and provide your own version of the openbabel python library.

Optional feature dependencies can be installed as follows:

pip install procaliper[nglview,pka]

The nglview extra provides the ability to visualize protein structures in a graphical notebook environment.

The pka extra provides additional methods for computing disassociation constants (typically denoted $pK_a$). Note that installing this extra requires obtaining a DelPhi license. Furthermore, these additional methods require an older version of numpy (version 1.26.4) and python version between 3.9 and 3.11 to properly function. If the pka extra is not installed, procaliper will use propka for $pK_a$ calculation.

Basic Usage

A basic example is provided here. See the examples folder for further examples.

import procaliper as pc

# Read in or download protein structure
protein = pc.Protein.from_uniprot_id("A0A0B4J2F0") # create a protein object from UniProt metadata using a UniProt ID
# alternatively, you can read in a protein from a UniProt Table using `Protein.from_uniprot_row`

# Download & save protein structure from AlphaFold
protein.fetch_pdb(save_path="A0A0B4J2F0.pdb") 
# Alternatively, `protein.register_local_pdb(file)` can be used to specify a previously downloaded pdb file

# Compute structure features
sasa = protein.get_sasa() # compute site-level SASA values
charge = protein.get_charge() # compute site-level charges
titr = protein.get_titration() # compute site-level titration (pKa) data
# The results from the above calculations are autmatically stored in the `protein` object.

# Get a table of site-level data
site_data = protein.unravel_sites() # returns a dictionary of lists; readable, e.g., by `pandas`

Contributing

Contributions are welcome!

See Contributing for detailed instructions.

License

This code is released under BSD 2-Clause "Simplified" License. See our License for detailed information.

By default, procaliper does not have any dependencies that are not freely licensed. However, additional features can be installed that rely on restricted software. That is, please note that some optional dependencies are not FOSS. Specifically, the pka extra requires a DelPhi license. We encourage caution when using software that is not free and open source, especially for contributions to the scientific literature.

Acknowledgements

The software described here was funded under the Predictive Phenomics Initiative (PPI) at Pacific Northwest National Laboratory (PNNL) under the Laboratory Directed Research and Development Program. PNNL is a multiprogram national laboratory operated by Battelle for the DOE under Contract No. DE-AC05-76RL01830.

Citation Guidance

1. Feng, S., Rozum, J. C., Ufford, H. S., Kim, D. N., & Im, A. K. (2025). ProCaliper. Zenodo. https://doi.org/10.5281/zenodo.15270417