pkaani 0.1.14

A Python package to calculate pKa values for proteins

INSTALLATION (using PyPI)

If you would like to use pKa-ANI in a python script, simply use the command below:

pip install pkaani

Python script usage

The snippet below shows how to use the calculate_pka function within a python script - the input argument is a list of strings which are PDB file names in the working directory. Given a list of PDBs titled "1brs.pdb" and "6oge_de.pdb":

from pkaani.pkaani import calculate_pka as calculate_pkaani
  
pKas = calculate_pkaani(["1brs.pdb","6oge_de.pdb"])

Command line usage

Note that command line usage (e.g. pkaani -i 1FDL.pdb on the command line) will not work with the simple pip install given above.

Command line usage performs energy minimization on the structure before the pKa calculation, which requires ambertools and can be installed as given below (only works with Python versions <3.14)

conda create -n pkaani python=3.13
conda activate pkaani
conda install conda-forge::ambertools

Note that this necessitates a numpy version earlier than 2.0, so if you are running into a numpy error use the following command to alleviate it:

pip install "numpy<2"

Example command line usages:

• If PDB file doesnt exist, it is downloaded and prepared for pKa calculations.

pkaani -i 1BNZ
      
pkaani -i 1BNZ.pdb

• Multiple files can be given as inputs

pkaani -i 1BNZ,1E8L

• If a specific directory is wanted:

pkaani -i path_to_file/1BNZ
      
pkaani -i path_to_file/1BNZ,path_to_file/1E8L

Arguments:

-h: Help

-i: Input files. Inputs can be given with or without file extension (.pdb). 
    If PDB file is under a specific directory (or will be downloaded) the path                 
    can also be given as path_to_file/PDBFILE. Multiple PDB files can be given 
    by using "," as separator (i.e. pkaani -i 1BNZ,1E8L).

INSTALLATION (from source code)

Navigate to this repository for the source code for this pyPI upload: https://github.com/adnaksskanda/pKa-ANI/tree/pyPI_upload

Prior to the installation of pKa-ANI, users should make sure they have installed conda.

To install pKa-ANI, navigate to the directory of the source that you've downloaded and;

conda env create -f pkaani_env.yaml

This will create a conda environment named pkaani and install all required packages. After the environment is created, activate the environment and install the package.

conda activate pkaani 
pip install .

PREREQUISITES:

• miniconda/anaconda

If pkaani_env.yaml is not used, users should make sure the following packages are installed.

• python>=3.10
• numpy
• scipy
• pytorch
• torchani==2.2.0
• scikit-learn==1.6.1
• ase
• joblib
• ambertools
• setuptools

Other notes

pKa-ANI requires PDB files to have H atoms that are added with default ionization states of residues: ASP, GLU, LYS, TYR, HIE.

Due to this reason, input PDB file(s) are prepared before the calculation of pKa values (output PDB file 'PDBID_pkaani.pdb').

We would like to warn users, that our models are trained to predict pKa values for apo-proteins. Due to this, any residue that is not an aminoacid is removed from PDB file(s) during the preparation.

CITATION

Gokcan, H.; Isayev, O. Prediction of Protein p K a with Representation Learning. Chem. Sci. 2022, 13 (8), 2462–2474. https://doi.org/10.1039/D1SC05610G.

LICENSING

Please read LICENSE file.