ChargeFW2

Application for computing partial atomic charges using selected empirical methods. ChargeFW2 is the computational core of Atomic Charge Calculator.

See the short description of implemented methods.

Compilation requirements

To compile ChargeFW2, several requirements have to be installed first. The compilation was tested on Ubuntu 25.10 with these versions of libraries:

• CMake 3.31
• GCC 15.2
• Boost 1.83
• Eigen 3.4
• nanoflann 1.7
• JSON for Modern C++ 3.11
• GEMMI 0.7.4
• pybind11 2.11

Other versions of the libraries might work too, but it was not tested. See the Dockerfile as the formal description of the dependencies.

Installation

After downloading and unpacking the sources, run the following in the ChargeFW2 directory:

mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=<WHERE-TO-INSTALL> -DPYTHON_MODULE=ON -DCMAKE_BUILD_TYPE=Release
make
make install

Docker

Rather than installing all dependencies, you can run ChargeFW2 directly inside a Docker container.

Using the pre-built image

A ready-to-use image is available on Docker Hub:

# Explicit pull of the image (optional)
docker pull sbncbr/chargefw2
# Check that it works
docker run --rm sbncbr/chargefw2 --help

Local build

You can also build the Docker image locally from the provided Dockerfile. This version will be optimised for your hardware as opposed to the pre-built general image from Docker Hub.

docker build -t sbncbr/chargefw2:local .
docker run --rm  sbncbr/chargefw2:local --help

Running

Suppose you want to compute partial atomic charges for a molecule stored in molecule.sdf located at /home/user/data/molecules on your host machine, and you want ChargeFW2 to write the results into /home/user/data/charges.

To make these host directories accessible inside the container, bind-mount them and expose them as /in and /out inside the container:

INPUT_DIR="/home/user/data/molecules"
OUTPUT_DIR="/home/user/data/charges"

docker run --rm \
  -v "$INPUT_DIR:/in" \
  -v "$OUTPUT_DIR:/out" \
  sbncbr/chargefw2 \
  --mode charges \
  --input-file /in/molecule.sdf \
  --chg-out-dir /out

Usage

The documentation for the application and its Python bindings is located in the doc folder.

How to cite

If you found ChargeFW2 or Atomic Charge Calculator helpful, please cite: Raček, T., Schindler, O., Toušek, D., Horský, V., Berka, K., Koča, J., & Svobodová, R. (2020). Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic Acids Research.