Installation

For general information on installing the module and downloading the example notebooks, please refer to the HQStage documentation.

Please note that HQS Molecules is currently only supported on Linux.

Parts of this module require third-party software packages that are not available for installation via pip: Open Babel, xTB and CREST.

The RDKit developers recommend installation via the conda-forge channel. Please note that the package on PyPI, which is installed by the pip command, may not necessarily contain the latest released version.

Specific installation commands for an environment with the conda package manager are provided below.

1. Installation of RDKit:
   To make use of the latest version of the program, RDKit should be installed from the conda-forge channel. Installation via the PyPI server is also possible, but we have sometimes observed its versions being behind the releases on GitHub and on conda-forge.

2. Installation of Open Babel:
   To benefit from the full scope of the 2D-to-3D structure conversion feature, we recommend installing Open Babel. Open Babel can be obtained via the package managers of various Linux distributions (e.g., apt on Debian 12) or alternatively from the conda-forge channel. Note: 2D-to-3D structure conversion in HQS Molecules uses the Open Babel package as a fallback option if RDKit fails to generate a reasonable three-dimensional structure. It is possible to use HQS Molecules without Open Babel, relying only on RDKit for structure conversion.

3. Installation of xTB:
   To make use of the interface to the xTB program for semiempirical calculations, the xtb binary must be provided by the user in the PATH variable. We strongly recommend to download the binary release 6.7.1 from GitHub, since Hessian calculations with the GFN-FF method are known to fail with version 6.7.0. Besides that, an installation from conda-forge is possible, in principle, but it is known to fail for specific calculations (like e.g. Hessian calculations for linear molecules).

4. Installation of CREST:
   To make use of the interface to the CREST program for conformer search, the crest binary must be provided by the user in the PATH variable. We recommend downloading the binary release 3.0.2 from GitHub.

Commands for the Installation of Third-Party Software

On Linux machines, we recommend working with a conda environment. It can be set up using distributions such as Anaconda, Miniforge or Mamba / Micromamba. The software packages mentioned above can be installed on Linux with the following commands:

# (1) Install Open Babel via apt
sudo apt install openbabel

# (2) Install RDKit in the current conda environment
conda install rdkit

# (3) Download and install the binaries of xTB
XTB_ARCHIVE="xtb-6.7.1-linux-x86_64.tar.xz"
XTB_URL="https://github.com/grimme-lab/xtb/releases/download/v6.7.1/${XTB_ARCHIVE}"
XTB_FOLDER="xtb-dist"
curl -LO ${XTB_URL}
tar -xvf ${XTB_ARCHIVE}
mv ${XTB_FOLDER} ${CONDA_PREFIX}/
ln -s ${CONDA_PREFIX}/${XTB_FOLDER}/bin/xtb ${CONDA_PREFIX}/bin/xtb
rm ${XTB_ARCHIVE}

# (4) Download and install the binaries of CREST
CREST_ARCHIVE="crest-intel-2023.1.0-ubuntu-latest.tar.xz"
CREST_URL="https://github.com/crest-lab/crest/releases/download/v3.0.2/${CREST_ARCHIVE}"
curl -LO ${CREST_URL}
tar -xvf ${CREST_ARCHIVE}
mv crest/crest ${CONDA_PREFIX}/bin/
rm ${CREST_ARCHIVE}