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.
-
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. -
Installation of
Open Babel
:
To benefit from the full scope of the 2D-to-3D structure conversion feature, we recommend installingOpen 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 inHQS Molecules
uses the Open Babel package as a fallback option ifRDKit
fails to generate a reasonable three-dimensional structure. It is possible to useHQS Molecules
withoutOpen Babel
, relying only onRDKit
for structure conversion. -
Installation of
xTB
:
To make use of the interface to the xTB program for semiempirical calculations, thextb
binary must be provided by the user in thePATH
variable. We strongly recommend to download the binary release6.7.1
from GitHub, since Hessian calculations with the GFN-FF method are known to fail with version6.7.0
. Besides that, an installation fromconda-forge
is possible, in principle, but it is known to fail for specific calculations (like e.g. Hessian calculations for linear molecules). -
Installation of
CREST
:
To make use of the interface to the CREST program for conformer search, thecrest
binary must be provided by the user in thePATH
variable. We recommend downloading the binary release3.0.2
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}