Installation
BespokeFit and its dependencies can be installed in several ways. The OpenFF Initiative recommends using the mamba package manager.
Using Mamba
The recommended way to install openff-bespokefit is via the mamba package
manager. A working installation also requires at least one package from each of
the two sections below (“Fragmentation Backends” and “Reference Data
Generators”)
mamba install -c conda-forge openff-bespokefit "qcportal <0.50"
If you do not have Mamba installed, see the OpenFF installation documentation.
Warning
Some upstream dependencies may not be supported on Apple Silicon. To force mamba to use the use of the Rosetta emulation layer, use CONDA_SUBDIR=osx-64, which is described in more detail here.
Fragmentation Backends
AmberTools Antechamber
AmberTools is free and open-source, and can generally be used fragment molecules up to 40 heavy atoms in under 10 minutes.
mamba install -c conda-forge ambertools
OpenEye Toolkits
If you have access to the OpenEye toolkits (namely oechem, oequacpac and oeomega) we recommend installing
these also as they can speed up certain operations significantly. OpenEye software requires a
free-for-academics license to run.
mamba install -c openeye openeye-toolkits
Reference Data Generators
Psi4
Psi4 is an open source quantum chemistry package that enables BespokeFit to generate bespoke QC data, and is recommended to be installed unless you intend to train against data generated using a surrogate such as ANI:
mamba install -c conda-forge psi4 dftd3-python
Warning
There are some incompatibilities between the AmberTools and Psi4 conda packages on macOS, and it may not be possible to create a working conda environment containing both.
Note
Installing Psi4 into an existing environment sometimes fails because of subtle differences in compiled dependencies found in multiple channels. An alternative is to install everything when initially creating the environment using, with AmberTools:
mamba create -n bespokefit-env -c conda-forge openff-bespokefit psi4 dftd3-python ambertools
or with OpenEye Toolkits:
mamba create -n bespokefit-env -c conda-forge -c openeye openff-bespokefit psi4 dftd3-python openeye-toolkits
XTB
The xtb-python package gives access to the XTB semi-empirical models produced by the Grimme group, which may be
used as a much faster surrogate when generating QC reference data:
mamba install -c conda-forge xtb-python
xtb-python can optionally be configured to use MKL as its compute backend by running
mamba install -c conda-forge xtb-python "libblas=*=*mkl"
This likely provides better performance on Intel CPUs. Note that use of the MKL backend may be subject to additional license agreements with Intel. We currently understand it to be free for use by academics and companies generally, but it is not strictly open source.
TorchANI
TorchANI is a PyTorch implementation of the ANI neural network potentials from the Roitberg group that can be used as a much faster surrogate when generating QC reference data:
mamba install -c conda-forge torchani
Note
TorchANI potentials are only suitable for molecules with a net neutral charge and have limited element coverage consisting of C, H, N, O, S, F and Cl
From source
To install openff-bespokefit from source, begin by cloning the repository from
GitHub:
git clone https://github.com/openforcefield/openff-bespokefit
cd openff-bespokefit
Create a custom conda environment which contains the required dependencies and activate it:
mamba env create --name openff-bespokefit --file devtools/conda-envs/test-env.yaml
mamba activate openff-bespokefit
Finally, install the package itself into the new environment:
python -m pip install -e .