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INSTALL.md

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Install XTB

For M1 Macs: Install using homebrew as described here: https://github.com/grimme-lab/homebrew-qc

Binaries can be downloaded here https://github.com/grimme-lab/xtb/releases/tag/v6.6.0 or directly installed using conda:

conda config --add channels conda-forge
conda search xtb --channel conda-forge

or alternatively

conda install mamba -c conda-forge

Current results were obtained using xtb version 6.5.1.

Install OPSIN

Used to convert iupac names -> smiles

As explained here https://anaconda.org/bioconda/opsin this can be achieved via:

conda install -c bioconda opsin

Alternatively, jar files can be obtained from https://github.com/dan2097/opsin/releases.

Install pip requirements

cd path/to/solvmate/
pip install -r requirements.txt

Advanced

Building Metadata DB for the Nearest Neighbor Search

To rebuild the metadata database, 7-zip is required. On mac this can be installed with

brew install p7zip

However, as we (will) make precompiled metadata available this should never be necessary from an end-user perspective.

Enabling the Ranked Pairs / PageRank algorithms

To enable the ranked pairs or pagerank advanced pair resolution algorithms the pair_rank module within solvmate/src/solvmate/pair_rank needs to be compiled and installed as a c extension on the target system. At the moment, this requires a working version of GNU make and a compiler on the target system. Running

cd solvmate/src/solvmate/pair_rank && make

should both build, install and test this extension.

TODO: The pagerank algo is actually implemented in pure python so should be much simpler to distribute. We should therefore cut it out of this ugly c extension hack and provide it directly within the ranksolv package. So that this annoying step is avoided...