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Readme for new release
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willfinnigan committed Sep 25, 2020
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Expand Up @@ -13,8 +13,9 @@ For more information, please see our preprint:
[Finnigan, William; Hepworth, Lorna J.; Turner, Nicholas J.; Flitsch, Sabine (2020): RetroBioCat: Computer-Aided Synthesis Planning for Biocatalytic Reactions and Cascades. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.12571235.v1](https://chemrxiv.org/articles/preprint/RetroBioCat_Computer-Aided_Synthesis_Planning_for_Biocatalytic_Reactions_and_Cascades/12571235?fbclid=IwAR3PBVXF-MGavQ2ejq3gdVQhdRxUYxNLPvI-EozTnqfm1Ut9R2eDJOD6i4I)

## Requirements and testing
python >= 3.7
rdkit >= 2020
python = 3.7
rdkit >= 2020
tensorflow >= 2.1.0
Python packages listed in requirements.txt. The lastest version of each package is recommended other than where specified.

Retrobiocat also requires a running mongodb and redis instance, for which we recommended using docker.
Expand All @@ -40,6 +41,10 @@ docker-compose build --no-cache
- Copy the building_blocks.db file from https://figshare.com/articles/software/RetroBioCat_database_files/12696482
into the `/docker/data/buyability` folder

- Copy the templates and policy model from
https://figshare.com/articles/AiZynthFinder_a_fast_robust_and_flexible_open-source_software_for_retrosynthetic_planning/12334577
into the `/docker/data/aizynthfinder` folder

- Run.
```
docker-compose up
Expand All @@ -64,6 +69,10 @@ git clone https://github.com/willfinnigan/retrobiocat.git

* Copy the building_blocks.db file from https://figshare.com/articles/software/RetroBioCat_database_files/12696482
into `/retrobiocat/retrobiocat_web/retro/data/buyability/`

- Copy the templates and policy model from
https://figshare.com/articles/AiZynthFinder_a_fast_robust_and_flexible_open-source_software_for_retrosynthetic_planning/12334577
into the `/retrobiocat/retrobiocat_web/retro/data/aizynthfinder` folder

* Install retrobiocat_web along with requirements.
```
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