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clangini a1462b0407 Merge branch 'master' of https://gitlab.com/CaflischLab/chem_library_preparation
2019-01-09 16:21:09 +01:00
otherfiles initial commit 2018-04-05 13:42:12 +02:00
pythonscripts added salt removal and occupancy threshold no longer hardcoded 2019-01-09 16:19:48 +01:00
conf_gen_test.ipynb added salt removal and occupancy threshold no longer hardcoded 2019-01-09 16:19:48 +01:00
library.sdf initial commit 2018-04-05 13:42:12 +02:00
library_preparation.sh added salt removal and occupancy threshold no longer hardcoded 2019-01-09 16:19:48 +01:00
README.md README.md was ugly, added spaces 2018-09-20 11:13:13 +02:00
Slides_librarypreparation_git.pdf initial commit 2018-04-05 13:42:12 +02:00

README.md

Suite of scripts for chemical library preparation -- JRM March 2018

Licence agreement: Feel free to reproduce it, modify it, add things to it But if you do so, keep the original reference and most importantly, continue to share it with your colleagues

This folder contains a meta script (library_preparation.sh), launching commands for preparing a chemical library for docking.

It relies heavily on python scripts, and other software:

SOFTWARE REQUIREMENTS generation of protomers: ChemAxon, with a working cxcalc binary

generation of conformers: RDKit > 2017

proper mol2 file conversion: corina

generation of parameters: cgenff, rdkit (for absinth)

Python scripts are in ROOT/pythonscripts/

Reference free energy of solvation structure are in ROOT/otherfiles/

It also contains a part of my group meeting of the 4th of April, with benchmark/considerations in ROOT/Slides_librarypreparation_git.pdf

Initial commit 5th April 2018

This version should replace the version shared on Slack.