This repository contains scripts, whose details are available in our preprint.

|-- 1_valence_parameter_fitting/
|   |-- README.md
|   |-- 1_dataset_generation/
|   |   |-- roche_set/
|   |   |   |-- 2019-05-16-Roche-Optimization_Set/ 
|   |   |   |-- 2019-07-09-OpenFF-Optimization-Set/ 
|   |   |   |-- 2019-05-01-OpenFF-Group1-Torsions/ 
|   |   |-- coverage_set/
|   |   |   |-- 2019-06-25-smirnoff99Frost-coverage/
|   |   |   |-- 2019-07-01-smirnoff99Frost-coverage-torsion/ 
|   |-- 2_forcebalance_optimization/
|   |   |-- 1_fb_target_gen/
|   |   |   |-- make_fb_optgeo_target.py 
|   |   |   |-- make_vib_freq_target.py 
|   |   |   |-- make_torsion_target_new.py 
|   |   |-- 2_input_components/ 
|   |   |   |-- optimize.in
|   |   |   |-- forcefield/
|-- 2_benchmarking/
|   |-- test_dataset_generation/ 
|   |   |-- divide_sets.ipynb
|-- 3_physical_property_datasets/
|   |-- physical_properties/

• 1_valence_parameter_fitting/README.md: OpenFF ForceBalance fitting tutorial(original location)

• 2019-05-16-Roche-Optimization_Set/: Roche optimization dataset construction and submission (original location)

• 2019-07-09-OpenFF-Optimization-Set/: Roche hessian dataset construction and submission (original location)

• 2019-05-01-OpenFF-Group1-Torsions/: Roche torsiondrive dataset construction and submission (original location)

• 019-06-25-smirnoff99Frost-coverage/: coverage optimization and hessian dataset construction and submission (original location)

• 2019-07-01-smirnoff99Frost-coverage-torsion/: coverage torsiondrive dataset construction and submission (original location)

• make_fb_optgeo_target.py: a python script for ForceBalance readable optgeo target generation (original location)

• make_vib_freq_target.py: a python script for ForceBalance readable vibfreq target generation (original location)

• make_torsion_target_new.py: a python script for ForceBalance readable torsiondrive target generation (original location)

• optimize.in: input file for ForceBalance optimization (original location)

• forcefield/: input forcefield directory for ForceBalance optimizaiton (original location)

• divide_sets.ipynb: script for dividing a large benchmark set into these two sets using path-based fingerprint method (original location)

• physical_properties/ : contains scripts for automated curation of physical property datasets and benchmarking results against condensed phase liquid properties (original location)

|-- forcefield_releases/
|   |-- parsley/
|   |   |-- v0.0.9/
|   |   |-- v1.0.0-RC1/ 
|   |   |-- v1.0.0-RC2/ 
|   |-- smirnoff99Frosst/
|   |   |-- smirnoff99Frosst-1.1.0/
|-- qm_datasets/
|   |-- training_datasets/
|   |   |-- 01_Roche_set/ 
|   |   |   |-- roche_optimization_set_gen.tar.gz
|   |   |   |-- roche_hessian_set_gen.tar.gz  
|   |   |   |-- roche_torsiondrive_set_gen.tar.gz
|   |   |-- 02_Coverage_set/
|   |   |   |-- Utility-All-Parameters.tar.gz 
|   |   |   |-- coverage_optimization_set_gen.tar.gz 
|   |   |   |-- coverage_torsiondrive_set_gen.tar.gz 
|   |-- test_datasets/ 
|   |   |-- discrepancy_optimization_set_gen.tar.gz
|   |   |-- pfizer_optimization_set_gen.tar.gz
|   |   |-- fda_drugs_optimization_set_gen.tar.gz
|-- physical_property_datasets/
|   |-- test_datasets/ 
|   |   |-- physical_properties_benchmark.tar.gz 
|-- utils/
|   |-- fragmenter-87b85a4.zip
|   |-- openforcefield-0.4.1/

• v0.0.9:

• v1.0.0-RC1/: contains assets from Parsley v1.0.0-RC1 release notes (original location)

• v1.0.0-RC2/: contains assets from Parsley v1.0.0-RC2 release notes (original location)

• smirnoff99Frosst-1.1.0/: contains assets from smirnoff99Frosst v1.1.0 release notes(https://github.com/openforcefield/smirnoff99Frosst/releases/tag/1.1.0)

• roche_optimization_set_gen.tar.gz: optimization data set construction (original location)

• roche_hessian_set_gen.tar.gz: vibrational data set construction (original location)

• roche_torsiondrive_set_gen.tar.gz: torsiondrive data set construction (original location)

• Utility-All-Parameters.tar.gz: Construction of the original coverage set (original location)

• coverage_optimization_set_gen.tar.gz: optimization, hessian data set construction (original location)

• coverage_torsiondrive_set_gen.tar.gz: torsiondrive data set construction (original location)

• discrepancy_optimization_set_gen.tar.gz: (original location)

• pfizer_optimization_set_gen.tar.gz: (original location)

• fda_drugs_optimization_set_gen.tar.gz: (original location)

• physical_properties_benchmark.tar.gz : contains scripts for automated curation of physical property datasets and benchmarking results against condensed phase liquid properties (original location)

• fragmenter-87b85a4.zip: fragmenter v0.0.2+121.g87b85a4 used for the datasets used for Parsley 1.0 (original location)

• openforcefield-0.4.1/: openforcefield toolkits v0.4.1 (original location)