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 fromParsley v1.0.0-RC1
release notes (original location) -
v1.0.0-RC2/
: contains assets fromParsley v1.0.0-RC2
release notes (original location) -
smirnoff99Frosst-1.1.0/
: contains assets fromsmirnoff99Frosst 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)