New analysis

[ldamore]

Description

This PR introduces two additional benchmark analysis proposed by B. Swope and X. Lucas.

Installation of new_analysis command group in a dev environment

First, follow the installation procedures for the openff-benchmark-optimization environment described in Deployment Procedure document

Once this is done, you can clone the environment into a development environment:

conda create -n openff-analysis --clone openff-benchmark-optimization
conda activate openff-analysis

Install the new_analysis branch from github:

git clone https://github.com/openforcefield/openff-benchmark
cd openff-benchmark
git checkout --track origin/new_analysis
pip install -e .

General comments

The two new analysis are typically executed at point (5) of the Optimization Benchmark Protocol

With openff-benchmark report bill the analysis proposed by B. Swope is executed. The command accepts the paths of the optimized molecules obtained from the optimization step. Additionally, the reference method (b3lyp-d3bj by default) and an output directory can be specified.

  openff-benchmark report bill --input-path 4-compute-qm-filtered --input-path 4-compute-mm-filtered --ref-method b3lyp-d3bj --output-directory 5-results-bill

The command creates one output csv file per method, which are named bill_<method>.csv, i.e. bill_openff-1.0.0.csv

The analysis proposed by B. Swope operates as follows:

• For each molecule MOL-00001-XX.sdf

  • Report the relative energy (dE) of each MM optimized conformer (MM_conf) with respect to the MM optimized conformer which is the global minimum (MM_min)

  • dE = E_{MM_conf} - E_{MM_min}

  • Report the RMSD between each MM_conf and the QM optimized conformer which is the global minimum (QM_min)

  • RMSD (MM_conf | QM_min)

With openff-benchmark report xavier the analysis proposed by X. Lucas is executed. The command accepts the paths of the optimized molecules obtained from the optimization step. Additionally, the reference method (b3lyp-d3bj by default) and an output directory can be specified.

openff-benchmark report xavier --input-path 4-compute-qm-filtered --input-path 4-compute-mm-filtered --ref-method b3lyp-d3bj --output-directory 5-results-xavier

The command creates one output csv file per method, which are named xavier_<method>.csv, i.e. xavier_openff-1.0.0.csv

The analysis proposed by X. Lucas operates as follows:

• For each molecule MOL-00001-XX.sdf

  • Find the MM reference conformer (MM_ref) with the lowest RMSD with respect to QM_min

  • Report the relative energy (dE) and RMSD between MM_ref and MM_min

  • dE = E_{MM_ref} - E_{MM_min}

  • RMSD (MM_ref | MM_min)

The final openff-benchmark report plots-bill and openff-benchmark report plots-xavier commands take the directories containing the csv files as an input (output of 5-results-bill or 5-results-xavier).

For 5-results-bill an rmsd-cutoff and de-cutoff should be set.

openff-benchmark report plots-bill --input-path 5-results-bill/ --ref-method bill_gaff-2.11 --de-cutoff 1.5 --rmsd-cutoff 1.0

The algorithm will generate a ridge plot of all the conformers within the rmsd-cutoff for a range of dE values, and another ridge plot of all the conformers within the de-cutoff for a range of rsmd values.

For 5-results-xavier

openff-benchmark report plots-xavier --input-path 5-results-xavier/ --ref-method xavier_gaff-2.11

The algorithm will generate similar plots as for compare-forcefields and match_minima

Please note

When generating plots, --ref-method is used for indexing purposes only. Hence, one could arbitrarly use any .*csv generated by the corresponding analysis. b3lyp-d3bj has been omitted in the analysis for the sake of computational time and cannot therefore be used for indexing.

Todos

• [ ] Fix an error that prevent the drawing of density plots when using the intersection of methods at the plotting stage.
• [ ] Fix overlapping ytics labels in ridge plots
• [x] Introduced the intersection of methods at the plotting stage.

Questions

• [ ] Question1

Status

• [ ] Ready to go

[ldamore]

Closed because based on master. Opened a new PR #86 based on season-1