From fa45247aa9867f504c02eb6f62d8459a94a0a936 Mon Sep 17 00:00:00 2001 From: Victoria Lim Date: Sun, 27 Sep 2020 15:17:06 -0700 Subject: [PATCH] Update README.md Add collaborators, add preprint, reorganize --- README.md | 57 ++++++++++++++++++++++++++++--------------------------- 1 file changed, 29 insertions(+), 28 deletions(-) diff --git a/README.md b/README.md index 1eb71b8..927e45f 100644 --- a/README.md +++ b/README.md @@ -1,34 +1,15 @@ # BenchmarkFF [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/vtlim/benchmarkff.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/vtlim/benchmarkff/context:python) -README last updated: Aug 2 2020 +README last updated: Sep 27 2020 ## About -Overview: Compare optimized geometries and energies from various force fields with respect to a QM reference. +**Objective**: Compare optimized geometries and energies from various force fields with respect to a QM reference. This repository comprises code to extract molecule datasets from [QCArchive](https://qcarchive.molssi.org/), run energy minimizations with various force fields, and analyze the resulting geometries and energies with respect to QM reference data from QCArchive. -## Python setup - -### Package dependencies - -* numpy, matplotlib, seaborn -* OpenEye -* RDKit (solely for TFD calculations) -* OpenMM -* OpenForceField -* QCFractal, QCPortal - - -### Conda setup -``` -conda create -n parsley python=3.6 matplotlib numpy seaborn -conda activate parsley -conda install -c openeye -c conda-forge -c omnia rdkit openeye-toolkits qcfractal qcportal openforcefield cmiles openmm -``` - -The packages in VTL's conda environment is documented in this repo as `parsley.yml`. +See our work in this [preprint](https://chemrxiv.org/articles/preprint/Benchmark_Assessment_of_Molecular_Geometries_and_Energies_from_Small_Molecule_Force_Fields/12551867): Lim et. al.; Benchmark Assessment of Molecular Geometries and Energies from Small Molecule Force Fields. 2020. ## Contents @@ -55,8 +36,28 @@ File descriptions: |`03_analysis`|`reader.py` |reader for molecule sets and text input files called by the other analysis scripts| |`03_analysis`|`tailed_parameters.py` |identify parameters that may be overrepresented in high RMSD/TFD tails for FFXML force fields| +## Python setup + +### Package dependencies + +* numpy, matplotlib, seaborn +* OpenEye +* RDKit (solely for TFD calculations) +* OpenMM +* OpenForceField +* QCFractal, QCPortal + + +### Conda setup +``` +conda create -n parsley python=3.6 matplotlib numpy seaborn +conda activate parsley +conda install -c openeye -c conda-forge -c omnia rdkit openeye-toolkits qcfractal qcportal openforcefield cmiles openmm +``` + +The packages in VTL's conda environment is documented in this repo as `parsley.yml`. -## Brief overview +## Brief overview of usage ### Setup 1. Write out from a QCArchive database which have completed QM calculations, using `extract_qcarchive_dataset.ipynb`. @@ -91,13 +92,13 @@ To explore the analyzed data, adjust plots, etc. without re-analyzing data, you input the pickle file written out from the previously run analysis. ## Contributors -* Victoria Lim (author) -* David Mobley (advising) -* Jeffrey Wagner, Daniel Smith (code review) -* Jessica Maat, Caitlin Bannan, Hyesu Jang, Lee-Ping Wang, Chris Bayly (discussions) +* **Authors**: Victoria T. Lim, David F. Hahn +* **Advising**: David Mobley, Gary Tresadern, Chris Bayly +* **Code review**: Jeffrey Wagner, Daniel Smith +* **Discussions**: Jessica Maat, Caitlin Bannan, Hyesu Jang, Lee-Ping Wang ## Big picture wish list / to do tasks -See more science-focused issues in the Github issue tracker. +See more focused issues in the [issue tracker](https://github.com/MobleyLab/benchmarkff/issues). * Format code with YAPF/Black * Use logging module instead of print statements * Look into automatically serializable representations (e.g., Pydantic) instead of pickle