conformer-scoring
Supporting data and scripts relevant to an evaluation of force field and quantum methods for conformer scoring via energy ranking.
Connected to the manuscript
"A Sobering Assessment of Small-Molecule Force Field Methods for Low Energy Conformer Predictions" arXiv: https://arxiv.org/abs/1705.04308
Brief description of files:
Jupyter / ipython notebooks for converting CSV data for analysis:
- MMAnalysis.ipynb
- OptAnalysis.ipynb
Output files and geometries:
- atoms.tar.bz2 - compiled ORCA output files for computing atomization energies
- conformers.tar.bz2 - compiled optimized geometries with MMFF94, PM7, and DFT
Compiled data:
- data.csv - energies corresponding to data-merge.csv mm-data.csv
Scripts:
- compile-conformers.py - read output files, compile conformer geometries and data.csv file
- consolidate-data.py - convert data.csv file into data-merge.csv file
Analysis CSV files created by OptAnalysis jupyter notebook:
- dft@mmff_dft@dft_stats.csv
- dft@mmff_dft@pm7_stats.csv
- dft@pm7_dft@dft_stats.csv
- mmff@mmff_dft@dft_stats.csv
- mmff@mmff_dft@pm7_stats.csv
- mmff@pm7_dft@dft_stats.csv
- pm7@dft_dft@dft_stats.csv
- pm7@dft_pm7@pm7_stats.csv
- pm7@mmff_pm7_stats.csv
- pm7@pm7_dft@dft_stats.csv
- pm7@pm7_dft@pm7_stats.csv
Analysis CSV files for MM vs. PM7 comparisons created by MMAnalysis jupyter notebook:
- mmff_pm7_stats.csv
- gaff_pm7_stats.csv
- uff_pm7_stats.csv
Auxillary scripts:
- rmsd.py - analyze the heavy-atom root mean square displacement (RMSD) using Open Babel