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