README last updated: Jan 8 2020

Overview: 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, run energy minimizations with various force fields, and analyze the resulting geometries and energies with respect to QM reference data from QCArchive.

• Python (numpy, matplotlib, seaborn)
• OpenEye
• RDKit (solely for TFD calculations)
• OpenMM
• OpenForceField
• QCFractal, QCPortal

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

Directories in this repo:

• 01_setup: Extract molecules from QCArchive, convert to OpenEye mols, and standardize conformers and titles.
• 02_calc
• 03_analysis
• examples: See this directory for example results and plots.

File descriptions:

1. Write out from a QCArchive database which have completed QM calculations, using extract_qcarchive_dataset.ipynb.
2. Reorganize up the molecule set for conformers which are labeled as different molecules:
   1. Group all the same conformers together since they are separated by intervening molecules, using combine_conformers.ipynb.
   2. Of the full set, write out the good molecules that don't need conformer reorganization, using molextract.py from OEChem.
   3. Combine the results of steps 2.1 and 2.2: cat whole_02_good.sdf whole_03_redosort.sdf > whole_04_combine.sdf
   4. Read in the whole set with proper conformers, and rename titles for numeric order, using combine_conformers.ipynb.
   5. (opt) Write out associated SMILES: awk '/SMILES/{getline; print}' whole_05_renew.sdf > whole_05_renew.smi
   6. (opt) Generate molecular structures in PDF format, using mols2pdf.py.
3. Break up the full set into smaller chunks for managable computations, using molchunk.py.
4. Run the minimizations, using minimize_ffs.py.
5. Remove the molecules that were unable to minimize (e.g., due to missing parameters) from all files, using cat_mols.py.
6. Cat all the constituent files back together, using cat or cat_mols.py.
7. Analyze with match_minima.py and compare_ffs.py.
   1. (opt) If some conformers (not full molecules) are outliers, can remove using get_by_tag.py

The OEChem scripts referred to above are located here.

• molextract.py
• molchunk.py -- VTL modified to use OEAbsCanonicalConfTest

• Victoria Lim
• David Mobley (advising)
• Lee-Ping Wang (discussions)
• Jeffrey Wagner (code review)
• Daniel Smith (code review)

See more science-focused issues in the Github issue tracker.

• Format code with YAPF/Black
• Use logging module instead of print statements
• Look into automatically serializable representations (e.g., Pydantic) instead of pickle
• Use type hints for functions
• Allow user to pass in dict for plotting parameters (i.e., talk or paper font sizes)
• Generate plots with Plotly