GetProperties

This repository contains an updated version of the Sigman group's "Get_Properties" script with parallelization. For the original script, please visit the original repository.

Installation

1. Create a conda environment using the gpenv_312.yml file.

   conda env create -f gpenv_312.yml

2. Activate the environment and use the notebook.

   conda activate gpenv_312

Usage

Use the notebook get_properties.ipynb to collect your properties. Be sure to set your Jupyter kernel to gpenv_312. Follow the instructions for each cell. Several comparisons between the old and new versions can be found in the /tests/ directory.

Parallelized Functions

1. get_goodvibes_data
2. get_frontierorbs
3. get_polarizability
4. get_dipole
5. get_volume
6. get_SASA
7. get_nbo
8. get_nmr
9. get_distance
10. get_angles
11. get_dihedral
12. get_vbur_scan
13. get_sterimol_morfeus
14. get_chelpg
15. get_hirshfeld
16. get_pyramidalization
17. get_planeangle
18. get_time

Non-parallelized Functions

1. get_IR
2. get_sterimol_dbstep
3. get_sterimol2vec

To-do

1. Implement get_IR
2. Implement get_sterimol_dbstep
3. Implement get_sterimol2vec
4. Implement get_enthalpies
5. Switch to computing properties for one file at a time to reduce I/O operations by ~90% (major overhaul)

Major changes

• Everything is parallelized
• Using logging module instead of print statements (easily redirected to file)
• Interactive 3D visualization of your files for easy atom name assignment
• get_buried_sterimol has been combined into get_sterimol_morfeus. Specifying a radius will automatically bury the molecule while regular sterimol is calculated if radius is None
• Logfiles are automatically converted to .mol files
• Logfiles can be in any directory instead of the same directory as the Jupyter notebook
• File reading failures are decreased using a .xyz correction process
• Failure to read in files notifies user

Contributors

• James R. Howard, PhD
• Brittany C. Haas, PhD
• Melissa A. Hardy, PhD
• Jordan P. Liles, PhD