Scripts for computational investigations of large and flexible chemical systems based on the conformation labelling system, ONIOM calculations in Python 3
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Filter_diversity_incl_label_generation_and_selection.ipynb
- The label generation and selection process have been integrated into the same script
- Take a xyz file + dihedral angle of interests and return the selected conformers as a list (numerical index from the conformation searching output file)
- Examples have been included
conformation_label_generation.ipynb
- Take a xyz file + dihedral angle of interests and return the conformation labels of the conformers in the file as a data frame
- Two Examples have been included
Selection_remove_repetitive_structures.ipynb
- Take a dataframe that contains the conformation label and ΔG‡ value of the conformers and return a list of selected conformers (as numerical index – inherit from the conformation searching output file)
- An Example has been included
gjf_generation.ipynb
- The output from ‘Filter_diversity_incl_label_generation_and_selection’ can be directly used as the input for generating the gjf
- The naming of the gjf file is controlled by ‘by_num’: by_num = ‘no’ -- filename given in the xyz file + a user-specified suffix (input as a string) by_num = ‘yes’ or other string -- filename of the xyz file + a number (the index of the conformer in the xyz file)
- Two examples have been included