Repository for the paper: Genetic algorithm-based re-optimization of the Schrock catalyst for dinitrogen fixation
For simple use of the GA install with conda
conda env create --file environment.yml
To run the ga activate the relevant environment and run:
python GA_schrock.py
A list of possible arguments.
| Arg | Description |
|---|---|
-h or --help |
Prints help message. |
--population_size |
Sets the size of the population pool. |
--mating_pool_size |
Sets the size of the mating pool. |
--n_confs |
Sets how many conformers to generate for each molecule. |
--n_tries |
Sets how many times the GA is restarted. Can be used to run multiple GA runs in a single submission. |
--cpus_per_task |
How many cores to use for each scoring job. |
--RMS_thresh |
RMS cutoff value for RDKit conformer embedding. |
--generations |
How many evolution cycles of the population is performed. |
--mutation_rate |
Decides the probability of performing a mutation operation instead of crossover. |
--prune_population |
If there are duplicates within the current population these are removed. |
--sa_screening |
Decides if synthetic accessibility score is enabled. Highly recommended to turn this on. |
--file_name |
Path to the database extract to create starting population. |
--output_dir |
Sets output directory for all files generated during generations. |
--timeout |
How many minutes each slurm job is allowed to run |
--debug |
If set the starting population is a set of 4 small molecules that can run fast locally. Used for debugging. |
--ga_scoring |
If set, removes all higher energy conformers in GA. |
--supress_amines |
Supress amine heavy molecules by converting any primary amines to hydrogen in generations. |
--method |
Which gfn method to use. |
--energy_cutoff |
Sets energy cutoff on the conformer filtering. |
--bond_opt |
Decides if a final Mo-N bond optimization is performed during scoring. |
--cleanup |
If enabled, all scoring files are removed after scoring. Only the optimized structures and their energies are saved. |
--scoring_func |
Which scoring function to use. |
--opt |
Set optimization convergence criteria for xTB. |
--gbsa |
Which type of solvent to use for xTB. |
--input |
Name of input control file created for xTB |
--average_size |
Average number of atoms in molecules resulting from crossover. |
--size-stdev |
STD of crossover molecule size distribution |
Magnus Strandgaard1
1 Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark. Heres my email: [email protected].
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