README.md

GB-GA for the Schrock catalyst

Repository for the paper Genetic algorithm-based re-optimization of the Schrock catalyst for dinitrogen fixation. The GA implementation is based on the GB_GA.

Note

This codebase is slightly outdated for the work we do on catalyst design with GAs. For the interested, this is a more robust codebase we are currently using for catalyst design: catalystGA. And for other updated work on the Schrock catalyst see: genetic_algorithm_for_nitrogen_fixation

1. How to run
2. Driver function arguments

How to run

For simple use of the GA install with conda install the env file.

conda env create --file environment.yml

To run the GA activate the relevant environment and run the following for a quick run on a local installation:

python GA_schrock.py --supress_amines --debug --average_size 10 --size_stdev 2 --scoring_func rdkit_embed_scoring_NH3toN2 --cpus_per_task 2 --population_size 3 --mating_pool_size 4

Driver function arguments

A list of possible commandline 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.
--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 size distribution for molecules.

Authors

Magnus Strandgaard¹ Julius Seumer¹ Jan H. Jensen¹

¹ Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark.

For any questions regarding the code, please do not hesitate to contact me at : [email protected].