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Discovery of nitrogen fixation catalysts with genetic algorithms

Code repository for the paper Discovery of molybdenum based nitrogen fixation catalysts with genetic algorithms.

  1. Run
  2. Parameters

How to run

To setup an environment for running the GA, activate a conda environment with pip installed and run:

pip install .

Then ensure you have installed xtb in the environment.

To do a simple GA run, activate the environment and run:

python genetic_algorithm_driver.py --scoring_func calculate_score --partition kemi1 --generations 1 --filename data/ligands.smi --debug --population_size 4 --molecules_per_chunk 2 --cpus_per_chunk 2 --sa_screening --CovalentLigands 3 --DativeLigands 1 --opt loose --n_confs 2

Input driver arguments

A list of possible arguments and their discriptions are seen below:

Arg Description
-h or --help Prints help message.
--population_size Sets the size of the population pool.
--n_confs Sets how many conformers to generate for each molecule.
--num_rotatable_bonds Set the limit for the number of rotatable bonds for new children.
--max_size Maximum number of heavy atoms allowed in crossover
--min_size Minimum number of heavy atoms allowed in crossover
--DativeLigands Number of dative ligands in each catalyst
--CovalentLigands Number of covalent ligands in each catalyst
--BidentateLigands Number of bidentate ligands in each catalyst
--molecules_per_chunk Parallelization option. How many molecules to put in each SLURM job
--cpus_per_chunk Parallelization option. How many cpus to reserve for each SLURM job
--memory_per_chunk Parallelization option. How much memory per cpu in a SLURM job
--partition Cluster to run on
--debug If set the starting population is a set of 4 small molecules that can run fast locally. Used for debugging.
--find_connection_point Pre-screen ligand candidates for connection points
--load_from_pickle Load starting population from pickle file
--minimize_score Minimize the score obtained from scoring function
--generations How many evolution cycles of the population is performed.
--n_tries Sets how many times the GA is restarted. Can be used to run multiple GA runs in a single submission.
--scoring_function Chose one of the specified scoring functions to run
--sa_screening Decides if synthetic accessibility score is enabled. Highly recommended to turn this on.
--filename Path to the database extract to create starting population.
--output_dir Sets output directory for all files generated during generations.
--scratch Path to put any intermediate scratch files
--cleanup If enabled, all scoring files are removed after scoring. Only the optimized structures and their energies are saved.
--method Which gfn method to use.
--timeout_min How many minutes each slurm job is allowed to run
--rms_prune Pruning value for RDKit conformer embedding
--energy_cutoff Sets energy cutoff on the conformer filtering.
--opt Set optimization convergence criteria for xTB.

Authors

Magnus Strandgaard1

1 Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark. Email: mastr@chem.ku.dk.