import json
import os
# Configuration dictionary
config = {
"_comment": "GENERAL CONFIGURATIONS",
"output_path": "sample_predictions",
"jobname": "abl_wt",
"_comment2": "CONFIGURATIONS TO BUILD MSA",
"sequence_path": "abl1.fasta",
"tmp_dir": "tmp",
"homooligomers": 1,
"use_ramdisk": True,
"_comment3": "CONFIGURATIONS TO MAKE PREDICTIONS",
"engine": "alphafold2",
"msa_path": None,
"msa_from": "mmseqs2",
"seq_pairs": [
[64, 128],
[128, 256],
[256, 512],
[512, 1024]
],
"seeds": 10,
"platform": "cpu",
"save_all": False,
"models": [1, 2, 3, 4, 5],
"recycles": 4,
"subset_msa_to": None,
"_comment4": "GENERAL ANALYSIS CONFIGURATIONS",
"align_range": "backbone",
"ref1d": None,
"ref2d1": None,
"ref2d2": None,
"predictions_path": "sample_preds/alphafold2",
"_comment5": "RMSF ANALYSIS CONFIGURATIONS",
"detect_mobile": True,
"peak_width": 3,
"peak_prominence": 1,
"peak_height": 2,
"starting_residue": 200,
"_comment6": "RMSD ANALYSIS CONFIGURATIONS",
"analysis_range": "backbone and resid 358-365",
"analysis_range_name": "aloop",
"_comment7": "RMSD_2D OR TMSCORE_2D CONFIGURATIONS",
"mode_results": None,
"n_stdevs": 5,
"_comment8": "TMSCORE CONFIGURATIONS",
"slice_predictions": "backbone and resid 210-459",
"_comment10": "PCA CONFIGURATIONS",
"n_pca_clusters": 3,
"_comment11": "TRAJECTORY SAVING CONFIGURATIONS",
"reorder": "rmsd_1d",
"traj_format": "pdb",
"n_clusters": None
}
[docs]
def main():
# Extract output path
output_path = config.get("output_path")
# Create directory if it doesn't exist
if not os.path.exists(output_path):
os.makedirs(output_path)
# Save the config dictionary to config.json
with open("config.json", "w") as config_file:
json.dump(config, config_file, indent=4)
if __name__ == "__main__":
main()