style: fix imports and order of os.make_dirs

jyaacoub · Oct 27, 2024 · e22a5a0 · e22a5a0
1 parent 653cf40
commit e22a5a0
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Showing 2 changed files with 28 additions and 29 deletions.
diff --git a/inference.py b/inference.py
@@ -1,4 +1,4 @@
-import argparse
+import os, logging, argparse
 parser = argparse.ArgumentParser(description='Runs inference on a given ligand SMILES and an input of pdb files.')
 parser.add_argument('-ls','--ligand_smile', type=str, required=True, help='Ligand SMILES string.')
 parser.add_argument('-pdb','--pdb_files', type=str, nargs='+', required=True, 
@@ -35,17 +35,16 @@
 FOLD = args.fold
 BATCH_SIZE = args.batch_size
 
-import logging
 logging.getLogger().setLevel(logging.DEBUG)
-logging.debug("#"*50)
-logging.debug(f"LIGAND_SMILE: {LIGAND_SMILES}")
-logging.debug(f"LIGAND_ID: {LIGAND_ID}")
-logging.debug(f"PDB_FILES: {PDB_FILES}")
-logging.debug(f"OUT_PATH: {CSV_OUT}")
-logging.debug(f"MODEL_OPT: {MODEL_OPT}")
-logging.debug(f"FOLD: {FOLD}")
-logging.debug(f"BATCH_SIZE: {BATCH_SIZE}")
-logging.debug("#"*50)
+logging.info("#"*50)
+logging.info(f"LIGAND_SMILE: {LIGAND_SMILES}")
+logging.info(f"LIGAND_ID: {LIGAND_ID}")
+logging.info(f"PDB_FILES: {PDB_FILES}")
+logging.info(f"OUT_PATH: {CSV_OUT}")
+logging.info(f"MODEL_OPT: {MODEL_OPT}")
+logging.info(f"FOLD: {FOLD}")
+logging.info(f"BATCH_SIZE: {BATCH_SIZE}")
+logging.info("#"*50)
 
 import os
 import numpy as np

diff --git a/run_mutagenesis.py b/run_mutagenesis.py
@@ -1,7 +1,7 @@
-import argparse
+import os, logging, argparse
 parser = argparse.ArgumentParser(description='Runs Mutagenesis on an input PDB file and a given ligand SMILES.')
 parser.add_argument('--ligand_smile', type=str, required=True, help='Ligand SMILES string.')
-parser.add_argument('--ligand_smile_name', type=str, required=True, help='Ligand SMILES name, required for output path.')
+parser.add_argument('--ligand_id', type=str, required=True, help='Ligand SMILES identifier, required for output path.')
 parser.add_argument('--pdb_file', type=str, required=True, help='Path to the PDB file.')
 parser.add_argument('--out_path', type=str, default='./', 
                     help='Output directory path to save resulting mutagenesis numpy matrix with predicted pkd values')
@@ -21,28 +21,30 @@
 
 # Assign variables
 LIGAND_SMILE = args.ligand_smile
-LIGAND_SMILE_NAME = args.ligand_smile_name
+LIGAND_ID = args.ligand_id
 PDB_FILE = args.pdb_file
 OUT_PATH = args.out_path
 MODEL_OPT = args.model_opt
 FOLD = args.fold
 RES_START = args.res_start
 RES_END = args.res_end
 
-import logging
+OUT_DIR = f'{OUT_PATH}/{LIGAND_ID}/{MODEL_OPT}'
+os.makedirs(OUT_DIR, exist_ok=True)
+
 logging.getLogger().setLevel(logging.DEBUG)
-logging.debug("#"*50)
-logging.debug(f"LIGAND_SMILE: {LIGAND_SMILE}")
-logging.debug(f"LIGAND_SMILE_NAME: {LIGAND_SMILE_NAME}")
-logging.debug(f"PDB_FILE: {PDB_FILE}")
-logging.debug(f"OUT_PATH: {OUT_PATH}")
-logging.debug(f"MODEL_OPT: {MODEL_OPT}")
-logging.debug(f"FOLD: {FOLD}")
-logging.debug(f"RES_START: {RES_START}")
-logging.debug(f"RES_END: {RES_END}")
-logging.debug("#"*50)
-
-import os
+logging.info("#"*50)
+logging.info(f"LIGAND_SMILE: {LIGAND_SMILE}")
+logging.info(f"LIGAND_ID: {LIGAND_ID}")
+logging.info(f"PDB_FILE: {PDB_FILE}")
+logging.info(f"OUT_PATH: {OUT_PATH}")
+logging.info(f"MODEL_OPT: {MODEL_OPT}")
+logging.info(f"FOLD: {FOLD}")
+logging.info(f"RES_START: {RES_START}")
+logging.info(f"RES_END: {RES_END}")
+logging.info(f"OUT_DIR: {OUT_DIR}")
+logging.info("#"*50)
+
 import numpy as np
 import torch
 import torch_geometric as torchg
@@ -148,8 +150,6 @@ def get_protein_features(pdb_file_path, cmap_thresh=8.0):
 
 
 # Save mutagenesis matrix
-OUT_DIR = f'{OUT_PATH}/{LIGAND_SMILE_NAME}/{MODEL_OPT}'
-os.makedirs(OUT_DIR, exist_ok=True)
 OUT_FP = f"{OUT_DIR}/{res_range[0]}_{res_range[1]}.npy"
 print("Saving mutagenesis numpy matrix to", OUT_FP)
 np.save(OUT_FP, muta)