Update for super

Docking/ProgressiveDocking/activation_script.sh

@@ -1,3 +1,4 @@
 echo Activating virtual environment
 source ~/.bashrc
-conda activate app-deepdocking-gui-remote
+conda activate app-deepdocking-gui-remote
+module load omega

Docking/ProgressiveDocking/phase_4.sh

@@ -59,7 +59,7 @@ if [ $? != 0 ]; then
 fi
 
 echo "Creating simple jobs"
-python simple_job_models.py -n_it $1 -time 00-04:00 -file_path $file_path/$project_name -nhp $num_hyperparameters -titr $5 -n_mol $num_molec --save_path $save_path --percent_first_mols $7 --percent_last_mols $8
+python simple_job_models.py -n_it $1 -file_path $file_path/$project_name -nhp $num_hyperparameters -titr $5 -n_mol $num_molec --save_path $save_path --percent_first_mols $7 --percent_last_mols $8
 
 # Executes all the files that were created in the simple_jobs directory
 echo "Running simple jobs"

Docking/ProgressiveDocking/prepare_ligands_ad.sh

@@ -1,6 +1,5 @@
 #!/bin/bash
 #SBATCH --job-name=prepare
-#SBATCH --time=04:00:00
 #SBATCH --output=slurm-phase_2-%x.%j.out
 #SBATCH --error=slurm-phase_2-%x.%j.err
 
@@ -31,7 +30,7 @@ cp $name'.'sdf $fld'/'
 cd $fld
 python $script_path'/'split_sdf.py $name'.'sdf
 rm $name'.'sdf
-obabel -isdf *sdf -opdbqt -m
+find . -type f -name '*.sdf' | xargs -d '\n' -n 10000 -P 24 bash -c 'obabel -isdf "$@" -opdbqt -m;' command
 wait $!
 rm *sdf
 

Docking/ProgressiveDocking/simple_job_models.py

@@ -22,7 +22,6 @@ def print(*args, **kwargs):
 
 parser = argparse.ArgumentParser()
 parser.add_argument('-n_it','--iteration_no',required=True)
-parser.add_argument('-time','--time',required=True)
 parser.add_argument('-file_path','--file_path',required=True)
 parser.add_argument('-nhp','--number_of_hyp',required=True)
 parser.add_argument('-titr','--total_iterations',required=True)
@@ -49,26 +48,6 @@ def print(*args, **kwargs):
 nhp = int(io_args.number_of_hyp)
 titr = int(io_args.total_iterations)
 
-
-# Handle the time
-# We pass the min training time (4 hours usually) and lerp between the min and max times using the ratio
-# current_iteration/max_iterations
-time_model = io_args.time
-# Initial date time
-date_time = time_model
-# Convert max time (20 hours) to seconds
-max_seconds = 20*60*60  # 20 hours in seconds
-# Convert min time to seconds
-converted_seconds = datetime_string_to_seconds(date_time)
-# Lerp between the the min and max seconds
-lerp_seconds = int(lerp(converted_seconds, max_seconds, n_it/titr))
-# Convert back to datetime
-h, m, s = seconds_to_datetime(lerp_seconds)
-# Format our date time
-new_time = f"00-{h}:{m}"
-print("Generated Time: ", new_time)
-
-
 num_molec = int(io_args.number_mol)
 percent_first_mols = float(io_args.percent_first_mols)
 percent_last_mols = float(io_args.percent_last_mols)
@@ -234,7 +213,6 @@ def print(*args, **kwargs):
         ref.write('#SBATCH --cpus-per-task=1\n')
         ref.write('#SBATCH --job-name=phase_4\n')
         ref.write('#SBATCH --mem=0               # memory per node\n')
-        ref.write('#SBATCH --time='+new_time+'            # time (DD-HH:MM)\n')
         ref.write("#SBATCH --output=slurm-phase_4-%x.%j.out\n")
         ref.write("#SBATCH --error=slurm-phase_4-%x.%j.err\n")
         ref.write('\n')

Docking/ProgressiveDocking/simple_job_predictions.py

@@ -33,8 +33,6 @@
 for f in glob.glob(SAVE_PATH + '/iteration_' + str(n_it) + '/simple_job_predictions/*'):
     os.remove(f)
 
-time = '0-10:30'
-
 # temp = []
 part_files = []
 
@@ -51,7 +49,6 @@
         ref.write('#SBATCH --cpus-per-task=1\n')
         ref.write('#SBATCH --job-name=phase_5\n')
         ref.write('#SBATCH --mem=0               # memory per node\n')
-        ref.write('#SBATCH --time=' + time + '            # time (DD-HH:MM)\n')
         ref.write("#SBATCH --output=slurm-phase_5-%x.%j.out\n")
         ref.write("#SBATCH --error=slurm-phase_5-%x.%j.err\n")
         ref.write('\n')