Update for super

Docking/ProgressiveDocking/autodock_gpu_ad.sh

@@ -48,28 +48,29 @@ rm -r $out_fold
 mkdir $out_fold
 mkdir $out_fold/pdbqt
 
-for i in $dlg_fold/*dlg
-do
-    name=$(grep -m 1 'Name' $i|awk '{print $5}')
-    if [ "$mode" == "be" ]; then
-       run=$(grep -m 1 'RANKING' $i|awk '{print $3}')
-       score=$(grep -m 1 'RANKING' $i|awk '{print $4}')
-    elif [ "$mode" == "lc" ]; then
-       score=$(grep '#' $i|awk '$9>a {a=$9; b=$3} END {print b}')
-       run=$(grep '#' $i|awk '$9>a {a=$9; b=$5} END {print b}')
-    fi
-    echo "ADSCOR   $score">>$out_fold/pdbqt/$name
-    awk -v p="DOCKED: MODEL        $run" '$0~p{f=1} f{print} f&&/DOCKED: ENDMDL/{exit}' $i|cut -c9-|sed '/USER/d;/REMARK/d;/MODEL/d;/TORSDOF/d'>>$out_fold/pdbqt/$name
-done
+find . -name "$dlg_fold/*dlg" -print0 | 
+    while IFS= read -r -d '' line; do 
+        name=$(grep -m 1 'Name' $i|awk '{print $5}')
+        if [ "$mode" == "be" ]; then
+        run=$(grep -m 1 'RANKING' $i|awk '{print $3}')
+        score=$(grep -m 1 'RANKING' $i|awk '{print $4}')
+        elif [ "$mode" == "lc" ]; then
+        score=$(grep '#' $i|awk '$9>a {a=$9; b=$3} END {print b}')
+        run=$(grep '#' $i|awk '$9>a {a=$9; b=$5} END {print b}')
+        fi
+        echo "ADSCOR   $score">>$out_fold/pdbqt/$name
+        awk -v p="DOCKED: MODEL        $run" '$0~p{f=1} f{print} f&&/DOCKED: ENDMDL/{exit}' $i|cut -c9-|sed '/USER/d;/REMARK/d;/MODEL/d;/TORSDOF/d'>>$out_fold/pdbqt/$name
+    done
 
-find $dlg_fold -name '*dlg' -delete
-find $dlg_fold -name '*xml' -delete
+perl -e "for(<$dlg_fold/*dlg>){((stat)[9]<(unlink))}"
+perl -e "for(<$dlg_fold/*xml>){((stat)[9]<(unlink))}"
 
 cd $out_fold/pdbqt
 mkdir ../sdf
-obabel -ipdbqt * -osdf -m
-cat *sdf>>../sdf/res_$out_file'.'sdf
+find . -type f | xargs -d '\n' -n 10000 bash -c 'obabel -ipdbqt "$@" -osdf -m;' command
+find . -type f | xargs -d '\n' -n 10000 bash -c "cat \"$@\" >> ../sdf/res_$out_file'.'sdf;" command
 cd ..
+perl -e "for(<pdbqt/*>){((stat)[9]<(unlink))}"
 rm -r pdbqt
 
 end=`date +%s`

Docking/ProgressiveDocking/setup_slurm_specifications.py

@@ -30,7 +30,7 @@ def save_slurm_arg(project_name, path, n_cpu, cpu_partition, gpu_partition, cust
         slurm_args_gpart += " --partition=" + gpu_partition if gpu_partition is not None and "partition" not in slurm_args else ""
         f.write(slurm_args_gpart + "\n") # 3: write without cpu arg for gpu req scripts 
 
-        slurm_args_gpart += " --cpus-per-task="+str(n_cpu) if n_cpu is not None and "cpus-per-task" not in slurm_args else ""
+        slurm_args_gpart += " --cpus-per-task=3" if "cpus-per-task" not in slurm_args else ""
         f.write(slurm_args_gpart + "\n") # 4: write with cpu arg for gpu req scripts