Update kissim scripts to run residue subsets

scripts/kissim_subsets.sh

@@ -0,0 +1,28 @@
+# @dominiquesydow
+# Subset and compare fingerprints
+# - DFG-in focused residues
+# - Martin et al. residues
+# 
+# Run this script only after having results from running the main script
+# https://github.com/volkamerlab/kissim_app/blob/master/scripts/kissim_encode_compare.sh
+#
+# Usage
+# -----
+# cd /path/to/kissim_app
+# bash kissim_subsets.sh
+
+KISSIM_APP="."
+NCORES=7
+
+# DFG-in focused residues
+for name_subset in dfg_in martin_set
+do
+    RESULTS=$KISSIM_APP/results/dfg_in_subset_${name_subset}
+    echo $RESULTS
+    echo "Select fingerprint subset..."
+    kissim subset -i $RESULTS/fingerprints_normalized.json -o $RESULTS/fingerprints_subset.json -s $name_subset
+    echo "Done."
+    echo "Compare fingerprints..."
+    kissim compare -i $RESULTS/fingerprints_subset.json -o $RESULTS -c $NCORES
+    echo "Done."
+done

scripts/kissim_ligand_subset.py → scripts/kissim_subsets_ligand.py

@@ -1,5 +1,5 @@
 """
-Generate KiSSim data for 
+Generate KiSSim data for ligand-based residue subsets.
 """
 
 from pathlib import Path
@@ -10,9 +10,10 @@
 
 PATH_RESULTS_DFG_IN = PATH_RESULTS / "dfg_in"
 
+
 def main(ligand_expo_id, path_fp_in=PATH_RESULTS_DFG_IN / "fingerprints_normalized.json"):
     """
-    Generate KiSSim fingerprint distances for a subset version of the fingerprint that 
+    Generate KiSSim fingerprint distances for a subset version of the fingerprint that
     is based only on residues that show interactions with co-crystallized structures
     (use KLIFS IFPS for this).
 
@@ -36,22 +37,23 @@ def main(ligand_expo_id, path_fp_in=PATH_RESULTS_DFG_IN / "fingerprints_normaliz
     # Subset fingerprints
     print("Subset fingerprints...")
     fingerprint_generator = subset(
-        fingerprints_path = path_fp_in,
+        fingerprints_path=path_fp_in,
         klifs_pocket_residue_subset_type=ligand_expo_id,
-        fingerprints_subset_path = path_out / "fingerprints_normalized.json",
-        klifs_pocket_residue_subset={ligand_expo_id: interacting_residues}
+        fingerprints_subset_path=path_out / "fingerprints_normalized.json",
+        klifs_pocket_residue_subset={ligand_expo_id: interacting_residues},
     )
-    
+
     print("All-against-all comparison...")
     compare(
         fingerprint_generator=fingerprint_generator,
         output_path=path_out,
         feature_weights=None,
-        n_cores=7
+        n_cores=7,
     )
 
+
 if __name__ == "__main__":
     main("IRE")
     main("STI")
     main("DB8")
-    main("B96")
+    main("B96")