added hbond residues in config for all genes

config/alr.R

@@ -1,33 +1,105 @@
 gene = "alr"
 drug = "cycloserine"
 
-aa_plip = c(66, 70, 112, 196, 237, 252, 254, 255, 295, 314, 343)
-aa_ligplus = c(66, 64, 70, 112, 196, 236, 237, 252, 253, 254, 255, 388 )
-#active_aa_pos = c(66, 64, 70, 112, 196, 236, 237, 252, 253, 254, 255, 295, 314, 343, 388)
-active_aa_pos = sort(unique(c(aa_plip, aa_ligplus)))
+#==========
+# LIGPLUS
+#===========
+aa_ligplus_dcs = c(66, 64, 70, 112, 196
+                   , 236, 237, 252, 253
+                   , 254, 255, 388)
 
-#aa_plip = c(66 = "hbond"
-#, 70 = "hbond"
-#, 112 = "hydrophobic"
-#, 196 = "hbond"
-#, 237 = "hbond"
-#, 252 = "hbond"
-#, 254 = "hbond"
-#, 255 = "hbond"
-#, 295 = "hbond"
-#, 314 = "hbond"
-#, 343 = "hbond")
+aa_ligplus_dcs_hbond = c(255, 254, 237, 66, 196)
+aa_ligplus_dcs_other = aa_ligplus_dcs[!aa_ligplus_dcs%in%aa_ligplus_dcs_hbond]
 
-#aa_ligplus = c(66  = "hbond"
-#, 64  = "hydrophobic"
-#, 70  = "hydrophobic"
-#, 112 = "hydrophobic"
-#, 196 = "hbond"
-#, 236 = "hydrophobic"
-#, 237 = "hbond"
-#, 252 = "hydrophobic"
-#, 253 = "hydrophobic"
-#, 254 = "hbond"
-#, 255 = "hbond"
-#, 388 = "hydrophobic"
-#)
+c1 = length(aa_ligplus_dcs_other) ==  length(aa_ligplus_dcs) - length(aa_ligplus_dcs_hbond)
+
+#==========
+# PLIP
+#===========
+aa_plip_dcs = c(66, 70, 112, 196, 237
+                , 252, 254, 255, 295
+                , 314, 343)
+aa_plip_dcs_hbond = c(66, 70, 196, 237
+                      , 252, 254, 255, 295
+                      , 314, 343)
+
+aa_plip_dcs_other = aa_plip_dcs[!aa_plip_dcs%in%aa_plip_dcs_hbond]
+
+c2 = length(aa_plip_dcs_other) == length(aa_plip_dcs) - length(aa_plip_dcs_hbond)
+    
+#==========
+# Arpeggio
+#===========
+aa_arpeg_dcs = c(64, 66, 70, 112, 157, 164
+                 , 194, 196, 200, 236, 237, 252, 253
+                 , 254, 255, 256, 295, 314, 342, 343
+                 , 344, 386, 388)
+
+aa_arpeg_dcs_other = aa_arpeg_dcs[!aa_arpeg_dcs%in%c(aa_ligplus_dcs_other
+                                                     , aa_plip_dcs_other)]
+
+c3 = length(aa_arpeg_dcs_other) == length(aa_arpeg_dcs) - ( length(aa_ligplus_dcs_other) + length(aa_plip_dcs_other) )
+
+#######################################################################
+
+#===============
+# Active site aa
+#===============
+active_aa_pos = sort(unique(c(aa_ligplus_dcs
+                              , aa_plip_dcs
+                              , aa_arpeg_dcs)))
+#=================
+# Drug binding aa
+#=================
+aa_pos_dcs = sort(unique(c(aa_ligplus_dcs
+                           , aa_plip_dcs
+                           , aa_arpeg_dcs)))
+aa_pos_drug = aa_pos_dcs
+
+#===============
+# Hbond aa
+#===============
+aa_pos_dcs_hbond = sort(unique(c(aa_ligplus_dcs_hbond
+                                 , aa_plip_dcs_hbond)))
+
+#=======================
+# Other interactions aa
+#=======================
+aa_pos_dcs_other = active_aa_pos[!active_aa_pos%in%aa_pos_dcs_hbond]
+
+c3 = length(aa_pos_dcs_other) == length(active_aa_pos) - length(aa_pos_dcs_hbond) 
+
+#######################################################################
+if ( all(c1, c2, c3) ) {
+    
+    cat("\nPASS:All active site residues and interctions checked and identified for"
+        , "\ngene:", gene
+        , "\ndrug:", drug
+        , "\n==================================================="
+        , "\nActive site residues for:", length(active_aa_pos) 
+        , "\n==================================================="
+        , "\n"
+        , active_aa_pos
+        
+        , "\n=================================================="
+        , "\nDrug binding residues:", length(aa_pos_drug)
+        , "\n==================================================="
+        , "\n"
+        #, aa_pos_dcs
+        , aa_pos_drug
+
+        , "\n==================================================="
+        , "\nHbond residues:", length(aa_pos_dcs_hbond)
+        , "\n==================================================="
+        , "\n"
+        , aa_pos_dcs_hbond
+        
+        , "\n=================================================="
+        , "\nOther interaction residues:",  length(aa_pos_dcs_other)
+        , "\n==================================================="
+        , "\n"
+        , aa_pos_dcs_other
+        , "\n\nNO other co-factors or ligands present\n")
+        
+}
+#######################################################################