added active site positions to all config.R

config/alr.R

@@ -1,2 +1,33 @@
 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)))
+
+#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 = 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"
+#)

config/embb.R

@@ -1,2 +1,7 @@
 gene = "embB"
 drug = "ethambutol"
+
+aa_plip = c(299, 302, 303, 327, 594, 988, 1028 )
+aa_ligplus = c(299, 302, 303, 306, 334, 594, 988, 1028)
+#active_aa_pos = c(299, 302, 303, 306, 327, 334, 594, 988, 1028 )
+active_aa_pos = sort(unique(c(aa_plip, aa_ligplus)))

config/gid.R

@@ -3,7 +3,13 @@ drug = "streptomycin"
 
 rna_bind_aa_pos = c(96, 97, 118, 163)
 binding_aa_pos = c(48, 51, 137, 200)
-active_aa_pos = sort(unique(c(rna_bind_aa_pos, binding_aa_pos)))
+aa_plip = c(118, 220, 223)
+aa_ligplus = c(118, 220, 223)
+
+active_aa_pos = sort(unique(c(rna_bind_aa_pos
+, binding_aa_pos
+, aa_plip
+, aa_ligplus)))
 #rna_site = G518
 
 cat("\nNo. of active site residues for gene"
@@ -18,4 +24,4 @@ cat("\n==================================================="
     , "\nRNA binding residues:"
     , rna_bind_aa_pos
     , "\nBinding site residues:"
-    , binding_aa_pos)
+    , binding_aa_pos)

config/katg.R

@@ -1,2 +1,6 @@
 gene = "katG"
 drug = "isoniazid"
+
+aa_plip = c(104, 229, 230)
+aa_ligplus = c(107, 108, 137, 229, 230) 
+active_aa_pos = sort(unique(c(aa_plip, aa_ligplus)))

config/pnca.R

@@ -7,6 +7,10 @@ drug = "pyrazinamide"
 #Substrate binding --> teal and blue
 #H-bond --> green
 #====================================
+#aa_plip = c(49, 51, 57, 71, 96 , 133, 134, 138)
+#aa_ligplus = c(8, 13 , 49 , 133, 134 , 138, 137)
+#active_aa_pos = sort(unique(c(aa_plip, aa_ligplus)))
+
 metal_aa_pos = c(49, 51, 57, 71) 
 catalytic_aa_pos = c(8, 96, 138)
 substrate_aa_pos = c(13, 68, 103, 137)
@@ -33,4 +37,4 @@ cat("\n==================================================="
     , "\nSubstrate binding residues:"
     , substrate_aa_pos
     , "\nH-bonding residues:"
-    , hbond_aa_pos)
+    , hbond_aa_pos)

config/rpob.R

@@ -1,2 +1,6 @@
 gene = "rpoB"
 drug = "rifampicin"
+
+aa_plip = c(429, 432, 491, 487)
+aa_plip_5uhc = c(430, 452, 483, 491, 432, 433, 448, 450, 459, 487)
+active_aa_pos = sort(unique(c(aa_plip, aa_plip_5uhc)))