added hbond residues in config for all genes

2022-02-09 15:59:18 +00:00 · 2022-02-09 15:59:18 +00:00 · 6ffb084546
commit 6ffb084546
parent 7a14655ecb
9 changed files with 686 additions and 110 deletions
--- a/config/rpob.R
+++ b/config/rpob.R
@ -1,6 +1,57 @@
 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)))
+#==========
+# LIGPLUS
+#===========
+# Error! No atom records found!
+
+#==========
+# PLIP
+#===========
+aa_plip_rfp = c(429, 432, 491, 487)
+aa_plip_rfp_hbond = c(429, 432, 487)
+
+# chainC: equivalent with offset (-6 from 5uhc) accounted
+aa_plip_5uhc_rfp = c(430, 452, 483
+                 , 491, 432, 433
+                 , 448, 450, 459, 487)
+aa_plip_5uhc_rfp_hbond = c(432, 433, 448, 450, 459, 487)
+
+#==========
+# Arpeggio
+#===========
+# rfp: 1894
+aa_arpeg_rfp = c(170, 428, 429, 430, 431, 432
+                 , 433, 435, 445, 448, 450, 452
+                 , 453, 458, 483, 487, 491, 604
+                 , 607, 674)
+
+##############################################################
+active_aa_pos = sort(unique(c(aa_plip_rfp
+                              , aa_plip_5uhc_rfp
+                              , aa_arpeg_rfp)))
+##############################################################
+cat("\nNo. of active site residues for gene"
+    , gene, ":"
+    , length(active_aa_pos)
+    , "\nThese are:\n"
+    , active_aa_pos)
+##############################################################
+aa_pos_rfp = sort(unique(c(aa_plip_rfp
+                           , aa_plip_5uhc_rfp
+                           , aa_arpeg_rfp)))
+
+aa_pos_drug = aa_pos_rfp
+
+aa_pos_rfp_hbond = sort(unique(c(aa_plip_rfp_hbond
+                           , aa_plip_5uhc_rfp_hbond)))
+
+cat("\n==================================================="
+    , "\nActive site residues for", gene, "comprise of..."
+    , "\n==================================================="
+    , "\nNo. of", drug, "binding residues:" , length(aa_pos_rfp), "\n"
+    , aa_pos_rfp
+    , "\n\nNO other co-factors or ligands present\n")
+
+##############################################################