111 lines
3.3 KiB
R
111 lines
3.3 KiB
R
gene = "katG"
|
|
drug = "isoniazid"
|
|
|
|
#==========
|
|
# LIGPLUS
|
|
#===========
|
|
# hem (1500)
|
|
aa_ligplus_inh = c(107, 108, 137, 229, 230)
|
|
#aa_ligplus_inh_hbond # none
|
|
|
|
aa_ligplus_hem = c(94, 276, 315, 274, 270, 381, 273, 104, 314, 275,
|
|
100, 101, 321, 103, 269, 107, 266, 230, 380, 275, 314)
|
|
|
|
aa_ligplus_hem_hbond = c(94, 276, 315, 274, 270, 381)
|
|
aa_ligplus_hem_other = aa_ligplus_hem[!aa_ligplus_hem%in%aa_ligplus_hem_hbond]
|
|
|
|
c1 = length(aa_ligplus_hem_other) == length(aa_ligplus_hem) - length(aa_ligplus_hem_hbond)
|
|
|
|
#==========
|
|
# PLIP
|
|
#===========
|
|
aa_plip_inh = c(104, 229, 230)
|
|
aa_plip_inh_hbond = c(104, 229, 230)
|
|
|
|
aa_plip_hem = c(104, 107, 248, 252, 265, 275, 321, 412, 274, 276, 315)
|
|
aa_plip_hem_hbond = c(274, 276, 315)
|
|
#aa_plip_hem_sb = c(104, 276)
|
|
#aa_plip_hem_pi = c(107)
|
|
aa_plip_hem_other = aa_plip_hem[!aa_plip_hem%in%aa_plip_hem_hbond]
|
|
|
|
c2 = length(aa_plip_hem_other) == length(aa_plip_hem) - length(aa_plip_hem_hbond)
|
|
|
|
#==========
|
|
# Arpeggio
|
|
#===========
|
|
aa_arpeg_inh = c(104, 107, 108, 136, 137, 228, 229, 230, 232, 315)
|
|
aa_arpeg_inh_hbond = c(104, 137)
|
|
|
|
aa_arpeg_hem = c(94, 100, 101, 103, 104, 107, 230, 231, 232, 248
|
|
, 252, 265, 266, 269, 270, 272, 273, 274, 275, 276, 314, 315
|
|
, 317, 321, 378, 380, 408, 412)
|
|
|
|
#from here
|
|
|
|
##############################################################
|
|
#===============
|
|
# Active site aa
|
|
#===============
|
|
active_aa_pos = sort(unique(c(aa_ligplus_inh
|
|
, aa_plip_inh
|
|
, aa_arpeg_inh
|
|
|
|
, aa_ligplus_hem
|
|
, aa_plip_hem
|
|
, aa_arpeg_hem
|
|
)))
|
|
cat("\nNo. of active site residues for gene"
|
|
, gene, ":"
|
|
, length(active_aa_pos)
|
|
, "\nThese are:\n"
|
|
, active_aa_pos)
|
|
|
|
#=================
|
|
# Drug binding aa
|
|
#=================
|
|
aa_pos_inh = sort(unique(c( aa_ligplus_inh
|
|
, aa_plip_inh
|
|
, aa_arpeg_inh)))
|
|
aa_pos_drug = aa_pos_inh
|
|
|
|
|
|
#===============
|
|
# Hbond aa
|
|
#===============
|
|
aa_pos_inh_hbond = sort(unique(c( aa_plip_inh_hbond
|
|
, aa_arpeg_inh_hbond)))
|
|
|
|
#=======================
|
|
# Other interactions aa
|
|
#=======================
|
|
|
|
|
|
|
|
#---------------------------------------------
|
|
|
|
aa_pos_hem = sort(unique(c( aa_ligplus_hem
|
|
, aa_plip_hem
|
|
, aa_arpeg_hem)))
|
|
|
|
aa_pos_hem_hbond = sort(unique(c( aa_ligplus_hem_hbond
|
|
, aa_plip_hem_hbond
|
|
#, aa_arpeg_hem_hbond
|
|
)))
|
|
|
|
|
|
cat("\n==================================================="
|
|
, "\nActive site residues for", gene, "comprise of..."
|
|
, "\n==================================================="
|
|
, "\nNo. of", drug, "binding residues:" , length(aa_pos_inh) , "\n"
|
|
, aa_pos_inh
|
|
, "\nNo. of 'HEM' binding residues:" , length(aa_pos_hem) , "\n"
|
|
, aa_pos_hem, "\n")
|
|
|
|
##############################################################
|
|
# var for position customisation for plots
|
|
aa_pos_lig1 = aa_pos_hem
|
|
aa_pos_lig2 = NULL
|
|
aa_pos_lig3 = NULL
|
|
tile_map=data.frame(tile=c("KAT","DPA","CDL","Ca"),
|
|
tile_colour=c("green","darkslategrey","navyblue","purple"))
|
|
|