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added hbond residues in config for all genes

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Tanushree Tunstall 2022-02-09 15:59:18 +00:00
parent 7a14655ecb
commit 6ffb084546
9 changed files with 686 additions and 110 deletions
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104
config/katg.R
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@ -1,6 +1,104 @@
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)))
#==========
# 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")
##############################################################