57 lines
1.7 KiB
R
57 lines
1.7 KiB
R
gene = "rpoB"
|
|
drug = "rifampicin"
|
|
|
|
#==========
|
|
# 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")
|
|
|
|
##############################################################
|