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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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44
config/pnca.R
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@ -11,16 +11,26 @@ drug = "pyrazinamide"
#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)
hbond_aa_pos = c(133, 134, 8, 138)
#aa_pos_substrate = c(13, 68, 103, 137)
aa_pos_pza = c(13, 68, 103, 137)
aa_pos_fe = c(49, 51, 57, 71)
aa_pos_catalytic = c(8, 96, 138)
aa_pos_hbond = c(133, 134, 8, 138)
aa_pos_drug = aa_pos_pza
#==========
# Arpeggio
#===========
# all same except one extra
aa_arpeg = c(102)
##############################################################
active_aa_pos = sort(unique(c(metal_aa_pos
, catalytic_aa_pos
, substrate_aa_pos
, hbond_aa_pos)))
, catalytic_aa_pos
, substrate_aa_pos
, hbond_aa_pos
, aa_arpeg)))
##############################################################
cat("\nNo. of active site residues for gene"
, gene, ":"
, length(active_aa_pos)
@ -30,11 +40,13 @@ cat("\nNo. of active site residues for gene"
cat("\n==================================================="
, "\nActive site residues for", gene, "comprise of..."
, "\n==================================================="
, "\nMetal coordination centre residues:"
, metal_aa_pos
, "\nCatalytic triad residues:"
, catalytic_aa_pos
, "\nSubstrate binding residues:"
, substrate_aa_pos
, "\nH-bonding residues:"
, hbond_aa_pos)
, "\nNo. of", drug, "binding residues:" , length(aa_pos_pza) , "\n"
, aa_pos_pza
, "\nMetal coordination centre residues:" , length(aa_pos_fe) , "\n"
, aa_pos_fe
, "\nCatalytic triad residues:" , length(aa_pos_catalytic) , "\n"
, aa_pos_catalytic
, "\nH-bonding residues:" , length(aa_pos_hbond) , "\n"
, aa_pos_hbond , "\n")
##############################################################