56 lines
No EOL
1.9 KiB
R
56 lines
No EOL
1.9 KiB
R
gene = "pncA"
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drug = "pyrazinamide"
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#===================================
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#Iron centre --> purple
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#Catalytic triad --> yellow
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#Substrate binding --> teal and blue
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#H-bond --> green
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#====================================
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#aa_plip = c(49, 51, 57, 71, 96 , 133, 134, 138)
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#aa_ligplus = c(8, 13 , 49 , 133, 134 , 138, 137)
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#active_aa_pos = sort(unique(c(aa_plip, aa_ligplus)))
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#aa_pos_substrate = c(13, 68, 103, 137)
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aa_pos_pza = c(13, 68, 103, 137)
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aa_pos_fe = c(49, 51, 57, 71)
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aa_pos_catalytic = c(8, 96, 138)
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aa_pos_hbond = c(133, 134, 8, 138)
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aa_pos_drug = aa_pos_pza
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#==========
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# Arpeggio
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#===========
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# all same except one extra
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aa_arpeg = c(102)
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##############################################################
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active_aa_pos = sort(unique(c(aa_pos_pza
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, aa_pos_fe
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, aa_pos_catalytic
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, aa_pos_hbond
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, aa_arpeg)))
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##############################################################
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cat("\nNo. of active site residues for gene"
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, gene, ":"
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, length(active_aa_pos)
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, "\nThese are:\n"
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, active_aa_pos)
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cat("\n==================================================="
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, "\nActive site residues for", gene, "comprise of..."
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, "\n==================================================="
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, "\nNo. of", drug, "binding residues:" , length(aa_pos_pza) , "\n"
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, aa_pos_pza
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, "\nMetal coordination centre residues:" , length(aa_pos_fe) , "\n"
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, aa_pos_fe
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, "\nCatalytic triad residues:" , length(aa_pos_catalytic) , "\n"
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, aa_pos_catalytic
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, "\nH-bonding residues:" , length(aa_pos_hbond) , "\n"
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, aa_pos_hbond , "\n")
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##############################################################
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# var for position customisation for plots
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aa_pos_lig1 = aa_pos_fe
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#aa_pos_lig2 = aa_pos_catalytic
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#aa_pos_lig3 = aa_pos_hbond |