64 lines
1.9 KiB
R
64 lines
1.9 KiB
R
gene = "rpoB"
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drug = "rifampicin"
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#==========
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# LIGPLUS
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#===========
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# Error! No atom records found!
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#==========
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# PLIP
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#===========
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aa_plip_rfp = c(429, 432, 491, 487)
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aa_plip_rfp_hbond = c(429, 432, 487)
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# chainC: equivalent with offset (-6 from 5uhc) accounted
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aa_plip_5uhc_rfp = c(430, 452, 483
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, 491, 432, 433
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, 448, 450, 459, 487)
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aa_plip_5uhc_rfp_hbond = c(432, 433, 448, 450, 459, 487)
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#==========
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# Arpeggio
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#===========
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# rfp: 1894
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aa_arpeg_rfp = c(170, 428, 429, 430, 431, 432
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, 433, 435, 445, 448, 450, 452
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, 453, 458, 483, 487, 491, 604
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, 607, 674)
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##############################################################
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active_aa_pos = sort(unique(c(aa_plip_rfp
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, aa_plip_5uhc_rfp
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, aa_arpeg_rfp)))
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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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##############################################################
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aa_pos_rfp = sort(unique(c(aa_plip_rfp
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, aa_plip_5uhc_rfp
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, aa_arpeg_rfp)))
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aa_pos_drug = aa_pos_rfp
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aa_pos_rfp_hbond = sort(unique(c(aa_plip_rfp_hbond
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, aa_plip_5uhc_rfp_hbond)))
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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_rfp), "\n"
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, aa_pos_rfp
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, "\n\nNO other co-factors or ligands present\n")
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##############################################################
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# FIXME: these should be populated!
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aa_pos_lig1 = NULL
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aa_pos_lig2 = NULL
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aa_pos_lig3 = NULL
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tile_map=data.frame(tile=c("RPO","DSL","CDL","Ca"),
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tile_colour=c("green","darkslategrey","navyblue","purple"))
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