139 lines
3.5 KiB
R
139 lines
3.5 KiB
R
gene = "gid"
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drug = "streptomycin"
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#rna_site = G518
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#rna_bind_aa_pos = c(96, 97, 118, 163)
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#binding_aa_pos = c(48, 51, 137, 200)
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# SAM: 226
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# SRY: 1601
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#==========
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# LIGPLUS
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#===========
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aa_ligplus_sry = c(118, 220, 223) # 526 (rna) and 7mg527
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aa_ligplus_sry_hbond = c(118, 220, 223)
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aa_ligplus_sam = c(148, 137, 138, 139
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, 93, 69, 119, 120
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, 220, 219, 118, 223)
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aa_ligplus_sam_hbond = c(220, 223)
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aa_ligplus_amp = c(123, 125, 213, 214)
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aa_ligplus_amp_hbond = c(125, 123, 213)
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aa_ligplus_rna = c(137, 47, 48, 38, 35, 36, 37, 94, 33, 97, 139, 138, 163, 165, 164, 199)
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aa_ligplus_rna_hbond = c(33, 97, 37, 47, 137)
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#==========
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# PLIP
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#===========
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aa_plip_sry = c(118, 220, 223)
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aa_plip_sry_hbond = c(118, 220, 223)
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aa_plip_sam = c(92, 118, 119, 120, 139, 220, 223, 148)
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aa_plip_sam_hbond = c(92, 118, 119, 120, 139, 220, 223)
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aa_plip_amp = c(123, 125, 213)
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aa_plip_amp_hbond = c(123, 125, 213)
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aa_plip_rna = c(33, 34, 36, 37, 47, 48, 51, 97, 137, 199)
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aa_plip_rna_hbond = c(33, 34, 36, 37, 47, 51, 137, 199)
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#==========
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# Arpeggio
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#===========
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aa_arpeg_sry = c(118, 148, 220, 223, 224)
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aa_arpeg_sam = c(68, 69, 92, 93, 97, 117
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, 118, 119, 120, 136, 137
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, 138, 139, 140, 148, 218
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, 219, 220, 221, 222, 223)
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aa_arpeg_amp = c(123, 125, 213)
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##############################################################
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#=============
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# Active site
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#=============
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active_aa_pos = sort(unique(c(
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#rna_bind_aa_pos
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#, binding_aa_pos
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aa_ligplus_sry
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, aa_ligplus_sam
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, aa_ligplus_amp
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, aa_ligplus_rna
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, aa_plip_sry
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, aa_plip_sam
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, aa_plip_amp
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, aa_plip_rna
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, aa_arpeg_sry
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, aa_arpeg_sam
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, aa_arpeg_amp
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)))
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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_sry = sort(unique(c(
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aa_ligplus_sry
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, aa_plip_sry
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, aa_arpeg_sry)))
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aa_pos_drug = aa_pos_sry
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aa_pos_sry_hbond = sort(unique(c(
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aa_ligplus_sry_hbond
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, aa_plip_sry_hbond)))
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aa_pos_rna = sort(unique(c(
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aa_ligplus_rna
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, aa_plip_rna)))
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aa_pos_rna_hbond = sort(unique(c(
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aa_ligplus_rna_hbond
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, aa_plip_rna_hbond)))
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aa_pos_sam = sort(unique(c(
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aa_ligplus_sam
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, aa_plip_sam
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, aa_arpeg_sam)))
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aa_pos_sam_hbond = sort(unique(c(
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aa_ligplus_sam_hbond
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, aa_plip_sam_hbond)))
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aa_pos_amp = sort(unique(c(
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aa_ligplus_amp
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, aa_plip_amp
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, aa_arpeg_amp)))
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aa_pos_amp_hbond = sort(unique(c(
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aa_ligplus_amp_hbond
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, aa_plip_amp_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_sry), "\n"
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, aa_pos_sry
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, "\nNo. of RNA binding residues:" , length(aa_pos_rna), "\n"
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, aa_pos_rna
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, "\nNo. of ligand 'SAM' binding residues:", length(aa_pos_sam), "\n"
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, aa_pos_sam
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, "\nNo. of ligand 'AMP' binding residues:", length(aa_pos_amp), "\n"
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, aa_pos_amp, "\n")
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##############################################################
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# var for position customisation for plots
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aa_pos_drug
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aa_pos_lig1 = aa_pos_sam
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aa_pos_lig2 = aa_pos_rna
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aa_pos_lig3 = aa_pos_amp
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tile_map=data.frame(tile=c("SRY","SAM","RNA","AMP"),
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tile_colour=c("green","darkslategrey","navyblue","purple"))
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