112 lines
3.7 KiB
R
112 lines
3.7 KiB
R
gene = "alr"
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drug = "cycloserine"
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#==========
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# LIGPLUS
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#===========
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aa_ligplus_dcs = c(66, 64, 70, 112, 196
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, 236, 237, 252, 253
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, 254, 255, 388)
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aa_ligplus_dcs_hbond = c(255, 254, 237, 66, 196)
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aa_ligplus_dcs_other = aa_ligplus_dcs[!aa_ligplus_dcs%in%aa_ligplus_dcs_hbond]
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c1 = length(aa_ligplus_dcs_other) == length(aa_ligplus_dcs) - length(aa_ligplus_dcs_hbond)
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#==========
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# PLIP
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#===========
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aa_plip_dcs = c(66, 70, 112, 196, 237
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, 252, 254, 255, 295
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, 314, 343)
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aa_plip_dcs_hbond = c(66, 70, 196, 237
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, 252, 254, 255, 295
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, 314, 343)
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aa_plip_dcs_other = aa_plip_dcs[!aa_plip_dcs%in%aa_plip_dcs_hbond]
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c2 = length(aa_plip_dcs_other) == length(aa_plip_dcs) - length(aa_plip_dcs_hbond)
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#==========
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# Arpeggio
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#===========
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aa_arpeg_dcs = c(64, 66, 70, 112, 157, 164
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, 194, 196, 200, 236, 237, 252, 253
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, 254, 255, 256, 295, 314, 342, 343
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, 344, 386, 388)
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aa_arpeg_dcs_other = aa_arpeg_dcs[!aa_arpeg_dcs%in%c(aa_ligplus_dcs_other
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, aa_plip_dcs_other)]
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c3 = length(aa_arpeg_dcs_other) == length(aa_arpeg_dcs) - ( length(aa_ligplus_dcs_other) + length(aa_plip_dcs_other) )
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#######################################################################
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#===============
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# Active site aa
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#===============
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active_aa_pos = sort(unique(c(aa_ligplus_dcs
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, aa_plip_dcs
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, aa_arpeg_dcs)))
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#=================
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# Drug binding aa
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#=================
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aa_pos_dcs = sort(unique(c(aa_ligplus_dcs
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, aa_plip_dcs
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, aa_arpeg_dcs)))
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aa_pos_drug = aa_pos_dcs
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#===============
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# Hbond aa
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#===============
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aa_pos_dcs_hbond = sort(unique(c(aa_ligplus_dcs_hbond
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, aa_plip_dcs_hbond)))
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#=======================
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# Other interactions aa
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#=======================
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aa_pos_dcs_other = active_aa_pos[!active_aa_pos%in%aa_pos_dcs_hbond]
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c3 = length(aa_pos_dcs_other) == length(active_aa_pos) - length(aa_pos_dcs_hbond)
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#######################################################################
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if ( all(c1, c2, c3) ) {
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cat("\nPASS:All active site residues and interctions checked and identified for"
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, "\ngene:", gene
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, "\ndrug:", drug
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, "\n==================================================="
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, "\nActive site residues for:", length(active_aa_pos)
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, "\n==================================================="
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, "\n"
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, active_aa_pos
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, "\n=================================================="
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, "\nDrug binding residues:", length(aa_pos_drug)
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, "\n==================================================="
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, "\n"
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#, aa_pos_dcs
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, aa_pos_drug
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, "\n==================================================="
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, "\nHbond residues:", length(aa_pos_dcs_hbond)
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, "\n==================================================="
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, "\n"
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, aa_pos_dcs_hbond
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, "\n=================================================="
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, "\nOther interaction residues:", length(aa_pos_dcs_other)
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, "\n==================================================="
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, "\n"
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, aa_pos_dcs_other
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, "\n\nNO other co-factors or ligands present\n")
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}
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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("ALR","DSL","CDL","Ca"),
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tile_colour=c("green","darkslategrey","navyblue","purple"))
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