renamed 2 to _v2
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18 changed files with 761 additions and 976 deletions
47
config/alr.R
47
config/alr.R
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@ -26,7 +26,8 @@ aa_plip_dcs_hbond = c(66, 70, 196, 237
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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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@ -40,6 +41,18 @@ aa_arpeg_dcs_other = aa_arpeg_dcs[!aa_arpeg_dcs%in%c(aa_ligplus_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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#NEW AFTER ADDING PLP to structure! huh
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# ADDED: 18 Aug 2022
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# PLIP server for co factor PLP (CONFUSING!)
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#and 2019 lit:lys42, M319, and Y364 : OFFSET is 24
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#K42: K66, Y271:Y295, M319:M343, W89: W113, W203: W227, H209:H233, Q321:Q345
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aa_pos_paper = sort(unique(c(66,70,112,113,164,196,227,233,237,252,254,255,295,342,343,344,345,388)))
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plp_pos_paper = sort(unique(c(66, 70, 112, 196, 227, 237, 252, 254, 255, 388)))
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#active_aa_pos = sort(unique(c(aa_pos_paper, active_aa_pos)))
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aa_pos_plp = sort(unique(c(plp_pos_paper, 66, 70, 112, 237, 252, 254, 255, 196)))
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#######################################################################
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#===============
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@ -47,7 +60,9 @@ c3 = length(aa_arpeg_dcs_other) == length(aa_arpeg_dcs) - ( length(aa_ligplus_dc
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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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, aa_arpeg_dcs
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, aa_pos_paper
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, aa_pos_plp)))
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#=================
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# Drug binding aa
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#=================
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@ -56,6 +71,12 @@ aa_pos_dcs = sort(unique(c(aa_ligplus_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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# Co-factor: PLP aa
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#===============
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aa_pos_plp = aa_pos_plp
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#===============
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# Hbond aa
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#===============
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@ -102,11 +123,25 @@ if ( all(c1, c2, c3) ) {
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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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######################################################################
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#NEW
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# PLIP server for co factor PLP (CONFUSING!)
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#and 2019 lit:lys42, M319, and Y364 : OFFSET is 24
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#K42: K66, Y271:Y295, M319:M343, W89: W113, W203: W227, H209:H233, Q321:Q345
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aa_pos_paper = sort(unique(c(66,70,112,113,164,196,227,233,237,252,254,255,295,342,343,344,345,388)))
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plp_pos_paper = sort(unique(c(66, 70, 112, 196, 227, 237, 252, 254, 255, 388)))
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active_aa_pos = sort(unique(c(aa_pos_paper, active_aa_pos)))
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aa_pos_plp = sort(unique(c(plp_pos_paper, 66, 70, 112, 237, 252, 254, 255, 196)))
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# add two key residues
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#aa_pos_drug = sort(unique(c(319, 364, aa_pos_drug)))
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#active_aa_pos = sort(unique(c(319, 364, active_aa_pos, aa_pos_plp)))
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# FIXME: these should be populated!
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aa_pos_lig1 = NULL
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aa_pos_lig1 = aa_pos_plp
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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","DPA","CDL","Ca"),
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tile_colour=c("green","darkslategrey","navyblue","purple"))
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tile_map=data.frame(tile=c("ALR","PLP"),
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tile_colour=c("green","darkslategrey"))
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