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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@ -70,30 +70,30 @@ cat("\nNo. of active site residues for gene"
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##############################################################
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aa_pos_emb = sort(unique(c( aa_ligplus_emb
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, aa_plip_emb
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, aa_arpeg_emb)))
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, aa_plip_emb
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, aa_arpeg_emb)))
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aa_pos_drug = aa_pos_emb
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aa_pos_emb_hbond = sort(unique(c( aa_ligplus_emb_hbond
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, aa_plip_emb_hbond)))
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, aa_plip_emb_hbond)))
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aa_pos_ca = sort(unique(c( aa_ligplus_ca
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, aa_plip_ca
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, aa_arpeg_ca)))
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, aa_plip_ca
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, aa_arpeg_ca)))
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aa_pos_cdl = sort(unique(c( aa_ligplus_cdl
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, aa_plip_cdl
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, aa_arpeg_cdl )))
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, aa_plip_cdl
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, aa_arpeg_cdl )))
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aa_pos_cdl_hbond = sort(unique(c( aa_ligplus_cdl_hbond )))
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aa_pos_dsl = sort(unique(c( aa_ligplus_dsl
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, aa_plip_dsl
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, aa_arpeg_dsl)))
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, aa_plip_dsl
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, aa_arpeg_dsl)))
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aa_pos_dsl_hbond = sort(unique(c( aa_ligplus_dsl_hbond
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, aa_plip_dsl_hbond)))
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, aa_plip_dsl_hbond)))
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cat("\n==================================================="
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, "\nActive site residues for", gene, "comprise of..."
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@ -120,3 +120,4 @@ aa_pos_lig3 = aa_pos_ca #purple
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tile_map=data.frame(tile=c("EMB","DPA","CDL","Ca"),
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tile_colour=c("green","darkslategrey","navyblue","purple"))
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drug_main_res = c(299 , 302, 303 , 306 , 327 , 592 , 594, 988, 1028)
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74
config/gid.R
74
config/gid.R
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@ -17,7 +17,7 @@ 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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@ -53,19 +53,19 @@ aa_arpeg_amp = c(123, 125, 213)
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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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#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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@ -77,42 +77,42 @@ cat("\nNo. of active site residues for gene"
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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_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_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_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_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_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_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_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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aa_ligplus_amp_hbond
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, aa_plip_amp_hbond)))
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cat("\n==================================================="
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@ -129,9 +129,11 @@ cat("\n==================================================="
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##############################################################
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# var for position customisation for plots
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aa_pos_lig1 = aa_pos_rna
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aa_pos_lig2 = aa_pos_sam
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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("GID","DPA","CDL","Ca"),
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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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