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renamed 2 to _v2

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This commit is contained in:
Tanushree Tunstall 2022-08-22 11:41:42 +01:00
parent c9d7ea9fad
commit 802d6f8495
18 changed files with 761 additions and 976 deletions
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47
config/alr.R
View file

@ -26,7 +26,8 @@ aa_plip_dcs_hbond = c(66, 70, 196, 237
aa_plip_dcs_other = aa_plip_dcs[!aa_plip_dcs%in%aa_plip_dcs_hbond]
c2 = length(aa_plip_dcs_other) == length(aa_plip_dcs) - length(aa_plip_dcs_hbond)
#==========
# Arpeggio
#===========
@ -40,6 +41,18 @@ aa_arpeg_dcs_other = aa_arpeg_dcs[!aa_arpeg_dcs%in%c(aa_ligplus_dcs_other
c3 = length(aa_arpeg_dcs_other) == length(aa_arpeg_dcs) - ( length(aa_ligplus_dcs_other) + length(aa_plip_dcs_other) )
#######################################################################
#NEW AFTER ADDING PLP to structure! huh
# ADDED: 18 Aug 2022
# PLIP server for co factor PLP (CONFUSING!)
#and 2019 lit:lys42, M319, and Y364 : OFFSET is 24
#K42: K66, Y271:Y295, M319:M343, W89: W113, W203: W227, H209:H233, Q321:Q345
aa_pos_paper = sort(unique(c(66,70,112,113,164,196,227,233,237,252,254,255,295,342,343,344,345,388)))
plp_pos_paper = sort(unique(c(66, 70, 112, 196, 227, 237, 252, 254, 255, 388)))
#active_aa_pos = sort(unique(c(aa_pos_paper, active_aa_pos)))
aa_pos_plp = sort(unique(c(plp_pos_paper, 66, 70, 112, 237, 252, 254, 255, 196)))
#######################################################################
#===============
@ -47,7 +60,9 @@ c3 = length(aa_arpeg_dcs_other) == length(aa_arpeg_dcs) - ( length(aa_ligplus_dc
#===============
active_aa_pos = sort(unique(c(aa_ligplus_dcs
, aa_plip_dcs
, aa_arpeg_dcs)))
, aa_arpeg_dcs
, aa_pos_paper
, aa_pos_plp)))
#=================
# Drug binding aa
#=================
@ -56,6 +71,12 @@ aa_pos_dcs = sort(unique(c(aa_ligplus_dcs
, aa_arpeg_dcs)))
aa_pos_drug = aa_pos_dcs
#===============
# Co-factor: PLP aa
#===============
aa_pos_plp = aa_pos_plp
#===============
# Hbond aa
#===============
@ -102,11 +123,25 @@ if ( all(c1, c2, c3) ) {
, "\n\nNO other co-factors or ligands present\n")
}
#######################################################################
######################################################################
#NEW
# PLIP server for co factor PLP (CONFUSING!)
#and 2019 lit:lys42, M319, and Y364 : OFFSET is 24
#K42: K66, Y271:Y295, M319:M343, W89: W113, W203: W227, H209:H233, Q321:Q345
aa_pos_paper = sort(unique(c(66,70,112,113,164,196,227,233,237,252,254,255,295,342,343,344,345,388)))
plp_pos_paper = sort(unique(c(66, 70, 112, 196, 227, 237, 252, 254, 255, 388)))
active_aa_pos = sort(unique(c(aa_pos_paper, active_aa_pos)))
aa_pos_plp = sort(unique(c(plp_pos_paper, 66, 70, 112, 237, 252, 254, 255, 196)))
# add two key residues
#aa_pos_drug = sort(unique(c(319, 364, aa_pos_drug)))
#active_aa_pos = sort(unique(c(319, 364, active_aa_pos, aa_pos_plp)))
# FIXME: these should be populated!
aa_pos_lig1 = NULL
aa_pos_lig1 = aa_pos_plp
aa_pos_lig2 = NULL
aa_pos_lig3 = NULL
tile_map=data.frame(tile=c("ALR","DPA","CDL","Ca"),
tile_colour=c("green","darkslategrey","navyblue","purple"))
tile_map=data.frame(tile=c("ALR","PLP"),
tile_colour=c("green","darkslategrey"))

25
config/embb.R
View file

@ -70,30 +70,30 @@ cat("\nNo. of active site residues for gene"
##############################################################
aa_pos_emb = sort(unique(c( aa_ligplus_emb
, aa_plip_emb
, aa_arpeg_emb)))
, aa_plip_emb
, aa_arpeg_emb)))
aa_pos_drug = aa_pos_emb
aa_pos_emb_hbond = sort(unique(c( aa_ligplus_emb_hbond
, aa_plip_emb_hbond)))
, aa_plip_emb_hbond)))
aa_pos_ca = sort(unique(c( aa_ligplus_ca
, aa_plip_ca
, aa_arpeg_ca)))
, aa_plip_ca
, aa_arpeg_ca)))
aa_pos_cdl = sort(unique(c( aa_ligplus_cdl
, aa_plip_cdl
, aa_arpeg_cdl )))
, aa_plip_cdl
, aa_arpeg_cdl )))
aa_pos_cdl_hbond = sort(unique(c( aa_ligplus_cdl_hbond )))
aa_pos_dsl = sort(unique(c( aa_ligplus_dsl
, aa_plip_dsl
, aa_arpeg_dsl)))
, aa_plip_dsl
, aa_arpeg_dsl)))
aa_pos_dsl_hbond = sort(unique(c( aa_ligplus_dsl_hbond
, aa_plip_dsl_hbond)))
, aa_plip_dsl_hbond)))
cat("\n==================================================="
, "\nActive site residues for", gene, "comprise of..."
@ -120,3 +120,4 @@ aa_pos_lig3 = aa_pos_ca #purple
tile_map=data.frame(tile=c("EMB","DPA","CDL","Ca"),
tile_colour=c("green","darkslategrey","navyblue","purple"))
drug_main_res = c(299 , 302, 303 , 306 , 327 , 592 , 594, 988, 1028)

74
config/gid.R
View file

@ -17,7 +17,7 @@ aa_ligplus_sam = c(148, 137, 138, 139
, 93, 69, 119, 120
, 220, 219, 118, 223)
aa_ligplus_sam_hbond = c(220, 223)
aa_ligplus_amp = c(123, 125, 213, 214)
aa_ligplus_amp_hbond = c(125, 123, 213)
@ -53,19 +53,19 @@ aa_arpeg_amp = c(123, 125, 213)
# Active site
#=============
active_aa_pos = sort(unique(c(
#rna_bind_aa_pos
#, binding_aa_pos
aa_ligplus_sry
, aa_ligplus_sam
, aa_ligplus_amp
, aa_ligplus_rna
, aa_plip_sry
, aa_plip_sam
, aa_plip_amp
, aa_plip_rna
, aa_arpeg_sry
, aa_arpeg_sam
, aa_arpeg_amp
#rna_bind_aa_pos
#, binding_aa_pos
aa_ligplus_sry
, aa_ligplus_sam
, aa_ligplus_amp
, aa_ligplus_rna
, aa_plip_sry
, aa_plip_sam
, aa_plip_amp
, aa_plip_rna
, aa_arpeg_sry
, aa_arpeg_sam
, aa_arpeg_amp
)))
##############################################################
@ -77,42 +77,42 @@ cat("\nNo. of active site residues for gene"
##############################################################
aa_pos_sry = sort(unique(c(
aa_ligplus_sry
, aa_plip_sry
, aa_arpeg_sry)))
aa_ligplus_sry
, aa_plip_sry
, aa_arpeg_sry)))
aa_pos_drug = aa_pos_sry
aa_pos_sry_hbond = sort(unique(c(
aa_ligplus_sry_hbond
, aa_plip_sry_hbond)))
aa_ligplus_sry_hbond
, aa_plip_sry_hbond)))
aa_pos_rna = sort(unique(c(
aa_ligplus_rna
, aa_plip_rna)))
aa_ligplus_rna
, aa_plip_rna)))
aa_pos_rna_hbond = sort(unique(c(
aa_ligplus_rna_hbond
, aa_plip_rna_hbond)))
aa_ligplus_rna_hbond
, aa_plip_rna_hbond)))
aa_pos_sam = sort(unique(c(
aa_ligplus_sam
, aa_plip_sam
, aa_arpeg_sam)))
aa_ligplus_sam
, aa_plip_sam
, aa_arpeg_sam)))
aa_pos_sam_hbond = sort(unique(c(
aa_ligplus_sam_hbond
, aa_plip_sam_hbond)))
aa_ligplus_sam_hbond
, aa_plip_sam_hbond)))
aa_pos_amp = sort(unique(c(
aa_ligplus_amp
, aa_plip_amp
, aa_arpeg_amp)))
aa_ligplus_amp
, aa_plip_amp
, aa_arpeg_amp)))
aa_pos_amp_hbond = sort(unique(c(
aa_ligplus_amp_hbond
, aa_plip_amp_hbond)))
aa_ligplus_amp_hbond
, aa_plip_amp_hbond)))
cat("\n==================================================="
@ -129,9 +129,11 @@ cat("\n==================================================="
##############################################################
# var for position customisation for plots
aa_pos_lig1 = aa_pos_rna
aa_pos_lig2 = aa_pos_sam
aa_pos_drug
aa_pos_lig1 = aa_pos_sam
aa_pos_lig2 = aa_pos_rna
aa_pos_lig3 = aa_pos_amp
tile_map=data.frame(tile=c("GID","DPA","CDL","Ca"),
tile_map=data.frame(tile=c("SRY","SAM","RNA","AMP"),
tile_colour=c("green","darkslategrey","navyblue","purple"))