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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
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@ -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"))