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added more scripts

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This commit is contained in:
Tanushree Tunstall 2022-08-24 20:04:29 +01:00
parent 9aed99e805
commit 11b936f09b
9 changed files with 148 additions and 117 deletions
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29
config/alr.R
View file

@ -54,7 +54,8 @@ plp_pos_paper = sort(unique(c(66, 70, 112, 196, 227, 237, 252, 254, 255, 388)))
aa_pos_plp = sort(unique(c(plp_pos_paper, 66, 70, 112, 237, 252, 254, 255, 196)))
#######################################################################
# this is post inspection on chimera
remove_pos = c(295, 314, 342, 343, 344)
#===============
# Active site aa
#===============
@ -63,31 +64,40 @@ active_aa_pos = sort(unique(c(aa_ligplus_dcs
, aa_arpeg_dcs
, aa_pos_paper
, aa_pos_plp)))
active_aa_pos = active_aa_pos[!active_aa_pos%in%remove_pos]
#=================
# Drug binding aa
#=================
aa_pos_dcs = sort(unique(c(aa_ligplus_dcs
, aa_plip_dcs
, aa_arpeg_dcs)))
aa_pos_drug = aa_pos_dcs
aa_pos_dcs = aa_pos_dcs[!aa_pos_dcs%in%remove_pos]
aa_pos_drug = aa_pos_dcs
#===============
# Co-factor: PLP aa
#===============
aa_pos_plp = aa_pos_plp
#aa_pos_plp = aa_pos_plp[!aa_pos_plp%in%remove_pos]
#===============
# Hbond aa
#===============
aa_pos_dcs_hbond = sort(unique(c(aa_ligplus_dcs_hbond
, aa_plip_dcs_hbond)))
aa_pos_dcs_hbond = aa_pos_dcs_hbond[!aa_pos_dcs_hbond%in%remove_pos]
#=======================
# Other interactions aa
#=======================
aa_pos_dcs_other = active_aa_pos[!active_aa_pos%in%aa_pos_dcs_hbond]
aa_pos_dcs_other = aa_pos_dcs_other[!aa_pos_dcs_other%in%remove_pos]
c3 = length(aa_pos_dcs_other) == length(active_aa_pos) - length(aa_pos_dcs_hbond)
#######################################################################
@ -144,4 +154,17 @@ aa_pos_lig2 = NULL
aa_pos_lig3 = NULL
tile_map=data.frame(tile=c("ALR","PLP"),
tile_colour=c("green","navyblue")) #darkslategrey
tile_colour=c("green","navyblue")) #darkslategrey
######
chain_suffix = ".A"
toString(paste0(aa_pos_drug, chain_suffix))
toString(paste0(aa_pos_plp, chain_suffix))
toString(paste0(active_aa_pos, chain_suffix))
common_pos = aa_pos_drug[aa_pos_drug%in%aa_pos_plp]
cat("\nCommon interacting partners:", length(common_pos))
common_pos
toString(paste0(common_pos, chain_suffix))

10
config/rpob.R
View file

@ -28,9 +28,12 @@ aa_arpeg_rfp = c(170, 428, 429, 430, 431, 432
, 607, 674)
##############################################################
remove_pos = c(170, 674, 604)
active_aa_pos = sort(unique(c(aa_plip_rfp
, aa_plip_5uhc_rfp
, aa_arpeg_rfp)))
active_aa_pos = active_aa_pos[!active_aa_pos%in%remove_pos]
##############################################################
cat("\nNo. of active site residues for gene"
, gene, ":"
@ -42,11 +45,14 @@ aa_pos_rfp = sort(unique(c(aa_plip_rfp
, aa_plip_5uhc_rfp
, aa_arpeg_rfp)))
aa_pos_rfp = aa_pos_rfp[!aa_pos_rfp%in%remove_pos]
aa_pos_drug = aa_pos_rfp
aa_pos_rfp_hbond = sort(unique(c(aa_plip_rfp_hbond
, aa_plip_5uhc_rfp_hbond)))
aa_pos_rfp_hbond = aa_pos_rfp_hbond[!aa_pos_rfp_hbond%in%remove_pos]
cat("\n==================================================="
, "\nActive site residues for", gene, "comprise of..."
, "\n==================================================="
@ -62,3 +68,7 @@ aa_pos_lig3 = NULL
tile_map=data.frame(tile=c("RPO","DPA","CDL","Ca"),
tile_colour=c("green","darkslategrey","navyblue","purple"))
####
chain_suffix = ".C"
print(toString(paste0(aa_pos_drug, chain_suffix)))