added hbond residues in config for all genes
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7a14655ecb
commit
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9 changed files with 686 additions and 110 deletions
128
config/alr.R
128
config/alr.R
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@ -1,33 +1,105 @@
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gene = "alr"
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gene = "alr"
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drug = "cycloserine"
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drug = "cycloserine"
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aa_plip = c(66, 70, 112, 196, 237, 252, 254, 255, 295, 314, 343)
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#==========
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aa_ligplus = c(66, 64, 70, 112, 196, 236, 237, 252, 253, 254, 255, 388 )
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# LIGPLUS
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#active_aa_pos = c(66, 64, 70, 112, 196, 236, 237, 252, 253, 254, 255, 295, 314, 343, 388)
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#===========
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active_aa_pos = sort(unique(c(aa_plip, aa_ligplus)))
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aa_ligplus_dcs = c(66, 64, 70, 112, 196
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, 236, 237, 252, 253
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, 254, 255, 388)
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#aa_plip = c(66 = "hbond"
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aa_ligplus_dcs_hbond = c(255, 254, 237, 66, 196)
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#, 70 = "hbond"
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aa_ligplus_dcs_other = aa_ligplus_dcs[!aa_ligplus_dcs%in%aa_ligplus_dcs_hbond]
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#, 112 = "hydrophobic"
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#, 196 = "hbond"
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#, 237 = "hbond"
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#, 252 = "hbond"
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#, 254 = "hbond"
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#, 255 = "hbond"
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#, 295 = "hbond"
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#, 314 = "hbond"
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#, 343 = "hbond")
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#aa_ligplus = c(66 = "hbond"
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c1 = length(aa_ligplus_dcs_other) == length(aa_ligplus_dcs) - length(aa_ligplus_dcs_hbond)
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#, 64 = "hydrophobic"
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#, 70 = "hydrophobic"
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#==========
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#, 112 = "hydrophobic"
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# PLIP
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#, 196 = "hbond"
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#===========
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#, 236 = "hydrophobic"
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aa_plip_dcs = c(66, 70, 112, 196, 237
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#, 237 = "hbond"
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, 252, 254, 255, 295
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#, 252 = "hydrophobic"
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, 314, 343)
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#, 253 = "hydrophobic"
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aa_plip_dcs_hbond = c(66, 70, 196, 237
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#, 254 = "hbond"
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, 252, 254, 255, 295
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#, 255 = "hbond"
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, 314, 343)
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#, 388 = "hydrophobic"
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#)
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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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aa_arpeg_dcs = c(64, 66, 70, 112, 157, 164
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, 194, 196, 200, 236, 237, 252, 253
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, 254, 255, 256, 295, 314, 342, 343
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, 344, 386, 388)
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aa_arpeg_dcs_other = aa_arpeg_dcs[!aa_arpeg_dcs%in%c(aa_ligplus_dcs_other
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, aa_plip_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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#===============
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# Active site aa
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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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#=================
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# Drug binding aa
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#=================
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aa_pos_dcs = 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_pos_drug = aa_pos_dcs
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#===============
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# Hbond aa
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#===============
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aa_pos_dcs_hbond = sort(unique(c(aa_ligplus_dcs_hbond
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, aa_plip_dcs_hbond)))
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#=======================
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# Other interactions aa
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#=======================
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aa_pos_dcs_other = active_aa_pos[!active_aa_pos%in%aa_pos_dcs_hbond]
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c3 = length(aa_pos_dcs_other) == length(active_aa_pos) - length(aa_pos_dcs_hbond)
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#######################################################################
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if ( all(c1, c2, c3) ) {
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cat("\nPASS:All active site residues and interctions checked and identified for"
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, "\ngene:", gene
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, "\ndrug:", drug
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, "\n==================================================="
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, "\nActive site residues for:", length(active_aa_pos)
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, "\n==================================================="
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, "\n"
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, active_aa_pos
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, "\n=================================================="
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, "\nDrug binding residues:", length(aa_pos_drug)
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, "\n==================================================="
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, "\n"
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#, aa_pos_dcs
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, aa_pos_drug
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, "\n==================================================="
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, "\nHbond residues:", length(aa_pos_dcs_hbond)
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, "\n==================================================="
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, "\n"
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, aa_pos_dcs_hbond
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, "\n=================================================="
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, "\nOther interaction residues:", length(aa_pos_dcs_other)
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, "\n==================================================="
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, "\n"
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, aa_pos_dcs_other
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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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111
config/embb.R
111
config/embb.R
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@ -1,7 +1,110 @@
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gene = "embB"
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gene = "embB"
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drug = "ethambutol"
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drug = "ethambutol"
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aa_plip = c(299, 302, 303, 327, 594, 988, 1028 )
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# interacting chain B
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aa_ligplus = c(299, 302, 303, 306, 334, 594, 988, 1028)
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#==========
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#active_aa_pos = c(299, 302, 303, 306, 327, 334, 594, 988, 1028 )
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# LIGPLUS
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active_aa_pos = sort(unique(c(aa_plip, aa_ligplus)))
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#===========
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aa_ligplus_emb = c(299, 302, 303, 306, 334, 594, 988, 1028)
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aa_ligplus_emb_hbond = c(299, 594)
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aa_ligplus_ca = c(952, 954, 959)
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aa_ligplus_ca_hbond = c(952, 954, 959)
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aa_ligplus_cdl = c(460, 665, 568, 601, 572, 579, 580, 583)
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aa_ligplus_cdl_hbond = c(601, 568, 665)
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aa_ligplus_dsl = c(435, 442, 489, 452, 330, 589, 509, 446, 445, 506, 592, 590, 514, 403, 515)
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aa_ligplus_dsl_hbond = c(445, 590, 592, 403)
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#==========
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# PLIP
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#===========
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aa_plip_emb = c(299, 302, 303, 327, 594, 988, 1028)
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aa_plip_emb_hbond = c(299, 327, 594)
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aa_plip_ca = c(952, 954, 959)
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aa_plip_cdl = c(456, 572, 579, 583, 568)
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#aa_plip_cdl_sb = c(537, 568, 601, 665)
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aa_plip_dsl = c(330, 435, 446, 452, 489, 506, 589, 590, 445, 403, 595)
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aa_plip_dsl_hbond = c(445, 590)
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#aa_plip_dsl_sb = c(403, 595)
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#==========
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# Arpeggio
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#===========
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# emb:1402, 1403
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aa_arpeg_emb = c(298, 299, 302, 303, 306, 318, 327, 334, 403, 445, 592, 594, 988, 1028)
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aa_arpeg_ca = c(847, 853, 854, 952, 954, 955, 956, 959, 960)
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aa_arpeg_cdl = c(456, 457, 460, 461, 521, 525, 533, 537, 554, 558, 568
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, 569, 572, 573, 575, 576, 579, 580, 582, 583, 586, 601, 605, 616, 658
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, 661, 662, 665)
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aa_arpeg_dsl = c(299, 322, 329, 330, 403, 435, 438, 439, 442, 445, 446
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, 449, 452, 455, 486, 489, 490, 493, 506, 509, 510, 513, 514
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, 515, 587, 589, 590, 592, 595)
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##############################################################
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active_aa_pos = 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_ligplus_ca
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, aa_plip_ca
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, aa_arpeg_ca
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, aa_ligplus_cdl
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, aa_plip_cdl
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, aa_arpeg_cdl
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, aa_ligplus_dsl
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, aa_plip_dsl
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, aa_arpeg_dsl)))
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##############################################################
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cat("\nNo. of active site residues for gene"
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, gene, ":"
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, length(active_aa_pos)
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, "\nThese are:\n"
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, active_aa_pos)
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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_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_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_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_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_pos_dsl_hbond = sort(unique(c( aa_ligplus_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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, "\n==================================================="
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, "\nNo. of", drug, "binding residues:" , length(aa_pos_emb), "\n"
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, aa_pos_emb
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, "\nNo. of co-factor 'Ca' binding residues:", length(aa_pos_ca) , "\n"
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, aa_pos_ca
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, "\nNo. of ligand 'CDL' binding residues:" , length(aa_pos_cdl), "\n"
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, aa_pos_cdl
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, "\nNo. of ligand 'DSL' binding residues:" , length(aa_pos_dsl), "\n"
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, aa_pos_dsl, "\n"
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)
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##############################################################
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128
config/gid.R
128
config/gid.R
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@ -1,27 +1,129 @@
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gene = "gid"
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gene = "gid"
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drug = "streptomycin"
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drug = "streptomycin"
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rna_bind_aa_pos = c(96, 97, 118, 163)
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binding_aa_pos = c(48, 51, 137, 200)
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aa_plip = c(118, 220, 223)
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aa_ligplus = c(118, 220, 223)
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active_aa_pos = sort(unique(c(rna_bind_aa_pos
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, binding_aa_pos
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, aa_plip
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, aa_ligplus)))
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#rna_site = G518
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#rna_site = G518
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#rna_bind_aa_pos = c(96, 97, 118, 163)
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#binding_aa_pos = c(48, 51, 137, 200)
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# SAM: 226
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# SRY: 1601
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#==========
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# LIGPLUS
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#===========
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aa_ligplus_sry = c(118, 220, 223) # 526 (rna) and 7mg527
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aa_ligplus_sry_hbond = c(118, 220, 223)
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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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aa_ligplus_rna = c(137, 47, 48, 38, 35, 36, 37, 94, 33, 97, 139, 138, 163, 165, 164, 199)
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aa_ligplus_rna_hbond = c(33, 97, 37, 47, 137)
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#==========
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# PLIP
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#===========
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aa_plip_sry = c(118, 220, 223)
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aa_plip_sry_hbond = c(118, 220, 223)
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aa_plip_sam = c(92, 118, 119, 120, 139, 220, 223, 148)
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aa_plip_sam_hbond = c(92, 118, 119, 120, 139, 220, 223)
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aa_plip_amp = c(123, 125, 213)
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aa_plip_amp_hbond = c(123, 125, 213)
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aa_plip_rna = c(33, 34, 36, 37, 47, 48, 51, 97, 137, 199)
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aa_plip_rna_hbond = c(33, 34, 36, 37, 47, 51, 137, 199)
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#==========
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# Arpeggio
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#===========
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aa_arpeg_sry = c(118, 148, 220, 223, 224)
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aa_arpeg_sam = c(68, 69, 92, 93, 97, 117
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, 118, 119, 120, 136, 137
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, 138, 139, 140, 148, 218
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, 219, 220, 221, 222, 223)
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aa_arpeg_amp = c(123, 125, 213)
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##############################################################
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#=============
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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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)))
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##############################################################
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cat("\nNo. of active site residues for gene"
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cat("\nNo. of active site residues for gene"
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, gene, ":"
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, gene, ":"
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, length(active_aa_pos)
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, length(active_aa_pos)
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, "\nThese are:\n"
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, "\nThese are:\n"
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, active_aa_pos)
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, active_aa_pos)
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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_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_pos_drug = aa_pos_sry
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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_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_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_pos_sam_hbond = sort(unique(c(
|
||||||
|
aa_ligplus_sam_hbond
|
||||||
|
, aa_plip_sam_hbond)))
|
||||||
|
|
||||||
|
aa_pos_amp = sort(unique(c(
|
||||||
|
aa_ligplus_amp
|
||||||
|
, aa_plip_amp
|
||||||
|
, aa_arpeg_amp)))
|
||||||
|
|
||||||
|
aa_pos_amp_hbond = sort(unique(c(
|
||||||
|
aa_ligplus_amp_hbond
|
||||||
|
, aa_plip_amp_hbond)))
|
||||||
|
|
||||||
|
|
||||||
cat("\n==================================================="
|
cat("\n==================================================="
|
||||||
, "\nActive site residues for", gene, "comprise of..."
|
, "\nActive site residues for", gene, "comprise of..."
|
||||||
, "\n==================================================="
|
, "\n==================================================="
|
||||||
, "\nRNA binding residues:"
|
, "\nNo. of", drug, "binding residues:" , length(aa_pos_sry), "\n"
|
||||||
, rna_bind_aa_pos
|
, aa_pos_sry
|
||||||
, "\nBinding site residues:"
|
, "\nNo. of RNA binding residues:" , length(aa_pos_rna), "\n"
|
||||||
, binding_aa_pos)
|
, aa_pos_rna
|
||||||
|
, "\nNo. of ligand 'SAM' binding residues:", length(aa_pos_sam), "\n"
|
||||||
|
, aa_pos_sam
|
||||||
|
, "\nNo. of ligand 'AMP' binding residues:", length(aa_pos_amp), "\n"
|
||||||
|
, aa_pos_amp, "\n")
|
||||||
|
|
||||||
|
##############################################################
|
||||||
|
|
|
||||||
104
config/katg.R
104
config/katg.R
|
|
@ -1,6 +1,104 @@
|
||||||
gene = "katG"
|
gene = "katG"
|
||||||
drug = "isoniazid"
|
drug = "isoniazid"
|
||||||
|
|
||||||
aa_plip = c(104, 229, 230)
|
#==========
|
||||||
aa_ligplus = c(107, 108, 137, 229, 230)
|
# LIGPLUS
|
||||||
active_aa_pos = sort(unique(c(aa_plip, aa_ligplus)))
|
#===========
|
||||||
|
# hem (1500)
|
||||||
|
aa_ligplus_inh = c(107, 108, 137, 229, 230)
|
||||||
|
#aa_ligplus_inh_hbond # none
|
||||||
|
|
||||||
|
aa_ligplus_hem = c(94, 276, 315, 274, 270, 381, 273, 104, 314, 275,
|
||||||
|
100, 101, 321, 103, 269, 107, 266, 230, 380, 275, 314)
|
||||||
|
|
||||||
|
aa_ligplus_hem_hbond = c(94, 276, 315, 274, 270, 381)
|
||||||
|
aa_ligplus_hem_other = aa_ligplus_hem[!aa_ligplus_hem%in%aa_ligplus_hem_hbond]
|
||||||
|
|
||||||
|
c1 = length(aa_ligplus_hem_other) == length(aa_ligplus_hem) - length(aa_ligplus_hem_hbond)
|
||||||
|
|
||||||
|
#==========
|
||||||
|
# PLIP
|
||||||
|
#===========
|
||||||
|
aa_plip_inh = c(104, 229, 230)
|
||||||
|
aa_plip_inh_hbond = c(104, 229, 230)
|
||||||
|
|
||||||
|
aa_plip_hem = c(104, 107, 248, 252, 265, 275, 321, 412, 274, 276, 315)
|
||||||
|
aa_plip_hem_hbond = c(274, 276, 315)
|
||||||
|
#aa_plip_hem_sb = c(104, 276)
|
||||||
|
#aa_plip_hem_pi = c(107)
|
||||||
|
aa_plip_hem_other = aa_plip_hem[!aa_plip_hem%in%aa_plip_hem_hbond]
|
||||||
|
|
||||||
|
c2 = length(aa_plip_hem_other) == length(aa_plip_hem) - length(aa_plip_hem_hbond)
|
||||||
|
|
||||||
|
#==========
|
||||||
|
# Arpeggio
|
||||||
|
#===========
|
||||||
|
aa_arpeg_inh = c(104, 107, 108, 136, 137, 228, 229, 230, 232, 315)
|
||||||
|
aa_arpeg_inh_hbond = c(104, 137)
|
||||||
|
|
||||||
|
aa_arpeg_hem = c(94, 100, 101, 103, 104, 107, 230, 231, 232, 248
|
||||||
|
, 252, 265, 266, 269, 270, 272, 273, 274, 275, 276, 314, 315
|
||||||
|
, 317, 321, 378, 380, 408, 412)
|
||||||
|
|
||||||
|
#from here
|
||||||
|
|
||||||
|
##############################################################
|
||||||
|
#===============
|
||||||
|
# Active site aa
|
||||||
|
#===============
|
||||||
|
active_aa_pos = sort(unique(c(aa_ligplus_inh
|
||||||
|
, aa_plip_inh
|
||||||
|
, aa_arpeg_inh
|
||||||
|
|
||||||
|
, aa_ligplus_hem
|
||||||
|
, aa_plip_hem
|
||||||
|
, aa_arpeg_hem
|
||||||
|
)))
|
||||||
|
cat("\nNo. of active site residues for gene"
|
||||||
|
, gene, ":"
|
||||||
|
, length(active_aa_pos)
|
||||||
|
, "\nThese are:\n"
|
||||||
|
, active_aa_pos)
|
||||||
|
|
||||||
|
#=================
|
||||||
|
# Drug binding aa
|
||||||
|
#=================
|
||||||
|
aa_pos_inh = sort(unique(c( aa_ligplus_inh
|
||||||
|
, aa_plip_inh
|
||||||
|
, aa_arpeg_inh)))
|
||||||
|
aa_pos_drug = aa_pos_inh
|
||||||
|
|
||||||
|
|
||||||
|
#===============
|
||||||
|
# Hbond aa
|
||||||
|
#===============
|
||||||
|
aa_pos_inh_hbond = sort(unique(c( aa_plip_inh_hbond
|
||||||
|
, aa_arpeg_inh_hbond)))
|
||||||
|
|
||||||
|
#=======================
|
||||||
|
# Other interactions aa
|
||||||
|
#=======================
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
#---------------------------------------------
|
||||||
|
|
||||||
|
aa_pos_hem = sort(unique(c( aa_ligplus_hem
|
||||||
|
, aa_plip_hem
|
||||||
|
, aa_arpeg_hem)))
|
||||||
|
|
||||||
|
aa_pos_hem_hbond = sort(unique(c( aa_ligplus_hem_hbond
|
||||||
|
, aa_plip_hem_hbond
|
||||||
|
#, aa_arpeg_hem_hbond
|
||||||
|
)))
|
||||||
|
|
||||||
|
|
||||||
|
cat("\n==================================================="
|
||||||
|
, "\nActive site residues for", gene, "comprise of..."
|
||||||
|
, "\n==================================================="
|
||||||
|
, "\nNo. of", drug, "binding residues:" , length(aa_pos_inh) , "\n"
|
||||||
|
, aa_pos_inh
|
||||||
|
, "\nNo. of 'HEM' binding residues:" , length(aa_pos_hem) , "\n"
|
||||||
|
, aa_pos_hem, "\n")
|
||||||
|
|
||||||
|
##############################################################
|
||||||
|
|
|
||||||
|
|
@ -11,16 +11,26 @@ drug = "pyrazinamide"
|
||||||
#aa_ligplus = c(8, 13 , 49 , 133, 134 , 138, 137)
|
#aa_ligplus = c(8, 13 , 49 , 133, 134 , 138, 137)
|
||||||
#active_aa_pos = sort(unique(c(aa_plip, aa_ligplus)))
|
#active_aa_pos = sort(unique(c(aa_plip, aa_ligplus)))
|
||||||
|
|
||||||
metal_aa_pos = c(49, 51, 57, 71)
|
#aa_pos_substrate = c(13, 68, 103, 137)
|
||||||
catalytic_aa_pos = c(8, 96, 138)
|
aa_pos_pza = c(13, 68, 103, 137)
|
||||||
substrate_aa_pos = c(13, 68, 103, 137)
|
aa_pos_fe = c(49, 51, 57, 71)
|
||||||
hbond_aa_pos = c(133, 134, 8, 138)
|
aa_pos_catalytic = c(8, 96, 138)
|
||||||
|
aa_pos_hbond = c(133, 134, 8, 138)
|
||||||
|
|
||||||
|
aa_pos_drug = aa_pos_pza
|
||||||
|
#==========
|
||||||
|
# Arpeggio
|
||||||
|
#===========
|
||||||
|
# all same except one extra
|
||||||
|
aa_arpeg = c(102)
|
||||||
|
|
||||||
|
##############################################################
|
||||||
active_aa_pos = sort(unique(c(metal_aa_pos
|
active_aa_pos = sort(unique(c(metal_aa_pos
|
||||||
, catalytic_aa_pos
|
, catalytic_aa_pos
|
||||||
, substrate_aa_pos
|
, substrate_aa_pos
|
||||||
, hbond_aa_pos)))
|
, hbond_aa_pos
|
||||||
|
, aa_arpeg)))
|
||||||
|
##############################################################
|
||||||
cat("\nNo. of active site residues for gene"
|
cat("\nNo. of active site residues for gene"
|
||||||
, gene, ":"
|
, gene, ":"
|
||||||
, length(active_aa_pos)
|
, length(active_aa_pos)
|
||||||
|
|
@ -30,11 +40,13 @@ cat("\nNo. of active site residues for gene"
|
||||||
cat("\n==================================================="
|
cat("\n==================================================="
|
||||||
, "\nActive site residues for", gene, "comprise of..."
|
, "\nActive site residues for", gene, "comprise of..."
|
||||||
, "\n==================================================="
|
, "\n==================================================="
|
||||||
, "\nMetal coordination centre residues:"
|
, "\nNo. of", drug, "binding residues:" , length(aa_pos_pza) , "\n"
|
||||||
, metal_aa_pos
|
, aa_pos_pza
|
||||||
, "\nCatalytic triad residues:"
|
, "\nMetal coordination centre residues:" , length(aa_pos_fe) , "\n"
|
||||||
, catalytic_aa_pos
|
, aa_pos_fe
|
||||||
, "\nSubstrate binding residues:"
|
, "\nCatalytic triad residues:" , length(aa_pos_catalytic) , "\n"
|
||||||
, substrate_aa_pos
|
, aa_pos_catalytic
|
||||||
, "\nH-bonding residues:"
|
, "\nH-bonding residues:" , length(aa_pos_hbond) , "\n"
|
||||||
, hbond_aa_pos)
|
, aa_pos_hbond , "\n")
|
||||||
|
|
||||||
|
##############################################################
|
||||||
|
|
@ -1,6 +1,57 @@
|
||||||
gene = "rpoB"
|
gene = "rpoB"
|
||||||
drug = "rifampicin"
|
drug = "rifampicin"
|
||||||
|
|
||||||
aa_plip = c(429, 432, 491, 487)
|
#==========
|
||||||
aa_plip_5uhc = c(430, 452, 483, 491, 432, 433, 448, 450, 459, 487)
|
# LIGPLUS
|
||||||
active_aa_pos = sort(unique(c(aa_plip, aa_plip_5uhc)))
|
#===========
|
||||||
|
# Error! No atom records found!
|
||||||
|
|
||||||
|
#==========
|
||||||
|
# PLIP
|
||||||
|
#===========
|
||||||
|
aa_plip_rfp = c(429, 432, 491, 487)
|
||||||
|
aa_plip_rfp_hbond = c(429, 432, 487)
|
||||||
|
|
||||||
|
# chainC: equivalent with offset (-6 from 5uhc) accounted
|
||||||
|
aa_plip_5uhc_rfp = c(430, 452, 483
|
||||||
|
, 491, 432, 433
|
||||||
|
, 448, 450, 459, 487)
|
||||||
|
aa_plip_5uhc_rfp_hbond = c(432, 433, 448, 450, 459, 487)
|
||||||
|
|
||||||
|
#==========
|
||||||
|
# Arpeggio
|
||||||
|
#===========
|
||||||
|
# rfp: 1894
|
||||||
|
aa_arpeg_rfp = c(170, 428, 429, 430, 431, 432
|
||||||
|
, 433, 435, 445, 448, 450, 452
|
||||||
|
, 453, 458, 483, 487, 491, 604
|
||||||
|
, 607, 674)
|
||||||
|
|
||||||
|
##############################################################
|
||||||
|
active_aa_pos = sort(unique(c(aa_plip_rfp
|
||||||
|
, aa_plip_5uhc_rfp
|
||||||
|
, aa_arpeg_rfp)))
|
||||||
|
##############################################################
|
||||||
|
cat("\nNo. of active site residues for gene"
|
||||||
|
, gene, ":"
|
||||||
|
, length(active_aa_pos)
|
||||||
|
, "\nThese are:\n"
|
||||||
|
, active_aa_pos)
|
||||||
|
##############################################################
|
||||||
|
aa_pos_rfp = sort(unique(c(aa_plip_rfp
|
||||||
|
, aa_plip_5uhc_rfp
|
||||||
|
, aa_arpeg_rfp)))
|
||||||
|
|
||||||
|
aa_pos_drug = aa_pos_rfp
|
||||||
|
|
||||||
|
aa_pos_rfp_hbond = sort(unique(c(aa_plip_rfp_hbond
|
||||||
|
, aa_plip_5uhc_rfp_hbond)))
|
||||||
|
|
||||||
|
cat("\n==================================================="
|
||||||
|
, "\nActive site residues for", gene, "comprise of..."
|
||||||
|
, "\n==================================================="
|
||||||
|
, "\nNo. of", drug, "binding residues:" , length(aa_pos_rfp), "\n"
|
||||||
|
, aa_pos_rfp
|
||||||
|
, "\n\nNO other co-factors or ligands present\n")
|
||||||
|
|
||||||
|
##############################################################
|
||||||
|
|
|
||||||
|
|
@ -193,6 +193,29 @@ map(paste0(func_path, source_files), source) # source all your R scripts!
|
||||||
# set plot script dir
|
# set plot script dir
|
||||||
plot_script_path = "~/git/LSHTM_analysis/scripts/plotting/"
|
plot_script_path = "~/git/LSHTM_analysis/scripts/plotting/"
|
||||||
|
|
||||||
|
####################################################
|
||||||
|
consurf_palette1 = c("0" = "yellow2"
|
||||||
|
, "1" = "cyan1"
|
||||||
|
, "2" = "steelblue2"
|
||||||
|
, "3" = "cadetblue2"
|
||||||
|
, "4" = "paleturquoise2"
|
||||||
|
, "5" = "thistle3"
|
||||||
|
, "6" = "thistle2"
|
||||||
|
, "7" = "plum2"
|
||||||
|
, "8" = "maroon"
|
||||||
|
, "9" = "violetred2")
|
||||||
|
|
||||||
|
consurf_palette2 = c("0" = "yellow2"
|
||||||
|
, "1" = "forestgreen"
|
||||||
|
, "2" = "seagreen3"
|
||||||
|
, "3" = "palegreen1"
|
||||||
|
, "4" = "darkseagreen2"
|
||||||
|
, "5" = "thistle3"
|
||||||
|
, "6" = "lightpink1"
|
||||||
|
, "7" = "orchid3"
|
||||||
|
, "8" = "orchid4"
|
||||||
|
, "9" = "darkorchid4")
|
||||||
|
|
||||||
##################################################
|
##################################################
|
||||||
|
|
||||||
# Function name clashes with plyr and dplyr
|
# Function name clashes with plyr and dplyr
|
||||||
|
|
|
||||||
|
|
@ -213,7 +213,7 @@ g = ggplot(df, aes(factor(position, ordered = T)))
|
||||||
# This is the key to generating the geom_tiles OUTside the plotting area on the x-axis!
|
# This is the key to generating the geom_tiles OUTside the plotting area on the x-axis!
|
||||||
OutPlot_aa_PS = g +
|
OutPlot_aa_PS = g +
|
||||||
coord_cartesian(xlim = c(1, my_xlim)
|
coord_cartesian(xlim = c(1, my_xlim)
|
||||||
#, ylim = c(0, 6)
|
#, ylim = c(0, 6)0.85
|
||||||
, ylim = c(0, max(snp_count))
|
, ylim = c(0, max(snp_count))
|
||||||
, clip = "off") +
|
, clip = "off") +
|
||||||
geom_bar(aes(fill = group), colour = "grey") +
|
geom_bar(aes(fill = group), colour = "grey") +
|
||||||
|
|
|
||||||
|
|
@ -1,30 +1,3 @@
|
||||||
consurf_palette1 = c("0" = "yellow2"
|
|
||||||
, "1" = "cyan1"
|
|
||||||
, "2" = "steelblue2"
|
|
||||||
, "3" = "cadetblue2"
|
|
||||||
, "4" = "paleturquoise2"
|
|
||||||
, "5" = "thistle3"
|
|
||||||
, "6" = "thistle2"
|
|
||||||
, "7" = "plum2"
|
|
||||||
, "8" = "maroon"
|
|
||||||
, "9" = "violetred2")
|
|
||||||
|
|
||||||
consurf_palette2 = c("0" = "yellow2"
|
|
||||||
, "1" = "forestgreen"
|
|
||||||
, "2" = "seagreen3"
|
|
||||||
, "3" = "palegreen1"
|
|
||||||
, "4" = "darkseagreen2"
|
|
||||||
, "5" = "thistle3"
|
|
||||||
, "6" = "lightpink1"
|
|
||||||
, "7" = "orchid3"
|
|
||||||
, "8" = "orchid4"
|
|
||||||
, "9" = "darkorchid4")
|
|
||||||
|
|
||||||
|
|
||||||
#myCOL <- colorRampPalette(c("yellow2", "palegreen1", "darkorchid4"))(10)
|
|
||||||
#plot(1:100, col = myCOL, pch = 19, cex = 2)
|
|
||||||
#myColors <- scale_color_brewer(palette = "Cyan-Magenta")
|
|
||||||
|
|
||||||
consurf_cols = consurf_palette1
|
consurf_cols = consurf_palette1
|
||||||
consurf_cols = consurf_palette2
|
consurf_cols = consurf_palette2
|
||||||
#consurf_cols = myCOL
|
#consurf_cols = myCOL
|
||||||
|
|
@ -42,17 +15,20 @@ length(unique(merged_df3[[aa_position_colname]]))
|
||||||
|
|
||||||
positionF <- levels(as.factor(merged_df3[[aa_position_colname]]))
|
positionF <- levels(as.factor(merged_df3[[aa_position_colname]]))
|
||||||
length(positionF)
|
length(positionF)
|
||||||
aa_pos_colours = ifelse(positionF%in%rna_bind_aa_pos, "purple"
|
aa_pos_colours = ifelse(positionF%in%aa_pos_sry, "purple"
|
||||||
, ifelse(positionF%in%binding_aa_pos, "orange", "black" ))
|
, ifelse(positionF%in%aa_pos_rna, "orange", "black" ))
|
||||||
bar = merged_df3
|
bar = merged_df3
|
||||||
bar[['lab_bg']] = ifelse(bar[[aa_position_colname]]%in%rna_bind_aa_pos
|
aa_colour_colname = "lab_bg"
|
||||||
|
|
||||||
|
bar[[aa_colour_colname]] = ifelse(bar[[aa_position_colname]]%in%aa_pos_sry
|
||||||
, "purple"
|
, "purple"
|
||||||
, ifelse(bar[[aa_position_colname]]%in%binding_aa_pos
|
, ifelse(bar[[aa_position_colname]]%in%aa_pos_rna
|
||||||
, "orange", "white" ))
|
, "orange", "white" ))
|
||||||
head(bar[[aa_position_colname]])
|
head(bar[[aa_position_colname]])
|
||||||
head(bar[['lab_bg']])
|
head(bar[[aa_colour_colname]])
|
||||||
|
|
||||||
my_xlim = length(unique(bar$position)); my_xlim
|
######################################################################
|
||||||
|
my_xlim = length(unique(bar[[aa_position_colname]])); my_xlim
|
||||||
|
|
||||||
ymin = min(bar$consurf_score)
|
ymin = min(bar$consurf_score)
|
||||||
ymax = max(bar$consurf_score)
|
ymax = max(bar$consurf_score)
|
||||||
|
|
@ -70,15 +46,38 @@ g = ggplot(bar, aes(x = factor(position)
|
||||||
) +
|
) +
|
||||||
geom_errorbar(aes(ymin = consurf_ci_lower, ymax = consurf_ci_upper))
|
geom_errorbar(aes(ymin = consurf_ci_lower, ymax = consurf_ci_upper))
|
||||||
|
|
||||||
g0 = g + geom_tile(aes(,-2, width = 0.95, height = -0.2)
|
# g0 = g + geom_tile(aes(,-2, width = 0.95, height = -0.2)
|
||||||
, fill = bar$lab_bg
|
# #, fill = bar$lab_bg
|
||||||
, colour = "white")
|
# , fill = bar[[aa_colour_colname]]
|
||||||
g0
|
# , colour = "white")
|
||||||
|
|
||||||
g1 = g0 + theme( axis.text.x = element_text(size = 10
|
g0 = g +
|
||||||
|
geom_tile(aes(,-1.7, width = 0.95, height = 0.3)
|
||||||
|
, fill = bar$ligD_colours
|
||||||
|
, colour = "black")
|
||||||
|
|
||||||
|
# g0 = g +
|
||||||
|
# geom_tile(aes(,-1.9, width = 0.95, height = 0.2)
|
||||||
|
# , fill = bar[[aa_colour_colname4]]
|
||||||
|
# , colour = "white") +
|
||||||
|
# geom_tile(aes(,-2, width = 0.95, height = 0.3)
|
||||||
|
# , fill = bar[[aa_colour_colname3]]
|
||||||
|
# , colour = "white"
|
||||||
|
# )+
|
||||||
|
# geom_tile(aes(,-2.1, width = 0.95, height = 0.35)
|
||||||
|
# , fill = bar[[aa_colour_colname2]]
|
||||||
|
# , colour = "white"
|
||||||
|
# )+
|
||||||
|
# geom_tile(aes(,-2.2, width = 0.95, height = 0.45)
|
||||||
|
# , fill = bar[[aa_colour_colname1]]
|
||||||
|
# , colour = "white"
|
||||||
|
# )
|
||||||
|
|
||||||
|
g1 = g + theme( axis.text.x = element_text(size = 10
|
||||||
, angle = 90
|
, angle = 90
|
||||||
, hjust = 1
|
, hjust = 1
|
||||||
, vjust = 0.4
|
, vjust = 0.4
|
||||||
|
, face = "bold"
|
||||||
#, colour = aa_pos_colours
|
#, colour = aa_pos_colours
|
||||||
)
|
)
|
||||||
, axis.text.y = element_text(size = 12
|
, axis.text.y = element_text(size = 12
|
||||||
|
|
@ -92,12 +91,128 @@ g1 = g0 + theme( axis.text.x = element_text(size = 10
|
||||||
, panel.grid.minor = element_line(color = "black")) +
|
, panel.grid.minor = element_line(color = "black")) +
|
||||||
guides(colour = guide_legend(title = "Consurf"
|
guides(colour = guide_legend(title = "Consurf"
|
||||||
, position = "top"
|
, position = "top"
|
||||||
#, direction = "horizontal"
|
#, direction = "horizontal"
|
||||||
)) +
|
)) +
|
||||||
labs(title = ""
|
labs(title = ""
|
||||||
, x = "Wild-type position"
|
#, x = "Wild-type position"
|
||||||
|
, x = ""
|
||||||
, y = "Consurf score")
|
, y = "Consurf score")
|
||||||
|
|
||||||
g1
|
g1
|
||||||
|
|
||||||
##########################################
|
# add tile afterwards
|
||||||
|
g2 = g1 + geom_tile(aes(,-1.7, width = 0.95, height = 0.3)
|
||||||
|
, fill = bar$ligD_colours
|
||||||
|
, colour = "black")
|
||||||
|
g2
|
||||||
|
|
||||||
|
g3 = g2 +
|
||||||
|
geom_tile(aes(,-1.9, width = 0.95, height = 0.3)
|
||||||
|
, fill = bar[[aa_colour_colname4]]
|
||||||
|
, colour = "white") +
|
||||||
|
geom_tile(aes(,-2, width = 0.95, height = 0.3)
|
||||||
|
, fill = bar[[aa_colour_colname3]]
|
||||||
|
, colour = "white"
|
||||||
|
)+
|
||||||
|
geom_tile(aes(,-2.1, width = 0.95, height = 0.35)
|
||||||
|
, fill = bar[[aa_colour_colname2]]
|
||||||
|
, colour = "white"
|
||||||
|
)+
|
||||||
|
geom_tile(aes(,-2.2, width = 0.95, height = 0.35)
|
||||||
|
, fill = bar[[aa_colour_colname1]]
|
||||||
|
, colour = "white"
|
||||||
|
)
|
||||||
|
|
||||||
|
g3
|
||||||
|
|
||||||
|
#==============================================
|
||||||
|
#Multiple legends in a plot with geom_tile
|
||||||
|
#==============================================
|
||||||
|
|
||||||
|
# https://stackoverflow.com/questions/24822621/multiple-legends-in-a-plot-with-geom-tile
|
||||||
|
g_legend<-function(a.gplot){
|
||||||
|
tmp <- ggplot_gtable(ggplot_build(a.gplot))
|
||||||
|
leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
|
||||||
|
legend <- tmp$grobs[[leg]]
|
||||||
|
legend
|
||||||
|
}
|
||||||
|
|
||||||
|
legend1 = g_legend(g1)
|
||||||
|
|
||||||
|
g2 = g1 + geom_tile(aes(,-1.7, width = 0.95, height = 0.3)
|
||||||
|
, fill = bar$ligD_colours
|
||||||
|
, colour = "black")
|
||||||
|
|
||||||
|
g2
|
||||||
|
|
||||||
|
legend2 = g_legend(g2)
|
||||||
|
|
||||||
|
grid.arrange(g1+theme(legend.position = 'none')
|
||||||
|
#, legend1
|
||||||
|
, legend2
|
||||||
|
, ncol = 2
|
||||||
|
, widths=c(4/6, 1/6))
|
||||||
|
###############################################################
|
||||||
|
###############################################################
|
||||||
|
|
||||||
|
lig_min = min(round(bar[[LigDist_colname]])); lig_min
|
||||||
|
lig_max = max(round(bar[[LigDist_colname]])); lig_max
|
||||||
|
lig_mean = round(mean(bar[[LigDist_colname]])); lig_mean
|
||||||
|
labels = seq(lig_min, lig_max, len = 5); labels
|
||||||
|
labelsD = round(labels, digits = 0); labelsD
|
||||||
|
|
||||||
|
g = ggplot(bar, aes( x = factor(.data[[aa_position_colname]])
|
||||||
|
, y = .data[[LigDist_colname]]))
|
||||||
|
g
|
||||||
|
# yayy
|
||||||
|
g1 = g + geom_tile(aes(fill = .data[[LigDist_colname]])
|
||||||
|
, colour = "white") +
|
||||||
|
#scale_fill_gradient(low = "green", high = "red")
|
||||||
|
scale_fill_gradient2(midpoint = lig_mean
|
||||||
|
, low = "green"
|
||||||
|
, mid = "yellow"
|
||||||
|
, high = "red"
|
||||||
|
, breaks = labels
|
||||||
|
#, n.breaks = 11
|
||||||
|
#, minor_breaks = c(2, 4, 6, 8, 10)
|
||||||
|
, limits = c(lig_min, lig_max)
|
||||||
|
, labels = labelsD
|
||||||
|
, name = "Ligand Distance")
|
||||||
|
g1
|
||||||
|
|
||||||
|
|
||||||
|
main_leg = g_legend(g2)
|
||||||
|
main_leg
|
||||||
|
|
||||||
|
ligD_leg = g_legend(g1)
|
||||||
|
grid.arrange(ligD_leg
|
||||||
|
, ncol = 2
|
||||||
|
, widths=c(4/6, 1/6))
|
||||||
|
|
||||||
|
grid.arrange(g2+theme(legend.position = 'none')
|
||||||
|
, main_leg
|
||||||
|
, ligD_leg
|
||||||
|
, ncol = 3
|
||||||
|
, widths=c(9/10, 0.5/10, 0.5/10))
|
||||||
|
|
||||||
|
|
||||||
|
##########################
|
||||||
|
g3 = g2 + theme(legend.position = 'none')
|
||||||
|
g3
|
||||||
|
g4 = g3 + geom_tile(aes(fill = .data[['consurf_score']])
|
||||||
|
, colour = "white")
|
||||||
|
|
||||||
|
g4 + geom_tile(scale_fill_gradient(consurf_palette2)
|
||||||
|
|
||||||
|
|
||||||
|
midpoint = lig_mean
|
||||||
|
, low = "green"
|
||||||
|
, mid = "yellow"
|
||||||
|
, high = "red"
|
||||||
|
, breaks = labels
|
||||||
|
#, n.breaks = 11
|
||||||
|
#, minor_breaks = c(2, 4, 6, 8, 10)
|
||||||
|
, limits = c(lig_min, lig_max)
|
||||||
|
, labels = labelsD
|
||||||
|
, name = "Ligand Distance")
|
||||||
|
g1
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue