Merge pull request protwis#1 from protwis/master

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pszgaspar · Feb 9, 2016 · 3af0fe2 · 3af0fe2
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diff --git a/docs/building_a_database.rst b/docs/building_a_database.rst
@@ -19,11 +19,11 @@ Building a local database from source data
 
 * Run migrations::
 
-    /protwis/env/bin/python3 manage.py migrate
+    /env/bin/python3 manage.py migrate
 
 * Start the build process::
 
-    /protwis/env/bin/python3 manage.py build_all -p 4 -t
+    /env/bin/python3 manage.py build_all -p 4 -t
 
 This will build a test version of the database using only the proteins for which a structure has been determined.
 For a full build, remove the -t flag from the build_all command (NOTE: a full build takes a long time, and should not

diff --git a/docs/meetings.rst b/docs/meetings.rst
@@ -4,9 +4,12 @@ Meetings with GPCRdb representation
 2016
 ----
 
+*   Apr 6-8,
+    `6th GLISTEN meeting`_ in Erlangen, Germany.
 *   Feb 21-25,
     `G Protein-Coupled Receptors\: Structure, Signaling and Drug Discovery`_ in Keystone, USA.
 
+.. _6th GLISTEN meeting: http://www.grk1910.de/glisten-2016.html
 .. _G Protein-Coupled Receptors\: Structure, Signaling and Drug Discovery: https://www.keystonesymposia.org/index.cfm?e=web.Meeting.Program&meetingid=1368
 
 2015
@@ -52,4 +55,4 @@ Meetings with GPCRdb representation
 *   Oct 7-9,
     `1st GLISTEN meeting`_ in Warsaw, Poland.
 
-.. _1st GLISTEN meeting: http://www.biomodellab.eu/1glisten/welcome/
+.. _1st GLISTEN meeting: http://www.biomodellab.eu/1glisten/welcome/
diff --git a/docs/reload_database.rst b/docs/reload_database.rst
@@ -14,6 +14,6 @@ Reload database from dump
     curl http://files.gpcrdb.org/protwis_sp.sql.gz > ~/protwis.sql.gz
     gunzip ~/protwis.sql.gz
 
-* Load the dump [Either from default location or a location of your choosing]::
+* Load the dump (Either from default location or a location of your choosing)::
 
     psql -U protwis -h localhost -o protwis < ~/protwis.sql;
diff --git a/protein_data/proteins_and_families.txt b/protein_data/proteins_and_families.txt
diff --git a/residue_data/generic_numbers/mapping_gpcrdba.txt b/residue_data/generic_numbers/mapping_gpcrdba.txt
@@ -59,11 +59,11 @@
 1x78    1x78
 1x79    1x79
 1x80    1x80
-12x46   12x46
 12x47   12x47
 12x48   12x48
 12x49   12x49
 12x50   12x50
+12x51   12x51
 2x30    2x30
 2x31    2x31
 2x32    2x32
@@ -518,4 +518,4 @@
 8x67    8x67
 8x68    8x68
 8x69    8x69
-8x70    8x70
+8x70    8x70
diff --git a/residue_data/generic_numbers/mapping_gpcrdbb.txt b/residue_data/generic_numbers/mapping_gpcrdbb.txt
@@ -59,6 +59,11 @@
 1x78    1x82
 1x79    1x83
 1x80    1x84
+12x47   12x47
+12x48   12x48
+12x49   12x49
+12x50   12x50
+12x51   12x51
 2x30    2x37
 2x31    2x38
 2x32    2x39
@@ -498,4 +503,4 @@
 8x67    8x67
 8x68    8x68
 8x69    8x69
-8x70    8x70
+8x70    8x70
diff --git a/residue_data/generic_numbers/mapping_gpcrdbc.txt b/residue_data/generic_numbers/mapping_gpcrdbc.txt
@@ -59,6 +59,11 @@
 1x78    1x82
 1x79    1x83
 1x80    1x84
+12x47   12x47
+12x48   12x48
+12x49   12x49
+12x50   12x50
+12x51   12x51
 2x30    2x26
 2x31    2x27
 2x32    2x28
@@ -498,4 +503,4 @@
 8x67    8x67
 8x68    8x68
 8x69    8x69
-8x70    8x70
+8x70    8x70
diff --git a/residue_data/generic_numbers/mapping_gpcrdbf.txt b/residue_data/generic_numbers/mapping_gpcrdbf.txt
@@ -59,6 +59,12 @@
 1x78    1x75
 1x79    1x76
 1x80    1x77
+12x46   12x46
+12x47   12x47
+12x48   12x48
+12x49   12x49
+12x50   12x50
+12x51   12x51
 2x30    2x29
 2x31    2x30
 2x32    2x31
@@ -498,4 +504,4 @@
 8x67    8x67
 8x68    8x68
 8x69    8x69
-8x70    8x70
+8x70    8x70
diff --git a/residue_data/reference_positions/5ht7r_human.yaml b/residue_data/reference_positions/5ht7r_human.yaml
@@ -9,4 +9,4 @@
 5x50: 251
 6x50: 342
 7x50: 381
-8x50: 387
+8x50: 391
diff --git a/residue_data/reference_positions/ackr1_human.yaml b/residue_data/reference_positions/ackr1_human.yaml
@@ -7,4 +7,4 @@
 5x50: 222
 6x50: 255
 7x50: 301
-8x50: 312
+8x50: 311
diff --git a/residue_data/reference_positions/ackr2_human.yaml b/residue_data/reference_positions/ackr2_human.yaml
@@ -1,6 +1,6 @@
 12x50: 77
 1x50: 64
-23x50: 108
+23x50: 110
 2x50: 92
 34x50: 149
 3x50: 142

diff --git a/residue_data/reference_positions/ackr4_human.yaml b/residue_data/reference_positions/ackr4_human.yaml
@@ -9,3 +9,4 @@
 5x50: 212
 6x50: 255
 7x50: 300
+8x50: 310
diff --git a/residue_data/reference_positions/adrb1_human.yaml b/residue_data/reference_positions/adrb1_human.yaml
@@ -9,4 +9,4 @@
 5x50: 236
 6x50: 339
 7x50: 374
-8x50: 383
+8x50: 384
diff --git a/residue_data/reference_positions/adrb2_human.yaml b/residue_data/reference_positions/adrb2_human.yaml
@@ -9,4 +9,4 @@
 5x50: 211
 6x50: 288
 7x50: 323
-8x50: 332
+8x50: 333
diff --git a/residue_data/reference_positions/adrb3_human.yaml b/residue_data/reference_positions/adrb3_human.yaml
@@ -9,4 +9,4 @@
 5x50: 216
 6x50: 307
 7x50: 343
-8x50: 352
+8x50: 353
diff --git a/residue_data/reference_positions/apj_human.yaml b/residue_data/reference_positions/apj_human.yaml
@@ -9,3 +9,4 @@
 5x50: 213
 6x50: 263
 7x50: 306
+8x50: 316
diff --git a/residue_data/reference_positions/bai1_human.yaml b/residue_data/reference_positions/bai1_human.yaml
@@ -1,5 +1,5 @@
-1x50: 931
-2x50: 975
+1x50: 962
+2x50: 991
 3x50: 1036
 45x50: 1083
 4x50: 1058

diff --git a/residue_data/reference_positions/bkrb2_human.yaml b/residue_data/reference_positions/bkrb2_human.yaml
@@ -9,3 +9,4 @@
 5x50: 236
 6x50: 285
 7x50: 329
+8x50: 339
diff --git a/residue_data/reference_positions/c3ar_human.yaml b/residue_data/reference_positions/c3ar_human.yaml
@@ -9,4 +9,4 @@
 5x50: 348
 6x50: 392
 7x50: 432
-8x50: 438
+8x50: 442
diff --git a/residue_data/reference_positions/c5ar2_human.yaml b/residue_data/reference_positions/c5ar2_human.yaml
@@ -9,4 +9,4 @@
 5x50: 212
 6x50: 248
 7x50: 288
-8x50: 294
+8x50: 298
diff --git a/residue_data/reference_positions/calcr_human.yaml b/residue_data/reference_positions/calcr_human.yaml
@@ -6,3 +6,4 @@
 5x50: 342
 6x50: 392
 7x50: 422
+12x50: 194
diff --git a/residue_data/reference_positions/calrl_human.yaml b/residue_data/reference_positions/calrl_human.yaml
@@ -6,3 +6,4 @@
 5x50: 301
 6x50: 351
 7x50: 381
+12x50: 169
diff --git a/residue_data/reference_positions/casr_human.yaml b/residue_data/reference_positions/casr_human.yaml
@@ -6,3 +6,4 @@
 5x50: 783
 6x50: 820
 7x50: 849
+12x50: 640
diff --git a/residue_data/reference_positions/ccrl2_human.yaml b/residue_data/reference_positions/ccrl2_human.yaml
@@ -1,5 +1,6 @@
 12x50: 69
 1x50: 56
+23x50: '-'
 2x50: 84
 34x50: 135
 3x50: 128

diff --git a/residue_data/reference_positions/cltr1_human.yaml b/residue_data/reference_positions/cltr1_human.yaml
@@ -9,3 +9,4 @@
 5x50: 201
 6x50: 248
 7x50: 292
+8x50: 302
diff --git a/residue_data/reference_positions/cltr2_human.yaml b/residue_data/reference_positions/cltr2_human.yaml
@@ -9,3 +9,4 @@
 5x50: 213
 6x50: 262
 7x50: 302
+8x50: 312
diff --git a/residue_data/reference_positions/crfr1_human.yaml b/residue_data/reference_positions/crfr1_human.yaml
@@ -6,3 +6,4 @@
 5x50: 308
 6x50: 358
 7x50: 389
+12x50: 147
diff --git a/residue_data/reference_positions/crfr2_human.yaml b/residue_data/reference_positions/crfr2_human.yaml
@@ -6,3 +6,4 @@
 5x50: 275
 6x50: 325
 7x50: 356
+12x50: 144
diff --git a/residue_data/reference_positions/cxcr2_human.yaml b/residue_data/reference_positions/cxcr2_human.yaml
@@ -9,3 +9,4 @@
 5x50: 223
 6x50: 266
 7x50: 311
+8x50: 321
diff --git a/residue_data/reference_positions/cxcr3_human.yaml b/residue_data/reference_positions/cxcr3_human.yaml
@@ -9,3 +9,4 @@
 5x50: 227
 6x50: 270
 7x50: 315
+8x50: 325
diff --git a/residue_data/reference_positions/cxcr4_human.yaml b/residue_data/reference_positions/cxcr4_human.yaml
@@ -9,3 +9,4 @@
 5x50: 211
 6x50: 254
 7x50: 299
+8x50: 309
diff --git a/residue_data/reference_positions/cxcr5_human.yaml b/residue_data/reference_positions/cxcr5_human.yaml
@@ -9,3 +9,4 @@
 5x50: 230
 6x50: 274
 7x50: 319
+8x50: 329
diff --git a/residue_data/reference_positions/cxcr6_human.yaml b/residue_data/reference_positions/cxcr6_human.yaml
@@ -9,3 +9,4 @@
 5x50: 203
 6x50: 246
 7x50: 285
+8x50: 295
diff --git a/residue_data/reference_positions/drd1_human.yaml b/residue_data/reference_positions/drd1_human.yaml
@@ -9,4 +9,4 @@
 5x50: 206
 6x50: 287
 7x50: 328
-8x50: 337
+8x50: 338
diff --git a/residue_data/reference_positions/drd5_human.yaml b/residue_data/reference_positions/drd5_human.yaml
@@ -9,4 +9,4 @@
 5x50: 237
 6x50: 311
 7x50: 356
-8x50: 365
+8x50: 366
diff --git a/residue_data/reference_positions/ednrb_human.yaml b/residue_data/reference_positions/ednrb_human.yaml
@@ -9,3 +9,4 @@
 5x50: 285
 6x50: 338
 7x50: 383
+8x50: 393
diff --git a/residue_data/reference_positions/eltd1_human.yaml b/residue_data/reference_positions/eltd1_human.yaml
@@ -4,5 +4,5 @@
 45x50: 562
 4x50: 538
 5x50: 581
-6x50: 633
+6x50: 639
 7x50: 661
diff --git a/residue_data/reference_positions/etbr2_human.yaml b/residue_data/reference_positions/etbr2_human.yaml
@@ -1,5 +1,6 @@
 12x50: 161
 1x50: 148
+23x50: '-'
 2x50: 176
 34x50: 235
 3x50: 228

diff --git a/residue_data/reference_positions/ffar1_human.yaml b/residue_data/reference_positions/ffar1_human.yaml
@@ -1,4 +1,4 @@
-12x50: 37
+12x50: 36
 1x50: 23
 23x50: 72
 2x50: 52

diff --git a/residue_data/reference_positions/ffar3_human.yaml b/residue_data/reference_positions/ffar3_human.yaml
@@ -9,3 +9,4 @@
 5x50: 196
 6x50: 240
 7x50: 273
+8x50: 283
diff --git a/residue_data/reference_positions/fshr_human.yaml b/residue_data/reference_positions/fshr_human.yaml
@@ -1,6 +1,6 @@
 12x50: 393
 1x50: 380
-23x50: 430
+23x50: '-'
 2x50: 408
 34x50: 474
 3x50: 467

diff --git a/residue_data/reference_positions/fzd10_human.yaml b/residue_data/reference_positions/fzd10_human.yaml
@@ -6,3 +6,4 @@
 5x50: 405
 6x50: 460
 7x50: 516
+12x50: 255
diff --git a/residue_data/reference_positions/fzd1_human.yaml b/residue_data/reference_positions/fzd1_human.yaml
@@ -6,3 +6,4 @@
 5x50: 498
 6x50: 553
 7x50: 615
+12x50: 347
diff --git a/residue_data/reference_positions/fzd2_human.yaml b/residue_data/reference_positions/fzd2_human.yaml
@@ -6,3 +6,4 @@
 5x50: 423
 6x50: 478
 7x50: 533
+12x50: 272
diff --git a/residue_data/reference_positions/fzd3_human.yaml b/residue_data/reference_positions/fzd3_human.yaml
@@ -6,3 +6,4 @@
 5x50: 382
 6x50: 437
 7x50: 492
+12x50: 230
diff --git a/residue_data/reference_positions/fzd4_human.yaml b/residue_data/reference_positions/fzd4_human.yaml
@@ -6,3 +6,4 @@
 5x50: 398
 6x50: 453
 7x50: 489
+12x50: 247
diff --git a/residue_data/reference_positions/fzd5_human.yaml b/residue_data/reference_positions/fzd5_human.yaml
@@ -6,3 +6,4 @@
 5x50: 411
 6x50: 466
 7x50: 515
+12x50: 263
diff --git a/residue_data/reference_positions/fzd6_human.yaml b/residue_data/reference_positions/fzd6_human.yaml
@@ -6,3 +6,4 @@
 5x50: 378
 6x50: 433
 7x50: 488
+12x50: 226
diff --git a/residue_data/reference_positions/fzd7_human.yaml b/residue_data/reference_positions/fzd7_human.yaml
@@ -6,3 +6,4 @@
 5x50: 432
 6x50: 487
 7x50: 542
+12x50: 281
diff --git a/residue_data/reference_positions/fzd8_human.yaml b/residue_data/reference_positions/fzd8_human.yaml
@@ -6,3 +6,4 @@
 5x50: 492
 6x50: 549
 7x50: 598
+12x50: 305
diff --git a/residue_data/reference_positions/fzd9_human.yaml b/residue_data/reference_positions/fzd9_human.yaml
@@ -6,3 +6,4 @@
 5x50: 409
 6x50: 464
 7x50: 522
+12x50: 259
diff --git a/residue_data/reference_positions/gabr1_human.yaml b/residue_data/reference_positions/gabr1_human.yaml
@@ -6,3 +6,4 @@
 5x50: 780
 6x50: 818
 7x50: 849
+12x50: 619
diff --git a/residue_data/reference_positions/gabr2_human.yaml b/residue_data/reference_positions/gabr2_human.yaml
@@ -6,3 +6,4 @@
 5x50: 667
 6x50: 705
 7x50: 736
+12x50: 509
diff --git a/residue_data/reference_positions/ghrhr_human.yaml b/residue_data/reference_positions/ghrhr_human.yaml
@@ -6,3 +6,4 @@
 5x50: 292
 6x50: 344
 7x50: 373
+12x50: 157
diff --git a/residue_data/reference_positions/ghsr_human.yaml b/residue_data/reference_positions/ghsr_human.yaml
@@ -1,5 +1,6 @@
+12x50: 74
 1x50: 61
-23x50: 104
+23x50: 109
 2x50: 89
 34x50: 148
 3x50: 141
@@ -8,4 +9,4 @@
 5x50: 224
 6x50: 278
 7x50: 320
-12x50: 74
+8x50: 330
diff --git a/residue_data/reference_positions/gipr_human.yaml b/residue_data/reference_positions/gipr_human.yaml
@@ -6,3 +6,4 @@
 5x50: 306
 6x50: 356
 7x50: 389
+12x50: 165
diff --git a/residue_data/reference_positions/glp1r_human.yaml b/residue_data/reference_positions/glp1r_human.yaml
@@ -6,3 +6,4 @@
 5x50: 316
 6x50: 366
 7x50: 399
+12x50: 172