-
Notifications
You must be signed in to change notification settings - Fork 7
/
pdb-mode.el
1642 lines (1533 loc) · 75.7 KB
/
pdb-mode.el
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
;; pdb-mode.el --- Major mode for editing Protein Data Bank files
;;; This file is not part of GNU Emacs.
;; Copyright (C) 1997 Charlie Bond, University of Sydney
;; 2000-2002 Charlie Bond, University of Dundee
;; 2000 David Love, CLRC Daresbury Laboratory (marked sections)
;; Author: [email protected]
;; X-URL: http://stein.bioch.dundee.ac.uk/~charlie/scripts/pdb-mode.el
;; Version: Major update Jan 2002
;; Keywords: data
;; This file is free software; you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation; either version 2, or (at your option)
;; any later version.
;; This file is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;; GNU General Public License for more details.
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs; see the file COPYING. If not, write to
;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
;; Boston, MA 02111-1307, USA.
;;{{{ Documentation
;;; Commentary:
;; PDB mode is set up to do a few useful things to PDB (protein databank
;; format) files.
;; Other programs (MOLEMAN and PDBSET etc) do all this and more, but not
;; within an editor.
;; To take benefit of the PDB mode, add the following
;; line to your .emacs (or get your sysadmin to
;; add it to the site-start.el) and visit a pdb file.
;; (load-file "/{path-to}/pdb-mode.el")
;; ;; Need (setq pdb-rasmol-name "\"c:/Program Files/Rasmol/rw32b2a.exe\"")
;; ;; or something similar for windows
;; (setq auto-mode-alist
;; (cons (cons "pdb$" 'pdb-mode)
;; auto-mode-alist ) )
;; (autoload 'pdb-mode "PDB")
;;; This package is known to work (insofar as it's tested) with XEmacs
;;; 20.4, XEmacs 21.1, Emacs 20.5 and Emacs 21.1.1
;;}}}
;;; Code:
(require 'easymenu)
(defvar pdb-mode nil
"This buffer specific variable tells if the pdb mode is active." )
(make-variable-buffer-local 'pdb-mode)
;; initialise menu and hooks
(defvar pdb-mode-map (make-sparse-keymap))
(defvar pdb-mode-hook nil "Mode hook for pdb-mode")
(defvar pdb-menu-hook nil "Menu hook for pdb-mode")
(defconst pdb-mode-menu-def
'("PDB"
("rna-tools ..."
["RNApuzzle ready" rna-puzzle-ready t]
)
("Select ..."
["Select chain" pdb-select-chain t]
["Select current chain" (pdb-select-chain "") t]
["Select current residue" pdb-select-residue t]
["Select zone of residues" pdb-select-zone t])
("Navigate"
["Jump to next residue" pdb-forward-residue t]
["Jump to previous residue" pdb-back-residue t]
["Jump to next chain" pdb-forward-chain t]
["Jump to previous chain" pdb-back-chain t])
("Change Values"
["Set alternate conformer" pdb-change-alternate t]
["Set B-factor" pdb-change-bfactor t]
["Set chain ID" pdb-change-chain t]
["Set atom name" pdb-change-name t]
["Set occupancy" pdb-change-occu t]
["Set residue number" pdb-change-residue t]
["Set SEGID" pdb-change-segid t]
["Set residue type" pdb-change-type t]
["Mutate residue(s)" pdb-change-mutate t]
["Convert frac->orth" pdb-change-frac2orth t]
["Convert orth->frac" pdb-change-orth2frac t]
)
("Increment Values"
["Add value to B-factor" pdb-increment-bfactor t]
["Change centroid" pdb-increment-centroid t]
["Add value to residue number" pdb-increment-residue t]
["Add vector to xyz (orthogonal)" pdb-increment-xyz t]
["Add vector to xyz (fractional)" pdb-increment-fractional t]
["Scale coordinates" pdb-scale-xyz t]
["Scale B-factors" pdb-scale-bfactor t]
["Rotate xyz by 3x3 matrix" pdb-increment-matrix t]
["Rotate xyz by Euler triplet" pdb-increment-euler t])
("Renumber"
["Consecutive atom numbers" pdb-renumber-atoms t]
["Consecutive water residue numbers" pdb-renumber-waters t])
("Tidy Up"
["Remove non-protein atoms" pdb-tidy-amino t]
["Convert ATOM -> HETATM" pdb-tidy-atom2hetatm t]
["Reduce to CA only" pdb-tidy-ca t]
["Remove hydrogens" pdb-tidy-dehydrogenate t]
["Convert HETATM -> ATOM" pdb-tidy-hetatm2atom t]
["Cut back to poly-ALA/GLY" pdb-tidy-polyalanine t]
["Remove all but ATOM/HETATM records" pdb-tidy-xyz t])
("New..."
["amino acid(s)" pdb-new-sequence t]
["DNA base(s)" pdb-new-dnaseq t]
["PDB entry" pdb-new-pdb t]
("HICUP compound"
["User defined..." pdb-new-hicup t]
["Selenomethionine" (pdb-new-hicup "mse") t]
("Nucleotide"
["ATP" (pdb-new-hicup "atp") t]
["ADP" (pdb-new-hicup "adp") t]
["AMP" (pdb-new-hicup "amp") t]
["CTP" (pdb-new-hicup "ctp") t]
["CDP" (pdb-new-hicup "cdp") t]
["CMP" (pdb-new-hicup "cmp") t]
["GTP" (pdb-new-hicup "gtp") t]
["GDP" (pdb-new-hicup "gdp") t]
["GMP" (pdb-new-hicup "gmp") t]
["NAD" (pdb-new-hicup "nad") t]
["NADP+" (pdb-new-hicup "nap") t]
["NADPH" (pdb-new-hicup "ndp") t]
["S-adenosylmethionine" (pdb-new-hicup "sam") t]
["FAD" (pdb-new-hicup "fad") t])
("Sugar"
["Glucose" (pdb-new-hicup "glc") t]
["Linear glucose" (pdb-new-hicup "glo") t]
["n-Glycosyl chain" (pdb-new-hicup "asf") t]
["NAG (N-acetyl glucosamine)" (pdb-new-hicup "nag") t]
["Fructose" (pdb-new-hicup "fru") t]
["Sucrose" (pdb-new-hicup "suc") t]
["Fucose" (pdb-new-hicup "fuc") t]
["Inositol hexaphosphate" (pdb-new-hicup "ihp") t])
("Small"
["Sodium" (pdb-new-hicup "na") t]
["Calcium" (pdb-new-hicup "ca") t]
["Magnesium" (pdb-new-hicup "mg") t]
["Zinc" (pdb-new-hicup "zn") t]
["Iron" (pdb-new-hicup "fe") t]
["Mercury" (pdb-new-hicup "hg") t]
["Chloride" (pdb-new-hicup "cl") t]
["Oxygen molecule" (pdb-new-hicup "o2") t]
["Ammonium (NH4+)" (pdb-new-hicup "nh4") t]
["Carbon dioxide" (pdb-new-hicup "co2") t]
["Acetate" (pdb-new-hicup "acy") t]
["Acetone" (pdb-new-hicup "acn") t]
["Sulfate (SO4)" (pdb-new-hicup "so4") t]
["Sulfite (SO3)" (pdb-new-hicup "so3") t]
["Azide" (pdb-new-hicup "azi") t]
["Phosphate" (pdb-new-hicup "po4") t]
["Nitrate" (pdb-new-hicup "no3") t]
["DMSO (dimethyl sulfoxide)" (pdb-new-hicup "dms") t]
["Urea" (pdb-new-hicup "ure") t])
("Organic"
["Citrate" (pdb-new-hicup "cit") t]
["Ascorbate" (pdb-new-hicup "asc") t]
["Salicylic acid" (pdb-new-hicup "sal") t]
["Tartaric acid" (pdb-new-hicup "tar") t]
["Benzoic acid" (pdb-new-hicup "box") t]
["Succinic acid" (pdb-new-hicup "sin") t]
["6-Amino hexanoic acid" (pdb-new-hicup "aha") t]
["2-Phenylethylamine" (pdb-new-hicup "pea") t]
["Beta-mercaptoethanol" (pdb-new-hicup "bme") t]
["DTT (1,4-dithiothreitol)" (pdb-new-hicup "dtt") t]
["Ethanol" (pdb-new-hicup "eoh") t]
["2-Propanol" (pdb-new-hicup "ipa") t]
["Ethanediol" (pdb-new-hicup "edo") t]
["MPD (2-methyl-2,4-pentanediol)" (pdb-new-hicup "mpd") t]
["Glycerol" (pdb-new-hicup "gol") t]
["Retinol" (pdb-new-hicup "rtl") t]
["Methylparaben" (pdb-new-hicup "mpb") t]
["Tylenol" (pdb-new-hicup "tyl") t]
["Camphor" (pdb-new-hicup "cam") t]
["Tris (tromethamine)" (pdb-new-hicup "trs") t])
("Miscellaneous"
["Aminopyridine" (pdb-new-hicup "4ap") t]
["Isoquinoline" (pdb-new-hicup "isq") t]
["AlF3" (pdb-new-hicup "af3") t]
["AlF4-" (pdb-new-hicup "alf") t]
["SC-58272 synthetic peptidic inhibitor" (pdb-new-hicup "mim") t]
["N1-carboxypiperazine" (pdb-new-hicup "bzp") t]
["4-(Acetylamino)-3-amino benzoic acid" (pdb-new-hicup "st3") t]
["Porphyrin Fe(III)" (pdb-new-hicup "por") t])
))
("Miscellaneous"
[" Open in PYMOL" pdb-view t]
[" Toggle Fontification" (font-lock-mode) :style toggle :selected font-lock-mode])))
;; initialise some variables
(eval-when-compile
(defvar pdb-start-user-region nil "PDB Mode: Used by some functions")
(defvar pdb-end-user-region nil "PDB Mode: Used by some functions")
(defvar pdb-rasmol-name "rasmol" "PDB Mode: Full path to rasmol executable (only necessary if typing rasmol in a shell doesn't work. In Windows \(setq pdb-rasmol-name \"c:/Program Files/Rasmol/rw32b2a.exe\"\) or something similar to .emacs for windows")
(defvar pdb-rasmol-filestamp nil "PDB Mode: Temporary filename for rasmol display. Of the form (concat (getenv \"PWD\") \"/#TMP-emacs-rasmol\" (number-to-string (elt (current-time) 1)) (number-to-string (emacs-pid)) \"#\")))")
(defvar pdb-amino-lookup nil "PDB Mode: Lookup table to convert single-letter to three-letter amino acid codes")
(defvar pdb-record-lookup nil "PDB Mode: Lookup table to access side-chain PDB coordinates for amino acids from their three-letter code.")
(defvar pdb-mode-syntax-table nil "Syntax table in use in set file mode buffers.")
(defvar pdb-font-lock-keywords nil "Table of set file font lock keywords."))
;; Default binding for pdb-rasmol-name
;; Need to add (setq pdb-rasmol-name "\"c:/Program Files/Rasmol/rw32b2a.exe\"")
;; or something similar to .emacs for windows
(unless (boundp 'pdb-rasmol-name)
(setq pdb-rasmol-name "pymol"))
;; Some necessary data
(setq pdb-amino-lookup '(("A" . "ALA") ("C" . "CYS") ("D" . "ASP") ("E" . "GLU") ("F" . "PHE") ("G" . "GLY") ("H" . "HIS") ("I" . "ILE") ("K" . "LYS") ("L" . "LEU") ("M" . "MET") ("N" . "ASN") ("P" . "PRO") ("Q" . "GLN") ("R" . "ARG") ("S" . "SER") ("T" . "THR") ("V" . "VAL") ("W" . "TRP") ("Y" . "TYR") ("dA" . "A ") ("dG" . "G ") ("dT" . "T ") ("dC" . "C ")))
(setq pdb-record-lookup '(("ALA" .
"ATOM 2 CB ALA A 1 -0.532 -0.774 -1.196 1.00 20.00 C\n")
("ARG" .
"ATOM 1 CB ARG A 1 -0.526 -0.779 -1.207 1.00 20.00 C
ATOM 1 CG ARG A 1 -2.041 -0.900 -1.254 1.00 20.00 C
ATOM 1 CD ARG A 1 -2.494 -1.684 -2.476 1.00 20.00 C
ATOM 1 NE ARG A 1 -3.946 -1.811 -2.537 1.00 20.00 N
ATOM 1 CZ ARG A 1 -4.600 -2.437 -3.509 1.00 20.00 C
ATOM 1 NH1 ARG A 1 -3.929 -3.023 -4.492 1.00 20.00 N
ATOM 1 NH2 ARG A 1 -5.923 -2.518 -3.476 1.00 20.00 N\n")
("ASN" .
"ATOM 1 CB ASN A 1 -0.526 -0.778 -1.208 1.00 20.00 C
ATOM 1 CG ASN A 1 -2.037 -0.888 -1.218 1.00 20.00 C
ATOM 1 OD1 ASN A 1 -2.638 -1.406 -0.276 1.00 20.00 O
ATOM 1 ND2 ASN A 1 -2.663 -0.345 -2.255 1.00 20.00 N\n")
("ASP" .
"ATOM 1 CB ASP A 1 -0.526 -0.779 -1.207 1.00 20.00 C
ATOM 1 CG ASP A 1 -2.039 -0.881 -1.221 1.00 20.00 C
ATOM 1 OD1 ASP A 1 -2.585 -1.504 -2.156 1.00 20.00 O
ATOM 1 OD2 ASP A 1 -2.680 -0.356 -0.287 1.00 20.00 O\n")
("CYS" .
"ATOM 1 CB CYS A 1 -0.526 -0.779 -1.207 1.00 20.00 C
ATOM 1 SG CYS A 1 -2.327 -0.928 -1.273 1.00 20.00 S\n")
("GLN" .
"ATOM 1 CB GLN A 1 -0.526 -0.778 -1.208 1.00 20.00 C
ATOM 1 CG GLN A 1 -2.039 -0.907 -1.254 1.00 20.00 C
ATOM 1 CD GLN A 1 -2.522 -1.683 -2.462 1.00 20.00 C
ATOM 1 OE1 GLN A 1 -2.803 -1.106 -3.513 1.00 20.00 O
ATOM 1 NE2 GLN A 1 -2.663 -2.995 -2.307 1.00 20.00 N\n")
("GLU" .
"ATOM 1 CB GLU A 1 -0.525 -0.778 -1.208 1.00 20.00 C
ATOM 1 CG GLU A 1 -2.039 -0.902 -1.255 1.00 20.00 C
ATOM 1 CD GLU A 1 -2.523 -1.677 -2.465 1.00 20.00 C
ATOM 1 OE1 GLU A 1 -2.792 -1.045 -3.508 1.00 20.00 O
ATOM 1 OE2 GLU A 1 -2.679 -2.911 -2.359 1.00 20.00 O\n")
("GLY" .
"")
("HIS" .
"ATOM 1 CB HIS A 1 -0.525 -0.779 -1.208 1.00 20.00 C
ATOM 1 CG HIS A 1 -2.017 -0.903 -1.245 1.00 20.00 C
ATOM 1 ND1 HIS A 1 -2.826 0.022 -1.867 1.00 20.00 N
ATOM 1 CE1 HIS A 1 -4.089 -0.341 -1.737 1.00 20.00 C
ATOM 1 NE2 HIS A 1 -4.129 -1.468 -1.049 1.00 20.00 N
ATOM 1 CD2 HIS A 1 -2.846 -1.841 -0.728 1.00 20.00 C\n")
("ILE" .
"ATOM 1 CB ILE A 1 -0.504 -0.800 -1.215 1.00 20.00 C
ATOM 1 CG1 ILE A 1 -2.032 -0.886 -1.201 1.00 20.00 C
ATOM 1 CG2 ILE A 1 0.111 -2.191 -1.229 1.00 20.00 C
ATOM 1 CD1 ILE A 1 -2.612 -1.659 -2.365 1.00 20.00 C\n")
("LEU" .
"ATOM 1 CB LEU A 1 -0.525 -0.777 -1.209 1.00 20.00 C
ATOM 1 CG LEU A 1 -2.045 -0.935 -1.304 1.00 20.00 C
ATOM 1 CD1 LEU A 1 -2.727 0.424 -1.304 1.00 20.00 C
ATOM 1 CD2 LEU A 1 -2.425 -1.730 -2.544 1.00 20.00 C\n")
("LYS" .
"ATOM 1 CB LYS A 1 -0.526 -0.781 -1.206 1.00 20.00 C
ATOM 1 CG LYS A 1 -2.041 -0.890 -1.262 1.00 20.00 C
ATOM 1 CD LYS A 1 -2.494 -1.671 -2.486 1.00 20.00 C
ATOM 1 CE LYS A 1 -4.008 -1.792 -2.534 1.00 20.00 C
ATOM 1 NZ LYS A 1 -4.466 -2.556 -3.727 1.00 20.00 N\n")
("MET" .
"ATOM 1 CB MET A 1 -0.525 -0.780 -1.206 1.00 20.00 C
ATOM 1 CG MET A 1 -2.039 -0.908 -1.252 1.00 20.00 C
ATOM 1 SD MET A 1 -2.617 -1.831 -2.688 1.00 20.00 S
ATOM 1 CE MET A 1 -4.389 -1.785 -2.430 1.00 20.00 C
ATOM 1 SE MET A 1 -2.652 -1.887 -2.776 1.00 20.00 S
ATOM 1 CE2 MET A 1 -4.533 -1.839 -2.502 1.00 20.00 C\n")
("PHE" .
"ATOM 1 CB PHE A 1 -0.525 -0.779 -1.208 1.00 20.00 C
ATOM 1 CG PHE A 1 -2.023 -0.890 -1.253 1.00 20.00 C
ATOM 1 CD1 PHE A 1 -2.784 0.081 -1.880 1.00 20.00 C
ATOM 1 CE1 PHE A 1 -4.161 -0.024 -1.934 1.00 20.00 C
ATOM 1 CZ PHE A 1 -4.794 -1.087 -1.322 1.00 20.00 C
ATOM 1 CE2 PHE A 1 -4.048 -2.050 -0.672 1.00 20.00 C
ATOM 1 CD2 PHE A 1 -2.672 -1.940 -0.624 1.00 20.00 C\n")
("PRO" .
"ATOM 1 CB PRO A 1 -0.525 -0.582 -1.313 1.00 20.00 C
ATOM 1 CG PRO A 1 -1.785 0.165 -1.573 1.00 20.00 C
ATOM 1 CD PRO A 1 -1.548 1.557 -1.063 1.00 20.00 C\n")
("SER" .
"ATOM 1 CB SER A 1 -0.526 -0.778 -1.207 1.00 20.00 C
ATOM 1 OG SER A 1 -0.146 -0.155 -2.421 1.00 20.00 O\n")
("THR" .
"ATOM 1 CB THR A 1 -0.504 -0.800 -1.216 1.00 20.00 C
ATOM 1 OG1 THR A 1 -0.087 -0.151 -2.424 1.00 20.00 O
ATOM 1 CG2 THR A 1 -2.021 -0.899 -1.197 1.00 20.00 C\n")
("TRP" .
"ATOM 1 CB TRP A 1 -0.525 -0.777 -1.208 1.00 20.00 C
ATOM 1 CG TRP A 1 -2.019 -0.894 -1.243 1.00 20.00 C
ATOM 1 CD1 TRP A 1 -2.895 -0.028 -1.831 1.00 20.00 C
ATOM 1 NE1 TRP A 1 -4.184 -0.464 -1.649 1.00 20.00 N
ATOM 1 CE2 TRP A 1 -4.161 -1.635 -0.937 1.00 20.00 C
ATOM 1 CZ2 TRP A 1 -5.210 -2.445 -0.505 1.00 20.00 C
ATOM 1 CH2 TRP A 1 -4.888 -3.567 0.205 1.00 20.00 C
ATOM 1 CZ3 TRP A 1 -3.556 -3.890 0.499 1.00 20.00 C
ATOM 1 CE3 TRP A 1 -2.514 -3.089 0.069 1.00 20.00 C
ATOM 1 CD2 TRP A 1 -2.814 -1.925 -0.646 1.00 20.00 C\n")
("TYR" .
"ATOM 1 CB TYR A 1 -0.525 -0.779 -1.207 1.00 20.00 C
ATOM 1 CG TYR A 1 -2.033 -0.894 -1.254 1.00 20.00 C
ATOM 1 CD1 TYR A 1 -2.799 0.051 -1.923 1.00 20.00 C
ATOM 1 CE1 TYR A 1 -4.177 -0.052 -1.971 1.00 20.00 C
ATOM 1 CZ TYR A 1 -4.802 -1.121 -1.366 1.00 20.00 C
ATOM 1 CE2 TYR A 1 -4.061 -2.087 -0.720 1.00 20.00 C
ATOM 1 CD2 TYR A 1 -2.684 -1.975 -0.676 1.00 20.00 C
ATOM 1 OH TYR A 1 -6.173 -1.228 -1.413 1.00 20.00 O\n")
("VAL" .
"ATOM 1 CB VAL A 1 -0.504 -0.802 -1.214 1.00 20.00 C
ATOM 1 CG1 VAL A 1 0.110 -2.194 -1.227 1.00 20.00 C
ATOM 1 CG2 VAL A 1 -2.023 -0.883 -1.206 1.00 20.00 C\n")
("A " .
"ATOM 1 N9 A A 1 0.213 0.660 1.287 1.00 20.00
ATOM 2 C4 A A 1 0.250 2.016 1.509 1.00 20.00
ATOM 3 N3 A A 1 0.016 2.995 0.619 1.00 20.00
ATOM 4 C2 A A 1 0.142 4.189 1.194 1.00 20.00
ATOM 5 N1 A A 1 0.451 4.493 2.459 1.00 20.00
ATOM 6 C6 A A 1 0.681 3.485 3.329 1.00 20.00
ATOM 7 N6 A A 1 0.990 3.787 4.592 1.00 20.00
ATOM 8 C5 A A 1 0.579 2.170 2.844 1.00 20.00
ATOM 9 N7 A A 1 0.747 0.934 3.454 1.00 20.00
ATOM 10 C8 A A 1 0.520 0.074 2.491 1.00 20.00\n")
("C " .
"ATOM 1 N1 C A 1 0.212 0.668 1.294 1.00 20.00
ATOM 2 C6 C A 1 0.193 -0.043 2.462 1.00 20.00
ATOM 3 C2 C A 1 0.374 2.055 1.315 1.00 20.00
ATOM 4 O2 C A 1 0.388 2.673 0.240 1.00 20.00
ATOM 5 N3 C A 1 0.511 2.687 2.504 1.00 20.00
ATOM 6 C4 C A 1 0.491 1.984 3.638 1.00 20.00
ATOM 7 N4 C A 1 0.631 2.649 4.788 1.00 20.00
ATOM 8 C5 C A 1 0.328 0.569 3.645 1.00 20.00\n")
("G " .
"ATOM 1 N9 G A 1 0.214 0.659 1.283 1.00 20.00
ATOM 2 C4 G A 1 0.254 2.014 1.509 1.00 20.00
ATOM 3 N3 G A 1 0.034 2.979 0.591 1.00 20.00
ATOM 4 C2 G A 1 0.142 4.190 1.110 1.00 20.00
ATOM 5 N2 G A 1 -0.047 5.269 0.336 1.00 20.00
ATOM 6 N1 G A 1 0.444 4.437 2.427 1.00 20.00
ATOM 7 C6 G A 1 0.676 3.459 3.389 1.00 20.00
ATOM 8 O6 G A 1 0.941 3.789 4.552 1.00 20.00
ATOM 9 C5 G A 1 0.562 2.154 2.846 1.00 20.00
ATOM 10 N7 G A 1 0.712 0.912 3.448 1.00 20.00
ATOM 11 C8 G A 1 0.498 0.057 2.485 1.00 20.00\n")
("T " .
"ATOM 1 N1 T A 1 0.214 0.668 1.296 1.00 20.00
ATOM 2 C6 T A 1 0.171 -0.052 2.470 1.00 20.00
ATOM 3 C2 T A 1 0.374 2.035 1.303 1.00 20.00
ATOM 4 O2 T A 1 0.416 2.705 0.284 1.00 20.00
ATOM 5 N3 T A 1 0.483 2.592 2.553 1.00 20.00
ATOM 6 C4 T A 1 0.449 1.933 3.767 1.00 20.00
ATOM 7 O4 T A 1 0.560 2.568 4.812 1.00 20.00
ATOM 8 C5 T A 1 0.279 0.500 3.685 1.00 20.00
ATOM 9 C5A T A 1 0.231 -0.299 4.949 1.00 20.00\n")
("U " .
"ATOM 5 N1 U A 1 0.212 0.676 1.281 1.00 20.00
ATOM 6 C6 U A 1 0.195 -0.023 2.466 1.00 20.00
ATOM 7 C2 U A 1 0.370 2.048 1.265 1.00 20.00
ATOM 8 O2 U A 1 0.390 2.698 0.235 1.00 20.00
ATOM 9 N3 U A 1 0.505 2.629 2.502 1.00 20.00
ATOM 11 C4 U A 1 0.497 1.990 3.725 1.00 20.00
ATOM 12 O4 U A 1 0.629 2.653 4.755 1.00 20.00
ATOM 13 C5 U A 1 0.329 0.571 3.657 1.00 20.00\n")
))
;; Set up font lock
(setq pdb-mode-syntax-table (make-syntax-table (standard-syntax-table)))
(make-face 'pdb-key1-face)
(set-face-background 'pdb-key1-face "dim gray")
(make-face 'pdb-comment-face)
(set-face-foreground 'pdb-comment-face "dark gray")
(if (string-match "GNU" (emacs-version))
(progn
(setq pdb-font-lock-keywords
(list
'("\\(^ATOM..\\|HETATM\\).....\\(.\\)....\\(.\\)...\\(.\\).\\(....\\)............\\(........\\)........\\(......\\)......\\(......\\)" (1 'pdb-key1-face) (2 'pdb-key1-face) (3 'pdb-key1-face) (4 'pdb-key1-face) (5 'pdb-key1-face) (6 'pdb-key1-face) (7 'pdb-key1-face) (8 'pdb-key1-face nil t))
'("\\(^\\([B-G]\\|[I-Z]\\|AU\\|HE[AL]\\).*$\\)" 1 'pdb-comment-face t))))
)
(if (string-match "XEmacs" (emacs-version))
(progn
(setq pdb-font-lock-keywords
(list
'("^\\(^ATOM..\\|HETATM\\).\\{74\\}\\(.\\{2\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{70\\}\\(.\\{2\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{60\\}\\(.\\{6\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{48\\}\\(.\\{6\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{32\\}\\(.\\{8\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{16\\}\\(.\\{4\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{14\\}\\(.\\{1\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{10\\}\\(.\\{1\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{5\\}\\(.\\{1\\}\\)" 2 pdb-key1-face t)
'("\\(^ATOM..\\|HETATM\\)" 1 pdb-key1-face t)
'("\\(^\\([B-G]\\|[I-Z]\\|AU\\|HE[AL]\\).*$\\)" 1 pdb-comment-face t)))
(add-hook 'pdb-mode-hook (function
(lambda()
(setq font-lock-mode-disable-list
(cons 'pdb-mode font-lock-mode-disable-list)))))))
;;Final blast of commands on startup
(add-hook 'pdb-mode-hook (function
(lambda()
;; If CRYST1 card is present, set pdb-cell-local as a list of 6 numbers
;; Spacegroup will be picked up too if present.
(save-excursion
(goto-char (point-min))
(if (re-search-forward "^CRYST1" nil t)
(let ((str (buffer-substring (+ (point-at-bol) 7) (+ (point-at-bol) 55))))
(string-match "[0-9].*[0-9]" str)
(let ((str (split-string (match-string 0 str))))
(setq pdb-cell-local (list (string-to-number (elt str 0)) (string-to-number (elt str 1)) (string-to-number (elt str 2)) (string-to-number (elt str 3)) (string-to-number (elt str 4)) (string-to-number (elt str 5)))))
(setq pdb-spacegroup-local (buffer-substring (+ (point-at-bol) 55) (+ (point-at-bol) 64)))
(if (eq (elt pdb-orth2frac-local 0) 0)
(progn
(pdb-sub-orth2frac)
(pdb-sub-frac2orth)))))))))
;; PDB-MODE
(defun pdb-mode ()
"PDB mode is set up to do a few useful things to PDB (protein databank
format) files.
Other programs (MOLEMAN and PDBSET etc) do all this and more, but not
within an editor.
pdb-mode commands can be accessed from the menu bar PDB or from the minibuffer
(M-x pdb SPACE gives you a list of commands).
Some mouse/key bindings aid PDB file navigation:
C-middlemouse selects residue where button clicked.
C-pageup and C-pagedown jump to the previous/next residue.
C-M-pageup and C-M-pagedown jump to the previous/next chain."
(interactive)
;; Set up mode stuff
(kill-all-local-variables)
(setq mode-name "PDB")
(setq major-mode 'pdb-mode)
(setq kill-whole-line t)
;; Set up menu stuff
(use-local-map pdb-mode-map)
(easy-menu-define pdb-mode-menu pdb-mode-map "Emacs menu for PDB mode"
pdb-mode-menu-def)
;; Need this for Xemacs
(easy-menu-add pdb-mode-menu)
;; Customise tabbing to match PDB definition - David Love
(set (make-local-variable 'indent-line-function) #'tab-to-tab-stop)
(set (make-local-variable 'tab-stop-list)
'(;; ATOM
6 ; serial no.
11 ; Chemical symbol
14 ; Remoteness indicator
15 ; Branch designator
16 ; Alternate location indicator
17 ; Residue name
20 ; Reserved
21 ; Chain identifier
22 ; Residue sequence number
26 ; Code for inserting residue
27 ; Reserved
30 ; X
38 ; Y
46 ; Z
54 ; Pdb-Occupancy
60 ; Isotropic B-factor
66 ; Reserved
72 ; Segment identifier
76 ; Element symbol
78 ; Charge on atom
80
))
;; Redefine some keys for easy navigation
(local-set-key '[(control tab)] 'move-to-tab-stop)
(local-set-key '[(control next)] 'pdb-forward-residue)
(local-set-key '[(control prior)] 'pdb-back-residue)
(local-set-key '[(control meta next)] 'pdb-forward-chain)
(local-set-key '[(control meta prior)] 'pdb-back-chain)
;; Setup unit cell data - used for fractional coordinates
(set (make-local-variable 'pdb-cell-local) (make-list 6 0))
(set (make-local-variable 'pdb-spacegroup-local) "")
(set (make-local-variable 'pdb-orth2frac-local) (make-list 9 0))
(set (make-local-variable 'pdb-frac2orth-local) (make-list 9 0))
;; Some things are handled differently in GNU- and X-emacs
(if (string-match "XEmacs" (emacs-version))
(progn (redraw-modeline)
(setq zmacs-region-stays t )
;; Bind C-mouse2 to select clicked residue
(define-key pdb-mode-map [(control button2)] 'pdb-sub-mouse-cmouse2)
;; Bind C-Mmouse2 to select clicked chain
(define-key pdb-mode-map [(control meta button2)] 'pdb-sub-mouse-cmmouse2)
;; Setup Popup menu
(if (boundp 'mode-popup-menu)
(setq mode-popup-menu
(cons (concat mode-name " Mode Commands") pdb-mode-menu)))))
(if (string-match "GNU Emacs" (emacs-version))
(progn
;; Get font-lock to work
(make-local-variable 'font-lock-defaults)
(setq font-lock-defaults '(pdb-font-lock-keywords nil nil ((?_ . "w"))))
;; Bind C-mouse2 to select clicked residue
(define-key pdb-mode-map [(control down-mouse-2)] 'pdb-sub-mouse-cmouse2)
;; Bind C-mmouse2 to select clicked chain
(define-key pdb-mode-map [(control meta down-mouse-2)] 'pdb-sub-mouse-cmmouse2)
;; Some aliases
(defalias 'point-at-bol 'line-beginning-position)
(defalias 'point-at-eol 'line-end-position)
(defun activate-region ()
(exchange-point-and-mark)
(exchange-point-and-mark))))
;; Individual Functions:
;; SELECT...
(defun pdb-select-chain (pdb-test-string)
"PDB mode: Select current chain\n"
(interactive "sWhich chain ?(1 char. RET signifies current chain):")
(if (= 0 (length pdb-test-string))
(progn
(goto-char (point-at-bol))
(re-search-forward "^\\(ATOM \\|HETATM\\|ANISOU\\)" nil t)
(setq pdb-test-string (buffer-substring (+ (point-at-bol) 21) (+ (point-at-bol) 22)))))
(pdb-sub-selectlocal (concat "..............." pdb-test-string)))
(defun pdb-select-residue ( )
"PDB mode: Select current residue"
(interactive "")
(let ((str (concat "..........." (buffer-substring (+ (point-at-bol) 17) (+ (point-at-bol) 26)))))
(pdb-sub-selectlocal str)))
(defun pdb-select-zone (pdb-test-string)
"PDB mode: Select zone"
(interactive "sEnter zone ([Chain][Res1] [Chain][Res2]):")
(let (
(vec (split-string pdb-test-string))
(start-chain " ")
(end-chain " ")
(start-number 0)
(end-number 0)
(str ""))
;; Input is a 2 element array - need to grok chain and numbers from it
(if (string-match "^[A-Z]" (elt vec 0))
(setq start-chain (match-string 0 (elt vec 0))))
(if (string-match "^[A-Z]" (elt vec 1))
(setq pdb-end-chain (match-string 0 (elt vec 1))))
(string-match "[-0-9]*$" (elt vec 0))
(setq start-number (match-string 0 (elt vec 0)))
(string-match "[-0-9]*$" (elt vec 1))
(setq pdb-end-number (match-string 0 (elt vec 1)))
;; Find the ends
(goto-char (point-min))
(setq str (concat "^\\(ATOM \\|HETATM\\)..............." start-chain (format "%4d" (string-to-number start-number))))
(re-search-forward str nil (point) nil)
(setq pdb-start-user-region (point-at-bol))
(setq str (concat "^\\(ATOM \\|HETATM\\)..............." pdb-end-chain (format "%4d" (string-to-number pdb-end-number))))
(goto-char (point-max))
(re-search-backward str nil (point) nil))
(setq pdb-end-user-region (+ (point-at-eol) 1))
(pdb-sub-markregion))
;; NAVIGATE
(defun pdb-forward-residue ( )
"PDB mode: Jump to start of next residue"
(interactive "")
(let ((str (concat "..... ....." (buffer-substring (+ (point-at-bol) 17) (+ (point-at-bol) 26)))))
(re-search-forward "^\\(ATOM \\|HETATM\\)" nil t)
(goto-char (point-at-bol))
;; elisp has no not (regexp) search, so this is complicated
(while (progn
(re-search-forward "^\\(ATOM \\|HETATM\\)" (point-max) (point) nil)
(cond ((not (looking-at str))
(progn
(goto-char (point-at-bol)))
nil)
(t)))))
(goto-char (point-at-bol))
(activate-region)
)
(defun pdb-forward-chain ( )
"PDB mode: Jump to start of next chain"
(interactive "")
(let ((str (concat "..............." (buffer-substring (+ (point-at-bol) 21) (+ (point-at-bol) 22)))))
(re-search-forward "^\\(ATOM \\|HETATM\\)" nil t)
(goto-char (point-at-bol))
(while (progn
(re-search-forward "^\\(ATOM \\|HETATM\\)" (point-max) (point) nil)
(cond ((not (looking-at str))
(progn
;; roll back to previous matching residue
(goto-char (point-at-bol)))
nil)
(t)))))
(setq pdb-end-user-region (point-at-bol))
;; mark out region
(goto-char pdb-end-user-region)
(activate-region))
(defun pdb-back-residue ( )
"PDB mode: Jump to start of current/previous residue"
(interactive "")
(re-search-backward "^\\(ATOM \\|HETATM\\)" nil t )
(let ((str (concat "................." (buffer-substring (+ (point-at-bol) 17) (+ (point-at-bol) 26)))))
(while (and
(re-search-backward "^\\(ATOM \\|HETATM\\)" nil t )
(looking-at str)))
(if (not (looking-at str)) (re-search-forward "^\\(ATOM \\|HETATM\\)" nil t 2)))
(setq pdb-end-user-region (point-at-bol))
(goto-char pdb-end-user-region)
(activate-region))
(defun pdb-back-chain ( )
"PDB mode: Jump to start of current/previous chain"
(interactive "")
(re-search-backward "^\\(ATOM \\|HETATM\\)" nil t )
(let ((str (concat "....................." (buffer-substring (+ (point-at-bol) 21) (+ (point-at-bol) 22)))))
(while (and
(re-search-backward "^\\(ATOM \\|HETATM\\)" nil t )
(looking-at str)))
(if (not (looking-at str)) (re-search-forward "^\\(ATOM \\|HETATM\\)" nil t 2)))
(setq pdb-end-user-region (point-at-bol))
(goto-char pdb-end-user-region)
(activate-region))
;; CHANGE VALUES
(defun pdb-change-bfactor (b e pdb-test-number)
"PDB mode: Change selected B-factors to requested value"
(interactive "r\nnRequested B-factor (max 999.99): ")
(if (> pdb-test-number 999.99) (error "ERROR[PDB]: Number too big"))
(if ( < pdb-test-number 0) (setq pdb-test-number 20 ))
(setq pdb-test-number (format "%6.2f" pdb-test-number))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-number 60 6)
(pdb-sub-markregion))
(defun pdb-change-occu (b e pdb-test-number)
"PDB mode: Change occupancy to requested value"
(interactive "r\nnRequested occupancy: ")
(if (> pdb-test-number 99.99) (error "ERROR[PDB]: Number too big"))
(if (> pdb-test-number 1) (print "WARNING: Occupancy greater than 1.00" t))
(if (< pdb-test-number 0) (setq pdb-test-number "0.00" ))
(setq pdb-test-number (format "%5.2f" pdb-test-number))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-number 55 5)
(pdb-sub-markregion))
(defun pdb-change-alternate (b e pdb-test-string)
"PDB mode: Change alternate conformation ID of selected atoms"
(interactive "r \ns:Alternate ID: ")
(if (= (length pdb-test-string) 0)
(error "ERROR[PDB]: One character please - try again"))
(setq pdb-test-string (upcase (substring pdb-test-string 0 1)))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-string 16 1)
(pdb-sub-markregion))
(defun pdb-change-chain (b e pdb-test-string)
"PDB mode: Change chain ID of selected atoms"
(interactive "r \nsChain ID: ")
(if (= (length pdb-test-string) 0)
(error "ERROR[PDB]: One character please - try again"))
(setq pdb-test-string (upcase (substring pdb-test-string 0 1)))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-string 21 1)
(pdb-sub-markregion))
(defun pdb-change-name (b e pdb-test-string)
"PDB mode: Change selected atom names"
(interactive "r \nsAtom Name (4 chars, space first if not metal): ")
(if (/= (length pdb-test-string) 4)
(error "ERROR[PDB]: 4 characters please. Space first if not a metal"))
(setq pdb-test-string (upcase pdb-test-string))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-string 12 4)
(pdb-sub-markregion))
(defun pdb-change-residue (b e pdb-test-number)
"PDB mode: Change residue number to given value"
(interactive "r \nnNew residue number:")
(setq pdb-test-number (format "%4d" pdb-test-number))
(pdb-sub-defineregion b e )
(pdb-sub-change pdb-test-number 22 4)
(pdb-sub-markregion))
(defun pdb-change-segid (b e pdb-test-string)
"PDB mode: Add SEGID to selected atoms"
(interactive "r \nsSEGID: ")
(if ( = (length pdb-test-string) 0)
(setq pdb-test-string (buffer-substring (+ (point-at-bol) 21) (+ (point-at-bol) 22))))
(setq pdb-test-string (upcase pdb-test-string))
(setq pdb-test-string (format "%-4s" pdb-test-string))
(pdb-sub-defineregion b e )
(pdb-sub-change pdb-test-string 72 4)
(pdb-sub-markregion))
(defun pdb-change-type (b e pdb-test-string)
"PDB mode: Change residue type of selected atoms"
(interactive "r \nsNew Residue type: ")
(if (< (length pdb-test-string) 3)
(error "ERROR[PDB]: Three characters please - try again"))
(setq pdb-test-string (upcase (substring pdb-test-string 0 3)))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-string 17 3)
(pdb-sub-markregion))
;; INCREMENT VALUES
(defun pdb-increment-bfactor (b e pdb-test-string)
"PDB mode: Increment B-factor by given value"
(interactive "r \nsNumber to add to B-factor:")
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let (( str (buffer-substring (+ (point-at-bol) 60) (+ (point-at-bol) 66))))
(setq str (+ (eval (string-to-number str)) (eval (string-to-number pdb-test-string))))
(pdb-sub-change2 (format "%6.2f" str) 60 6)))))
(pdb-sub-markregion))
(defun pdb-scale-bfactor (b e pdb-test-string)
"PDB mode: Scale B-factor by given value"
(interactive "r \nsNumber to scale B-factor by:")
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let (( str (buffer-substring (+ (point-at-bol) 60) (+ (point-at-bol) 66))))
(setq str (* (eval (string-to-number str)) (eval (string-to-number pdb-test-string))))
(pdb-sub-change2 (format "%6.2f" str) 60 6)))))
(pdb-sub-markregion))
(defun pdb-increment-residue (b e pdb-test-string)
"PDB mode: Increment residue number by given value"
(interactive "r \nsNumber to increase residue number by:")
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\|ANISOU\\|TER \\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let ((str (buffer-substring (+ (point-at-bol) 22) (+ (point-at-bol) 26))))
(let ((str (+ (eval (string-to-number str)) (eval (string-to-number pdb-test-string)))))
(pdb-sub-change2 (format "%4d" str) 22 4))))))
(pdb-sub-markregion))
(defun pdb-increment-fractional (b e pdb-test-string)
"PDB mode: Translate selected atoms by given fractional vector"
(interactive "r \nsGive fractional vector (3 numbers, space delimited):")
(pdb-sub-defineregion b e)
(pdb-change-orth2frac pdb-start-user-region pdb-end-user-region )
(let* ((vec (split-string pdb-test-string))
(xadd (string-to-number (elt vec 0)))
(yadd (string-to-number (elt vec 1)))
(zadd (string-to-number (elt vec 2))))
(pdb-increment-xyz pdb-start-user-region pdb-end-user-region (format "%f %f %f" xadd yadd zadd)))
(pdb-change-frac2orth pdb-start-user-region pdb-end-user-region)
(pdb-sub-markregion))
(defun pdb-scale-xyz (b e sf)
"PDB mode: Scale coordinates by given factor.\nIf one number is given, x,y and z are scaled by this number.\n If 3 numbers given, they apply to x,y and z independently."
(interactive "r \nsScale factor (1 number or 3 numbers:")
(pdb-sub-defineregion b e)
(let* ((sf (concat sf " " sf " " sf))
(vec (split-string sf))
(xadd (string-to-number (elt vec 0)))
(yadd (string-to-number (elt vec 1)))
(zadd (string-to-number (elt vec 2))))
(while (and (progn
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil))
(not (progn
(pdb-sub-pad)
(let ((xyz (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54))))))
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" (* xadd (elt xyz 0)) (* yadd (elt xyz 1)) (* zadd (elt xyz 2))) 30 24))))))
(pdb-sub-markregion)))
(defun pdb-increment-xyz (b e pdb-test-string)
"PDB mode: Translate selected atoms by given vector"
(interactive "r \nsGive vector (3 numbers, space delimited):")
(let* ((li (split-string pdb-test-string))
(xadd (string-to-number (elt li 0)))
(yadd (string-to-number (elt li 1)))
(zadd (string-to-number (elt li 2))))
(pdb-sub-defineregion b e)
(while (and (progn
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil))
(not (progn
(pdb-sub-pad)
(let ((str (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54))))))
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" (+ (elt str 0) xadd) (+ (elt str 1) yadd) (+ (elt str 2) zadd)) 30 24)))))))
(pdb-sub-markregion))
(defun pdb-change-frac2orth (b e)
"PDB mode: Change fractional to orthogonal coordinates"
(interactive "r")
(pdb-sub-defineregion b e)
(if (eq (elt pdb-cell-local 1) 0)
(call-interactively 'pdb-data-cell))
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let* ((frac (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54)))))
(newx (+ (* (elt pdb-frac2orth-local 0) (elt frac 0)) (* (elt pdb-frac2orth-local 1) (elt frac 1)) (* (elt pdb-frac2orth-local 2) (elt frac 2))))
(newy (+ (* (elt pdb-frac2orth-local 4) (elt frac 1)) (* (elt pdb-frac2orth-local 5) (elt frac 2))))
(newz (* (elt pdb-frac2orth-local 8) (elt frac 2))))
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" newx newy newz) 30 24)))))
(pdb-sub-markregion))
(defun pdb-change-orth2frac (b e)
"PDB mode: Change orthogonal to fractional coordinates"
(interactive "r")
(pdb-sub-defineregion b e)
(if (eq (elt pdb-cell-local 1) 0)
(call-interactively 'pdb-data-cell))
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let* ((orth (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54)))))
(newx (+ (* (elt pdb-orth2frac-local 0) (elt orth 0)) (* (elt pdb-orth2frac-local 1) (elt orth 1)) (* (elt pdb-orth2frac-local 2) (elt orth 2))))
(newy (+ (* (elt pdb-orth2frac-local 4) (elt orth 1)) (* (elt pdb-orth2frac-local 5) (elt orth 2))))
(newz (* (elt pdb-orth2frac-local 8) (elt orth 2)))
)
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" newx newy newz) 30 24)))))
(pdb-sub-markregion))
(defun pdb-increment-matrix (b e rm)
"PDB mode: Rotate selected atoms by given 3x3 matrix"
(interactive "r \nsGive matrix (9 numbers, space delimited):")
(let* ((rm (split-string rm))
(rm (list (string-to-number (elt rm 0)) (string-to-number (elt rm 1)) (string-to-number (elt rm 2)) (string-to-number (elt rm 3)) (string-to-number (elt rm 4)) (string-to-number (elt rm 5)) (string-to-number (elt rm 6)) (string-to-number (elt rm 7)) (string-to-number (elt rm 8)))))
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let* ((xyz (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54)))))
(nx (+ (* (nth 0 rm) (nth 0 xyz)) (* (nth 1 rm ) (nth 1 xyz)) (* (nth 2 rm ) (nth 2 xyz))))
(ny (+ (* (nth 3 rm) (nth 0 xyz)) (* (nth 4 rm ) (nth 1 xyz)) (* (nth 5 rm ) (nth 2 xyz))))
(nz (+ (* (nth 6 rm) (nth 0 xyz)) (* (nth 7 rm ) (nth 1 xyz)) (* (nth 8 rm ) (nth 2 xyz)))))
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" nx ny nz) 30 24)
)))))
(pdb-sub-markregion))
(defun pdb-increment-euler (b e pdb-test-string)
"PDB mode: Rotate selected atoms by given euler triplet"
(interactive "r \nsGive eulers (3 numbers, space delimited):")
(pdb-sub-defineregion b e)
(let* ((pdb-test-vector (split-string pdb-test-string))
(rad (/ 3.141593 180))
(al (* rad (string-to-number (elt pdb-test-vector 0))))
(be (* rad (string-to-number (elt pdb-test-vector 1))))
(ga (* rad (string-to-number (elt pdb-test-vector 2))))
(rm (list
(- (* (cos al) (cos be) (cos ga)) (* (sin al) (sin ga)))
(- (* -1 (cos al) (cos be) (sin ga)) (* (sin al) (cos ga)))
(* (cos al) (sin be))
(+ (* (sin al) (cos be) (cos ga)) (* (cos al) (sin ga)))
(- (* (cos al) (cos ga)) (* (sin al) (cos be) (sin ga)))
(* (sin al) (sin be))
(* -1 (sin be) (cos ga))
(* (sin be) (sin ga))
(cos be)
)))
(message (format "Matrix: %f %f %f %f %f %f %f %f %f" (elt rm 0) (elt rm 1) (elt rm 2) (elt rm 3) (elt rm 4) (elt rm 5) (elt rm 6) (elt rm 7) (elt rm 8)))
(pdb-increment-matrix b e (format "%f %f %f %f %f %f %f %f %f" (elt rm 0) (elt rm 1) (elt rm 2) (elt rm 3) (elt rm 4) (elt rm 5) (elt rm 6) (elt rm 7) (elt rm 8))))
(pdb-sub-markregion))
(defun pdb-increment-centroid (b e pdb-test-string)
"PDB mode: Translate selected atoms by given vector"
(interactive "r \nsGive vector (3 numbers, space delimited):")
(let* ((inc (split-string pdb-test-string))
(inc (list (string-to-number (elt inc 0)) (string-to-number (elt inc 1)) (string-to-number (elt inc 2))))
(vec (make-list 3 0))
(cnt 0)
(xyz (make-list 3 0))
(str ""))
;; first pass to calculate average
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
;; get current xyz
(setq xyz (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54)))))
;; add current xyz to running total (vec)
(setq vec (vector (+ (elt xyz 0) (elt vec 0)) (+ (elt xyz 1) (elt vec 1)) (+ (elt xyz 2) (elt vec 2))))
;; keep count of atoms
(setq cnt (+ cnt 1)))))
;; calculate average xyz and store in pdb-test-vec
(setq vec (vector (/ (elt vec 0) cnt)(/ (elt vec 1) cnt)(/ (elt vec 2) cnt)))
(message (format "Old centroid: %8.3f %8.3f %8.3f" (elt vec 0) (elt vec 1) (elt vec 2)))
;; second pass to adjust numbers
(goto-char pdb-start-user-region)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(setq str (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54)))))
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" (- (elt str 0) (- (elt vec 0) (elt inc 0))) (- (elt str 1) (- (elt vec 1) (elt inc 1))) (- (elt str 2) (- (elt vec 2) (elt inc 2)))) 30 24))))
(pdb-sub-markregion)))
;; RENUMBER
(defun pdb-renumber-atoms (b e pdb-start-number)
"PDB mode: Renumber selected atoms consecutively"
(interactive "r \nnRenumber atoms, starting at?:")
(if ( = pdb-start-number 0) (setq pdb-start-number 1))
(pdb-sub-defineregion b e)
(let ((i (- pdb-start-number 1)))
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\|TER \\|ANISOU\\)" pdb-end-user-region 1 nil)
(unless (string= (buffer-substring (point-at-bol) (+ 6 (point-at-bol))) "ANISOU")
(setq i (+ 1 i)))
(cond ((< (point) pdb-end-user-region)
(goto-char (+ (point-at-bol) 11))
(delete-backward-char 5)
(insert (format "%5s" (int-to-string i))))))
(pdb-sub-markregion)))
(defun pdb-renumber-waters (b e pdb-start-number)
"PDB mode: Renumber selected waters consecutively"
(interactive "r \nnRenumber waters, starting at?:")
(if ( = pdb-start-number 0) (setq pdb-start-number 1))
(pdb-sub-defineregion b e)
(let ((i (- pdb-start-number 1)))
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\|TER \\|ANISOU\\)" pdb-end-user-region 1 nil)
(if (string-match (buffer-substring (point-at-bol) (+ 6 (point-at-bol))) "\\(ATOM \\|HETATM\\)")
(setq i (+ 1 i)))
(cond ((< (point) pdb-end-user-region)
(goto-char (+ (point-at-bol) 26))
(delete-backward-char 4)
(insert (format "%4s" (int-to-string i))))))
(pdb-sub-markregion)))
;;TIDY UP
(defun pdb-tidy-atom2hetatm (b e)
"PDB mode: Replace selected ATOMs with HETATM"
(interactive "r")
(pdb-sub-defineregion b e)
(goto-char pdb-start-user-region)
(while (and (progn
(re-search-forward "^ATOM" pdb-end-user-region 1 nil))
(not (progn
(beginning-of-line)
(delete-char 6)
(insert "HETATM")))))
(pdb-sub-markregion))
(defun pdb-tidy-hetatm2atom (b e)
"PDB mode: Replace selected HETATMS with ATOM"
(interactive "r")
(pdb-sub-defineregion b e)
(goto-char pdb-start-user-region)
(while (and (progn
(re-search-forward "^HETATM" pdb-end-user-region 1 nil))
(not (progn
(beginning-of-line)
(delete-char 6)
(insert "ATOM ")))))
(pdb-sub-markregion))
(defun pdb-tidy-ca ( b e )
"PDB mode: Reduce to CAs only"
(interactive "r" )
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^." pdb-end-user-region pdb-end-user-region nil)
(if (and (< (point) pdb-end-user-region) (not (looking-at "TOM ..... CA" )))
(progn
(beginning-of-line)
(setq pdb-end-user-region (- pdb-end-user-region (+ 1 (- (point-at-eol) (point-at-bol)))))
(kill-line))))
(pdb-sub-markregion))
(defun pdb-tidy-dehydrogenate (b e )
"PDB mode: Remove hydrogen atoms"
(interactive "r" )
(pdb-sub-defineregion b e)
(while (< (point) e)
(re-search-forward "^\\(ATOM \\|HETATM\\)..... .?H.*$" e 1 nil)
(if (< (point) e)
(progn
(beginning-of-line)