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
|
#! /usr/bin/perl
#
# pdb2fasta.pl - generate FASTA nonredundant sequence file from SEQRES records of globbed pdb files.
# HHsuite version 3.0.0 (15-03-2015)
#
# Reference:
# Remmert M., Biegert A., Hauser A., and Soding J.
# HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.
# Nat. Methods, epub Dec 25, doi: 10.1038/NMETH.1818 (2011).
# (C) Johannes Soeding, 2012
# This program 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 3 of the License, or
# (at your option) any later version.
# This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
# We are very grateful for bug reports! Please contact us at soeding@mpibpc.mpg.de
use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
use strict;
$|= 1; # Activate autoflushing on STDOUT
# Default parameters
my $v=2;
my $help="
pdb2fasta.pl - Generate FASTA nonredundant sequence file from SEQRES records of
globbed pdb files.
For updating purposes, you can write only those sequences to pdb_new.fas that are not
already contained in an old file by giving as third argument the old pdb.fas file.
Usage: pdb2fasta.pl 'pdb-fileglob' pdb_newseqs.fas [options]
Options:
-u oldfile update: write only those sequences to pdb_new.fas that are not contained in oldfile
-scop file read dir.cla.scop.txt_1.65 and list SCOP fold(s) in sequence name
-dali dir read FoldIndex.html and domain_definitions.txt in DALI directory and list DALI fold(s)
in sequence name
-v int verbose mode
-t MTH-YR use only structures released until the given month and year, e.g. APR-12 or SEP-99
-all include all sequences instead of nonredundant set
Examples:
pdb2fasta.pl '*.ent' /data/pdbfas/pdb_20Apr2012.fas
pdb2fasta.pl '*.pdb' pdb_new.fas -u pdb.fas -dali /data/dali -scop /data/scop/dir.cla.scop.txt_1.75
\n";
my $TOTLEN=160; # maximum length of name, description, and keywords
my $DESCLEN=80; # maximum length of description
if (@ARGV<2) {die($help);}
my @pdbfiles;
my $newseqfile;
my $oldfile="";
my $dalidir="";
my $scopfile="";
my $date="";
my %months=("JAN"=>1,"FEB"=>2,"MAR"=>3,"APR"=>4,"MAY"=>5,"JUN"=>6,"JUL"=>7,"AUG"=>8,"SEP"=>9,"OCT"=>10,"NOV"=>11,"DEC"=>12);
my %oldpdbids=(); # hash contains all pdbids in $oldfile
our $pdbfile;
my $pdbid; # four-letter PDB identifier, e.g. 1hz4
my $resolution; # experimental resolution in Angstrom
my $rvalue; # R-value
my $free_rvalue; # free R-value
my $molid=0; # molecule id (for multichain structures)
my $length; # number of residues in a chain
my @seqres=(); # three-letter code of chain currently read in
my $seqres; #
my %descript; # $descript{"A"} contains the description for chain A
my $descript;
my %organism; # $organism{"A"} contains the organism for chain A
my $organism;
my $organism_common;
my @chain; # $chain[$molid]
my $chain; # either A for chain A or "" if no chain id
my @chains; #
my @keywds; # keywords for the structure
my $keywds; # keywords for the structure
my $token;
my $synonym; # read from COMPND SYNONYM records of pdb files
my @synonyms; # read from COMPND SYNONYM records of pdb files
my $line; # line read in from file
my @sequences=(); # contains all sequences of chains to be printed to outfile
my @resolution=(); # $resolution[$nc] contains resolution of $nc'th sequence, where $nc=$nchains{$seqres}
my %nchains; # $nchains{$seqres} is index in @sequences of sequence with these residues
my $nchains=0; # number of chains written to $newseqfile
my $k=0; # counts pdb files processed
my @equiv_pdbs; # list of pdbids (including _chain) with identical residues (maximum one pdbid_chain per pdb file)
my %dalifamids=(); # $foldids{$pdbid} contains a list of (one or more) DALI or SCOP foldids
my %scopfamids=(); # $foldids{$pdbid} contains a list of (one or more) DALI or SCOP foldids
my $het; # $het contains list of hetero ligands with at least 10 atoms in current pdb file (e.g. "DAC,PTR")
my %words; # for debugging upper case -> lower case
my $nr=1; # 1: create nonredundant set 0:do not eliminate redundant sequences
my %three2one=(
"ALA"=>"A","VAL"=>"V","PHE"=>"F","PRO"=>"P","MET"=>"M","ILE"=>"I","LEU"=>"L","ASP"=>"D","GLU"=>"E","LYS"=>"K",
"ARG"=>"R","SER"=>"S","THR"=>"T","TYR"=>"Y","HIS"=>"H","CYS"=>"C","ASN"=>"N","GLN"=>"Q","TRP"=>"W","GLY"=>"G",
"2AS"=>"D","3AH"=>"H","5HP"=>"E","ACL"=>"R","AIB"=>"A","ALM"=>"A","ALO"=>"T","ALY"=>"K","ARM"=>"R","ASA"=>"D",
"ASB"=>"D","ASK"=>"D","ASL"=>"D","ASQ"=>"D","AYA"=>"A","BCS"=>"C","BHD"=>"D","BMT"=>"T","BNN"=>"A","BUC"=>"C",
"BUG"=>"L","C5C"=>"C","C6C"=>"C","CCS"=>"C","CEA"=>"C","CHG"=>"A","CLE"=>"L","CME"=>"C","CSD"=>"A","CSO"=>"C",
"CSP"=>"C","CSS"=>"C","CSW"=>"C","CXM"=>"M","CY1"=>"C","CY3"=>"C","CYG"=>"C","CYM"=>"C","CYQ"=>"C","DAH"=>"F",
"DAL"=>"A","DAR"=>"R","DAS"=>"D","DCY"=>"C","DGL"=>"E","DGN"=>"Q","DHA"=>"A","DHI"=>"H","DIL"=>"I","DIV"=>"V",
"DLE"=>"L","DLY"=>"K","DNP"=>"A","DPN"=>"F","DPR"=>"P","DSN"=>"S","DSP"=>"D","DTH"=>"T","DTR"=>"W","DTY"=>"Y",
"DVA"=>"V","EFC"=>"C","FLA"=>"A","FME"=>"M","GGL"=>"E","GLZ"=>"G","GMA"=>"E","GSC"=>"G","HAC"=>"A","HAR"=>"R",
"HIC"=>"H","HIP"=>"H","HMR"=>"R","HPQ"=>"F","HTR"=>"W","HYP"=>"P","IIL"=>"I","IYR"=>"Y","KCX"=>"K","LLP"=>"K",
"LLY"=>"K","LTR"=>"W","LYM"=>"K","LYZ"=>"K","MAA"=>"A","MEN"=>"N","MHS"=>"H","MIS"=>"S","MLE"=>"L","MPQ"=>"G",
"MSA"=>"G","MSE"=>"M","MVA"=>"V","NEM"=>"H","NEP"=>"H","NLE"=>"L","NLN"=>"L","NLP"=>"L","NMC"=>"G","OAS"=>"S",
"OCS"=>"C","OMT"=>"M","PAQ"=>"Y","PCA"=>"E","PEC"=>"C","PHI"=>"F","PHL"=>"F","PR3"=>"C","PRR"=>"A","PTR"=>"Y",
"SAC"=>"S","SAR"=>"G","SCH"=>"C","SCS"=>"C","SCY"=>"C","SEL"=>"S","SEP"=>"S","SET"=>"S","SHC"=>"C","SHR"=>"K",
"SOC"=>"C","STY"=>"Y","SVA"=>"S","TIH"=>"A","TPL"=>"W","TPO"=>"T","TPQ"=>"A","TRG"=>"K","TRO"=>"W","TYB"=>"Y",
"TYQ"=>"Y","TYS"=>"Y","TYY"=>"Y","AGM"=>"R","GL3"=>"G","SMC"=>"C","ASX"=>"B","CGU"=>"E","CSX"=>"C","GLX"=>"Z",
"LED"=>"L"
);
# Read command line options
my $options="";
for (my $i=0; $i<=$#ARGV; $i++) {$options.=" $ARGV[$i]";}
if ($options=~s/ -u\s+(\S+)//) {$oldfile=$1;}
if ($options=~s/ -dali\s+(\S+)//) {$dalidir=$1;}
if ($options=~s/ -scop\s+(\S+)//) {$scopfile=$1;}
if ($options=~s/ -v\s*(\d+)//) {$v=$1;}
if ($options=~s/ -v//) {$v=2;}
if ($options=~s/ -all//) {$nr=0;}
if ($options=~s/ -t (\w\w\w)-(\d\d)//) {$date=($months{$1}-1)/12+$2+100*($2<50);}
if ($options=~s/^\s*([^- ]\S+)\s*//) {
if ($v>=2) {print("Globbing...")};
@pdbfiles=glob($1);
if ($v>=2) {print(" found ".scalar(@pdbfiles)." files\n")};
}
if ($options=~s/^\s*([^- ]\S+)\s*//) {$newseqfile=$1;}
# Warn if unknown options found or no infile/newseqfile
if ($options!~/^\s*$/) {$options=~s/^\s*(.*?)\s*$/$1/g; die("Error: unknown options '$options'\n");}
if (!@pdbfiles) {print($help); print("Error: no input files given\n"); exit;}
if (!$newseqfile) {print($help); print("Error: no output file given\n"); exit;}
# Updating option?
if ($oldfile) {
# Reading pdb codes from $oldfile
if ($v>=3) {printf("Reading pdb codes from $oldfile ... \n");}
open (OLDFILE,"<$oldfile") || die ("ERROR: cannot open $oldfile for writing: $!\n");
while ($line=<OLDFILE>) {
if ($line=~/^>(\S\S\S\S)/o) {$oldpdbids{$1}=1;}
}
close(OLDFILE);
}
# Add fold identifiers?
if ($dalidir) {&ReadDaliFiles();}
if ($scopfile) {&ReadScopFile();}
############################################################################################
# Read one pdb file after the other
foreach $pdbfile (@pdbfiles) {
$k++;
if ($pdbfile=~/^.*\/(.*?)$/) {$pdbid=$1;} else {$pdbid=$pdbfile;} # remove path
if ($pdbid=~/^(pdb)?(.*)\..*$/) {$pdbid=lc($2);} else {die("Error: globbed file $pdbfile has no extension\n");}
if (exists $oldpdbids{$pdbid}) {next;}
if ($v>=1) {
print(".");
if (!($k%100)) {print("$k\n");}
} elsif ($v>=2) {printf("Reading %4i %s\n",$k,$pdbfile);}
open (PDBFILE, "<$pdbfile") || die ("Error: couldn't open $pdbfile: $!\n");
if ($v>=4) {print("Reading $pdbfile...\n");}
$line=<PDBFILE>;
# Initialize before reading new pdb file
$resolution=0;
$rvalue=0;
$free_rvalue=0;
$molid=0;
$token="MOLECULE";
$descript="";
$organism="";
$organism_common="";
$keywds="";
$chain="";
%organism=();
%descript=();
@keywds=();
@chain=();
@seqres=();
$synonym="";
@synonyms=();
$het=""; # will contain list of hetero groups (if found)
# COMPND ASPARTATE AMINOTRANSFERASE (E.C.2.6.1.1) WILD TYPE COMPLEXED 1ASA 3
# COMPND 2 WITH PYRIDOXAL-5'-PHOSPHATE AND MALEATE 1ASA 4
# or
# COMPND MOL_ID: 1;
# COMPND 2 MOLECULE: ACTIN-LIKE PROTEIN 3;
# COMPND 3 CHAIN: A;
# COMPND 4 SYNONYM: ARP3; ACTIN-RELATED PROTEIN 3; ACTIN-2;
# COMPND 5 OTHER_DETAILS: PART OF THE ARP2/3 COMPLEX;
# COMPND 6 MOL_ID: 2;
# COMPND 7 MOLECULE: ACTIN-LIKE PROTEIN 2;
# COMPND 8 CHAIN: B;
# COMPND 9 SYNONYM: ARP2; ACTIN-RELATED PROTEIN 2;
# COMPND 10 OTHER_DETAILS: PART OF THE ARP2/3 COMPLEX;
# or
# COMPND MOL_ID: 1;
# COMPND 2 MOLECULE: PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN
# COMPND 3 PHO4;
# COMPND 4 CHAIN: A, B;
# COMPND 5 FRAGMENT: DNA BINDING DOMAIN;
# COMPND 6 SYNONYM: BHLH;
# COMPND 7 ENGINEERED: YES;
# COMPND 8 BIOLOGICAL_UNIT: DIMER;
while ($line && $line!~/^COMPND /o && $line!~/^REMARK /o) {$line=<PDBFILE>;}
if (!$line || $line!~/^COMPND /)
{
if ($v>=2) {print("\n\nWarning: no COMPND line found in $pdbfile; skipping pdb file\n");}
next;
}
while ($line && $line=~/^COMPND /o && $line!~/^REMARK /o) {
$line=~s/^(.{70}).*/$1/;
if ($line=~/^COMPND\s+\d*\s+MOL_ID:\s*(\d+)/) {
if ($molid>0) {
&SetDescript();
} else {$molid=$1;}
$descript="";
$synonym="";
}
elsif ($line=~/^COMPND\s+\d*\s+MOLECULE:\s*(.*\S)/) {$descript=$1; $token="MOLECULE";}
elsif ($line=~/^COMPND\s+\d*\s+CHAIN:\s*(.*\S)/) {$chain=$1; $token="CHAIN";}
elsif ($line=~/^COMPND\s+\d*\s+SYNONYM:\s*(.*\S)/) {$synonym=$1;}
elsif ($line=~/^COMPND\s+\d*\s+FRAGMENT:/) {$token="";}
elsif ($line=~/^COMPND\s+\d*\s+EC:/) {$token="";}
elsif ($line=~/^COMPND\s+\d*\s+ENGINEERED:/) {$token="";}
elsif ($line=~/^COMPND\s+\d*\s+MUTATION:/) {$token="";}
elsif ($line=~/^COMPND\s+\d*\s+BIOLOGICAL UNIT:/) {$token="";}
elsif ($line=~/^COMPND\s+\d*\s+OTHER_DETAILS:/) {$token="";}
else {
$line=~/^COMPND\s+\d*\s+(.*\S)/;
if ($token eq "MOLECULE") {$descript.=" ".$1;}
elsif ($token eq "SYNONYM") {$synonym.=" ".$1;}
elsif ($token eq "CHAIN") {$chain.=" ".$1;}
}
$line=<PDBFILE>;
}
&SetDescript();
if (!$line) {if ($v>=2) {print("\nFormat error in $pdbfile. Skipping file ...\n");} next;}
# SOURCE (ESCHERICHIA COLI) 1ASA 5
# or
# SOURCE MOL_ID: 1;
# SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS;
# SOURCE 3 ORGANISM_COMMON: BOVINE;
# SOURCE 4 ORGAN: THYMUS;
# SOURCE 5 MOL_ID: 2;
# SOURCE 6 ORGANISM_SCIENTIFIC: BOS TAURUS;
# SOURCE 7 ORGANISM_COMMON: BOVINE;
# SOURCE 8 ORGAN: THYMUS;
$molid=0;
$token="ORGANISM";
# $organism="Synthetic?";
while ($line && $line!~/^SOURCE /o && $line!~/^REMARK /o) {$line=<PDBFILE>;}
if (!$line) {if ($v>=2) {print("\nFormat error in $pdbfile. Skipping file ...\n");} next;}
if ($v>=2 && $line!~/^SOURCE /) {print("\n\nWarning: no SOURCE line found in $pdbfile\n");}
while ($line=~/^SOURCE /o && $line!~/^REMARK /o) {
$line=~s/^(.{70}).*/$1/;
if ($line=~/^SOURCE\s+\d*\s+MOL_ID:\s*(\d+)/) {
if ($molid>0) {
&SetOrganism();
} else {$molid=$1;}
}
elsif ($line=~/^SOURCE\s+\d*\s+ORGANISM_SCIENTIFIC:\s*(.*\S)/) {$organism=$1; $token="ORGANISM";}
elsif ($line=~/^SOURCE\s+\d*\s+SYNTHETIC/) {if ($organism eq "") {$organism="Synthetic"; $token="";}}
elsif ($line=~/^SOURCE\s+\d*\s+FRAGMENT:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+ORGANISM_COMMON:\s+(.*\S)/) {$organism_common=$1; $token="";}
elsif ($line=~/^SOURCE\s+\d*\s+STRAIN:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+VARIANT:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+CELL_LINE:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+ATCC:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+ORGAN:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+TISSUE:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+CELL:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+ORGANELLE:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+SECRETION:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+CELLULAR_LOCATION:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+PLASMID:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+GENE:/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+EXPRESSION_/) {$token="";}
elsif ($line=~/^SOURCE\s+\d*\s+OTHER_DETAILS:/) {$token="";}
else {
$line=~/^SOURCE\s+\d*\s+(.*\S)/;
if ($token eq "ORGANISM") {$organism.=$1;}
}
$line=<PDBFILE>;
}
&SetOrganism();
if (!$line) {if ($v>=2) {print("\nFormat error in $pdbfile. Skipping file ...\n");} next;}
# KEYWDS KETOLISOMERASE, XYLOSE METABOLISM, GLUCOSE-FRUCTOSE
# KEYWDS 2 INTERCONVERSION, HYDRIDE TRANSFER, ALPHA-BETA BARREL,
# KEYWDS 3 METALLOENZYME, THERMOPHILE
while ($line && $line!~/^KEYWDS /o && $line!~/^REMARK /o) {$line=<PDBFILE>;}
if (!$line) {if ($v>=2) {print("\nFormat error in $pdbfile. Skipping file ...\n");} next;}
while ($line=~/^KEYWDS /o) {
$line=~s/^(.{70}).*/$1/;
if ($line=~/^KEYWDS\s+\d*\s+(.*\S)/) {$keywds.=" ".$1;}
$line=<PDBFILE>;
}
$keywds=~s/CRYSTAL STRUCTURE,?\s*//i;
$keywds=~s/X-RAY STRUCTURE,?\s*//i;
$keywds=~s/THREE-DIMENSIONAL STR.CTURE,?\s*//i;
$keywds=~s/NMR,?\s*//i;
if ($keywds) {
$keywds=~s/\s+/ /g;
$keywds=~s/^\s+/ /;
$keywds=~s/\s*;?$/;/;
@keywds=split(/[,;]\s+/,$keywds);
} else {@keywds=();}
# Include keywords up to 50 chars taken
my @these_keywds=@keywds;
if (@these_keywds) {
# Remove keywords that are substring of description or organism
for (my $k=0; $k<@these_keywds; $k++) {
$keywds=$these_keywds[$k];
my $ddescript=$descript;
my $kkeywds=$keywds;
my $oorganism=$organism;
$ddescript=~tr/a-zA-Z//cd;
$kkeywds=~tr/a-zA-Z//cd;
$oorganism=~tr/a-zA-Z//cd;
if ($ddescript=~/$kkeywds/i) {splice(@these_keywds,$k,1); $k--;}
elsif ($kkeywds=~/$ddescript/i) {splice(@these_keywds,$k,1); $k--;}
elsif ($oorganism=~/$kkeywds/i) {splice(@these_keywds,$k,1); $k--;}
}
# Add keywords until length limitation is exceeded ($TOTLEN chars)
if (@these_keywds) {
$keywds=$these_keywds[0];
for (my $k=1; $k<@these_keywds && length($descript.$keywds.", ".$these_keywds[$k].$organism)<$TOTLEN; $k++) {
$keywds.=", ".$these_keywds[$k];
}
$keywds=~s/^(\S)/ $1/; # add space at first position
} else {$keywds="";}
} else {$keywds="";}
foreach my $chain (keys(%descript)) {$descript{$chain}.=$keywds;}
# Check date?
if ($date) {
while ($line && $line!~/^REVDAT 1/o && $line!~/^REMARK /o) {$line=<PDBFILE>;}
if ($line=~/^REVDAT 1/) {
if ($line=~/^.{16}(\w\w\w)-(\d\d)/) {
my $thisdate=($months{$1}-1)/12+$2+100*($2<50);
# print("This date: $thisdate date=$date\n$line");
if ($thisdate>$date) {next;}
} elsif ($v>=2) {
print("WARNING: no valid date in header: \n$line");
}
}
}
# REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
while ($line && $line!~/^REMARK 2 /o && $line!~/^SEQRES /o) {$line=<PDBFILE>;}
if (!$line) {if ($v>=2) {print("\nFormat error in $pdbfile. Skipping file ...\n");} next;}
if ($v>=2 && $line!~/^REMARK 2 /) {print("\n\nWarning: no REMARK 2 line found in $pdbfile\n");}
while ($line=~/^REMARK 2 /o && $line!~/^SEQRES /o) {
if ($line=~/^REMARK 2\s+RESOLUTION\.\s+(\d+\.?\d*)/) {$resolution=$1; last;}
$line=<PDBFILE>;
}
# REMARK 3 R VALUE (WORKING SET) : 0.216
# REMARK 3 FREE R VALUE : 0.251
while ($line && $line!~/^REMARK 3 /o && $line!~/^SEQRES /o) {$line=<PDBFILE>;}
if (!$line) {if ($v>=2) {print("\nFormat error in $pdbfile. Skipping file ...\n");} next;}
if ($v>=2 && $line!~/^REMARK 3 /) {print("\n\nWarning: no REMARK 3 line found in $pdbfile\n");}
while ($line=~/^REMARK 3 /o && $line!~/^SEQRES /o) {
if ($line=~/^REMARK 3\s+R VALUE\s+\(WORKING SET\)\s*:\s*(\d+\.?\d*)/o) {$rvalue=$1;}
if ($line=~/^REMARK 3\s+FREE R VALUE\s*:\s*(\d+\.?\d*)/o) {$free_rvalue=$1;}
$line=<PDBFILE>;
}
# Record current position in PDBFILE
my $file_pos = tell(PDBFILE);
# Search for hetero groups BEFORE adding seqeunces => read pdb file twice :(
while ($line && $line!~/^HET /o && $line!~/^ATOM /o) {$line=<PDBFILE>;}
if (defined $line && $line=~/^HET /o) {
while ($line) {
# ----+----1----+----2----+----3
# HET DAC A 172 18
if ($line=~/^HET\s+(\S+) ..........\s*(\d+)/) {
if ($2>=10 ) {
my $this_het=$1;
if ($het!~/$this_het/) { # don't list any hetgoup twice
if ($het eq "") {$het=" HET: $1";} else {$het.=" $1";}
}
}
} else {
last;
}
$line=<PDBFILE>;
}
}
if ($het ne "") {$het.=";";}
# Rewind the current position in PDBFILE back before SEQRES records
seek (PDBFILE,$file_pos,0);
# SEQRES 1 396 MET PHE GLU ASN ILE THR ALA ALA PRO ALA ASP PRO ILE 1ASA 60
# SEQRES 1 A 366 SER ARG MET PRO SER PRO PRO MET PRO VAL PRO PRO ALA
@seqres=();
my $newchain="@"; # make sure that sequence is not printed before first chain has been read
my $newlength; # compare previous to current chain to find out when one chain is finished
while ($line && $line!~/^SEQRES /o) {$line=<PDBFILE>;}
if (!defined $line) {
if ($v>=2) {print("\n\nWarning: no SEQRES line found in $pdbfile. Skipping file ...\n");}
close (PDBFILE);
next;
}
while ($line=~/^SEQRES /o) {
if (length($line) >= 20) {
$chain = $newchain;
$newchain = substr($line, 10, 2);
$newchain =~ /\s*(\S*)/; #if newchain=" " -> ""
$newchain = $1;
$length = $newlength;
$newlength = substr($line, 13, 4);
$seqres = substr($line, 19, 51);
$seqres =~ s/\s*$//;
# Compare previous to current chain to find out when one chain is finished
if ($chain ne $newchain && $chain ne "@") {
if (scalar(@seqres)!=$length) {
if ($v>=2) {printf("\nWarning: in $pdbfile, line $., sequence length=$length, counted residues = %i\n",scalar(@seqres));}
}
&AddSequence();
@seqres=();
}
push(@seqres,split(/\s+/,$seqres));
} else {
print("\nError: found invalid SEQRES record in $pdbfile, line $. : line=$line");
}
$line=<PDBFILE>;
}
$chain=$newchain;
$length=$newlength;
&AddSequence();
close (PDBFILE);
} # end foreach $pdbfile
############################################################################################
# Print all sequences
open (NEWSEQFILE,">$newseqfile") || die ("ERROR: cannot open $newseqfile for writing: $!\n");
for (my $nc=0; $nc<@sequences; $nc++) {
if ($equiv_pdbs[$nc] ne "") {
$sequences[$nc]=~s/^(.*)/$1 PDB:$equiv_pdbs[$nc]/; # Add list of equivalent pdb codes
}
printf(NEWSEQFILE "%s",$sequences[$nc]);
}
close(NEWSEQFILE);
foreach my $word (keys(%words)) {print("$word ");}
print("\n");
print("Written $nchains chains to $newseqfile\n");
exit;
##################################################################################
# Set description when a new MOL_ID line is found, or at the end of COMPND records
##################################################################################
sub SetDescript() {
my $i;
# print("chain=$chain\n");
if ($chain eq "NULL;") {$chain="";}
$chain[$molid]=$chain;
$molid=$1;
if ($descript=~/^DNA[ ;]/) {$het=" HET: DNA";}
# Cut description down to max. $DESCLEN letters
$descript=~s/\s*;\s*$//;
if (length($descript)>$DESCLEN) {
$descript=~s/(.{$DESCLEN}\S*).*/$1.../; # remove everything after first comma
}
# Add synonyms with a maximum of 16 letters to description
if ($synonym ne "") {
@synonyms=split(/;\s+/,$synonym);
for ($i=0; $i<scalar(@synonyms); $i++) {
if (length($synonyms[$i])>16) {
splice(@synonyms,$i,1);
} else {
$synonyms[$i]=~s/;\s*//;
$token="SYNONYM";
}
}
}
# Choose shortname (<=16 characters) from synonyms
unshift(@synonyms,$descript);
for ($i=0; $i<scalar(@synonyms); $i++) {
if (length($synonyms[$i])<=16) {last;}
}
if ($i>=scalar(@synonyms)) {$i=0;}
$descript=$synonyms[$i];
$descript=~s/^\s*//;
$descript=~s/\s*$//;
splice(@synonyms,$i,1);
for $synonym (@synonyms) {$descript.=", ".$synonym;}
if ($descript ne "") {
$descript=~s/\s+/ /g;
$descript=~s/^\s+//g;
$descript=~s/\s*;*\s*$//; # remove ';'
}
$descript.=";"; # append a semicolon ';'
if ($chain ne "") {
$chain=~s/\s*;\s*$//;
@chains=split(/[,; ]\s*/,$chain);
foreach $chain (@chains) {
$descript{$chain}=$descript;
# printf("chain='$chain' description='$descript'\n");
}
} else {
$descript{$chain}=$descript;
# printf("chain='$chain' description='$descript'\n");
}
}
##################################################################################
# Set organism when a new MOL_ID line is found, or at the end of SOURCE records
##################################################################################
sub SetOrganism() {
if ($organism eq "" && $organism_common ne "") {$organism=$organism_common;}
if (!exists $chain[$molid]) {$molid=1-$molid;}
$chain=$chain[$molid];
$molid=$1;
$organism=~tr/$//d;
$organism=~s/^\s*([^;:]*).*/$1/;
if ($organism=~/^\S*\s*\(([\w ]*)/) {$organism=$1;} # bovine (Bos taurus)
elsif ($organism=~/^([\w -]+)/) {$organism=$1;} # BACTERIOPHAGE T4 (MUTANT GENE DERIVED ...)
elsif ($organism=~/^(\S+\s+\S+)/) {$organism=$1;} # maximum two words
elsif ($organism=~/^(\S+)/) {$organism=$1;}
$organism=~s/\s*$//g;
if ($chain ne "") {
$chain=~s/\s*;\s*$//;
@chains=split(/[,; ]\s*/,$chain);
foreach $chain (@chains) {
$organism{$chain}=$organism;
# printf("chain='%s' organism{chain}='%s'\n",$chain,$organism{$chain});
}
} else {
$organism{$chain}=$organism;
# printf("chain='%s' organism{chain}='%s'\n",$chain,$organism{$chain});
}
}
##################################################################################
# Print out sequence of last chain read in
##################################################################################
sub AddSequence() {
my $seqres="";
my $pdbidchain;
my $nc; # $nc= either next chain number OR, if identical seq exists with better resolution, index of this seq
foreach my $aa (@seqres) {$seqres.=&Three2OneLetter($aa);}
if ($v>=3) {
printf("CHAIN ='%s'\n",$chain);
printf("DESCRP='%s'\n",$descript{$chain});
printf("KEYWDS='$keywds'\n");
printf("ORGANI='%s'\n",$organism{$chain});
printf("SEQRES='%s'\n",$seqres);
}
if (length($seqres)<=20) {return 1;} # skip short protein/DNA chains (for DNA's ADGT &Three2OneLetter() returns "")
if ($chain ne "") {$pdbidchain=$pdbid."_".$chain;} else {$pdbidchain=$pdbid;}
# Check for nonredundancy
if ($nr==1 && defined $nchains{$seqres} ) {
$nc=$nchains{$seqres};
# $sequences[$nchains{$seqres}]=~/^(\S+)/;
# print("Sequence $pdbid"."_$chain redundant with $1. Res now: $resolution Res before: $resolution[$nc]\n");
if ($resolution==0 || $resolution[$nc]<=$resolution) {
# PDB identifier not yet contained in list of equivalent pdb ids?
if ($equiv_pdbs[$nc]!~/$pdbid/ && $sequences[$nc]!~/^>$pdbid/) {
$equiv_pdbs[$nc].=" $pdbidchain"; # Add new pdbid_chain to list $equiv_pdbs[$nc]
if ($het ne "") {$equiv_pdbs[$nc].="*";}
}
return 1;
} else {
# Sequence redundant
# => Throw out earlier sequence and keep this one
# => Keep list $equiv_pdbs[$nc] from earlier sequence and append its pdbid
$sequences[$nc]=~/>(\S+)/;
$equiv_pdbs[$nc].=" $1";
if ($het ne "") {$equiv_pdbs[$nc].="*";}
}
} else {
$nc=$nchains{$seqres}=$nchains;
$nchains++;
$equiv_pdbs[$nc]="";
}
$resolution[$nc]=$resolution;
# If descript{chain} does not exist, it was not specified seperately for each chain
if (exists $descript{$chain}) {$descript=$descript{$chain}}
$descript=~s/;*$//; # remove ; at the end
# If organism{chain} does not exist, it was not specified seperately for each chain
if (exists $organism{$chain}) {
$organism=lc($organism{$chain});
} else {
if($organism=~/\((.*)\)/) {$organism=$1;}
$organism=lc($organism);
}
if ($v>=3) {
printf("Accept:\n",$chain);
printf("CHAIN ='%s'\n",$chain);
printf("DESCRP='%s'\n",$descript);
printf("KEYWDS='$keywds'\n");
printf("ORGANI='%s'\n",$organism);
printf("SEQRES='%s'\n",$seqres);
}
# Correct upper/lower case
$descript=" $descript ";
$descript=~s/([a-zA-Z]{5,})/\L$1/g; # make everything longer than 5 word characters lower case
$descript=~s/([\s]OF[\s])/\L$1/g;
$descript=~s/([\s]OR[\s])/\L$1/g;
$descript=~s/([\s]ON[\s])/\L$1/g;
$descript=~s/([\s]NO[\s])/\L$1/g;
$descript=~s/([\s]IN[\s])/\L$1/g;
$descript=~s/([\s]IS[\s])/\L$1/g;
$descript=~s/([\s]BY[\s])/\L$1/g;
$descript=~s/([\s]AT[\s])/\L$1/g;
$descript=~s/([\s]TO[\s])/\L$1/g;
$descript=~s/([ -]ALL[ -])/\L$1/g;
$descript=~s/([ -]AND[ -])/\L$1/g;
$descript=~s/([ -]ARM[ -])/\L$1/g;
$descript=~s/([ -]BOX[ -])/\L$1/g;
$descript=~s/([ -]BOX[ -])/\L$1/g;
$descript=~s/([ -]EGG[ -])/\L$1/g;
$descript=~s/([ -]EYE[ -])/\L$1/g;
$descript=~s/([ -]FOR[ -])/\L$1/g;
$descript=~s/([ -]HAS[ -])/\L$1/g;
$descript=~s/([ -]HEN[ -])/\L$1/g;
$descript=~s/([ -]HOT[ -])/\L$1/g;
$descript=~s/([ -]LOW[ -])/\L$1/g;
$descript=~s/([ -]MOL[ -])/\L$1/g;
$descript=~s/([ -]NON[ -])/\L$1/g;
$descript=~s/([ -]ONE[ -])/\L$1/g;
$descript=~s/([\s]OUT[\s])/\L$1/g;
$descript=~s/([ -]SEX[ -])/\L$1/g;
$descript=~s/([ -]SIX[ -])/\L$1/g;
$descript=~s/([ -]TEN[ -])/\L$1/g;
$descript=~s/([\s]THE[\s])/\L$1/g;
$descript=~s/([ -]TWO[ -])/\L$1/g;
$descript=~s/([ -]WAY[ -])/\L$1/g;
$descript=~s/([\W]ACID[\W])/\L$1/g;
$descript=~s/([\W]ACYL[\W])/\L$1/g;
$descript=~s/([\W]ALDO[\W])/\L$1/g;
$descript=~s/([\W]ANTI[\W])/\L$1/g;
$descript=~s/([\W]AUTO[\W])/\L$1/g;
$descript=~s/([\W]AXIN[\W])/\L$1/g;
$descript=~s/([\W]BASE[\W])/\L$1/g;
$descript=~s/([\W]BEAN[\W])/\L$1/g;
$descript=~s/([\W]BETA[\W])/\L$1/g;
$descript=~s/([\W]BILE[\W])/\L$1/g;
$descript=~s/([\W]BLUE[\W])/\L$1/g;
$descript=~s/([\W]BONE[\W])/\L$1/g;
$descript=~s/([\W]BOND[\W])/\L$1/g;
$descript=~s/([\W]CELL[\W])/\L$1/g;
$descript=~s/([\W]COAT[\W])/\L$1/g;
$descript=~s/([\W]COIL[\W])/\L$1/g;
$descript=~s/([\W]COLD[\W])/\L$1/g;
$descript=~s/([\W]COLI[\W])/\L$1/g;
$descript=~s/([\W]CORE[\W])/\L$1/g;
$descript=~s/([\W]CRYO[\W])/\L$1/g;
$descript=~s/([\W]DRUG[\W])/\L$1/g;
$descript=~s/([\W]DUAL[\W])/\L$1/g;
$descript=~s/([\W]DUCK[\W])/\L$1/g;
$descript=~s/([\W]ENDO[\W])/\L$1/g;
$descript=~s/([\W]FAST[\W])/\L$1/g;
$descript=~s/([\W]FIVE[\W])/\L$1/g;
$descript=~s/([\W]FOLD[\W])/\L$1/g;
$descript=~s/([\W]FOOT[\W])/\L$1/g;
$descript=~s/([\W]FORM[\W])/\L$1/g;
$descript=~s/([\W]FOUR[\W])/\L$1/g;
$descript=~s/([\W]FROM[\W])/\L$1/g;
$descript=~s/([\W]FLAP[\W])/\L$1/g;
$descript=~s/([\W]FREE[\W])/\L$1/g;
$descript=~s/([\W]GENE[\W])/\L$1/g;
$descript=~s/([\W]GOOD[\W])/\L$1/g;
$descript=~s/([\W]HALF[\W])/\L$1/g;
$descript=~s/([\W]HAND[\W])/\L$1/g;
$descript=~s/([\W]HAVE[\W])/\L$1/g;
$descript=~s/([\W]HEAD[\W])/\L$1/g;
$descript=~s/([\W]HEAT[\W])/\L$1/g;
$descript=~s/([\W]HEME[\W])/\L$1/g;
$descript=~s/([\W]HEXA[\W])/\L$1/g;
$descript=~s/([\W]HIGH[\W])/\L$1/g;
$descript=~s/([\W]HOLO[\W])/\L$1/g;
$descript=~s/([\W]IRON[\W])/\L$1/g;
$descript=~s/([\W]KETO[\W])/\L$1/g;
$descript=~s/([\W]KNOT[\W])/\L$1/g;
$descript=~s/([\W]LATE[\W])/\L$1/g;
$descript=~s/([\W]LENS[\W])/\L$1/g;
$descript=~s/([\W]LIKE[\W])/\L$1/g;
$descript=~s/([\W]LONG[\W])/\L$1/g;
$descript=~s/([\W]LOOP[\W])/\L$1/g;
$descript=~s/([\W]MAIN[\W])/\L$1/g;
$descript=~s/([\W]MEAN[\W])/\L$1/g;
$descript=~s/([\W]MINI[\W])/\L$1/g;
$descript=~s/([\W]MITE[\W])/\L$1/g;
$descript=~s/([\W]MODE[\W])/\L$1/g;
$descript=~s/([\W]MONO[\W])/\L$1/g;
$descript=~s/([\W]MUCH[\W])/\L$1/g;
$descript=~s/([\W]NINE[\W])/\L$1/g;
$descript=~s/([\W]NULL[\W])/\L$1/g;
$descript=~s/([\W]ONLY[\W])/\L$1/g;
$descript=~s/([\W]OPEN[\W])/\L$1/g;
$descript=~s/([\W]PARA[\W])/\L$1/g;
$descript=~s/([\W]PLUS[\W])/\L$1/g;
$descript=~s/([\W]POST[\W])/\L$1/g;
$descript=~s/([\W]POLY[\W])/\L$1/g;
$descript=~s/([\W]PORE[\W])/\L$1/g;
$descript=~s/([\W]PUMP[\W])/\L$1/g;
$descript=~s/([\W]RICH[\W])/\L$1/g;
$descript=~s/([\W]RING[\W])/\L$1/g;
$descript=~s/([\W]ROLE[\W])/\L$1/g;
$descript=~s/([\W]ROLL[\W])/\L$1/g;
$descript=~s/([\W]SALT[\W])/\L$1/g;
$descript=~s/([\W]SEMI[\W])/\L$1/g;
$descript=~s/([\W]SITE[\W])/\L$1/g;
$descript=~s/([\W]STEM[\W])/\L$1/g;
$descript=~s/([\W]TAIL[\W])/\L$1/g;
$descript=~s/([\W]TATA[\W])/\L$1/g;
$descript=~s/([\W]TRAP[\W])/\L$1/g;
$descript=~s/([\W]TUBE[\W])/\L$1/g;
$descript=~s/([\W]TURN[\W])/\L$1/g;
$descript=~s/([\W]TWIN[\W])/\L$1/g;
$descript=~s/([\W]TYPE[\W])/\L$1/g;
$descript=~s/([\W]WELL[\W])/\L$1/g;
$descript=~s/([\W]WILD[\W])/\L$1/g;
$descript=~s/([\W]WITH[\W])/\L$1/g;
$descript=~s/([\W]WROM[\W])/\L$1/g;
$descript=~s/([\W]ZETA[\W])/\L$1/g;
$descript=~s/([\W]ZINC[\W])/\L$1/g;
$descript=~s/DE NOVO/de novo/ig;
$descript=~s/(\W)KDA(\W)/$1kDa$2/g;
$descript=~s/(\S+[CBDFGJKLMNPQRTVWXZ]{4,}\S+)/\U$1/ig;
$descript=~s/(\W)(\S[CBDFGHJKLMNPQRSTVWXZ]{4,}\W)/$1\U$2/ig; # no vowels for at least 4 letters -> abbreviation -> upper case
$descript=~s/(\W)([CBDFGHJKLMNPQRSTVWXZ]{4,}\S\W)/$1\U$2/ig; # no vowels for at least 4 letters -> abbreviation -> upper case
$descript=~s/(\w+ii+\w+)/\U$1/ig;
$descript=~s/([\W]rossman[\W])/\u$1/g;
$descript=~s/([\W]nadph[\W])/\U$1/g;
$descript=~s/([\W]gapdh[\W])/\U$1/g;
$descript=~s/([\W]f[\W])/\u$1/g;
$descript=~s/(\W)(\w{0,3})RNP(\W)/$1\L$2\URNP$3/ig;
$descript=~s/(\W)(\w{0,3})RNA(\W)/$1\L$2\URNA$3/ig;
$descript=~s/(\W)(\w{0,3})DNA(\W)/$1\L$2\UDNA$3/ig;
$descript=~s/RNASE(\W)/RNAse$1/ig;
$descript=~s/DNASE(\W)/DNAse$1/ig;
$descript=~s/barnase/barnase/ig;
$descript=~s/atpase(\W)/ATPase$1/ig;
$descript=~s/gtpase(\W)/GTPase$1/ig;
# Write amino acid three letter symbols with one capital letter
foreach my $aa ("Ala","Cys","Asp","Glu","Phe","Gly","His","Ile","Lys","Leu","Met","Asn","Pro","Gln","Arg","Ser","Thr","Val","Trp","Tyr","MSe") {
$descript=~s/$aa([ -;:.+])/$aa$1/ig;
}
# Write ions as chemical elements
foreach my $ion ("Zn","Mg","Na","Ka","Ca","Fe","Cu","Se","Al","Mn") {
$descript=~s/([ -:;])$ion([ -;:.+])/$1$ion$2/ig;
$descript=~s/([ -:;])$ion([ -;:.+])/$1$ion$2/ig;
}
$descript=~s/^\s*//;
$descript=~s/\s*$//;
$descript="\u$descript"; # first letter of description upper case
$organism="\u$organism"; # first letter of organism upper case
$organism=~s/ ([\w\d]{0,2})$/ \U$1/; # Influenza A virus
$organism=~s/ (\w+\d+\w*)$/ \U$1/; # Influenza A virus
if ($v>=2 && $organism eq "") {print("\n\nWarning: no organism found for chain $chain in $pdbfile\n");}
my $foldid="";
if ($dalifamids{$pdbidchain}) {$foldid=" $dalifamids{$pdbidchain}".$foldid;}
if ($scopfamids{$pdbidchain}) {$foldid=" $scopfamids{$pdbidchain}".$foldid;}
my $res;
if ($resolution>0) {$res=$resolution."A";} else {$res="NMR";}
# Set sequence record
$seqres=~s/(\S{1,100})/$1\n/g; # insert newlines after each 70 characters
$sequences[$nc]=sprintf(">%-6.6s %s;%s %s {%s}%s\n",$pdbidchain,$descript,$het,$res,$organism,$foldid);
$sequences[$nc].=sprintf("$seqres");
if($v>=3) {print($sequences[$nc]);}
return 0;
}
sub ReadScopFile()
{
# Read dir.cla.scop.txt_1.65
if ($v>=2) {print("Reading $scopfile ... ");}
open (SCOPFILE,"<$scopfile") || die ("ERROR: cannot open $scopfile: $!\n");
#d1dlwa_ 1dlw A: a.1.1.1 14982 cl=46456,cf=46457,sf=46458,fa=46459,dm=46460,sp=46461,px=14982
my $n=0;
my $scopfamid;
my $chain;
my $pdbidchain;
while($line=<SCOPFILE>) {
if ($line=~/^\S+\s+(\S\S\S\S)\s+(\S+)\s+(\w\.\d+\.\d+\.\d+)/) {
$pdbid=$1;
$chain=$2;
$scopfamid=$3;
$pdbidchain=$1;
# printf("chain=$chain\n");
if ($chain!~/([A-Za-z\d]):/) {
if ($scopfamids{$pdbidchain}) {
$scopfamids{$pdbidchain}.=" ".$scopfamid;
# printf("scopfamids($pdbidchain)=%s\n",$scopfamids{$pdbidchain});
} else {
$scopfamids{$pdbidchain}="SCOP: ".$scopfamid;
# printf("scopfamids($pdbidchain)=%s\n",$scopfamids{$pdbidchain});
}
$n++;
} else {
my %chains=();
while ($chain=~/([A-Za-z\d]):/) {
$chain=~s/([A-Za-z\d]):[^A-Za-z:]*//;
if ($chains{$1}) {next;}
if ($1 ne "") {$pdbidchain="$pdbid"."_$1";}
$chains{$1}=1;
if ($scopfamids{$pdbidchain}) {
$scopfamids{$pdbidchain}.=" ".$scopfamid;
# printf("scopfamids($pdbidchain)=%s\n",$scopfamids{$pdbidchain});
} else {
$scopfamids{$pdbidchain}="SCOP: ".$scopfamid;
# printf("scopfamids($pdbidchain)=%s\n",$scopfamids{$pdbidchain});
}
$n++;
}
}
}
}
close(SCOPFILE);
print(" found $n domains in SCOP file $scopfile\n");
}
sub ReadDaliFiles()
{
# Read FoldIndex.html
if ($v>=2) {print("Reading $dalidir/FoldIndex.html ... ");}
open (FOLDINEXFILE,"<$dalidir/FoldIndex.html") || die ("ERROR: cannot open $dalidir/FoldIndex.html: $!\n");
# 1.1.1.1.1.1 1cunA_2 ...
# 1.1.1.2.1.1 ___1lvfA_1 ...
my $n=0;
my $dalifamid;
my %fold_for_repr;
while($line=<FOLDINEXFILE>) {
if ($line=~/(\d+\.\d+\.\d+\.\d+\.\d+\.\d+)\s+_*(\S+)(_\d+)/) {
$fold_for_repr{$2.$3}=$1;
if ($3 eq "_0") {
$dalifamid=$1;
$pdbid=$2;
$pdbid=~s/^(\S\S\S\S)(\S)/$1_$2/;
$dalifamids{$pdbid}="DALI: ".$dalifamid;
}
$n++;
}
}
close(FOLDINEXFILE);
if ($v>=1) {print(" found $n representative domains in DALI's FoldIndex.html\n");}
# Read domain_definitions.txt
my $domainfile="$dalidir/domain_definitions.txt";
my $repr;
if ($v>=2) {print("Reading $domainfile ... ");}
open (DOMAINFILE,"<$domainfile") || die ("ERROR: cannot open $domainfile: $!\n");
# 1cunA/1-106 1cunA_1 1 ALPHA SPECTRIN
$n=0;
while($line=<DOMAINFILE>) {
if ($line=~/^(\S+)\/\S+\s+(\S+)/) {
if (!$fold_for_repr{$2}) {
if ($v>=2) {print("WARNING: no fold for DALI representative $2 in $domainfile\n");}
next;
}
$pdbid=$1;
$repr=$2;
$pdbid=~s/^(\S\S\S\S)(\S)/$1_$2/;
if ($dalifamids{$pdbid}) {
$dalifamids{$pdbid}.=" ".$fold_for_repr{$repr};
} else {
$dalifamids{$pdbid}=" DALI: ".$fold_for_repr{$repr};
}
$n++;
}
}
close(DOMAINFILE);
print(" found $n domains in DALI file $domainfile\n");
}
##################################################################################
# Convert three-letter amino acid code into one-letter code
##################################################################################
sub Three2OneLetter {
my $res = $three2one{uc($_[0])};
if (defined $res) {
return $res;
} elsif ($_[0] =~ /^\s+$/) {
return "";
} else {
return "X";
}
}
|
