-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathrotbond
1832 lines (1520 loc) · 53.4 KB
/
rotbond
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
#! /usr/bin/perl -w
# Modified by Naomi Haworth 17/3/2015
#
# If you haven't have environment set up, maker sure you Chage $HOME setting!!!!
#
# USAGE rotbond.pl $mol
# INPUT $mol.xyz and $mol.bonds where $mol.bonds are a file containing two columns with atomic number of bonds
# if a third column is presented, rotation angle can be manually set instead.
# OUTPUT $mol.abc.com and $mol.a.rfg where com is all the conformer files and rfg is the rotational fragment
#
#
#####################################################################
#
# Works out the inter-atomic distances in a molecule, and also
# determines if they are 'bonded' according to the covalent radii.
#
#####################################################################
# use Math::Matrix;
# use Iterator::Array::Jagged;
## Perl Library /System/Library/Perl/5.8.8/
## Require Math/Matrix.pm Iterator/Array/Jagged.pm
## http://search.cpan.org/~ulpfr/Math-Matrix-0.5/Matrix.pm
## http://search.cpan.org/~johnd/Iterator-Array-Jagged-0.05/lib/Iterator/Array/Jagged.pm
$print = 0;
$tsbond1 = 0;
$tsbond2 = 0;
for ($i = 1; $i <= 3; $i++) {
$hbond1[$i] = 0;
$hbond2[$i] = 0;
}
$HOME="home/$ENV{REMOTE_DIR}/$ENV{REMOTE_USER}"; #<--- change here!!!
$mol = $ARGV[0];
@rot = ('a','b','c','d','e','f','g','h','i','j','k','l','m','n','o','p','q','r','s','t','u','v','w','x','y','z');
$rot_i = 0;
$Rassolov = 0;
$solRassolov = 0;
$heavy = 0;
$heavybasis = "lacvp + polarisation + ecp";
@symbo=("xx","h" , "he",
"li","be", "b", "c", "n", "o", "f","ne",
"na","mg", "al","si", "p", "s","cl","ar",
"k" ,"ca","sc","ti", "v","cr","mn","fe","co","ni","cu","zn","ga","ge","as","se","br","kr",
"rb","sr", "y","zr","nb","mo","tc","ru","rh","pd","ag","cd","in","sn","sb","te", "i","xe",
"cs","ba",
"la","ce","pr","nd","pm","sm","eu","gd","tb","dy","ho","er","tm","yb","lu",
"hf","ta", "w","re","os","ir","pt","au","hg","tl","pb","bi","po","at","rn",
"fr","ra",
"ac","th","pa", "u","np","pu","am","cm","bk","cf","es","fm","md","no","lr");
$pi = atan2(1,1) * 4;
$nat = 0;
(@A,@X,@Y,@Z,@B) = ();
open XYZ, "$mol.xyz" or die $!;
while (<XYZ>) {
next if (m/molecule/);
next if (m/scf/);
last if (m/end/);
@F = split(/\s+/,$_);
next unless(m/\S/ && @F > 2);
$nat++;
@_ = split(/\s+/,$_);
($z,$y,$x,$a) = reverse(@_);
$a = ToSymbol($a) if ($a =~ m/\d/);
#print "$a\n$x $y $z\n";
push(@A,$a); push(@X,$x); push(@Y,$y); push(@Z,$z);
$atomn = atomicN($a) ;
if ($atomn > 18){
$Rassolov = 1;
$solRassolov = 1;
if ($atomn > 36){
$heavy=1;
$heavyatom = $a;
}
}
}
close XYZ;
$radiiline= "";
$genbasis = "";
$pseudo = "";
$scrf = "";
$heavyline = "";
$nonelec ="";
$solvnline = "";
$qnew = "";
$charge = &promptUser(" What is the charge of $mol?","0");
$multiplicity = &promptUser(" What is the multiplicity of $mol?","1");
$level = &promptUser(" What level of theory do you want to use?","M062X");
# $level = &promptUser(" What level of theory do you want to use?","B3LYP");
$basis = &promptUser(" What basis set do you want to use?","6-31+G*");
# $basis = &promptUser(" What basis set do you want to use?","6-31G*");
if (($basis =~ /6-31G\*/) || ($basis =~ /6-31\+G\*/) || ($basis =~ /6-31G\(d\)/) || ($basis =~ /6-31\+G\(d\)/)) {
$qnew = &promptUser(" Do you want to use the Rassolov version?","Y");
if ($qnew =~ /[yY]/) { $Rassolov = 1 }
}
$optight = &promptUser(" Do you want to use Opt=Tight?","No");
$opts = &promptUser(" Is this an optimization for transition structure?","No");
if ($opts eq "No"){
if ($optight eq "No") {
$opts = "Opt";
}
else {
$opts = "OPT(Tight)";
}
}
else{
print"\n If this is a bond forming/breaking transition state, Please specify the atomic number of the two atoms forming the bond:\n\n";
$tsbond1 = &promptUser(" what is the first atom:","");
$tsbond2 = &promptUser(" what is the second atom:","");
if ($optight eq "No") {
$opts = "OPT(TS,calcfc,noeigentest,maxcyc=200)";
}
else {
$opts = "OPT(TS,calcfc,noeigentest,maxcyc=200,tight)";
}
}
$optcpx = &promptUser(" Is this an optimization for a complex?","No");
$nhb = 0;
if ($optcpx eq "No"){
}
else{
$nhb = &promptUser(" Please specify the number of hydrogen bonds (must be <= 3):","1");
for ($ij = 1; $ij <= $nhb; $ij++) {
print" Please specify the atom numbers of the two atoms forming hydrogen bond $ij:\n";
$hbond1[$ij] = &promptUser(" What is the first atom:","");
$hbond2[$ij] = &promptUser(" What is the second atom:","");
}
}
$solvent = &promptUser(" Do you want to consider solvent effects?","No");
# $opts="No";
# $solvent="No";
# $level="";
# $basis="";
# $charge="";
# $multiplicity="";
$sollevel = $level;
if ($solvent ne "No"){
$solv = &promptUser(" What solvent model do you want to use (uaks, smd)?","smd");
$solvent = &promptUser(" What is the solvent you want to use (toluene,etac,h2o)?","h2o");
if ($qnew !~ [yYnN]) {
$qnew = &promptUser(" Do you want to use the Rassolov 6-31(+)G* basis sets for the solvent calculations?","Y");
if ($qnew =~ /[yY]/) { $solRassolov = 1 }
}
$solgenbasis = "";
if ($solv eq "uaks") {
print "PCM(uaks) was parameterised using B3LYP/6-31(+)G* - this model chemisty must (and will) be used.\n";
$sollevel = "B3LYP";
if ($basis =~ /\+/) {
$solbas = "6-31+G*";
}
else {
$solbas = "6-31G*";
}
if ($solvent eq "toluene"){
$scrf = "SCRF=(CPCM,Solvent=$solvent,Read)";
$scrf2 = "SCRF=(CPCM,Solvent=$solvent,Read,dovac,self)";
$radiiline = "RADII=UAKS\nAlpha=1.3\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
}
elsif ($solvent eq "etac"){
$scrf = "SCRF=(CPCM,Solvent=DiethylEther,Read)";
$scrf2 = "SCRF=(CPCM,Solvent=DiethylEther,Read,dovac,self)";
$radiiline = "RADII=UAKS\nAlpha=1.2\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "DENSITY=0.00613\nRSOLV=2.648\nEPS=5.9867\nVMOL=89.4\n";
}
elsif ($solvent eq "h2o"){
$scrf = "SCRF=(PCM,Solvent=water,Read)";
$scrf2 = "SCRF=(PCM,Solvent=water,Read,dovac,self)";
$radiiline = "RADII=UAKS\nAlpha=1.2\n";
$nonelec = "Cav\nDis\nRep\n";
$solvnline = "";
}
}
elsif ($solv eq "smd") {
$sollevel = &promptUser(" SMD was parameterised with M052X however other functionals are acceptable to use.\n What level of theory do you want to use with the solvent model?","M052X");
if ($basis =~ /\+/) {
$solbas = "6-31+G*";
}
else {
$solbas = "6-31G*";
}
$scrf = "SCRF=(SMD,Solvent=$solvent)";
$scrf2 = "SCRF=(SMD,Solvent=$solvent,dovac,self)";
$solvnline ="";
$radiiline = "";
$nonelec = "";
}
#$scrf = "SCRF=($pcm,Solvent=$solvent,Read)";
#$nonelec = "CAV\nDIS\nREP\n";
#if ($level =~/B/i or $level =~/M/i){
# $radiiline = "Radii=UAKS Alpha=1.2\n\n";
#$radiiline = "SCFVAC\n\n"; doesn't work in g09
#}
#elsif ($level =~ /HF/i){
#$radiiline = "Radii=UAHF\n\n";
#}
#else{
#$radii = &promptUser(" What radii do you want to use?","UFF");
#$radiiline = "Radii=$radii SCFVAC\n\n";
#}
}
$freq = &promptUser(" Do you want to calculate frequencies?","No");
$solfreqtype = "na";
if (($solvent ne "No") && ($freq ne "No")) {
$solfreqtype = &promptUser(" Do you want to 1. calculate frequencies in solution (recommended)\n or 2. calculate frequencies in gas phase and apply dGsoln?","1");
}
$grid="INT(grid=ultrafine)";
if (($level =~ /CCSD/) || ($level =~ /ccsd/) || ($level =~ /QCI/) || ($level =~ /qci/) || ($level =~ /mp2/) || ($level =~ /mp2/) || ($level =~ /HF/) || ($level =~ /hf/)) {
$grid = "";
}
if (($basis eq "6-31G*" or $basis eq "6-31G(d)") and $Rassolov == 1){
$basis = "gen 6D";
$genbasis = "@/$HOME/Basis/6-31Gd.gbs/N\n\n";
$heavybasis = "lacvp + polarisation + ecp";
}
elsif ( ($basis eq "6-31+G*" or $basis eq "6-31+G(d)") and $Rassolov == 1){
$basis = "gen 6D";
$genbasis = "@/$HOME/Basis/6-31pGd.gbs/N\n\n";
$heavybasis = "lacvp + polarisation + diffuse + ecp";
}
$solRassolov = 0;
if ($solvent ne "No" and ($solbas eq "6-31G*" or $solbas eq "6-31G(d)") and $solRassolov == 1){
print "$solvent $solbas $solRassolov\n";
$solbas = "gen 6D";
$solgenbasis = "@/$HOME/Basis/6-31Gd.gbs/N\n\n";
$heavybasis = "lacvp + polarisation + ecp";
}
elsif ($solvent ne "No" and ($solbas eq "6-31+G*" or $solbas eq "6-31+G(d)") and $solRassolov == 1){
print "$solvent $solbas $solRassolov\n";
$solbas = "gen 6D";
$solgenbasis = "@/$HOME/Basis/6-31pGd.gbs/N\n\n";
$heavybasis = "lacvp + polarisation + diffuse + ecp";
}
if ($heavy == 1){
print "\n use $heavybasis for $heavyatom\n";
$pseudo = "pseudo=read";
$heavyline = "@/$HOME/Basis/lacvp.ecp/N\n\n";
}
for $i (0..$nat-1) {
for $j (0..$nat-1) {
$b = ($X[$i]-$X[$j])**2 + ($Y[$i]-$Y[$j])**2 + ($Z[$i]-$Z[$j])**2;
$b = sprintf("%6.4f",sqrt($b));
$B[$i][$j] = $b;
}
}
print "\n";
open BONDLIST, "$mol.bonds" or die $!;
while (<BONDLIST>) {
@abc = split(/\s+/,$_);
if ($#abc == 1){
($atom1,$atom2) = @abc;
$data2[$rot_i][0] = $atom1;
$data2[$rot_i][1] = $atom2;
DistMatrix($nat,\@A,\@B,$rot_i,$atom1,$atom2); # print out connectivity table but don't print out distance matrix
if ($n_group[$rot_i] == 2){
#@theta = (0,$pi);
@aaa = [$rot[$rot_i]."1",$rot[$rot_i]."4"];
push(@data1,@aaa);
}
elsif ($n_group[$rot_i] == 3){
#@theta = (0,120/180*$pi,240/180*$pi);
@aaa = [$rot[$rot_i]."1",$rot[$rot_i]."2",$rot[$rot_i]."3"];
push(@data1,@aaa);
}
}
elsif ($#abc ==2) {
($atom1,$atom2,$theta_user) = @abc;
$data2[$rot_i][0] = $atom1;
$data2[$rot_i][1] = $atom2;
DistMatrix($nat,\@A,\@B,$rot_i,$atom1,$atom2); # print out connectivity table but don't print out distance matrix
$data2[$rot_i][2] = $theta_user/180*$pi;
if ($theta_user =~/180/){
#@theta = (0,$pi);
@aaa = [$rot[$rot_i]."1",$rot[$rot_i]."4"];
push(@data1,@aaa);
}
elsif ($theta_user =~/120/){
#@theta = (0,120/180*$pi,240/180*$pi);
@aaa = [$rot[$rot_i]."1",$rot[$rot_i]."2",$rot[$rot_i]."3"];
push(@data1,@aaa);
}
elsif ($theta_user =~/60/){
#@theta = (0,60,120,180,240,300);
@aaa = [$rot[$rot_i]."1",$rot[$rot_i]."5",$rot[$rot_i]."2",$rot[$rot_i]."4",$rot[$rot_i]."3",$rot[$rot_i]."6"];
push(@data1,@aaa);
}
elsif ($theta_user =~/90/){
#@theta = (0,90,180,270)
@aaa = [$rot[$rot_i]."1",$rot[$rot_i]."7",$rot[$rot_i]."4",$rot[$rot_i]."8"];
push(@data1,@aaa);
}
else{
die ("Sorry, you have specified $theta_user degree rotation, however we haven't implement other than 2/3/4/6 folds rotations");
}
}
else{
die "format in $mol.bonds is incorrect\n two columns or three columns only\n ";
}
$rot_i++;
}
close BONDLIST;
for $i (0..$rot_i-1){
if ($data2[$i][2] ){
print " for bond ",$data2[$i][0],"-",$data2[$i][1],", rotate ",$data2[$i][2]*180/$pi," degree\n";
}
else{
print " for bond ",$data2[$i][0],"-",$data2[$i][1],", rotate ",360/$n_group[$i]," degree\n";
}
}
print "\n";
open LIST, ">$mol.list" or die $!;
my $iterator = Iterator::Array::Jagged->new( data => \@data1 );
while( my @set = $iterator->next )
{
for $i (0..$nat-1) {
$original[$i] = new Math::Matrix( [$X[$i]],[$Y[$i]],[$Z[$i]],[1.0] );
}
if ($print){
print "Confmer sets: '" . join(" ", @set) . "'\n";
}
for $g (0..$#set){
if ($set[$g] =~/1/){
$theta = 0.;
}
elsif($set[$g] =~/2/){
$theta = 120/180*$pi;
}
elsif($set[$g] =~/3/){
$theta = 240/180*$pi;
}
elsif($set[$g] =~/4/){
$theta = $pi;
}
elsif($set[$g] =~/5/){
$theta = 60/180*$pi;
}
elsif($set[$g] =~/6/){
$theta = 300/180*$pi;
}
elsif($set[$g] =~/7/){
$theta = 90/180*$pi;
}
elsif($set[$g] =~/8/){
$theta = 270/180*$pi;
}
Rotate($data2[$g][0],$data2[$g][1],$theta);
foreach $i (@{$frag_atoms[$g]}) {
$original[$i] = Math::Matrix::multiply($TRRRRRT,$original[$i]);
}
}
$name = join("",@set);
$name =~s/\w1//g;
# $name =~s/4/2/g;
if ($name =~ /a/){
}
else{
$name =~s/^/a1/g;
}
print LIST "$name\n";
# # print xyz for debugging
# open ROTXYZ, ">$mol.$name.xyz" or die $!;
# print ROTXYZ "$nat\n\n"; # for XYZ format
# for $i (0..$nat-1) {
# printf ROTXYZ "$A[$i]\t%f\t%f\t%f\n",$original[$i]->[0][0],$original[$i]->[1][0],$original[$i]->[2][0];
# }
# print ROTXYZ "\n";
# close ROTXYZ;
# #end here
if ($solfreqtype !~ 2) {
open ROTCOM, ">$mol.$name.com" or die $!;
if ($freq =~ /[Yy]/) { print ROTCOM "%chk=check.chk\n" }
print ROTCOM "#$sollevel/$basis SCF=Tight IOP(2/17=4) $grid $opts $pseudo $scrf\n\n";
print ROTCOM "@set\n\n";
print ROTCOM "$charge $multiplicity\n";
for $i (0..$nat-1) {
printf ROTCOM "$A[$i]\t%f\t%f\t%f\n",$original[$i]->[0][0],$original[$i]->[1][0],$original[$i]->[2][0];
}
print ROTCOM "\n";
print ROTCOM "$genbasis";
print ROTCOM "$heavyline";
print ROTCOM "$radiiline";
print ROTCOM "$nonelec";
print ROTCOM "$solvnline";
print ROTCOM "\n\n";
if ($freq =~ /[Yy]/) {
print ROTCOM "--Link1--\n";
print ROTCOM "%chk=check.chk\n";
print ROTCOM "#$sollevel/$basis Geom=check Guess=tcheck SCF=Tight IOP(2/17=4) $grid Freq(NoRaman) $pseudo $scrf\n\n";
print ROTCOM "@set\n\n";
print ROTCOM "$charge $multiplicity\n";
print ROTCOM "\n";
print ROTCOM "$genbasis";
print ROTCOM "$heavyline";
print ROTCOM "$radiiline";
print ROTCOM "$nonelec";
print ROTCOM "$solvnline";
print ROTCOM "\n\n";
}
# print ROTCOM "--Link1--\n";
# print ROTCOM "%chk=check.chk\n";
# print ROTCOM "#$level/$basis SCF=Tight IOP(2/17=4) $grid $opts $pseudo \n\n";
# print ROTCOM "@set\n\n";
# print ROTCOM "$charge $multiplicity\n";
# print ROTCOM "\n";
# print ROTCOM "$genbasis";
# print ROTCOM "\n\n";
# print ROTCOM "--Link1--\n";
# print ROTCOM "%chk=check.chk\n";
# print ROTCOM "#$level/$basis Geom=check Guess=tcheck SCF=Tight IOP(2/17=4) $grid Freq(NoRaman) $pseudo \n\n";
# print ROTCOM "@set\n\n";
# print ROTCOM "$charge $multiplicity\n";
# print ROTCOM "\n";
# print ROTCOM "$genbasis";
# print ROTCOM "\n";
close ROTCOM;
}
else {
open ROTCOM, ">$mol.$name.com" or die $!;
if ($freq =~ /[Yy]/) { print ROTCOM "%chk=check.chk\n" }
print ROTCOM "#$level/$basis SCF=Tight IOP(2/17=4) $grid $opts $pseudo \n\n";
print ROTCOM "@set\n\n";
print ROTCOM "$charge $multiplicity\n";
for $i (0..$nat-1) {
printf ROTCOM "$A[$i]\t%f\t%f\t%f\n",$original[$i]->[0][0],$original[$i]->[1][0],$original[$i]->[2][0];
}
print ROTCOM "\n";
print ROTCOM "$genbasis";
print ROTCOM "\n\n";
print ROTCOM "--Link1--\n";
print ROTCOM "%chk=check.chk\n";
print ROTCOM "#$level/$basis Geom=check Guess=tcheck SCF=Tight IOP(2/17=4) $grid Freq(NoRaman) $pseudo \n\n";
print ROTCOM "@set\n\n";
print ROTCOM "$charge $multiplicity\n";
print ROTCOM "\n";
print ROTCOM "$genbasis";
print ROTCOM "\n\n";
print ROTCOM "--Link1--\n";
print ROTCOM "%chk=check.chk\n";
print ROTCOM "#$sollevel/6-31G* Geom=check Guess=tcheck SCF=Tight IOP(2/17=4) $grid $opts $pseudo $scrf\n\n";
print ROTCOM "@set\n\n";
print ROTCOM "$charge $multiplicity\n";
print ROTCOM "\n";
print ROTCOM "$solgenbasis";
print ROTCOM "$heavyline";
print ROTCOM "$radiiline";
print ROTCOM "$nonelec";
print ROTCOM "$solvnline";
print ROTCOM "\n\n";
print ROTCOM "--Link1--\n";
print ROTCOM "%chk=check.chk\n";
print ROTCOM "#$sollevel/6-31G* Geom=check Guess=tcheck SCF=Tight IOP(2/17=4) $grid Freq(NoRaman) $pseudo $scrf\n\n";
print ROTCOM "@set\n\n";
print ROTCOM "$charge $multiplicity\n";
print ROTCOM "\n";
print ROTCOM "$solgenbasis";
print ROTCOM "$heavyline";
print ROTCOM "$radiiline";
print ROTCOM "$nonelec";
print ROTCOM "$solvnline";
print ROTCOM "\n\n";
print ROTCOM "--Link1--\n";
print ROTCOM "%chk=check.chk\n";
print ROTCOM "#$sollevel/6-31G* Geom=check Guess=tcheck SCF=Tight IOP(2/17=4) $grid $pseudo $scrf2\n\n";
print ROTCOM "@set\n\n";
print ROTCOM "$charge $multiplicity\n";
print ROTCOM "\n";
print ROTCOM "$solgenbasis";
print ROTCOM "$heavyline";
print ROTCOM "$radiiline";
print ROTCOM "$nonelec";
print ROTCOM "$solvnline";
print ROTCOM "\n\n";
print ROTCOM "--Link1--\n";
print ROTCOM "%chk=check.chk\n";
print ROTCOM "#$level/$basis Geom=check Guess=tcheck SCF=Tight IOP(2/17=4) $grid $opts $pseudo \n\n";
print ROTCOM "@set\n\n";
print ROTCOM "$charge $multiplicity\n";
print ROTCOM "\n";
print ROTCOM "$genbasis";
print ROTCOM "\n\n";
print ROTCOM "--Link1--\n";
print ROTCOM "%chk=check.chk\n";
print ROTCOM "#$level/$basis Geom=check Guess=tcheck SCF=Tight IOP(2/17=4) $grid Freq(NoRaman) $pseudo \n\n";
print ROTCOM "@set\n\n";
print ROTCOM "$charge $multiplicity\n";
print ROTCOM "\n";
print ROTCOM "$genbasis";
print ROTCOM "\n\n";
close ROTCOM;
}
$total++;
}
close LIST;
print " Total number of conformers $total\n\n";
#----------------------------------------------------------------------
sub DistMatrix {
# Print out Distance Matrix and FInd out the fragment of bond between atom1 and atom2
my ($n,$A,$B,$rot_i,$atom1,$atom2) = @_;
my @A = @$A;
my @B = @$B;
my ($batom1,$batom2);
@{$frag_atoms[$rot_i]} = ();
@{$frag_atoms_1[$rot_i]} = ();
my @new=();
for $i (0..$n-1) {
$new[$i]=1;
}
my @group2=() ;
my @group1=() ;
my @group=() ;
my @group1_element=() ;
my @group2_element=() ;
my ($g,$gs);
for $i (0..$n-1) {
if (connected($i,$atom2-1)) {
if ($i != $atom1-1){
if ($print){
print "group2 $A[$i]",$i+1,"\n";
}
push (@group2,$i);
$new[$i]=0;
}
}
}
#push (@group,@group2);
#print "$atom2 has ",$#group2+1,"\n";
for $i (0..$n-1) {
if (connected($i,$atom1-1)) {
if ($i != $atom2-1){
if ($print){
print "group1 $A[$i]",$i+1,"\n";
}
push (@group1,$i);
$new[$i]=0;
}
}
}
# print "$atom1 has ",$#group1+1,"\n";
# print "atom2, atom1 are $atom2 ,$atom1\n";
# if ( ($atom1 eq $tsbond1) or ($atom1 eq $tsbond2) ){
# if ( ($atom2 eq $tsbond1) or ($atom2 eq $tsbond2) ){
# $#group2 = $#group2;
# $#group1 = $#group1;
# }
# else{
# # ts bond so, ngroup -1
# $#group1 = $#group1-1;
# }
# }
# elsif ( ($atom2 eq $tsbond1) or ($atom2 eq $tsbond2) ){
# if ( ($atom1 eq $tsbond1) or ($atom1 eq $tsbond2) ){
# $#group2 = $#group2;
# $#group1 = $#group1;
# }
# else{
# $#group2 = $#group2-1;
# }
# }
# print "$atom2 has ",$#group2+1,"\n";
#print "$atom1 has ",$#group1+1,"\n";
$n_group[$rot_i] = max($#group1,$#group2) +1;
# print "max is ",$n_group[$rot_i],"\n";
for $g(0..$#group1){
push (@{$group1_element[$g]},$group1[$g]);
for $i (0..$n-1) {
if (connected($group1[$g],$i)) {
if ($i != $atom1-1 and $i != $atom2-1){
if ($print){
print "group1 $g has $A[$i]",$i+1,"\n";
}
push (@{$group1_element[$g]},$i);
$new[$i]=0;
}
}
}
}
for $g(0..$#group2){
push (@{$group2_element[$g]},$group2[$g]);
for $i (0..$n-1) {
if (connected($group2[$g],$i)) {
if ($i != $atom1-1 and $i != $atom2-1){
if ($print){
print "group2 $g has $A[$i]",$i+1,"\n";
}
push (@{$group2_element[$g]},$i);
$new[$i]=0;
}
}
}
}
$tot_frag1[$rot_i] = 0;
$tot_frag2[$rot_i] = 0;
# Recursive
while( $tot_frag1[$rot_i]+ $tot_frag2[$rot_i] <$n){
$tot_frag1[$rot_i] = 0;
$tot_frag2[$rot_i] = 0;
for $i(0..$n-1){
if ($i != $atom1-1 && $i != $atom2-1){
for $g(0..$#group1){
for $gs(0..$#{$group1_element[$g]}){
if (connected($i,$group1_element[$g][$gs]) and $new[$i] != 0){
push (@{$group1_element[$g]},$i);
$new[$i] = 0;
}
}
}
}
}
for $i(0..$n-1){
if ($i != $atom1-1 && $i != $atom2-1){
for $g(0..$#group2){
for $gs(0..$#{$group2_element[$g]}){
if (connected($i,$group2_element[$g][$gs]) and $new[$i] != 0){
push (@{$group2_element[$g]},$i);
$new[$i] = 0;
}
}
}
}
}
for $g(0..$#group1){
if ($print){
print "Good group1 $g has ";
}
for $gs(0..$#{$group1_element[$g]}){
if ($print){
print $group1_element[$g][$gs]+1,"\t";
}
}
if ($print){
print "\n";
}
$tot_frag1[$rot_i] += $#{$group1_element[$g]}+1;
}
for $g(0..$#group2){
if ($print){
print "Good group2 $g has ";
}
for $gs(0..$#{$group2_element[$g]}){
if ($print){
print $group2_element[$g][$gs]+1,"\t";
}
}
if ($print){
print "\n";
}
$tot_frag2[$rot_i] += $#{$group2_element[$g]}+1;
}
$tot_frag1[$rot_i] = $tot_frag1[$rot_i]+1; # total number of fragments
$tot_frag2[$rot_i] = $tot_frag2[$rot_i]+1; # total number of fragments
#print "tot_frag1 is $tot_frag1[$rot_i]\n\n\n";
#print "tot_frag2 is $tot_frag2[$rot_i]\n\n\n";
}
open RFGFILE, ">$mol.$rot[$rot_i].rfg" or die $!;
print RFGFILE "$tot_frag2[$rot_i]\n";
push (@{$frag_atoms[$rot_i]},$atom2-1);
push (@{$frag_atoms_1[$rot_i]},$atom2);
for $g(0..$#group2){
for $gs(0..$#{$group2_element[$g]}){
push (@{$frag_atoms[$rot_i]},$group2_element[$g][$gs]);
push (@{$frag_atoms_1[$rot_i]},$group2_element[$g][$gs]+1);
}
}
print RFGFILE "@{$frag_atoms_1[$rot_i]}\n";
close RFGFILE;
return $tot_frag2[$rot_i],@{$frag_atoms[$rot_i]};
}
sub connected {
my ($a,$b) = @_;
if (( $B[$a][$b] < Bond($A[$a],$A[$b]) && $B[$a][$b] > 0 ) || ($a+1 == $tsbond1 && $b+1 == $tsbond2) ||($a+1 == $tsbond2 && $b+1 == $tsbond1) || (($a+1 == $hbond1[1]) && ($b+1 == $hbond2[1])) || (($a+1 == $hbond2[1]) && ($b+1 == $hbond1[1])) || (($a+1 == $hbond1[2]) && ($b+1 == $hbond2[2])) || (($a+1 == $hbond2[2]) && ($b+1 == $hbond1[2]))|| (($a+1 == $hbond1[3]) && ($b+1 == $hbond2[3])) || (($a+1 == $hbond2[3]) && ($b+1 == $hbond1[3]))){
return 1;
}
else{
return 0;
}
}
sub dot {
my ($a,$b,$c) = @_;
return ($X[$a]-$X[$b])*($X[$c]-$X[$b])+($Y[$a]-$Y[$b])*($Y[$c]-$Y[$b])+($Z[$a]-$Z[$b])*($Z[$c]-$Z[$b]);
}
sub min {
my ($a,$b) = @_;
return $b < $a ? $b : $a;
}
sub max {
my ($a,$b) = @_;
return $b > $a ? $b : $a;
}
sub Bond {
my ($a1,$a2) = @_;
#CSD covalent radii (Rcov) are used to assign bonded connections in
#crystal structures. A bonded connection is established if the distance
#(d) between two elements A and B is in the range from Rcov(A) + Rcov(B)
#- t to Rcov(A) + Rcov(B) + t, where the tolerance (t) is usually set to
#0.4 A. The tolerance and Rcov values can be altered by CSD Editors to
#force bonds in certain situations. The Rcov values have been refined
#over the years to minimise the need for editorial changes for specific
#structures. Elements not yet encountered in the CSD have Rcov = 1.50 A.
%cov = ( xx => 0.0, h => 0.23, he => 1.50, li => 0.68, be => 0.35, b => 0.83,
c => 0.68, n => 0.68, o => 0.68, f => 0.64, ne => 1.50,
na => 0.97, mg => 1.10, al => 1.35, si => 1.20, p => 1.05,
s => 1.02, cl => 0.99, ar => 1.51, k => 1.33, ca => 0.99,
sc => 1.44, ti => 1.47, v => 1.33, cr => 1.35, mn => 1.35,
fe => 1.34, co => 1.33, ni => 1.50, cu => 1.52, zn => 1.45,
ga => 1.22, ge => 1.17, as => 1.21, se => 1.22, br => 1.21,
kr => 1.50, bi => 1.48, x => 0.00 , i => 1.40);
return $cov{lc($a1)}+$cov{lc($a2)} + 0.4 ;
}
sub ToSymbol {
my $n = shift;
#my @sym = qw/H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr/;
return $symbo[$n];
}
sub atomicN {
my ($a1) = @_;
my %index ;
@index{@symbo} = (0..$#symbo);
my $index = $index{lc($a1)} ;
return $index;
}
sub Rotate{
my ($atom1,$atom2,$theta) = @_;
# http://paulbourke.net/geometry/rotate/
# Rotate along an arbitray axis, in this case, the bond we selected. theta angle is 120 or 180 depends on how many $group are there on the bond, min(2,3)
my ($XX1,$YY1,$ZZ1) = ($original[$atom1-1]->[0][0],$original[$atom1-1]->[1][0],$original[$atom1-1]->[2][0]);
my ($XX2,$YY2,$ZZ2) = ($original[$atom2-1]->[0][0],$original[$atom2-1]->[1][0],$original[$atom2-1]->[2][0]);
$T = new Math::Matrix ([1.0,0.0,0.0,-$XX1 ],
[0.0,1.0,0.0,-$YY1 ],
[0.0,0.0,1.0,-$ZZ1 ],
[0.0,0.0,0.0,1.0 ]);
$Ti = new Math::Matrix ([1.0,0.0,0.0, $XX1 ],
[0.0,1.0,0.0, $YY1 ],
[0.0,0.0,1.0, $ZZ1 ],
[0.0,0.0,0.0, 1.0 ]);
$Vlength = sqrt( ($XX1-$XX2)**2+($YY1-$YY2)**2+($ZZ1-$ZZ2)**2 );
$Va = ($XX1-$XX2)/$Vlength;
$Vb = ($YY1-$YY2)/$Vlength;
$Vc = ($ZZ1-$ZZ2)/$Vlength;
$Vd = sqrt( $Vb**2 + $Vc**2 );
$Rx = new Math::Matrix ([1.0, 0.0 , 0.0,0.0 ],
[0.0, $Vc/$Vd, -$Vb/$Vd,0.0 ],
[0.0, $Vb/$Vd, $Vc/$Vd,0.0 ],
[0.0, 0.0, 0.0,1.0 ]);
$Rxi = new Math::Matrix ([1.0, 0.0, 0.0,0.0 ],
[0.0, $Vc/$Vd, $Vb/$Vd,0.0 ],
[0.0,-$Vb/$Vd, $Vc/$Vd,0.0 ],
[0.0, 0.0, 0.0,1.0 ]);
$Ry = new Math::Matrix ([$Vd, 0.0, -$Va,0.0 ],
[0.0, 1.0, 0.0,0.0 ],
[$Va, 0.0, $Vd,0.0 ],
[0.0, 0.0, 0.0,1.0 ]);
$Ryi = new Math::Matrix ([$Vd, 0.0, $Va,0.0 ],
[0.0, 1.0, 0.0,0.0 ],
[-$Va, 0.0, $Vd,0.0 ],
[0.0, 0.0, 0.0,1.0 ]);
$Rz = new Math::Matrix ([cos($theta),-sin($theta),0.0,0.0 ],
[sin($theta), cos($theta),0.0,0.0 ],
[0.0 ,0.0 ,1.0,0.0 ],
[0.0 ,0.0 ,0.0,1.0 ]);
# [x',y',z',1] = Ti * Rxi * Ryi * Rz * Ry * Rx * T * [x,y,z,1]
$TRRRRRT = Math::Matrix::multiply(Math::Matrix::multiply(Math::Matrix::multiply(Math::Matrix::multiply(Math::Matrix::multiply(Math::Matrix::multiply($Ti,$Rxi),$Ryi),$Rz),$Ry),$Rx),$T);
#$TRRRRRT->print("TRRRRRT,\n");
}
#############################################################################
## promptUser #
##############################################################################
#
##----------------------------( promptUser )-----------------------------#
## #
## FUNCTION: promptUser #
## #
## PURPOSE: Prompt the user for some type of input, and return the #
## input back to the calling program. #
## #
## ARGS: $promptString - what you want to prompt the user with #
## $defaultValue - (optional) a default value for the prompt #
## #
##-------------------------------------------------------------------------#
sub promptUser {
#-------------------------------------------------------------------#
# two possible input arguments - $promptString, and $defaultValue #
# make the input arguments local variables. #
#-------------------------------------------------------------------#
local($promptString,$defaultValue) = @_;
#-------------------------------------------------------------------#
# if there is a default value, use the first print statement; if #
# no default is provided, print the second string. #
#-------------------------------------------------------------------#
print $promptString, "[", $defaultValue, "]: ";
$| = 1; # force a flush after our print
$_ = <STDIN>; # get the input from STDIN (presumably the keyboard)
#------------------------------------------------------------------#
# remove the newline character from the end of the input the user #
# gave us. #
#------------------------------------------------------------------#
chomp;
#-----------------------------------------------------------------#
# if we had a $default value, and the user gave us input, then #
# return the input; if we had a default, and they gave us no #
# no input, return the $defaultValue. #
# #
# if we did not have a default value, then just return whatever #
# the user gave us. if they just hit the <enter> key, #
# the calling routine will have to deal with that. #
#-----------------------------------------------------------------#
return $_ ? $_ : $defaultValue; # return $_ if it has a value
}
package Iterator::Array::Jagged;
use strict;
use warnings 'all';
our $VERSION = '0.05';
#==============================================================================
sub new
{
my ($class, %args) = @_;
my $s = bless {
idx => [
map { 0 } 0...scalar(@{$args{data}}) - 1
],
sizes => [
map { scalar(@$_) - 1 } @{$args{data}}
],
data => $args{data},
_max => scalar(@{$args{data}}),
_is_finished => 0,
}, $class;
return $s;
}# end new()
#==============================================================================
sub _increment
{
my ($s, $index) = @_;
if( $s->{idx}->[ $index ] < $s->{sizes}->[ $index ] )
{
$s->{idx}->[ $index ]++;
}
else
{
$s->{idx}->[ $index ] = 0;
if( $index + 1 < $s->{_max} )
{
$s->_increment( $index + 1 );
}
else
{
$s->{_is_finished} = 1;
}# end if()
}# end if()
}# end _increment()
#==============================================================================
sub next
{
my ($s) = @_;
return if $s->{_is_finished};
# Calculate and return the current value:
my @parts = ();
for( 0...$s->{_max} - 1 )
{
my $part_idx = $s->{idx}->[ $_ ];
push @parts, $s->{data}->[ $_ ]->[ $part_idx ];
}# end for()
$s->_increment( 0 );
return @parts;
}# end next()
#==============================================================================
sub permute
{
my ($class, $func, @data) = @_;
my @idx = map { 0 } 0...scalar(@data) - 1;
my @sizes = map { scalar(@$_) - 1 } @data;
my $max = scalar(@data);
PERMUTATION: while( 1 )
{
# Prepare a 'set':
my @parts = ();
for my $num ( 0...$max - 1 )
{
push @parts, $data[ $num ]->[ $idx[ $num ] ];
}# end for()
# Execute 'func':
$func->( @parts );