I have a text files that consists of blocks of text. Each block of text represents a set of Cartesian coordinates for a molecule. Each block of text starts with a line that has a only a number, which is equal to the total number of atoms in the molecule. After this number is a line with "Frame #" where the # symbol is the number of the frame i.e. 1, 2, 3... This is line are the Cartesian coordinates, one set (x, y, z) per line. There are the same number of Cartesian coordinates as the number of atoms in the molecule.
Here is a sample:
14
Frame 1
Ir 0.4482 -1.2980 -0.2902
P 1.8759 -2.1654 1.4038
P -1.2305 -0.8418 -1.9134
H -2.5605 -0.7775 -1.4067
H -1.3820 -1.8515 -2.9058
H -1.1987 0.3321 -2.7223
H 2.5359 -3.3920 1.1065
H 1.2161 -2.5072 2.6182
H 2.9669 -1.3899 1.8960
C 1.3685 0.2571 -0.5341
O 1.9671 1.2795 -0.7004
Cl -0.8142 -3.4101 0.0318
H -0.8380 -0.5636 2.1141
H -1.0869 -0.4380 2.8141
14
Frame 2
Ir 0.4490 -1.2978 -0.2903
P 1.8738 -2.1613 1.4076
P -1.2367 -0.8359 -1.9047
H -2.5634 -0.7722 -1.3897
H -1.3955 -1.8409 -2.9008
H -1.2083 0.3415 -2.7087
H 2.5186 -3.3989 1.1226
H 1.2155 -2.4815 2.6289
H 2.9753 -1.3923 1.8863
C 1.3731 0.2542 -0.5394
O 1.9771 1.2723 -0.7122
Cl -0.8091 -3.4129 0.0288
H -0.9491 -0.6267 2.0929
H -1.2309 -0.4996 2.7795
.
.
.
14
Frame 72
Ir 0.2799 -1.1423 -0.0744
P 1.5830 -2.0634 1.6851
P -1.4956 -0.6824 -1.5757
H -2.5240 0.2145 -1.1716
H -2.2321 -1.8577 -1.8841
H -1.2106 -0.1808 -2.8791
H 2.8807 -2.5381 1.3446
H 0.9971 -3.2308 2.2364
H 1.8734 -1.3013 2.8541
C 1.7346 -0.5673 -1.1992
O 2.6174 -0.1436 -1.8621
Cl 0.2051 -3.5805 -0.9057
H 0.1695 0.2982 0.6158
H -0.9713 -1.5095 0.9427
I would like to be able to remove every other frame (which corresponds to a block of text that starts with number of atoms in the molecule, followed by the "Frame #" followed by the coordinates.
The trick is that not every file has the same number of atoms, so the script has to have a variable such that the user can tell it how many atoms are in the coordinates section and then it should remove every other block of data.
So I am trying to remove Frames 2, 4, 6, 8 and so on.
Thus the above sample would become:
14
Frame 1
Ir 0.4482 -1.2980 -0.2902
P 1.8759 -2.1654 1.4038
P -1.2305 -0.8418 -1.9134
H -2.5605 -0.7775 -1.4067
H -1.3820 -1.8515 -2.9058
H -1.1987 0.3321 -2.7223
H 2.5359 -3.3920 1.1065
H 1.2161 -2.5072 2.6182
H 2.9669 -1.3899 1.8960
C 1.3685 0.2571 -0.5341
O 1.9671 1.2795 -0.7004
Cl -0.8142 -3.4101 0.0318
H -0.8380 -0.5636 2.1141
H -1.0869 -0.4380 2.8141
.
.
.
Frame 71
Ir 0.2798 -1.1422 -0.0743
P 1.5833 -2.0636 1.6848
P -1.4955 -0.6824 -1.5761
H -2.5237 0.2149 -1.1727
H -2.2322 -1.8577 -1.8839
H -1.2099 -0.1819 -2.8797
H 2.8810 -2.5379 1.3438
H 0.9977 -3.2312 2.2359
H 1.8739 -1.3017 2.8539
C 1.7345 -0.5673 -1.1991
O 2.6175 -0.1439 -1.8621
Cl 0.2052 -3.5805 -0.9056
H 0.1693 0.2983 0.6159
H -0.9714 -1.5096 0.9427
Also, if possible, I would like also to be able to remove every 3rd frame as well.
By setting "Frame" as record separator , i must get rid off the leading line "^14$", i must adjust the offset of record, this is why the NR-1 instead of NR
This works exactly as you said, but is there a way to make it print blocks 1,3,5, 7 and 1,4,7,9 etc..?
---------- Post updated at 01:36 PM ---------- Previous update was at 01:29 PM ----------
Thanks for your reply but this doesn't work.
It seems that this command adds spaces into certain spots of the file at the begining but does remove the correct blocks towards the end. Here is the the first few blocks:
Frame 1
Rh -0.3793 -0.3188 -0.3617
C -1.4181 0.5185 -1.7491
P 1.8313 -0.3365 -1.4708
H 2.0493 0.2251 -2.7751
H 2.9159 0.3283 -0.8096
H 2.5143 -1.5807 -1.7041
P -1.0881 -2.6725 -0.6945
H -0.1078 -3.7030 -0.9106
H -1.7533 -3.3073 0.4056
H -2.0033 -3.0952 -1.7185
H 0.4760 -0.9847 0.8641
O -2.0655 1.0426 -2.5964
C -1.5647 0.4833 1.2803
C -0.4855 1.3783 1.0023
H -2.5722 0.7321 0.9603
H -1.5075 -0.1757 2.1410
H -0.6724 2.3044 0.4670
H 0.3854 1.3885 1.6488
18
Frame 2
Rh -0.3799 -0.3194 -0.3618
C -1.4163 0.5199 -1.7496
P 1.8296 -0.3352 -1.4732
H 2.0452 0.2282 -2.7771
H 2.9144 0.3296 -0.8125
H 2.5134 -1.5785 -1.7089
P -1.0872 -2.6741 -0.6913
H -0.1063 -3.7039 -0.9069
H -1.7499 -3.3073 0.4112
H -2.0037 -3.0998 -1.7128
H 0.4765 -0.9847 0.8635
O -2.0594 1.0478 -2.5979
C -1.5655 0.4814 1.2805
C -0.4871 1.3774 1.0028
H -2.5732 0.7295 0.9607
H -1.5077 -0.1779 2.1409
H -0.6748 2.3035 0.4679
H 0.3839 1.3880 1.6492
and here are the blocks at the end:
Frame 287
Rh -0.4360 -0.2696 -0.6220
C -1.1646 1.0045 -1.7330
P 1.7166 -0.5355 -1.8645
H 1.8842 0.0740 -3.1515
H 2.8434 0.0882 -1.2285
H 2.3789 -1.7764 -2.1787
P -0.6673 -2.6176 0.1277
H 0.3305 -3.6308 0.3709
H -1.4676 -2.8685 1.2952
H -1.4465 -3.3795 -0.8014
H -0.3658 -0.4659 2.3069
O -1.7130 1.6942 -2.5406
C -1.8697 0.1962 0.8475
C -0.9955 0.4085 2.0867
H -2.4370 1.0967 0.5998
H -2.5883 -0.6253 0.9828
H -0.3321 1.2698 1.9625
H -1.6058 0.5920 2.9832
18
Frame 289
Rh -0.4362 -0.2701 -0.6236
C -1.1618 1.0091 -1.7307
P 1.7142 -0.5392 -1.8686
H 1.8803 0.0675 -3.1571
H 2.8442 0.0827 -1.2365
H 2.3725 -1.7824 -2.1820
P -0.6607 -2.6166 0.1343
H 0.3410 -3.6262 0.3757
H -1.4536 -2.8644 1.3074
H -1.4437 -3.3837 -0.7873
H -0.3808 -0.4699 2.3130
O -1.7083 1.7048 -2.5345
C -1.8742 0.1934 0.8435
C -1.0063 0.4059 2.0871
H -2.4418 1.0934 0.5946
H -2.5926 -0.6289 0.9752
H -0.3391 1.2644 1.9635
H -1.6207 0.5944 2.9797
18
Frame 291
Rh -0.4365 -0.2705 -0.6252
C -1.1590 1.0137 -1.7283
P 1.7117 -0.5429 -1.8727
H 1.8763 0.0608 -3.1628
H 2.8450 0.0772 -1.2446
H 2.3659 -1.7885 -2.1852
P -0.6541 -2.6156 0.1410
H 0.3512 -3.6217 0.3813
H -1.4405 -2.8599 1.3191
H -1.4403 -3.3880 -0.7734
H -0.3944 -0.4731 2.3185
O -1.7034 1.7154 -2.5282
C -1.8788 0.1901 0.8395
C -1.0170 0.4034 2.0873
H -2.4472 1.0893 0.5894
H -2.5964 -0.6335 0.9678
H -0.3474 1.2601 1.9648
H -1.6358 0.5956 2.9761
As you can see, it does remove every second block at the end but it also adds in spaces for some reason...
---------- Post updated at 01:39 PM ---------- Previous update was at 01:36 PM ----------
Thanks for your suggestion. This does remove blocks of text but it seems it is removing 2 or 3 or 4 blocks rather than removing every second block.
Here is a sample:
Frame 1
Rh -0.3793 -0.3188 -0.3617
C -1.4181 0.5185 -1.7491
P 1.8313 -0.3365 -1.4708
H 2.0493 0.2251 -2.7751
H 2.9159 0.3283 -0.8096
H 2.5143 -1.5807 -1.7041
P -1.0881 -2.6725 -0.6945
H -0.1078 -3.7030 -0.9106
H -1.7533 -3.3073 0.4056
H -2.0033 -3.0952 -1.7185
H 0.4760 -0.9847 0.8641
O -2.0655 1.0426 -2.5964
C -1.5647 0.4833 1.2803
C -0.4855 1.3783 1.0023
H -2.5722 0.7321 0.9603
H -1.5075 -0.1757 2.1410
H -0.6724 2.3044 0.4670
H 0.3854 1.3885 1.6488
18
Frame 5
Rh -0.3814 -0.3213 -0.3621
C -1.4104 0.5238 -1.7517
P 1.8239 -0.3291 -1.4809
H 2.0315 0.2434 -2.7820
H 2.9094 0.3353 -0.8209
H 2.5109 -1.5685 -1.7278
P -1.0864 -2.6784 -0.6804
H -0.1049 -3.7078 -0.8957
H -1.7414 -3.3064 0.4296
H -2.0081 -3.1123 -1.6940
H 0.4791 -0.9850 0.8613
O -2.0384 1.0622 -2.6046
C -1.5674 0.4749 1.2816
C -0.4913 1.3740 1.0054
H -2.5758 0.7210 0.9626
H -1.5076 -0.1858 2.1409
H -0.6814 2.3004 0.4719
H 0.3800 1.3854 1.6513
18
Frame 7
Rh -0.3823 -0.3227 -0.3624
C -1.4064 0.5263 -1.7531
P 1.8201 -0.3247 -1.4859
H 2.0225 0.2538 -2.7852
H 2.9058 0.3396 -0.8263
H 2.5096 -1.5612 -1.7402
P -1.0862 -2.6812 -0.6731
H -0.1046 -3.7105 -0.8884
H -1.7358 -3.3054 0.4422
H -2.0117 -3.1204 -1.6809
H 0.4809 -0.9852 0.8597
O -2.0243 1.0716 -2.6091
C -1.5686 0.4703 1.2824
C -0.4940 1.3715 1.0071
H -2.5775 0.7151 0.9639
H -1.5074 -0.1914 2.1408
H -0.6858 2.2982 0.4746
H 0.3775 1.3835 1.6527
18
Frame 11
Rh -0.3843 -0.3255 -0.3630
C -1.3984 0.5314 -1.7560
P 1.8126 -0.3158 -1.4960
H 2.0050 0.2739 -2.7918
H 2.8983 0.3492 -0.8369
H 2.5076 -1.5464 -1.7639
P -1.0859 -2.6867 -0.6582
H -0.1046 -3.7161 -0.8740
H -1.7243 -3.3027 0.4680
H -2.0199 -3.1361 -1.6538
H 0.4848 -0.9857 0.8561
O -1.9959 1.0901 -2.6179
C -1.5709 0.4610 1.2839
C -0.4995 1.3664 1.0108
H -2.5808 0.7031 0.9666
H -1.5070 -0.2029 2.1405
H -0.6944 2.2936 0.4804
H 0.3725 1.3793 1.6557
.
.
.
Hi on my system my suggestion prints
m=2: 1,3,5,7 . so 2,4,6,.. are deleted
m=3: 1,2,4,5,7 .. so 3,6,9.... are deleted
etc..
Does it not do that on your system? What platform are you on?
I meant to remove 2,4,6,8.... and then output this as only file. This essentially cuts the total number of frames by half.
Another option would be to remove frames 3,6,9,12... and then output this as a different file. This essentially cuts the total number of frames by a third.
You have to tell more about what you want to keep or exclude :
Do you want to keep Frames that are multiple of 3 ( Frame 6 and Frame 9 ) ???
or you want to display Frame 9 but exclude Frame 6 ???
Of course if we use a formula that filter out all multiple of 3 , the Frame 9 will be filtered out ...
# awk -F"\n" -vRS="Frame" -vORS="Frame" 'BEGIN{printf "%s",RS};((NR-1)%3==1)' infile
Frame 1
Ir 0.4482 -1.2980 -0.2902
H -0.8380 -0.5636 2.1141
...
H -1.0869 -0.4380 2.8141
14
Frame 4
Ir 0.2799 -1.1423 -0.0744
P 1.5830 -2.0634 1.6851
P -1.4956 -0.6824 -1.5757
H -2.5240 0.2145 -1.1716
14
Frame 7
Ir 0.2799 -1.1423 -0.0744
P 1.5830 -2.0634 1.6851
14
Frame 10
Ir 0.2799 -1.1423 -0.0744
P 1.5830 -2.0634 1.6851
14
#
---------- Post updated at 07:23 PM ---------- Previous update was at 07:20 PM ----------
$
$
$ # show the content of the input data file "f1"
$ cat f1
14
Frame 1
Ir 0.4482 -1.2980 -0.2902
P 1.8759 -2.1654 1.4038
P -1.2305 -0.8418 -1.9134
H -2.5605 -0.7775 -1.4067
H -1.3820 -1.8515 -2.9058
H -1.1987 0.3321 -2.7223
H 2.5359 -3.3920 1.1065
H 1.2161 -2.5072 2.6182
H 2.9669 -1.3899 1.8960
C 1.3685 0.2571 -0.5341
O 1.9671 1.2795 -0.7004
Cl -0.8142 -3.4101 0.0318
H -0.8380 -0.5636 2.1141
H -1.0869 -0.4380 2.8141
14
Frame 2
Ir 0.4490 -1.2978 -0.2903
P 1.8738 -2.1613 1.4076
P -1.2367 -0.8359 -1.9047
H -2.5634 -0.7722 -1.3897
H -1.3955 -1.8409 -2.9008
H -1.2083 0.3415 -2.7087
H 2.5186 -3.3989 1.1226
H 1.2155 -2.4815 2.6289
H 2.9753 -1.3923 1.8863
C 1.3731 0.2542 -0.5394
O 1.9771 1.2723 -0.7122
Cl -0.8091 -3.4129 0.0288
H -0.9491 -0.6267 2.0929
H -1.2309 -0.4996 2.7795
14
Frame 3
Ir 0.2799 -1.1423 -0.0744
P 1.5830 -2.0634 1.6851
P -1.4956 -0.6824 -1.5757
H -2.5240 0.2145 -1.1716
H -2.2321 -1.8577 -1.8841
H -1.2106 -0.1808 -2.8791
H 2.8807 -2.5381 1.3446
H 0.9971 -3.2308 2.2364
H 1.8734 -1.3013 2.8541
C 1.7346 -0.5673 -1.1992
O 2.6174 -0.1436 -1.8621
Cl 0.2051 -3.5805 -0.9057
H 0.1695 0.2982 0.6158
H -0.9713 -1.5095 0.9427
14
Frame 4
Ir 0.1111 -1.1111 -0.1111
P 1.2222 -2.2222 1.2222
P -1.3333 -0.3333 -1.3333
H -2.4444 0.4444 -1.4444
H -2.5555 -1.5555 -1.5555
H -1.6666 -0.6666 -2.6666
H 2.7777 -2.7777 1.7777
H 0.8888 -3.8888 2.8888
H 1.9999 -1.9999 2.9999
C 1.1010 -0.1010 -1.1010
O 2.1111 -0.1111 -1.1111
Cl 0.1212 -3.1212 -0.1212
H 0.1313 0.1313 0.1313
H -0.1414 -1.1414 0.1414
14
Frame 5
Ir 0.1515 -1.1515 -0.1515
P 1.1616 -2.1616 1.1616
P -1.1717 -0.1717 -1.1717
H -2.1818 0.1818 -1.1818
H -2.1919 -1.1919 -1.1919
H -1.2020 -0.2020 -2.2020
H 2.2121 -2.2121 1.2121
H 0.2222 -3.2222 2.2222
H 1.2323 -1.2323 2.2323
C 1.2424 -0.2424 -1.2424
O 2.2525 -0.2525 -1.2525
Cl 0.2626 -3.2626 -0.2626
H 0.2727 0.2727 0.2727
H -0.2828 -1.2828 0.2828
14
Frame 6
Ir 0.2929 -1.2929 -0.2929
P 1.3030 -2.3030 1.3030
P -1.3131 -0.3131 -1.3131
H -2.3232 0.3232 -1.3232
H -2.3333 -1.3333 -1.3333
H -1.3434 -0.3434 -2.3434
H 2.3535 -2.3535 1.3535
H 0.3636 -3.3636 2.3636
H 1.3737 -1.3737 2.3737
C 1.3838 -0.3838 -1.3838
O 2.3939 -0.3939 -1.3939
Cl 0.4040 -3.4040 -0.4040
H 0.4141 0.4141 0.4141
H -0.4242 -1.4242 0.4242
$
$
$ # show the content of the Perl program "f1.pl"
$
$ cat -n f1.pl
1 #!perl -w
2 print "Enter number of atoms: ";
3 chomp($x = <STDIN>);
4 print "Enter <n> if every nth frame is to be removed: ";
5 chomp($y = <STDIN>);
6 $file = "f1";
7 open (F, "f1") or die "Can't open $file: $!";
8 while (<F>) { # iterate through the records
9 chomp; # chomp newline
10 if (/^\d+$/) { # if the number is here all by itself
11 $atoms = $_; # then it is the number of atoms
12 $iter = 1; # initialize the iterator
13 $show = 0; # don't show/print the records just yet
14 } elsif (/^Frame (\d+)$/ and $1%$y != 0) { # if the frame number is not a multiple of <n>
15 print $atoms,"\n"; # then print the number of atoms
16 print $_,"\n"; # and print the current line
17 $show = 1; # and set the flag so that the block could be printed
18 } elsif ($show and $iter <= $x) { # if flag is set and we haven't reached the upper limit
19 print $_,"\n"; # then keep printing the record
20 $iter++; # and incrementing the iterator
21 }
22 }
23 close (F) or die "Can't close $file: $!"; # clean up after ourselves
$
$
$ # test the Perl program
$
$ perl f1.pl
Enter number of atoms: 14
Enter <n> if every nth frame is to be removed: 2
14
Frame 1
Ir 0.4482 -1.2980 -0.2902
P 1.8759 -2.1654 1.4038
P -1.2305 -0.8418 -1.9134
H -2.5605 -0.7775 -1.4067
H -1.3820 -1.8515 -2.9058
H -1.1987 0.3321 -2.7223
H 2.5359 -3.3920 1.1065
H 1.2161 -2.5072 2.6182
H 2.9669 -1.3899 1.8960
C 1.3685 0.2571 -0.5341
O 1.9671 1.2795 -0.7004
Cl -0.8142 -3.4101 0.0318
H -0.8380 -0.5636 2.1141
H -1.0869 -0.4380 2.8141
14
Frame 3
Ir 0.2799 -1.1423 -0.0744
P 1.5830 -2.0634 1.6851
P -1.4956 -0.6824 -1.5757
H -2.5240 0.2145 -1.1716
H -2.2321 -1.8577 -1.8841
H -1.2106 -0.1808 -2.8791
H 2.8807 -2.5381 1.3446
H 0.9971 -3.2308 2.2364
H 1.8734 -1.3013 2.8541
C 1.7346 -0.5673 -1.1992
O 2.6174 -0.1436 -1.8621
Cl 0.2051 -3.5805 -0.9057
H 0.1695 0.2982 0.6158
H -0.9713 -1.5095 0.9427
14
Frame 5
Ir 0.1515 -1.1515 -0.1515
P 1.1616 -2.1616 1.1616
P -1.1717 -0.1717 -1.1717
H -2.1818 0.1818 -1.1818
H -2.1919 -1.1919 -1.1919
H -1.2020 -0.2020 -2.2020
H 2.2121 -2.2121 1.2121
H 0.2222 -3.2222 2.2222
H 1.2323 -1.2323 2.2323
C 1.2424 -0.2424 -1.2424
O 2.2525 -0.2525 -1.2525
Cl 0.2626 -3.2626 -0.2626
H 0.2727 0.2727 0.2727
H -0.2828 -1.2828 0.2828
$
$
$ # once more
$
$ perl f1.pl
Enter number of atoms: 14
Enter <n> if every nth frame is to be removed: 3
14
Frame 1
Ir 0.4482 -1.2980 -0.2902
P 1.8759 -2.1654 1.4038
P -1.2305 -0.8418 -1.9134
H -2.5605 -0.7775 -1.4067
H -1.3820 -1.8515 -2.9058
H -1.1987 0.3321 -2.7223
H 2.5359 -3.3920 1.1065
H 1.2161 -2.5072 2.6182
H 2.9669 -1.3899 1.8960
C 1.3685 0.2571 -0.5341
O 1.9671 1.2795 -0.7004
Cl -0.8142 -3.4101 0.0318
H -0.8380 -0.5636 2.1141
H -1.0869 -0.4380 2.8141
14
Frame 2
Ir 0.4490 -1.2978 -0.2903
P 1.8738 -2.1613 1.4076
P -1.2367 -0.8359 -1.9047
H -2.5634 -0.7722 -1.3897
H -1.3955 -1.8409 -2.9008
H -1.2083 0.3415 -2.7087
H 2.5186 -3.3989 1.1226
H 1.2155 -2.4815 2.6289
H 2.9753 -1.3923 1.8863
C 1.3731 0.2542 -0.5394
O 1.9771 1.2723 -0.7122
Cl -0.8091 -3.4129 0.0288
H -0.9491 -0.6267 2.0929
H -1.2309 -0.4996 2.7795
14
Frame 4
Ir 0.1111 -1.1111 -0.1111
P 1.2222 -2.2222 1.2222
P -1.3333 -0.3333 -1.3333
H -2.4444 0.4444 -1.4444
H -2.5555 -1.5555 -1.5555
H -1.6666 -0.6666 -2.6666
H 2.7777 -2.7777 1.7777
H 0.8888 -3.8888 2.8888
H 1.9999 -1.9999 2.9999
C 1.1010 -0.1010 -1.1010
O 2.1111 -0.1111 -1.1111
Cl 0.1212 -3.1212 -0.1212
H 0.1313 0.1313 0.1313
H -0.1414 -1.1414 0.1414
14
Frame 5
Ir 0.1515 -1.1515 -0.1515
P 1.1616 -2.1616 1.1616
P -1.1717 -0.1717 -1.1717
H -2.1818 0.1818 -1.1818
H -2.1919 -1.1919 -1.1919
H -1.2020 -0.2020 -2.2020
H 2.2121 -2.2121 1.2121
H 0.2222 -3.2222 2.2222
H 1.2323 -1.2323 2.2323
C 1.2424 -0.2424 -1.2424
O 2.2525 -0.2525 -1.2525
Cl 0.2626 -3.2626 -0.2626
H 0.2727 0.2727 0.2727
H -0.2828 -1.2828 0.2828
$
$
$
I don't know if I am doing something wrong, but it doesn't work on my end.
Any suggestions to try and log what is going wrong?
---------- Post updated at 07:57 AM ---------- Previous update was at 07:54 AM ----------
Would it be possible to modify any of the suggestions so far such that frames 2,3,5,6,8,9,11,12, etc would be removed and the output file would have only frames 1,4,7,10,13,16,19,...etc?
This would remove 2 frames at a time instead of one.
Many many thanks to all of you for your help with this.
You could pass a comma-delimited list of frame numbers that should not be displayed. Frame numbers not in the list would be displayed by default.
$
$
$ cat -n frames1.pl
1 #!perl -w
2 print "Enter number of atoms: ";
3 chomp($x = <STDIN>);
4 print "Enter comma-delimited list of frame nos. that should be removed: ";
5 chomp($y = <STDIN>);
6 @noshow = split(",", $y); # store non-displaying frames in array @noshow
7 $file = "frames";
8 open (F, "frames") or die "Can't open $file: $!";
9 while (<F>) { # iterate through the records
10 chomp; # chomp newline
11 if (/^\d+$/) { # if the number is here all by itself
12 $atoms = $_; # then it is the number of atoms
13 $iter = 1; # initialize the iterator
14 $show = 0; # don't show/print the records just yet
15 } elsif (/^Frame (\d+)$/) { # if this line has the Frame number
16 if (grep(/^$1$/,@noshow) == 0) { # that should be displayed
17 print $atoms,"\n"; # then print the number of atoms
18 print $_,"\n"; # and print the current line
19 $show = 1; # and set the flag so that the block could be printed
20 }
21 } elsif ($show and $iter <= $x) { # if flag is set and we haven't reached the upper limit
22 print $_,"\n"; # then keep printing the record
23 $iter++; # and incrementing the iterator
24 }
25 }
26 close (F) or die "Can't close $file: $!"; # clean up after ourselves
$
$ perl frames1.pl
Enter number of atoms: 14
Enter comma-delimited list of frame nos. that should be removed: 2,3,5
14
Frame 1
Ir 0.4482 -1.2980 -0.2902
P 1.8759 -2.1654 1.4038
P -1.2305 -0.8418 -1.9134
H -2.5605 -0.7775 -1.4067
H -1.3820 -1.8515 -2.9058
H -1.1987 0.3321 -2.7223
H 2.5359 -3.3920 1.1065
H 1.2161 -2.5072 2.6182
H 2.9669 -1.3899 1.8960
C 1.3685 0.2571 -0.5341
O 1.9671 1.2795 -0.7004
Cl -0.8142 -3.4101 0.0318
H -0.8380 -0.5636 2.1141
H -1.0869 -0.4380 2.8141
14
Frame 4
Ir 0.1111 -1.1111 -0.1111
P 1.2222 -2.2222 1.2222
P -1.3333 -0.3333 -1.3333
H -2.4444 0.4444 -1.4444
H -2.5555 -1.5555 -1.5555
H -1.6666 -0.6666 -2.6666
H 2.7777 -2.7777 1.7777
H 0.8888 -3.8888 2.8888
H 1.9999 -1.9999 2.9999
C 1.1010 -0.1010 -1.1010
O 2.1111 -0.1111 -1.1111
Cl 0.1212 -3.1212 -0.1212
H 0.1313 0.1313 0.1313
H -0.1414 -1.1414 0.1414
14
Frame 6
Ir 0.2929 -1.2929 -0.2929
P 1.3030 -2.3030 1.3030
P -1.3131 -0.3131 -1.3131
H -2.3232 0.3232 -1.3232
H -2.3333 -1.3333 -1.3333
H -1.3434 -0.3434 -2.3434
H 2.3535 -2.3535 1.3535
H 0.3636 -3.3636 2.3636
H 1.3737 -1.3737 2.3737
C 1.3838 -0.3838 -1.3838
O 2.3939 -0.3939 -1.3939
Cl 0.4040 -3.4040 -0.4040
H 0.4141 0.4141 0.4141
H -0.4242 -1.4242 0.4242
$
$
tyler_durden
---------- Post updated at 11:46 AM ---------- Previous update was at 11:13 AM ----------
In the script posted earlier, it might be a tad cumbersome to input a comma-delimited list of all frame numbers that should not be displayed.
If "S" means "Show" and "NS" means "(Do) Not Show", then you could input the smallest non-repeating display pattern to the script. And the script can keep on implementing the pattern for all the frames.
For example, if the input pattern is "S,NS,NS", then it means:
(1) Show block 1.
(2) Do not show block 2.
(3) Do not show block 3.
(4) Repeat the above pattern (i.e. "S,NS,NS") for each block of 3 frames that follows.
You could come up with more complex patterns for varying block counts.
For example, an input pattern of "S,NS,NS,NS,S" means -
(1) Show block 1.
(2) Do not show block 2.
(3) Do not show block 3.
(4) Do not show block 4.
(5) Show block 5.
------
(6) Show block 6.
(7) Do not show block 7.
(8) Do not show block 8.
(9) Do not show block 9.
(10) Show block 10.
------
and so on...
The boundary condition - "S" means "show all blocks" and "NS" means "do not show any block".
Here's the code -
$
$
$ cat -n frames2.pl
1 #!perl -w
2 print "Enter number of atoms: ";
3 chomp($x = <STDIN>);
4 print "Enter comma-delimited display pattern: ";
5 chomp($y = <STDIN>);
6 @action = split(",", $y); # store the "show/noshow" action in an array
7 @acopy = @action; # copy the array because we'll modify the original
8 $file = "frames";
9 open (F, "frames") or die "Can't open $file: $!";
10 while (<F>) { # iterate through the records
11 chomp; # chomp newline
12 if (/^\d+$/) { # if the number is here all by itself
13 $atoms = $_; # then it is the number of atoms
14 $iter = 1; # initialize the iterator
15 $show = 0; # don't show/print the records just yet
16 } elsif (/^Frame (\d+)$/) { # if this line has the Frame number
17 $act = shift @action; # then pick up an element from array @action
18 if ($act eq "S") { # if this action is "Show"
19 print $atoms,"\n"; # then print the number of atoms
20 print $_,"\n"; # and print the current line
21 $show = 1; # and set the flag so that the block could be printed
22 }
23 if ($#action == -1) { # if the original array @action is empty
24 @action = @acopy; # then replenish it
25 }
26 } elsif ($show and $iter <= $x) { # if flag is set and we haven't reached the upper limit
27 print $_,"\n"; # then keep printing the record
28 $iter++; # and incrementing the iterator
29 }
30 }
31 close (F) or die "Can't close $file: $!"; # clean up after ourselves
$
$
$ perl frames2.pl
Enter number of atoms: 14
Enter comma-delimited display pattern: S,NS,NS
14
Frame 1
Ir 0.4482 -1.2980 -0.2902
P 1.8759 -2.1654 1.4038
P -1.2305 -0.8418 -1.9134
H -2.5605 -0.7775 -1.4067
H -1.3820 -1.8515 -2.9058
H -1.1987 0.3321 -2.7223
H 2.5359 -3.3920 1.1065
H 1.2161 -2.5072 2.6182
H 2.9669 -1.3899 1.8960
C 1.3685 0.2571 -0.5341
O 1.9671 1.2795 -0.7004
Cl -0.8142 -3.4101 0.0318
H -0.8380 -0.5636 2.1141
H -1.0869 -0.4380 2.8141
14
Frame 4
Ir 0.1111 -1.1111 -0.1111
P 1.2222 -2.2222 1.2222
P -1.3333 -0.3333 -1.3333
H -2.4444 0.4444 -1.4444
H -2.5555 -1.5555 -1.5555
H -1.6666 -0.6666 -2.6666
H 2.7777 -2.7777 1.7777
H 0.8888 -3.8888 2.8888
H 1.9999 -1.9999 2.9999
C 1.1010 -0.1010 -1.1010
O 2.1111 -0.1111 -1.1111
Cl 0.1212 -3.1212 -0.1212
H 0.1313 0.1313 0.1313
H -0.1414 -1.1414 0.1414
$
$
$ perl frames2.pl
Enter number of atoms: 14
Enter comma-delimited display pattern: S,NS
14
Frame 1
Ir 0.4482 -1.2980 -0.2902
P 1.8759 -2.1654 1.4038
P -1.2305 -0.8418 -1.9134
H -2.5605 -0.7775 -1.4067
H -1.3820 -1.8515 -2.9058
H -1.1987 0.3321 -2.7223
H 2.5359 -3.3920 1.1065
H 1.2161 -2.5072 2.6182
H 2.9669 -1.3899 1.8960
C 1.3685 0.2571 -0.5341
O 1.9671 1.2795 -0.7004
Cl -0.8142 -3.4101 0.0318
H -0.8380 -0.5636 2.1141
H -1.0869 -0.4380 2.8141
14
Frame 3
Ir 0.2799 -1.1423 -0.0744
P 1.5830 -2.0634 1.6851
P -1.4956 -0.6824 -1.5757
H -2.5240 0.2145 -1.1716
H -2.2321 -1.8577 -1.8841
H -1.2106 -0.1808 -2.8791
H 2.8807 -2.5381 1.3446
H 0.9971 -3.2308 2.2364
H 1.8734 -1.3013 2.8541
C 1.7346 -0.5673 -1.1992
O 2.6174 -0.1436 -1.8621
Cl 0.2051 -3.5805 -0.9057
H 0.1695 0.2982 0.6158
H -0.9713 -1.5095 0.9427
14
Frame 5
Ir 0.1515 -1.1515 -0.1515
P 1.1616 -2.1616 1.1616
P -1.1717 -0.1717 -1.1717
H -2.1818 0.1818 -1.1818
H -2.1919 -1.1919 -1.1919
H -1.2020 -0.2020 -2.2020
H 2.2121 -2.2121 1.2121
H 0.2222 -3.2222 2.2222
H 1.2323 -1.2323 2.2323
C 1.2424 -0.2424 -1.2424
O 2.2525 -0.2525 -1.2525
Cl 0.2626 -3.2626 -0.2626
H 0.2727 0.2727 0.2727
H -0.2828 -1.2828 0.2828
$
$
$ perl frames2.pl
Enter number of atoms: 14
Enter comma-delimited display pattern: NS
$
$
$
$
