| line |
true |
false |
branch |
|
74
|
0 |
245 |
defined $options && ref $options eq 'CODE' ? : |
|
75
|
35 |
210 |
unless defined $options and ref $options eq "HASH" |
|
85
|
228 |
17 |
unless exists $options->{'explicit_aromatic_bonds'} |
|
95
|
213 |
32 |
unless exists $options->{'explicit_parentheses'} |
|
106
|
238 |
7 |
unless exists $options->{'immediately_reuse_ring_numbers'} |
|
116
|
202 |
43 |
unless exists $options->{'remove_implicit_hydrogens'} |
|
127
|
198 |
47 |
unless exists $options->{'unsprout_hydrogens'} |
|
140
|
56 |
189 |
if $options->{'order_sub'} |
|
153
|
0 |
245 |
$options->{'write_atom_sub'} ? : |
|
161
|
20 |
225 |
if ref $what eq "HASH" |
|
163
|
200 |
25 |
ref $what eq 'ARRAY' ? : |
|
173
|
0 |
1328 |
if $seen{$v} |
|
193
|
1 |
244 |
if (@order != $graph->vertices) |
|
197
|
0 |
245 |
unless @order |
|
199
|
219 |
26 |
if ($options->{'unsprout_hydrogens'}) |
|
217
|
1146 |
90 |
unless &is_chiral($atom) |
|
218
|
2 |
13 |
unless &is_chiral_tetrahedral($atom) or &is_chiral_planar($atom) or &is_chiral_trigonal_bipyramidal($atom) or &is_chiral_octahedral($atom) |
|
225
|
75 |
13 |
if ($atom->{'chirality'} =~ /^@(\@?|SP[123])$/) |
|
226
|
0 |
75 |
if (scalar @neighbours < 3 or scalar @neighbours > 4) |
|
235
|
8 |
80 |
if ($atom->{'chirality'} =~ /^\@TB..?$/) |
|
236
|
0 |
8 |
if (scalar @neighbours < 4 or scalar @neighbours > 5) |
|
245
|
5 |
83 |
if ($atom->{'chirality'} =~ /^\@OH..?$/) |
|
246
|
0 |
5 |
if (scalar @neighbours < 5 or scalar @neighbours > 6) |
|
256
|
0 |
88 |
unless exists $atom->{'chirality_neighbours'} |
|
260
|
0 |
88 |
if (@neighbours != @chirality_neighbours) |
|
269
|
8 |
80 |
if ($has_lone_pair) |
|
287
|
88 |
0 |
if ($$rings{&$order_by_vertex($atom)}) |
|
301
|
71 |
17 |
if ($options->{'unsprout_hydrogens'}) |
|
302
|
194 |
16 |
if defined $_ |
|
|
57 |
14 |
if (&any(sub {
$_ < $order if defined $_;
}
, map({&$order_by_vertex($_);} @neighbours))) { } |
|
312
|
8 |
80 |
if ($has_lone_pair) |
|
319
|
69 |
19 |
if ($atom->{'chirality'} =~ /^\@\@?$/) { } |
|
|
6 |
13 |
elsif ($atom->{'chirality'} =~ /^\@SP[123]$/) { } |
|
|
8 |
5 |
elsif ($atom->{'chirality'} =~ /^\@TB..?$/) { } |
|
321
|
12 |
57 |
if (join("", _permutation_order(@permutation)) ne "0123") |
|
322
|
10 |
2 |
$chirality_now eq '@' ? : |
|
342
|
995 |
241 |
if ($discovered_from{$vertex}) |
|
343
|
385 |
610 |
if ($options->{'explicit_parentheses'} or _has_more_unseen_children($discovered_from{$vertex}, $i, $order_by_vertex, $graph, $rings)) |
|
349
|
88 |
1148 |
if ($chirality{$vertex}) { } |
|
360
|
233 |
1003 |
if ($rings->{$i}) |
|
363
|
77 |
77 |
if ($i < $j) { } |
|
364
|
0 |
77 |
unless (@ring_ids) |
|
373
|
77 |
0 |
$rings->{$i}{$j}{'ring'} < 10 ? : |
|
376
|
77 |
0 |
$rings->{$i}{$j}{'ring'} < 10 ? : |
|
377
|
71 |
6 |
if ($options->{'immediately_reuse_ring_numbers'}) { } |
|
379
|
0 |
71 |
unless ($a == 0) - ($b == 0) |
|
386
|
11 |
222 |
unless ($options->{'immediately_reuse_ring_numbers'}) |
|
387
|
0 |
11 |
unless ($a == 0) - ($b == 0) |
|
391
|
991 |
245 |
$i < $#order ? : |
|
393
|
385 |
606 |
if ($options->{'explicit_parentheses'} or _has_more_unseen_children($discovered_from{$vertex}, $i, $order_by_vertex, $graph, $rings)) |
|
414
|
0 |
88 |
unless @$A == @$B |
|
426
|
0 |
1256 |
unless $options |
|
436
|
3 |
1253 |
if (exists $vertex->{'isotope'}) |
|
441
|
1236 |
20 |
if (exists $options->{'chirality'}) { } |
|
|
0 |
20 |
elsif (&is_chiral($vertex)) { } |
|
442
|
88 |
1148 |
if ($options->{'chirality'}) |
|
451
|
6 |
1250 |
$vertex->{'hcount'} ? : |
|
452
|
998 |
238 |
if ($graph and $options->{'unsprout_hydrogens'} and $atom ne "H") |
|
458
|
429 |
28 |
if ($is_simple and $graph and not $raw and $Chemistry::OpenSMILES::Writer::normal_valence{ucfirst $atom} and not $vertex->{'charge'} and not $vertex->{'class'}) |
|
461
|
407 |
22 |
if (_has_unambiguous_normal_valence($graph, $vertex, $hcount)) { } |
|
463
|
366 |
41 |
if $options->{'remove_implicit_hydrogens'} |
|
470
|
49 |
1207 |
if ($hcount) |
|
471
|
31 |
18 |
$hcount == 1 ? : |
|
474
|
84 |
590 |
if $raw and exists $vertex->{'hcount'} |
|
476
|
12 |
1244 |
if ($vertex->{'charge'}) |
|
477
|
4 |
8 |
$vertex->{'charge'} > 0 ? : |
|
482
|
26 |
1230 |
if ($vertex->{'class'}) |
|
487
|
934 |
322 |
$is_simple ? : |
|
498
|
823 |
326 |
unless ($graph->has_edge_attribute($u, $v, "bond")) |
|
499
|
5 |
818 |
$n_aromatic == 2 ? : |
|
503
|
144 |
0 |
if $bond eq ":" and $n_aromatic and not $options->{'explicit_aromatic_bonds'} |
|
504
|
158 |
24 |
if $u->{'number'} < $v->{'number'} |
|
515
|
654 |
1088 |
if (defined &$order_by_vertex($vertex) and $$rings{&$order_by_vertex($vertex)}) |
|
526
|
0 |
429 |
unless exists $Chemistry::OpenSMILES::Writer::normal_valence{$element} |
|
530
|
21 |
408 |
unless $normal_valence |
|
544
|
3 |
89 |
if (scalar @_ != 4 or &any(sub {
not defined $_ && /^[0-3]$/;
}
, @_) or join(",", sort(@_)) ne "0,1,2,3") |
|
555
|
42 |
47 |
if ($_[0] != 0) |
|
570
|
0 |
6 |
if (join(",", sort(@_)) ne "0,1,2,3") |
|
582
|
3 |
3 |
if ($source[3] == $target[1]) |
|
588
|
3 |
3 |
if ($source[2] == $target[1]) |
|
594
|
3 |
3 |
if ($source[3] == $target[2]) |
|
608
|
0 |
4810 |
if (join(",", sort(@target)) ne "0,1,2,3,4") |
|
621
|
19240 |
4810 |
if $_ != $axis[0] |
|
626
|
19240 |
4810 |
if $_ != $axis[0] |
|
629
|
2402 |
2408 |
if ($axis_location[0] > $axis_location[1]) |
|
639
|
1203 |
1202 |
$order eq '@' ? : |
|
|
2405 |
2405 |
unless $sides[1] == $target[1] |
|
643
|
9614 |
40892 |
if $Chemistry::OpenSMILES::Writer::TB[$_]{'order'} eq $order and $Chemistry::OpenSMILES::Writer::TB[$_]{'axis'}[0] == $axis_location[0] + 1 |
|
653
|
0 |
43205 |
if (join(",", sort(@target)) ne "0,1,2,3,4,5") |
|
664
|
216025 |
43205 |
if $_ != $axis[0] |
|
666
|
14401 |
28804 |
if ($Chemistry::OpenSMILES::Writer::OH[$chirality - 1]{'shape'} eq "Z") |
|
670
|
14401 |
28804 |
if ($Chemistry::OpenSMILES::Writer::OH[$chirality - 1]{'shape'} eq 4) |
|
675
|
21604 |
21601 |
if $Chemistry::OpenSMILES::Writer::OH[$chirality - 1]{'order'} eq "\@" |
|
678
|
7201 |
36004 |
if ($axis[0] == $target[0]) { } |
|
|
7201 |
28803 |
elsif ($axis[1] == $target[0]) { } |
|
703
|
7201 |
36004 |
if ($target[0] == $sides[0] and $target[1] == $sides[1]) { } |
|
|
7201 |
28803 |
elsif ($target[0] == $sides[0] and $target[1] == $sides[2]) { } |
|
|
7200 |
21603 |
elsif ($target[0] == $sides[1] and $target[1] == $sides[0]) { } |
|
|
7202 |
14401 |
elsif ($target[0] == $sides[1] and $target[1] == $sides[2]) { } |
|
|
7200 |
7201 |
elsif ($target[0] == $sides[2] and $target[1] == $sides[0]) { } |
|
|
7201 |
0 |
elsif ($target[0] == $sides[2] and $target[1] == $sides[1]) { } |
|
720
|
129611 |
540043 |
if $Chemistry::OpenSMILES::Writer::OH[$_]{'shape'} eq $shape and $Chemistry::OpenSMILES::Writer::OH[$_]{'order'} eq $order |