package Chemistry::Canonicalize; # $Id: Canonicalize.pm,v 1.2 2009/05/10 20:16:22 itubert Exp $ $VERSION = '0.11'; use strict; use warnings; use Math::BigInt; use Carp; use base 'Exporter'; our @EXPORT_OK = qw(canonicalize); our %EXPORT_TAGS = ( all => \@EXPORT_OK ); =head1 NAME Chemistry::Canonicalize - Number the atoms in a molecule in a unique way =head1 SYNOPSIS use Chemistry::Canonicalize ':all'; # $mol is a Chemistry::Mol object canonicalize($mol); print "The canonical number for atom 1 is: ", $mol->atoms(1)->attr("canon/class"); print "The symmetry class for for atom 1 is: ", $mol->atoms(1)->attr("canon/symmetry_class"); =head1 DESCRIPTION This module provides functions for "canonicalizing" a molecular structure; that is, to number the atoms in a unique way regardless of the input order. The canonicalization algorithm is based on: Weininger, et. al., J. Chem. Inf. Comp. Sci. 29[2], 97-101 (1989) This module is part of the PerlMol project, L. =head1 ATOM ATTRIBUTES During the canonicalization process, the following attributes are set on each atom: =over =item canon/class The unique canonical number; it is an integer going from 1 to the number of atoms. =item canon/symmetry_class The symmetry class number. Atoms that have the same symmetry class are considered to be topologicaly equivalent. For example, the two methyl carbons on 2-propanol would have the same symmetry class. =back =head1 FUNCTIONS These functions may be exported, although nothing is exported by default. =over =cut my @PRIMES = qw( 1 2 3 5 7 11 13 17 19 23 29 31 37 41 43 47 53 59 61 67 71 73 79 83 89 97 101 103 107 109 113 127 131 137 139 149 151 157 163 167 173 179 181 191 193 197 199 211 223 227 229 233 239 241 251 257 263 269 271 277 281 283 293 307 311 313 317 331 337 347 349 353 359 367 373 379 383 389 397 401 409 419 421 431 433 439 443 449 457 461 463 467 479 487 491 499 503 509 521 523 541 547 557 563 569 571 577 587 593 599 601 607 613 617 619 631 641 643 647 653 659 661 673 677 683 691 701 709 719 727 733 739 743 751 757 761 769 773 787 797 809 811 821 823 827 829 839 853 857 859 863 877 881 883 887 907 911 919 929 937 941 947 953 967 971 977 983 991 997 1009 1013 1019 1021 1031 1033 1039 1049 1051 1061 1063 1069 1087 1091 1093 1097 1103 1109 1117 1123 1129 1151 1153 1163 1171 1181 1187 1193 1201 1213 1217 1223 1229 1231 1237 1249 1259 1277 1279 1283 1289 1291 1297 1301 1303 1307 1319 1321 1327 1361 1367 1373 1381 1399 1409 1423 1427 1429 1433 1439 1447 1451 1453 1459 1471 1481 1483 1487 1489 1493 1499 1511 1523 1531 1543 1549 1553 1559 1567 1571 1579 1583 1597 1601 1607 1609 1613 1619 1621 1627 1637 1657 1663 1667 1669 1693 1697 1699 1709 1721 1723 1733 1741 1747 1753 1759 1777 1783 1787 1789 1801 1811 1823 1831 1847 1861 1867 1871 1873 1877 1879 1889 1901 1907 1913 1931 1933 1949 1951 1973 1979 1987 1993 1997 1999 2003 2011 2017 2027 2029 2039 2053 2063 2069 2081 2083 2087 2089 2099 2111 2113 2129 2131 2137 2141 2143 2153 2161 2179 2203 2207 2213 2221 2237 2239 2243 2251 2267 2269 2273 2281 2287 2293 2297 2309 2311 2333 2339 2341 2347 2351 2357 2371 2377 2381 2383 2389 2393 2399 2411 2417 2423 2437 2441 2447 2459 2467 2473 2477 2503 2521 2531 2539 2543 2549 2551 2557 2579 2591 2593 2609 2617 2621 2633 2647 2657 2659 2663 2671 2677 2683 2687 2689 2693 2699 2707 2711 2713 2719 2729 2731 2741 2749 2753 2767 2777 2789 2791 2797 2801 2803 2819 2833 2837 2843 2851 2857 2861 2879 2887 2897 2903 2909 2917 2927 2939 2953 2957 2963 2969 2971 2999 ); =item canonicalize($mol, %opts) Canonicalizes the molecule. It adds the canon/class and canon/symmetry class to every atom, as discussed above. This function may take the following options: =over =item sort If true, sort the atoms in the molecule in ascending canonical number order. =item invariants This should be a subroutine reference that takes an atom and returns a number. These number should be based on the topological invariant properties of the atom, such as symbol, charge, number of bonds, etc. =back =cut sub canonicalize { my ($mol, %opts) = @_; if ($mol->atoms > @PRIMES - 1) { croak "maximum number of atoms exceeded for canonicalization\n"; } my $invariants_sub = $opts{invariants} || \&atom_invariants; # set up initial classes for my $atom ($mol->atoms) { $atom->attr("canon/class", $invariants_sub->($atom)); $atom->attr("canon/prev_class", 1); } #printf "$_: %s\n", $_->attr("canon/class") for $mol->atoms; # run one canonicalization step my $atoms; my $n_classes; ($atoms, $n_classes) = rank_classes($mol); ($atoms, $n_classes) = canon($mol, $n_classes); my $n_atom = $mol->atoms; # atoms with the same class are topologically symmetric for my $atom ($mol->atoms) { $atom->attr("canon/symmetry_class", $atom->attr("canon/class")); } #printf "$_: %s\n", $_->attr("canon/class") for $mol->atoms; # break symmetry to get a canonical numbering while ($n_classes < $n_atom) { # multiply all classes by 2 for my $atom (@$atoms) { my $class = $atom->attr("canon/class"); $atom->attr("canon/class", $class * 2); } # break first tie my $last_class = -1; my $last_atom; for my $atom (@$atoms) { my $class = $atom->attr("canon/class"); if ($class == $last_class) { # tie #print "breaking tie for $last_atom\n"; $last_atom->attr("canon/class", $class - 1); last; } $last_class = $class; $last_atom = $atom; } #printf "$_: %s\n", $_->attr("canon/class") for $mol->atoms; #print "---\n"; # run another canonicalization step ($atoms, $n_classes) = canon($mol, $n_classes); #printf "$_: %s\n", $_->attr("canon/class") for $mol->atoms; } if ($opts{'sort'}) { $mol->sort_atoms( sub { $_[0]->attr("canon/class") <=> $_[1]->attr("canon/class") } ); } # clean up temporary classes $_->del_attr("canon/new_class") for $mol->atoms; $n_classes; } sub atom_invariants { no warnings 'uninitialized'; my ($atom) = @_; my $n_bonds = $atom->bonds; my $valence = 0; #$valence += $_->order for $atom->bonds; for ($atom->bonds) { $valence += $_->order if defined $_ } my $Z = $atom->Z; my $q = $atom->formal_charge + 5; return $n_bonds*10_000 + $valence*1000 + $q*100 + $Z; } # atom class comparison function. Only compare the class if the # previous classes are equal sub _cmp { $a->attr("canon/prev_class") <=> $b->attr("canon/prev_class") or $a->attr("canon/class") <=> $b->attr("canon/class") } sub rank_classes { my ($mol) = @_; my @atoms = sort _cmp $mol->atoms; # consider Schwartzian transform? my $n = 0; local ($a, $b); for $b (@atoms) { $n++ if (!$a || _cmp); $a = $b; $b->attr("canon/new_class", $n); } #use diagnostics; for my $atom (@atoms) { $atom->attr("canon/class", $atom->attr("canon/new_class")); } (\@atoms, $n); } sub canon { my ($mol, $n) = @_; my $old_classes = 0; my $n_atom = $mol->atoms; my $atoms; while ($n > $old_classes and $n < $n_atom) { $old_classes = $n; # save current classes for my $atom ($mol->atoms) { $atom->attr("canon/prev_class", $atom->attr("canon/class")); } # set new class to product of neighbor's primes for my $atom ($mol->atoms) { my $class = Math::BigInt->new('1'); #my $class = 1; for my $neighbor ($atom->neighbors) { $class *= $PRIMES[$neighbor->attr("canon/prev_class")]; } #print "$class\n"; $atom->attr("canon/class", $class); } ($atoms, $n) = rank_classes($mol); } ($atoms, $n); } 1; =back =head1 VERSION 0.11 =head1 TO DO Add some tests. =head1 CAVEATS Currently there is an atom limit of about 430 atoms. These algorithm is known to fail to discriminate between non-equivalent atoms for some complicated cases. These are usually highly bridged structures explicitly designed to break canonicalization algorithms; I don't know of any "real-looking structure" (meaning something that someone would actually synthesize or find in nature) that fails, but don't say I didn't warn you! =head1 SEE ALSO L, L, L, L. =head1 AUTHOR Ivan Tubert Eitub@cpan.orgE =head1 COPYRIGHT Copyright (c) 2009 Ivan Tubert. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut