Chemistry::File::Formula - Molecular formula reader/formatter
use Chemistry::File::Formula; my $mol = Chemistry::Mol->parse("H2O"); print $mol->print(format => formula); print $mol->formula; # this is a shorthand for the above print $mol->print(format => formula, formula_format => "%s%d{<sub>%d</sub>});
This module converts a molecule object to a string with the formula and back. It registers the 'formula' format with Chemistry::Mol. Besides its obvious use, it is included in the Chemistry::Mol distribution because it is a very simple example of a Chemistry::File derived I/O module.
The format can be specified as a printf-like string with the following control sequences, which are specified with the formula_format parameter to $mol->print or $mol->write.
If no format is specified, the default is "%s%d". Some examples follow. Let's assume that the formula is C2H6O, as it would be formatted by default.
%s%D
Like the default, but include explicit indices for all atoms. The formula would be formatted as "C2H6O1"
%s%d{<sub>%d</sub>}
HTML format. The output would be "C<sub>2</sub>H<sub>6</sub>O".
%D %s%j{, }
Use a comma followed by a space as a joiner. The output would be "2 C, 6 H, 1 O".
The elements in the formula are sorted by default in the "Hill order", which means that:
1) if the formula contains carbon, C goes first, followed by H, and the rest of the symbols in alphabetical order. For example, "CH2BrF".
2) if there is no carbon, all the symbols (including H) are listed alphabetically. For example, "BrH".
It is possible to supply a custom sorting subroutine with the 'formula_sort' option. It expects a subroutine reference that takes a hash reference describing the formula (similar to what is returned by parse_formula, discussed below), and that returns a list of symbols in the desired order.
For example, this will sort the symbols in reverse asciibetical order:
my $formula = $mol->print( format => 'formula', formula_sort => sub { my $formula_hash = shift; return reverse sort keys %$formula_hash; } );
Formulas can also be parsed back into Chemistry::Mol objects. The formula may have parentheses and square or triangular brackets, and it may have the following abbreviations:
Me => '(CH3)', Et => '(CH3CH2)', Bu => '(C4H9)', Bn => '(C6H5CH2)', Cp => '(C5H5)', Ph => '(C6H5)', Bz => '(C6H5CO)',
The formula may also be preceded by a number, which multiplies the whole formula. Some examples of valid formulas:
Formula Equivalent to -------------------------------------------------------------- CH3(CH2)3CH3 C5H12 C6H3Me3 C9H12 2Cu[NH3]4(NO3)2 Cu2H24N12O12 2C(C[C<C>5]4)3 C152 2C(C(C(C)5)4)3 C152 C 1 0 H 2 2 C10H22 (whitespace is completely ignored)
When a formula is parsed, a molecule object is created which consists of the set of the atoms in the formula (no bonds or coordinates, of course). The atoms are created in alphabetical order, so the molecule object for C2H5Br would have the atoms in the following sequence: Br, C, C, H, H, H, H, H.
If you don't want to create a molecule object, but would rather have a simple hash with the number of atoms for each element, use the parse_formula
method:
my %formula = Chemistry::File::Formula->parse_formula("C2H6O"); use Data::Dumper; print Dumper \%formula;
which prints something like
$VAR1 = { 'H' => 6, 'O' => 1, 'C' => 2 };
The parse_formula
method is called internally by the parse_string
method.
The parse_formula
method can also accept formulas that contain floating-point numbers, such as H1.5N0.5. The numbers must be positive, and numbers smaller than one should include a leading zero (e.g., 0.9, not .9).
When formulas with non-integer numbers of atoms are turned into molecule objects as described in the previous section, the number of atoms is always rounded up. For example, H1.5N0.5 will produce a molecule object with two hydrogen atoms and one nitrogen atom.
There is currently no way of producing formulas with non-integer numbers; perhaps a future version will include an "occupancy" property for atoms that will result in non-integer formulas.
0.37
Chemistry::Mol, Chemistry::File
For discussion about Hill order, just search the web for formula "hill order"
. The original reference is J. Am. Chem. Soc. 1900, 22, 478-494. http://dx.doi.org/10.1021/ja02046a005.
The PerlMol website http://www.perlmol.org/
Ivan Tubert-Brohman <itub@cpan.org>.
Formula parsing code contributed by Brent Gregersen.
Patch for non-integer formulas by Daniel Scott.
Copyright (c) 2005 Ivan Tubert-Brohman. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.