Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / lib / HPM.pm

diff --git a/binaries/src/jpred/lib/HPM.pm b/binaries/src/jpred/lib/HPM.pm
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+package HPM;
+
+use strict;
+use warnings;
+use Carp;
+
+use base qw(Exporter);
+
+our @EXPORT_OK = qw(hydrophobic_moment);
+
+=head1 NAME
+
+HPM - module to calculate hydrophobic moments of a peptide sequence
+
+=head1 $moment = hydrophobic_moment($angle, @sequence)
+
+Calculate the hydrophobic moment (Eisenberg et al.) of a series of amino acids in @sequence for angle $angle in degrees. This is 100 for alpha helices and between 160 and 180.
+
+An example helix is: RIIRRIIRRIRRIIRRII which has a maximum at 100 degrees.
+An example sheet is: ALALALALAL, with a maximum at between 160-180 degrees.
+
+See Eisenberg et al., PNAS, 1984, v81, p140-144 for more details.
+
+=cut
+
+# Hydrophobic moments from Eisenberg et al., PNAS, 1984, v81, p140.
+my %moments = (
+       I => 0.73,
+       F => 0.61,
+       V => 0.54,
+       L => 0.53,
+       W => 0.37,
+       M => 0.26,
+       A => 0.25,
+       G => 0.16,
+       C => 0.04,
+       Y => 0.02,
+       P => -0.07,
+       T => -0.18,
+       S => -0.26,
+       H => -0.40,
+       E => -0.62,
+       N => -0.64,
+       Q => -0.69,
+       D => -0.72,
+       K => -1.10,
+       R => -1.76
+);
+
+# Hydrophobic moments from EMBOSS 2.9.0 hmoment program. Gives similar graphs
+# to the above moments.
+my %e_moments = (
+       A => 0.62,
+       B => -100,
+       C => 0.29,
+       D => -0.90,
+       E => -0.74,
+       F => 1.19,
+       G => 0.48,
+       H => -0.4,
+       I => 1.38,
+       J => -100,
+       K => -1.5,
+       L => 1.06,
+       M => 0.64,
+       N => -0.78,
+       O => -100,
+       P => 0.12,
+       Q => -0.85,
+       R => -2.53,
+       S => -0.18,
+       T => -0.05,
+       U => -100,
+       V => 1.08,
+       W => 0.81,
+       X => -100,
+       Y => 0.26,
+       Z => -100,
+);
+
+sub deg2rad { $_[0] and return $_[0] * (3.141593 / 180) }
+
+sub hydrophobic_moment {
+       my ($angle, @seq) = @_;
+       my $tangle = $angle;
+
+       my ($sum_sin, $sum_cos) = (0, 0);
+       for (@seq) {
+               $sum_sin += ($moments{ $_ } * sin(deg2rad $tangle));
+               $sum_cos += ($moments{ $_ } * cos(deg2rad $tangle));
+               $tangle = ($tangle + $angle) % 360;
+       }
+       return sqrt($sum_sin * $sum_sin + $sum_cos * $sum_cos) / @seq;
+}