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Contents
#
# bio/util/color_scheme/hydropathy.rb - Color codings for hydrophobicity
#
# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
# License:: The Ruby License
#
# $Id: hydropathy.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
#
require 'bio/util/color_scheme'
module Bio::ColorScheme
# Hydropathy index
# Kyte, J., and Doolittle, R.F., J. Mol. Biol.
# 1157, 105-132, 1982
class Hydropathy < Score #:nodoc:
#########
protected
#########
def self.score_to_rgb_hex(score, min, max)
percent = score_to_percent(score, min, max)
rgb_percent_to_hex(percent, 0.0, 1.0-percent)
end
@colors = {}
@scores = {
'A' => 1.8,
'C' => 2.5,
'D' => -3.5,
'E' => -3.5,
'F' => 2.8,
'G' => -0.4,
'H' => -3.2,
'I' => 4.5,
'K' => -3.9,
'L' => 3.8,
'M' => 1.9,
'N' => -3.5,
'P' => -1.6,
'Q' => -3.5,
'R' => -4.5,
'S' => -0.8,
'T' => -0.7,
'U' => 0.0,
'V' => 4.2,
'W' => -0.9,
'Y' => -1.3,
'B' => -3.5,
'X' => -0.49,
'Z' => -3.5,
}
@min = -3.9
@max = 4.5
@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
@colors.default = 'FFFFFF' # return white by default
end
end
Version data entries
33 entries across 33 versions & 5 rubygems