qu-thermo 1.0.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: c76137b4b3ca987df2112ff6ed774e2aace0be69
+  data.tar.gz: bb0c6b08e3b262344a3a441f069a812797c0450b
+SHA512:
+  metadata.gz: 3af235456aad35965f49abeda1771313a27122ec846bc029d55ebf434ce82286588783796c5f7f022e38596ba41fe0ec29f7fa91f70a9542df966a18ffd9eeea
+  data.tar.gz: 97420eaaeb38f51cbfdab5be8974e90769b031eb4c3a2fa6d623c4f8e6bafc7a5687d6415b94fa02a6fdc5a6016d7063fd7a88a9d5a84246b682a7dc3ad41671

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in qu-thermo.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2013 Wubin Qu
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# Qu::Thermo
+
+A thermodynamics library for calculating DNA/DNA binding energy
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'qu-thermo'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install qu-thermo
+
+## Usage
+
+`tm = Qu::Thermo::Hybrid.new(seq_1, seq_2).tm`
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"

data/lib/qu/thermo.rb

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+require "qu/thermo/version"
+require_relative "thermo/parameters"
+
+
+module Qu
+  module Thermo
+    class Hybrid
+      def initialize(qseq, sseq, mono=50, diva=1.5, dntp=0.25, oligo=50)
+        # qseq: 5' -> 3'
+        # sseq: 3' -> 5'
+        @qseq = qseq.upcase
+        @sseq = sseq.upcase
+        @mono = mono.to_f
+        @diva = diva.to_f
+        @dntp = dntp.to_f
+        @oligo = oligo.to_f
+
+        @dh, @ds = delta_hs
+        @adjusted_mono = (@mono + diva2mono) / 1000.0
+        @adjusted_ds = @ds + 0.368 * (@sseq.size - 1) * Math.log(@adjusted_mono, Math::E)
+      end
+
+      def dg
+        (@dh * 1000 - (273.15 + 37) * @adjusted_ds) / 1000.0
+      end
+
+      def tm
+        @dh * 1000.0 / (@adjusted_ds + 1.987 * Math.log(@oligo / 1000000000.0 / 4, Math::E)) - 273.15
+      end
+
+      def dg_tm
+        return dg, tm
+      end
+
+      private
+
+      def diva2mono
+        @dntp = 0 if @diva == 0
+
+        $stderr.puts "Error conc for diva and mono" if @diva < 0 or @dntp < 0
+
+        @diva = @dntp if @diva < @dntp
+
+        return 120 * (Math.sqrt(@diva - @dntp))
+      end
+
+      def delta_hs
+        init_start = "init#{@qseq[0]}#{@sseq[0]}"
+        init_stop = "init#{@qseq[-1]}#{@sseq[-1]}"
+
+        dh = ds = 0
+        if DH.include?(init_start) and DH.include?(init_stop)
+          dh = DH[init_start] + DH[init_stop]
+          ds = DS[init_start] + DS[init_stop]
+        end
+
+        (0...(@qseq.size - 1)).each do |i|
+          dinuc = "#{@qseq[i...(i+2)]}#{@sseq[i...(i+2)]}"
+          if DH.include?(dinuc) and DS.include?(dinuc)
+            dh += DH[dinuc]
+            ds += DS[dinuc]
+          end
+        end
+
+        return dh, ds
+      end
+    end
+  end
+end

data/lib/qu/thermo/parameters.rb

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+#!/usr/bin/env ruby 
+# -*- coding: utf-8 -*- #
+=begin
+Thermodynamics Parameters for calculating Tm and Gibbs free energy
+
+References
+
+ Matched base-pair =>
+
+ [1] SantaLucia JR (1998) "A unified view of polymer, dumbbell
+ and oligonucleotide DNA nearest-neighbor thermodynamics", Proc Natl
+ Acad Sci 95=>1460-65 http=>//dx.doi.org/10.1073/pnas.95.4.1460.
+
+ Mismatched base-pair =>
+
+ [1]. Allawi, H.T. and SantaLucia, J. (1997) Thermodynamics and NMR 
+ of internal GT mismatches in DNA, Biochemistry, 36, 10581-10594.
+ [2]. Allawi, H.T. and SantaLucia, J. (1998) Nearest-neighbor 
+ thermodynamics of internal A center dot C mismatches in 
+ DNA=> Sequence dependence and pH effects, Biochemistry, 37, 9435-9444.
+ [3]. Allawi, H.T. and SantaLucia, J. (1998) Nearest neighbor 
+ thermodynamic parameters for internal G center dot A mismatches 
+ in DNA, Biochemistry, 37, 2170-2179.
+ [4]. Allawi, H.T. and Santalucia, J. (1998) Thermodynamics of 
+ internal C center dot T mismatches in DNA, Nucleic Acids 
+ Research, 26, 2694-2701.
+
+ NN model =>
+
+ [1] SantaLucia, J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proceedings of the National Academy of Sci-ences of the United States of America, 95, 1460-1465.
+
+ [2] von Ahsen, N., Wittwer, C.T. and Schutz, E. (2001) Oligonucleotide melting tempera-tures under PCR conditions=> Nearest-neighbor corrections for Mg2+, deoxynu-cleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas, Clinical Chemistry, 47, 1956-1961.
+
+by Wubin Qu <quwubin@gmail.com>
+Copyright @ 2010, All Rights Reserved.
+=end
+
+module Qu
+  module Thermo
+      DH = {
+      'AATT' => -7.9, 'TTAA' => -7.9,
+      'ATTA' => -7.2, 'TAAT' => -7.2,
+      'CAGT' => -8.5, 'TGAC' => -8.5,
+      'GTCA' => -8.4, 'ACTG' => -8.4,
+      'CTGA' => -7.8, 'AGTC' => -7.8,
+      'GACT' => -8.2, 'TCAG' => -8.2,
+      'CGGC' => -10.6, 'GCCG' => -9.8, 
+      'GGCC' => -8.0, 'CCGG' => -8.0, 
+      'initCG' => 0.1, 'initGC' => 0.1, 
+      'initAT' => 2.3, 'initTA' => 2.3, 
+      # Like pair mismatches 
+      'AATA' => 1.2, 'ATAA' => 1.2, 
+      'CAGA' => -0.9, 'AGAC' => -0.9, 
+      'GACA' => -2.9, 'ACAG' => -2.9, 
+      'TAAA' => 4.7, 'AAAT' => 4.7, 
+      'ACTC' => 0.0, 'CTCA' => 0.0, 
+      'CCGC' => -1.5, 'CGCC' => -1.5, 
+      'GCCC' => 3.6, 'CCCG' => 3.6, 
+      'TCAC' => 6.1, 'CACT' => 6.1, 
+      'AGTG' => -3.1, 'GTGA' => -3.1, 
+      'CGGG' => -4.9, 'GGGC' => -4.9, 
+      'GGCG' => -6.0, 'GCGG' => -6.0, 
+      'TGAG' => 1.6, 'GAGT' => 1.6, 
+      'ATTT' => -2.7, 'TTTA' => -2.7, 
+      'CTGT' => -5.0, 'TGTC' => -5.0, 
+      'GTCT' => -2.2, 'TCTG' => -2.2, 
+      'TTAT' => 0.2, 'TATT' => 0.2, 
+      # G.T mismatches 
+      'AGTT' => 1.0, 'TTGA' => 1.0, 
+      'ATTG' => -2.5, 'GTTA' => -2.5, 
+      'CGGT' => -4.1, 'TGGC' => -4.1, 
+      'CTGG' => -2.8, 'GGTC' => -2.8, 
+      'GGCT' => 3.3, 'TCGG' => 3.3, 
+      'GGTT' => 5.8, 'TTGG' => 5.8, 
+      'GTCG' => -4.4, 'GCTG' => -4.4, 
+      'GTTG' => 4.1, 'GTTG' => 4.1, 
+      'TGAT' => -0.1, 'TAGT' => -0.1, 
+      'TGGT' => -1.4, 'TGGT' => -1.4, 
+      'TTAG' => -1.3, 'GATT' => -1.3, 
+      #G.A mismatches
+      'AATG' => -0.6, 'GTAA' => -0.6, 
+      'AGTA' => -0.7, 'ATGA' => -0.7, 
+      'CAGG' => -0.7, 'GGAC' => -0.7, 
+      'CGGA' => -4.0, 'AGGC' => -4.0, 
+      'GACG' => -0.6, 'GCAG' => -0.6, 
+      'GGCA' => 0.5, 'ACGG' => 0.5, 
+      'TAAG' => 0.7, 'GAAT' => 0.7, 
+      'TGAA' => 3.0, 'AAGT' => 3.0, 
+      #C.T mismatches
+      'ACTT' => 0.7, 'TTCA' => 0.7, 
+      'ATTC' => -1.2, 'CTTA' => -1.2, 
+      'CCGT' => -0.8, 'TGCC' => -0.8, 
+      'CTGC' => -1.5, 'CGTC' => -1.5, 
+      'GCCT' => 2.3, 'TCCG' => 2.3, 
+      'GTCC' => 5.2, 'CCTG' => 5.2, 
+      'TCAT' => 1.2, 'TACT' => 1.2, 
+      'TTAC' => 1.0, 'CATT' => 1.0, 
+      #A.C mismatches
+      'AATC' => 2.3, 'CTAA'=>2.3, 
+      'ACTA' => 5.3, 'ATCA'=>5.3, 
+      'CAGC' => 1.9, 'CGAC'=>1.9, 
+      'CCGA' => 0.6, 'AGCC'=>0.6, 
+      'GACC' => 5.2, 'CCAG'=>5.2, 
+      'GCCA' => -0.7, 'ACCG'=>-0.7, 
+      'TAAC' => 3.4, 'CAAT'=>3.4, 
+      'TCAA' => 7.6, 'AACT'=>7.6,
+
+      #tandem mismatch
+      'GGTT' => 5.8,  'TTGG' => 5.8,   
+      'GTTG' => 4.1,  'TGGT' => -1.4, 
+      'GTTT' => 5.8,  'TTTG' => 5.8,
+      'GTAT' => -0.1, 'TATG' => -0.1,
+      #single bulge loop 
+      'AAAT-T' => -4.0,  'AATT-A' => -13.5, 'AACT-G' => 10.2,  'AAGT-C' => -0.2,
+      'ATAT-T' => 9.8,   'ATTT-A' => -19.5, 'ATCT-G' => -4.8,  'ATGT-C' => 5.6,
+      'ACAT-T' => 6.1,   'ACTT-A' => -3.4,  'ACCT-G' => -29.1, 'ACGT-C' => -1.2,
+      'AGAT-T' => 15.5,  'AGTT-A' => 5.3,   'AGCT-G' => -7.2,  'AGGT-C' => 5.7,
+      'TAAA-T' => 15.3,  'TATA-A' => 19.8,  'TACA-G' => -2.3,  'TAGA-C' => 15,
+      'TTAA-T' => -2.7,  'TTTA-A' => -8.2,  'TTCA-G' => 8.8,   'TTGA-C' => 7.0,
+      'TCAA-T' => 1.6,   'TCTA-A' => 9.9,   'TCCA-G' => -15.2, 'TCGA-C' => -0.7,
+      'TGAA-T' => -12.3, 'TGTA-A' => 20.9,  'TGCA-G' => 2.6,   'TGGA-C' => -9.2,
+      'CAAG-T' => -14.4, 'CATG-A' => -7.0,  'CACG-G' => 4.3,   'CAGG-C' => -2.9,
+      'CTAG-T' => -18.7, 'CTTG-A' => -4.6,  'CTCG-G' => -14.5, 'CTGG-C' => -4.7,
+      'CCAG-T' => 5.8,   'CCTG-A' => -5.3,  'CCCG-G' => -2.6,  'CCGG-C' => 9.1,
+      'CGAG-T' => -14.7, 'CGTG-A' => 2.1,   'CGCG-G' => -4.4,  'CGGG-C' => -16.4,
+      'GAAC-T' => -6.8,  'GATC-A' => -9.8,  'GACC-G' => -4.8,  'GAGC-C' => -6.5,
+      'GTAC-T' => -7.4,  'GTTC-A' => 1.8,   'GTCC-G' => -12.3, 'GTGC-C' => -2.3,
+      'GCAC-T' => -2.1,  'GCTC-A' => -3.5,  'GCCC-G' => 0.4,   'GCGC-C' => 13.8,
+      'GGAC-T' => 2.7,   'GGTC-A' => -1.2,  'GGCC-G' => -1.7,  'GGGC-C' => 3.5,
+      # single dangling_end
+      'AA-T' => 0.2,  'TA-T' => -6.9,  'GA-T' => -1.1, 'CA-T' => 0.6,
+      'AC-G' => -6.3, 'TC-G' => -4.0,  'GC-G' => -5.1, 'CC-G' => -4.4,
+      'AG-C' => -3.7, 'TG-C' => -4.9,  'GG-C' => -3.9, 'CG-C' => -4.0,
+      'AT-A' => -2.9, 'TT-A' => -0.2,  'GT-A' => -4.2, 'CT-A' => -4.1,
+      'AAT-' => -0.5, 'ACT-' => 4.7,   'AGT-' => -4.1, 'ATT-' => -3.8,
+      'TAA-' => -0.7, 'TCA-' => 4.4,   'TGA-' => -1.6, 'TTA-' => 2.9,
+      'GAC-' => -2.1,  'GCC-' => -0.2,  'GGC-' => -3.9, 'GTC-' => -4.4,
+      'CAG-' => -5.9, 'CCG-' => -2.6,  'CGG-' => -3.2, 'CTG-' => -5.2,  
+      # long dangling_end
+      'CAAG--' => -2.15, 'CAAAG---' => -3.3,  'CAAAAG----' => -4.85,
+      'TAAA--' => -1.0,  'TAAAA---' => -1.95, 'TAAAAA----' => -2.35,
+      'AAA--T' => -1.5,  'AAAA---T' => -1.75, 'AAAAA----T' => -3.95,
+      'AAG--C' => -0.25, 'AAAG---C' => -0.15, 'AAAAG----C' => -0.75,    
+      }
+
+      #--------------------#
+      # deltaS (cal/K.mol) #
+      #--------------------#
+      DS = {
+      'AATT' => -22.2, 'TTAA'=>-22.2, 
+      'ATTA' => -20.4, 'TAAT'=>-21.3, 
+      'CAGT' => -22.7, 'TGAC'=>-22.7, 
+      'GTCA' => -22.4, 'ACTG'=>-22.4, 
+      'CTGA' => -21.0, 'AGTC'=>-21.0, 
+      'GACT' => -22.2, 'TCAG'=>-22.2, 
+      'CGGC' => -27.2, 'GCCG'=>-24.4, 
+      'GGCC' => -19.9, 'CCGG'=>-19.9, 
+      'initCG' => -2.8, 'initGC'=>-2.8, 
+      'initAT' => 4.1, 'initTA'=>4.1, 
+      'sym' => -1.4, 
+      # => Like=>pair=>mismatches
+      'AATA' => 1.7, 'ATAA'=>1.7, 
+      'CAGA' => -4.2, 'AGAC'=>-4.2, 
+      'GACA' => -9.8, 'ACAG'=>-9.8, 
+      'TAAA' => 12.9, 'AAAT'=>12.9, 
+      'ACTC' => -4.4, 'CTCA'=>-4.4, 
+      'CCGC' => -7.2, 'CGCC'=>-7.2, 
+      'GCCC' => 8.9, 'CCCG'=>8.9, 
+      'TCAC' => 16.4, 'CACT'=>16.4, 
+      'AGTG' => -9.5, 'GTGA'=>-9.5, 
+      'CGGG' => -15.3, 'GGGC'=>-15.3, 
+      'GGCG' => -15.8, 'GCGG'=>-15.8, 
+      'TGAG' => 3.6, 'GAGT'=>3.6, 
+      'ATTT' => -10.8, 'TTTA'=>-10.8, 
+      'CTGT' => -15.8, 'TGTC'=>-15.8, 
+      'GTCT' => -8.4, 'TCTG'=>-8.4, 
+      'TTAT' => -1.5, 'TATT'=>-1.5, 
+      # => G.T=>mismatches
+      'AGTT' => 0.9, 'TTGA'=>0.9, 
+      'ATTG' => -8.3, 'GTTA'=>-8.3, 
+      'CGGT' => -11.7, 'TGGC'=>-11.7, 
+      'CTGG' => -8.0, 'GGTC'=>-8.0, 
+      'GGCT' => 10.4, 'TCGG'=>10.4, 
+      'GGTT' => 16.3, 'TTGG'=>16.3, 
+      'GTCG' => -12.3, 'GCTG'=>-12.3, 
+      'GTTG' => 9.5, 'GTTG'=>9.5, 
+      'TGAT' => -1.7, 'TAGT'=>-1.7, 
+      'TGGT' => -6.2, 'TGGT'=>-6.2, 
+      'TTAG' => -5.3, 'GATT'=>-5.3, 
+      #  G.A mismatches
+      'AATG' => -2.3, 'GTAA' => -2.3, 
+      'AGTA' => -2.3, 'ATGA' => -2.3, 
+      'CAGG' => -2.3, 'GGAC' => -2.3, 
+      'CGGA' => -13.2, 'AGGC' => -13.2, 
+      'GACG' => -1.0, 'GCAG' => -1.0, 
+      'GGCA' => 3.2, 'ACGG' => 3.2, 
+      'TAAG' => 0.7, 'GAAT' => 0.7, 
+      'TGAA' => 7.4, 'AAGT' => 7.4, 
+      # C.T mismatches
+      'ACTT' => 0.2, 'TTCA' => 0.2, 
+      'ATTC' => -6.2, 'CTTA' => -6.2, 
+      'CCGT' => -4.5, 'TGCC' => -4.5, 
+      'CTGC' => -6.1, 'CGTC' => -6.1, 
+      'GCCT' => 5.4, 'TCCG' => 5.4, 
+      'GTCC' => 13.5, 'CCTG' => 13.5, 
+      'TCAT' => 0.7, 'TACT' => 0.7, 
+      'TTAC' => 0.7, 'CATT' => 0.7, 
+      # A.C mismatches
+      'AATC' => 4.6, 'CTAA' => 4.6, 
+      'ACTA' => 14.6, 'ATCA' => 14.6, 
+      'CAGC' => 3.7, 'CGAC' => 3.7, 
+      'CCGA' => -0.6, 'AGCC' => -0.6, 
+      'GACC' => 14.2, 'CCAG' => 14.2, 
+      'GCCA' => -3.8, 'ACCG' => -3.8, 
+      'TAAC' => 8.0, 'CAAT' => 8.0, 
+      'TCAA' => 20.2, 'AACT' => 20.2,
+      # tandem mismatch
+      'GGTT' => 16.3, 'TTGG' => 16.3,   
+      'GTTG' => 9.5,  'TGGT' => -6.2, 
+      'GTTT' => 16.3, 'TTTG' => 16.3,
+      'GTAT' => -1.7, 'TATG' => -1.7, 
+      # single bulge loop
+      'AAAT-T' => -17.5, 'AATT-A' => -44.6, 'AACT-G' => 25.8,  'AAGT-C' => -4.6,
+      'ATAT-T' => 24.7,  'ATTT-A' => -61.8, 'ATCT-G' => -20.0, 'ATGT-C' => 12.9,
+      'ACAT-T' => 14.0,  'ACTT-A' => -15.3, 'ACCT-G' => -91.3, 'ACGT-C' => -7.4,
+      'AGAT-T' => 43.1,  'AGTT-A' => 10.6,  'AGCT-G' => -28.4, 'AGGT-C' => 14.4,
+      'TAAA-T' => 38.5,  'TATA-A' => 56.7,  'TACA-G' => -12.7, 'TAGA-C' => 40.4,
+      'TTAA-T' => -16.0, 'TTTA-A' => -30.1, 'TTCA-G' => 23.2,  'TTGA-C' => 17.5,
+      'TCAA-T' => -3.9,  'TCTA-A' => 30.5,  'TCCA-G' => -48.7, 'TCGA-C' => -7.0,
+      'TGAA-T' => -47.0, 'TGTA-A' => 59.8,  'TGCA-G' => 1.6,   'TGGA-C' => -31.4,
+      'CAAG-T' => -46.6, 'CATG-A' => -25.8, 'CACG-G' => 8.8,   'CAGG-C' => -13.0,
+      'CTAG-T' => -61.7, 'CTTG-A' => -17.0, 'CTCG-G' => -48.1, 'CTGG-C' => -18.8,
+      'CCAG-T' => 13.4,  'CCTG-A' => -24.8, 'CCCG-G' => -9.4,  'CCGG-C' => 24.4,
+      'CGAG-T' => -49.6, 'CGTG-A' => 6.5,   'CGCG-G' => -17.8, 'CGGG-C' => -51.6,
+      'GAAC-T' => -25.2, 'GATC-A' => -35.6, 'GACC-G' => -18.3, 'GAGC-C' => -21.0,
+      'GTAC-T' => -27.0, 'GTTC-A' => -0.6,  'GTCC-G' => -40.0, 'GTGC-C' => -10.0,
+      'GCAC-T' => -12.5, 'GCTC-A' => -16.1, 'GCCC-G' => -1.0,  'GCGC-C' => 42.9,
+      'GGAC-T' => 3.6,   'GGTC-A' => -9.3,  'GGCC-G' => -7.2,  'GGGC-C' => 8.5,
+      # single dangling_end
+      'AA-T' => 2.3,   'TA-T' => -20.0, 'GA-T' => -1.6,  'CA-T' => 3.3,
+      'AC-G' => -17.1, 'TC-G' => -10.9, 'GC-G' => -14.0, 'CC-G' => -12.6,
+      'AG-C' => -10,   'TG-C' => -13.8, 'GG-C' => -10.9, 'CG-C' => -11.9,
+      'AT-A' => -7.6,  'TT-A' => -0.5,  'GT-A' => -15.0, 'CT-A' => -13.0,
+      'AAT-' => -1.1,  'ACT-' => 14.2,  'AGT-' => -13.1, 'ATT-' => -12.6,
+      'TAA-' => -0.8,  'TCA-' => 14.9,  'TGA-' => -3.6,  'TTA-' => 10.4,
+      'GAC-' => -3.9,  'GCC-' => -0.1,  'GGC-' => -11.2, 'GTC-' => -13.1,
+      'CAG-' => -16.5, 'CCG-' => -7.4,  'CGG-' => -10.4, 'CTG-' => -15.0, 
+      # long dangling_end
+      'CAAG--' => -5.5, 'CAAAG---' => -8.5, 'CAAAAG----' => -13.5,
+      'TAAA--' => -1.0, 'TAAAA---' => -4.5, 'TAAAAA----' => -6.0,
+      'AAA--T' => -2.5, 'AAAA---T' => -3.5, 'AAAAA----T' => -10.5,
+      'AAG--C' => 0.5,  'AAAG---C' => 1.5,  'AAAAG----C' => -0.5, 
+      }
+
+      LONG_BULGE_LOOP_DS = {
+         '2' => -9.35,    '3' => -10.0,   '4' => -10.32,   '5' => -10.64,  '6' => -11.28,
+         '7' => -11.93,   '8' => -12.57,  '9' => -13.22,  '10' => -13.86, '11' => -14.15,
+         '12' => -14.51,  '13' => -15.00, '14' => -15.48,  '15' => -15.65,  '16' => -16.12,
+         '17' => -16.26,  '18' => -16.77, '19' => -16.80,  '20' => -17.09,
+      }
+
+      TANDEM_MISMATCH = {
+        'GT' => ['TT', 'AT', 'TG'],
+        'TT' => ['TG', 'GG'],
+        'TG' => ['GT'],
+        'GG' => ['TT'],
+        'TA' => ['TG'],
+      }
+
+      PERFECT_MATCH = {
+          'A' => 'T',
+          'T' => 'A',
+          'C' => 'G',
+          'G' => 'C',
+      }
+
+      
+  end
+end
+
+if $0 == __FILE__
+   p Qu::Thermo::DH
+end

data/lib/qu/thermo/version.rb

@@ -0,0 +1,5 @@
+module Qu
+  module Thermo
+    VERSION = "1.0.0"
+  end
+end

data/qu-thermo.gemspec

@@ -0,0 +1,23 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'qu/thermo/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "qu-thermo"
+  spec.version       = Qu::Thermo::VERSION
+  spec.authors       = ["Wubin Qu"]
+  spec.email         = ["quwubin@gmail.com"]
+  spec.description   = %q{A thermodynamics library for calculating DNA/DNA binding energy}
+  spec.summary       = %q{Thermodynamics parameters and calculations}
+  spec.homepage      = "https://github.com/quwubin/qu-thermo"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+end

metadata

@@ -0,0 +1,81 @@
+--- !ruby/object:Gem::Specification
+name: qu-thermo
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+platform: ruby
+authors:
+- Wubin Qu
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-04-28 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: A thermodynamics library for calculating DNA/DNA binding energy
+email:
+- quwubin@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/qu/thermo.rb
+- lib/qu/thermo/parameters.rb
+- lib/qu/thermo/version.rb
+- qu-thermo.gemspec
+homepage: https://github.com/quwubin/qu-thermo
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.0
+signing_key: 
+specification_version: 4
+summary: Thermodynamics parameters and calculations
+test_files: []