mspire-molecular_formula 0.0.1 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8aa1b3d4118e17b3ca2c9092e9c355f6e376a46c
-  data.tar.gz: 14d52e1251c536369476ec68bab41f903a366a11
+  metadata.gz: 61ab058e6c8b53fa54ff7c743e322e52ca866ea8
+  data.tar.gz: 2fb66783ec477d4d4f87df12e98b7dc7ae4ed597
 SHA512:
-  metadata.gz: ee4729ebc0ff0276ffbd299bdec26a3eea81a05603895c1061b333031c8c22b53c1bac56789734a7e071dd776df728041f1dd67f0ca2ae4f61be6192aca87a77
-  data.tar.gz: d6301ed9ef9b458c80b80ea92615c059f6a49bbedc15ed76c1a5f089aac3766cb2d52d7063858bbb4704080fff8ade679bc18049f0d223e44e945c33d8f4ea65
+  metadata.gz: 1da09fe7a26f3cf3a069bb7762aba72fe62667ab9cdf30f46ee7f1b480bbed61ebb5274d9472fff88d1b660e0b7f6a4a0d7aedee5caf6f8faf4efa88100a78e7
+  data.tar.gz: 41c96037b3e850df81caf5405adcdc2fe5b96105efb6db7fa4a4424bfbb9af30ecac16e272297a832f47f35412b77a69993950e794c03a2746ec66de3dd23c86

data/README.md

@@ -21,7 +21,7 @@ mf = Mspire::MolecularFormula.new( C:3, H:4, O:2 )
 mf = Mspire::MolecularFormula.new( {C:3, H:4, O:2}, 2)
 ```
 
-### Create with a string formula
+### Create with a string formula or AA seq
 
 ```ruby
 mf = Mspire::MolecularFormula[ 'C3H4O2' ]
@@ -30,11 +30,25 @@ mf = Mspire::MolecularFormula[ 'C3H4O2' ]
 mf = Mspire::MolecularFormula[ 'C3H4O2', 2 ]
 mf = Mspire::MolecularFormula[ 'C3H4O2+2' ]  # alternatively
 mf = Mspire::MolecularFormula[ 'C3H4O2++' ]  # alternatively
+
+# from amino acid sequence
+Mspire::MolecularFormula.from_aaseq('APEPTIDE') # .to_s => "C37H58N8O16"
+Mspire::MolecularFormula.from_aaseq('APEPTIDE', -2) # w/ -2 charge .to_s => "C37H58N8O16-2"
+```
+
+### Output string or hash formula
+
+```ruby
+mf = Mspire::MolecularFormula[ 'C3H4O2', 2 ]
+mf.inspect     # => {MolecularFormula :C=>3, :H=>4, :O=>2, @charge=2}
+mf.to_s        # => 'C3H4O2+2'
+mf.to_s(false) # (hide charge) => 'C3H4O2'
+mf.to_h        # => {:C=>3, :H=>4, :O=>2}
 ```
 
 ### Arithmetic
 
-Walk through the arithmetic of combustion of ethene using this equation:
+Walk through the arithmetic of combustion of ethene:
 
     CH2=CH2 + 3 O2 -> 2 CO2 + 2 H2O 
 
@@ -48,11 +62,58 @@ two_carbon_dioxide = combustion - (water*2)
 carbon_dioxide = two_carbon_dioxide / 2
 ```
 
-Note that there are no methods defined on fixnum to deal with MolecularFormula
-objects, so fixnums need to follow the MolecularFormula (i.e., "3 * oxygen"
+Note: there are no methods defined on fixnum to deal with MolecularFormula
+objects, so fixnums need to go after the MolecularFormula (i.e., "3 * oxygen"
 will throw an error but "oxygen * 3" is fine)
 
+### Isotope Distribution
+
+[Note, currently requires the fftw3 gem to be installed and accessible.]
+
+#### isotope\_intensity\_distribution
 
-require 'mspire/isotope/distribution'  # requires fftw gem
-puts butane.isotope_distribution  # :total, :max, :first as arg to normalize
+```ruby
+# by default normalizes by total intensity with no peak or percent cuttoff
+ethene.isotope_intensity_distribution
+#   => [0.9777084818979036, 0.02215911350461325, 0.0001323273147371948, 7.726507349638125e-08, 
+#       1.7670756693524035e-11, 1.81473621216667e-15, 2.6146991408856273e-17]
+
+# return/use only first 4 peaks and normalize by max peak 
+ethene.isotope_intensity_distribution(normalize: :max, peak_cutoff: 4)
+#   => [1.0, 0.022664335959936163, 0.00013534434566868467, 7.902669857828807e-08]
+
+# cut at less than 0.01% total intensity and normalize by max peak 
+ethene.isotope_intensity_distribution(normalize: :first, percent_cutoff: 0.01)
+#   => [1.0, 0.022664335959936163, 0.00013534434566868467]
+```
+
+#### isotope\_distribution
+
+Returns an array of masses (mz's if charged) and intensities.  Although the
+monoisotopic mass will be, the other peaks are not quite as accurate as those
+from [emass](https://github.com/princelab/emass) or
+[BRAIN](https://code.google.com/p/brain-isotopic-distribution/); however, they
+should be accurate enough for many purposes.
+
+```ruby
+# zero charge, so returns masses and intensities
+ethene.isotope_distribution
+#   => [[28.03130012828, 29.039965043880002, 30.048629959480003, ...], 
+#       [0.9777084818979036, 0.02215911350461325, 0.0001323273147371948, ...]]
+
+# if charged, will return m/z's and intensities
+ethene.charge = 2
+#   => [[14.01510146414, 14.519433921940001, 15.023766379740001, 15.528098837540002...], 
+#       [0.9777084818979036, 0.02215911350461325, 0.0001323273147371948, ...]]
+```
+
+## Convenience method to get at formulas fast
+
+```
+require 'mspire/mf'
+ethene = Mspire::MF['C2H4']
+```
 
+This is just like calling 'mspire/molecular_formula' but it sets the MF
+constant equal to MolecularFormula.  Include Mspire or set your own constant
+if you want something even shorter.

data/lib/mspire/molecular_formula.rb

@@ -45,6 +45,7 @@ module Mspire
   end
 end
 
+
 require "mspire/molecular_formula/version"
 
 # class methods for reading from different string input
@@ -53,7 +54,23 @@ require 'mspire/molecular_formula/reader'
 # the modules for these 3 are included at the bottom
 require 'mspire/molecular_formula/arithmetic'
 require 'mspire/molecular_formula/mass'
-require 'mspire/molecular_formula/isotope_distribution'
+
+# currently can't execute isotope dist code without this gem
+# TODO: remove dep.
+def have_fftw3?
+  begin
+    response = require('fftw3')
+    true
+  rescue
+    begin
+      Kernel.const_get('FFTW3')
+    rescue
+      false
+    end
+  end
+end
+
+require 'mspire/molecular_formula/isotope_distribution' if have_fftw3?
 
 module Mspire
   class MolecularFormula
@@ -64,6 +81,8 @@ module Mspire
     ####################################################
     include Arithmetic
     include Mass
-    include IsotopeDistribution
+    if have_fftw3?
+      include IsotopeDistribution 
+    end
   end
 end

data/lib/mspire/molecular_formula/isotope_distribution.rb

@@ -1,7 +1,7 @@
 require 'mspire/mass'
 require 'mspire/isotope'
 
-require 'fftw3'
+# depends on FFTW3 from mspire/molecular_formula right which does the: require 'fftw3'
 
 module Mspire
   class MolecularFormula

data/lib/mspire/molecular_formula/version.rb

@@ -1,5 +1,5 @@
 module Mspire
   class MolecularFormula < Hash
-    VERSION = "0.0.1"
+    VERSION = "0.1.0"
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: mspire-molecular_formula
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.1.0
 platform: ruby
 authors:
 - John T. Prince
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-02 00:00:00.000000000 Z
+date: 2014-08-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: mspire-mass