Mspire::MolecularFormula

mspire library to handle molecular formulas (including an optional charge state), complete with relevant chemical properties such as mass, m/z, and isotope distribution.

Installation

gem install mspire-molecular_formula

Usage

require 'mspire/molecular_formula'

Create with a hash

mf = Mspire::MolecularFormula.new( C:3, H:4, O:2 )

# with a +2 charge
mf = Mspire::MolecularFormula.new( {C:3, H:4, O:2}, 2)

Create with a string formula or AA seq

mf = Mspire::MolecularFormula[ 'C3H4O2' ]

# with a +2 charge
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

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:

CH2=CH2 + 3 O2 -> 2 CO2 + 2 H2O 

ethene = Mspire::MolecularFormula['C2H4']
oxygen = Mspire::MolecularFormula['O2']
water = Mspire::MolecularFormula['H2O']

combustion = ethene + (oxygen*3)
two_carbon_dioxide = combustion - (water*2)
carbon_dioxide = two_carbon_dioxide / 2

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

# 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 or BRAIN; however, they should be accurate enough for many purposes.

# 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.