Hello community,
here is the log from the commit of package ghc-isotope for openSUSE:Factory
checked in at 2017-08-31 20:56:48
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/ghc-isotope (Old)
and /work/SRC/openSUSE:Factory/.ghc-isotope.new (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "ghc-isotope"
Thu Aug 31 20:56:48 2017 rev:2 rq:513408 version:0.5.0.1
Changes:
--------
--- /work/SRC/openSUSE:Factory/ghc-isotope/ghc-isotope.changes 2017-04-11
09:38:30.689459377 +0200
+++ /work/SRC/openSUSE:Factory/.ghc-isotope.new/ghc-isotope.changes
2017-08-31 20:56:49.936307676 +0200
@@ -1,0 +2,5 @@
+Thu Jul 27 14:06:43 UTC 2017 - psim...@suse.com
+
+- Update to version 0.5.0.1.
+
+-------------------------------------------------------------------
Old:
----
isotope-0.4.0.0.tar.gz
New:
----
isotope-0.5.0.1.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ ghc-isotope.spec ++++++
--- /var/tmp/diff_new_pack.PLp2z4/_old 2017-08-31 20:56:50.588216081 +0200
+++ /var/tmp/diff_new_pack.PLp2z4/_new 2017-08-31 20:56:50.596214957 +0200
@@ -19,7 +19,7 @@
%global pkg_name isotope
%bcond_with tests
Name: ghc-%{pkg_name}
-Version: 0.4.0.0
+Version: 0.5.0.1
Release: 0
Summary: Isotopic masses and relative abundances
License: GPL-3.0+
++++++ isotope-0.4.0.0.tar.gz -> isotope-0.5.0.1.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/isotope-0.4.0.0/README.md
new/isotope-0.5.0.1/README.md
--- old/isotope-0.4.0.0/README.md 2017-03-11 09:42:03.000000000 +0100
+++ new/isotope-0.5.0.1/README.md 2017-04-30 01:08:04.000000000 +0200
@@ -1,5 +1,5 @@
[](https://travis-ci.org/Michaelt293/isotope)
-[](https://gitter.im/Michaelt293/isotope)
+[](https://gitter.im/Michaelt293/isotope)
@@ -13,6 +13,7 @@
* [ToElementalComposition type class](#elementalcomposition-type-class)
* [Behaviour of ElementalComposition, MolecularFormula, CondensedFormula
and EmpiricalFormula data
types](#behaviour-of-elementalcomposition-molecularformula-condensedformula-and-empiricalformula-data-types)
* [Additional functions accepting an ElementSymbol as
input](#additional-functions-accepting-an-elementsymbol-as-input)
+ * [Representing ions in Isotope](#representing-ions-in-isotope)
* [Comparison to other chemistry
libraries](#comparison-to-other-chemistry-libraries)
* [Radium](#radium)
* [Ouch](#ouch)
@@ -108,13 +109,13 @@
### `ToElementalComposition` type class
-`ToElementalComposition` is a superclass of `ToMolecularFormula`,
`ToCondensedFormula` and `ToEmpiricalFormula`. In addition to the
`toElementalComposition` method, the `ToElementalComposition` type class has
three other methods; `monoisotopicMass`, `nominalMass` and `averageMass`.
(`toElementalComposition` is the minimal complete definition.) `ElementSymbol`,
`ElementalComposition`, `MolecularFormula`, `CondensedFormula` and
`EmpiricalFormula` all have instances of `ToElementalComposition`. This
provides a uniform approach to working with elements, elemental compositions,
molecular formulae, condensed formulae and empirical formulae.
+`ToElementalComposition` is a superclass of `ToMolecularFormula`,
`ToCondensedFormula` and `ToEmpiricalFormula`. In addition to the
`toElementalComposition` method, the `ToElementalComposition` type class has
four other methods; `charge`, `monoisotopicMass`, `nominalMass` and
`averageMass`. (`toElementalComposition` and `charge` is the minimal complete
definition.) `ElementSymbol`, `ElementalComposition`, `MolecularFormula`,
`CondensedFormula` and `EmpiricalFormula` all have instances of
`ToElementalComposition`. This provides a uniform approach to working with
elements, elemental compositions, molecular formulae, condensed formulae and
empirical formulae.
```haskell
ghci> nominalMass C
NominalMass {getNominalMass = 12}
ghci> averageMass [mol|CH4|]
AverageMass {getAverageMass = 16.042498912958358}
-ghci> monoisotopicMass [mol|N(CH3)3|]
+ghci> monoisotopicMass [con|N(CH3)3|]
MonoisotopicMass {getMonoisotopicMass = 59.073499294499996}
```
@@ -158,6 +159,36 @@
[IsotopicMass {getIsotopicMass = 45.95262772},IsotopicMass {getIsotopicMass =
46.95175879},IsotopicMass {getIsotopicMass = 47.94794198},IsotopicMass
{getIsotopicMass = 48.94786568},IsotopicMass {getIsotopicMass = 49.94478689}]
```
+### Representing ions in Isotope
+
+Ions are represented in `Isotope` using the `Ion` type class. The `Ion` type
class has two methods, `mz` and `polarity`; where `mz` is mass-to-charge ratio
and `polarity` is either `Positive` or `Negative`. Any type with an
`ToElementalComposition` instance can have an `Ion` instance if charge is not
equal to zero. If charge is equal to zero, a runtime exception will occur!
Ideally, the type system should be put better use to catch this error at
compile-time.
+
+```haskell
+data Ammonium = Ammonium deriving Show
+
+instance ToElementalComposition Ammonium where
+ toElementalComposition _ = mkElementalComposition [(N, 1), (H, 4)]
+ charge _ = Just 1
+
+instance Ion Ammonium
+
+ghci> mz Ammonium
+Mz {getMz = 18.03437413335}
+```
+
+`Protonated` and `Deprotonated` types, with `Ion` instances, are provided to
represent protonated and deprotonated ions, respectively.
+
+```haskell
+ghci> mz . Protonated $ mkMolecularFormula [(H, 2), (O, 1)]
+Mz {getMz = 19.01838971626}
+ghci> mz . Deprotonated $ mkMolecularFormula [(H, 2), (O, 1)]
+Mz {getMz = 17.0027396518}
+ghci> polarity . Protonated $ mkMolecularFormula [(H, 2), (O, 1)]
+Positive
+ghci> polarity . Deprotonated $ mkMolecularFormula [(H, 2), (O, 1)]
+Negative
+```
+
## Comparison to other chemistry libraries
In addition to Isotope, there are two other open-source chemistry libraries
written in Haskell; Radium [2] and Ouch [3].
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/isotope-0.4.0.0/isotope.cabal
new/isotope-0.5.0.1/isotope.cabal
--- old/isotope-0.4.0.0/isotope.cabal 2017-03-11 09:41:07.000000000 +0100
+++ new/isotope-0.5.0.1/isotope.cabal 2017-04-30 01:07:25.000000000 +0200
@@ -1,5 +1,5 @@
name: isotope
-version: 0.4.0.0
+version: 0.5.0.1
synopsis: Isotopic masses and relative abundances.
description: Please see README.md
homepage:
https://github.com/Michaelt293/Element-isotopes/blob/master/README.md
@@ -18,6 +18,7 @@
exposed-modules: Isotope
, Isotope.Base
, Isotope.Parsers
+ , Isotope.Ion
build-depends: base >= 4.7 && < 5
, containers >= 0.5 && < 0.6
, megaparsec >= 5 && < 6
@@ -37,5 +38,6 @@
, megaparsec
other-modules: Isotope.BaseSpec
, Isotope.ParsersSpec
+ , Isotope.IonSpec
ghc-options: -threaded -rtsopts -with-rtsopts=-N
default-language: Haskell2010
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/isotope-0.4.0.0/src/Isotope/Base.hs
new/isotope-0.5.0.1/src/Isotope/Base.hs
--- old/isotope-0.4.0.0/src/Isotope/Base.hs 2017-03-11 09:41:07.000000000
+0100
+++ new/isotope-0.5.0.1/src/Isotope/Base.hs 2017-04-29 12:29:38.000000000
+0200
@@ -189,6 +189,8 @@
-- neutron number) for an isotope.
type MassNumber = Int
+type Charge = Int
+
--------------------------------------------------------------------------------
-- 'Isotope' and 'Element' data types
@@ -638,13 +640,14 @@
-- 'monoisotopicMass', 'nominalMass' and 'averageMass'.
class ToElementalComposition a where
toElementalComposition :: a -> ElementalComposition
+ charge :: a -> Maybe Charge
monoisotopicMass :: a -> MonoisotopicMass
nominalMass :: a -> NominalMass
averageMass :: a -> AverageMass
monoisotopicMass = getFormulaSum elementMonoisotopicMass
nominalMass = getFormulaSum elementNominalMass
averageMass = getFormulaSum elementAverageMass
- {-# MINIMAL (toElementalComposition) #-}
+ {-# MINIMAL (toElementalComposition, charge) #-}
-- Helper function for the calculating monoistopic masses, average mass and
-- nominal masses for molecular formulae.
@@ -672,9 +675,11 @@
instance ToElementalComposition ElementSymbol where
toElementalComposition sym = mkElementalComposition [(sym, 1)]
+ charge _ = Nothing
instance ToElementalComposition ElementalComposition where
toElementalComposition = id
+ charge _ = Nothing
instance Formula ElementalComposition where
renderFormula f = foldMap renderFoldfunc
@@ -742,6 +747,7 @@
instance ToElementalComposition MolecularFormula where
toElementalComposition (MolecularFormula m) = ElementalComposition m
+ charge _ = Nothing
instance Formula MolecularFormula where
renderFormula f = foldMap renderFoldfunc
@@ -766,6 +772,7 @@
instance ToElementalComposition CondensedFormula where
toElementalComposition =
ElementalComposition . getMolecularFormula . toMolecularFormula
+ charge _ = Nothing
instance ToMolecularFormula CondensedFormula where
toMolecularFormula c = foldMap foldFunc (getCondensedFormula c)
@@ -814,6 +821,7 @@
instance ToElementalComposition EmpiricalFormula where
toElementalComposition (EmpiricalFormula a) = ElementalComposition a
+ charge _ = Nothing
instance Formula EmpiricalFormula where
renderFormula f = foldMap renderFoldfunc
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/isotope-0.4.0.0/src/Isotope/Ion.hs
new/isotope-0.5.0.1/src/Isotope/Ion.hs
--- old/isotope-0.4.0.0/src/Isotope/Ion.hs 1970-01-01 01:00:00.000000000
+0100
+++ new/isotope-0.5.0.1/src/Isotope/Ion.hs 2017-04-29 12:29:38.000000000
+0200
@@ -0,0 +1,70 @@
+{-|
+Module : Isotope.Ion
+Description : Provides support for ions.
+Copyright : Michael Thomas
+License : GPL-3
+Maintainer : Michael Thomas <michaelt...@gmail.com>
+Stability : Experimental
+
+This module allows the mass-to-charge ratio and polarity of ions to be
+calculated.
+-}
+module Isotope.Ion where
+
+import Isotope.Base
+import Data.Maybe (fromMaybe)
+import Data.Monoid
+
+-- | The polarity of a charge. A charge can be either `Positive` or `Negative`.
+data Polarity = Positive | Negative
+ deriving (Show, Read, Eq, Ord)
+
+-- | The mass-to-charge ratio of an ion.
+newtype Mz = Mz { getMz :: Double }
+ deriving (Show, Read, Eq, Ord)
+
+-- | The `Ion` type class. This type class has two methods: `mz` and
`polarity`.
+class ToElementalComposition a => Ion a where
+ mz :: a -> Mz
+ polarity :: a -> Polarity
+ mz a = Mz . abs $ monoisotopicMass' / charge'
+ where
+ monoisotopicMass' = getMonoisotopicMass $ monoisotopicMass a
+ charge' = let charge'' = fromMaybe 0 (charge a)
+ in if charge'' /= 0
+ then fromIntegral charge''
+ else error "An ion can't have a charge of 0!"
+ polarity a = polarity' $ fromMaybe 0 (charge a)
+ where
+ polarity' c
+ | c > 0 = Positive
+ | c < 0 = Negative
+ | c == 0 = error "An ion can't have a charge of 0!"
+
+-- | Protonated represents a protonated ion.
+newtype Protonated a = Protonated a deriving (Show, Read, Eq, Ord)
+
+instance ToElementalComposition a => ToElementalComposition (Protonated a)
where
+ toElementalComposition (Protonated a) = toElementalComposition a |+|
+ mkElementalComposition [(H, 1)]
+ charge (Protonated a) = getSum <$> Just (Sum 1) <> (Sum <$> charge a)
+
+instance ToElementalComposition a => Ion (Protonated a)
+
+-- | `doublyProtonated` takes a type and returns a doubly `Protonated` ion.
+doublyProtonated :: a -> Protonated (Protonated a)
+doublyProtonated = Protonated . Protonated
+
+-- | `Deprotonated` represents a deprotonated ion.
+newtype Deprotonated a = Deprotonated a deriving (Show, Read, Eq, Ord)
+
+instance ToElementalComposition a => ToElementalComposition (Deprotonated a)
where
+ toElementalComposition (Deprotonated a) = toElementalComposition a |-|
+ mkElementalComposition [(H, 1)]
+ charge (Deprotonated a) = getSum <$> Just (Sum (-1)) <> (Sum <$> charge a)
+
+instance ToElementalComposition a => Ion (Deprotonated a)
+
+-- | `doublyDeprotonated` takes a type and returns a doubly `Deprotonated` ion.
+doublyDeprotonated :: a -> Deprotonated (Deprotonated a)
+doublyDeprotonated = Deprotonated . Deprotonated
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/isotope-0.4.0.0/test/Isotope/BaseSpec.hs
new/isotope-0.5.0.1/test/Isotope/BaseSpec.hs
--- old/isotope-0.4.0.0/test/Isotope/BaseSpec.hs 2017-03-11
09:41:07.000000000 +0100
+++ new/isotope-0.5.0.1/test/Isotope/BaseSpec.hs 2017-04-29
12:29:38.000000000 +0200
@@ -115,6 +115,8 @@
describe "ToElementalComposition - ElementalComposition instance" $ do
it "toElementalComposition" . property $
\ec -> toElementalComposition ec == (ec :: ElementalComposition)
+ it "charge of an elemental composition should Just 0" . property $
+ \ec -> charge (ec :: ElementalComposition) == Nothing
it "monoisotopic mass of ethanol" $
withinTolerance (getMonoisotopicMass (monoisotopicMass [ele|C2H6O|]))
46.04186 0.0001
`shouldBe` True
@@ -130,9 +132,11 @@
it "should give the correct formula" $
mkElementalComposition [(C, 2), (H, 6), (O, 1)] `shouldBe` [ele|C2H6O|]
- describe "ToElementalComposition - ElementSymbol instance" .
+ describe "ToElementalComposition - ElementSymbol instance" $ do
it "monoisotopicMass" . property $
\sym -> monoisotopicMass sym == monoisotopicMass
(mkElementalComposition [(sym, 1)])
+ it "charge of a symbol should be Just 0" . property $
+ \sym -> charge (sym :: ElementSymbol) == Nothing
describe "Monoid instance for MolecularFormula" $ do
it "associativity" . property $
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/isotope-0.4.0.0/test/Isotope/IonSpec.hs
new/isotope-0.5.0.1/test/Isotope/IonSpec.hs
--- old/isotope-0.4.0.0/test/Isotope/IonSpec.hs 1970-01-01 01:00:00.000000000
+0100
+++ new/isotope-0.5.0.1/test/Isotope/IonSpec.hs 2017-04-29 12:29:38.000000000
+0200
@@ -0,0 +1,22 @@
+module Isotope.IonSpec (spec) where
+
+import Isotope
+import Isotope.Ion
+import Test.Hspec
+
+spec :: Spec
+spec = do
+ describe "mz" $ do
+ it "The mass-to-charge ratio of protonated water should be 19.01838971626"
$
+ mz (Protonated water) `shouldBe` Mz {getMz = 19.01838971626}
+ it "The mass-to-charge ratio of deprotonated water should be
17.0027396518" $
+ mz (Deprotonated water) `shouldBe` Mz {getMz = 17.0027396518}
+
+ describe "polarity" $ do
+ it "The polarity of protonated water should be Positive" $
+ polarity (Protonated water) `shouldBe` Positive
+ it "The polarity of deprotonated water should be Negative" $
+ polarity (Deprotonated water) `shouldBe` Negative
+
+water :: MolecularFormula
+water = mkMolecularFormula [(H, 2), (O, 1)]
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/isotope-0.4.0.0/test/Spec.hs
new/isotope-0.5.0.1/test/Spec.hs
--- old/isotope-0.4.0.0/test/Spec.hs 2016-11-12 04:43:36.000000000 +0100
+++ new/isotope-0.5.0.1/test/Spec.hs 2017-04-29 12:29:38.000000000 +0200
@@ -4,8 +4,10 @@
import Test.QuickCheck
import Isotope.BaseSpec
import Isotope.ParsersSpec
+import Isotope.IonSpec
main :: IO ()
main = hspec $ do
describe "Base" Isotope.BaseSpec.spec
describe "Parsers" Isotope.ParsersSpec.spec
+ describe "Ion" Isotope.IonSpec.spec
