Merge pull request #6 from n-elie/master

Fix add/sub Formula objects

src/lipyd/formula.py

@@ -179,7 +179,7 @@ def __iadd__(self, other):
 
     def __sub__(self, other):
 
-        new = copy.copy(self)
+        new = copy.deepcopy(self)
         new.__isub__(other)
         return new
 
@@ -203,6 +203,9 @@ def __isub__(self, other):
         self.charge -= (other.charge if hasattr(other, 'charge') else 0)
         self.isotope -= (other.isotope if hasattr(other, 'isotope') else 0)
 
+        self.calc_mass()
+        self.update_mz()
+
         return self
 
     def __imul__(self, other):
@@ -211,12 +214,12 @@ def __imul__(self, other):
 
             return self
 
-        for elem, cnt in iteritems(self.atoms):
+        for elem, cnt in iteritems(self._atoms):
 
             self.counts[elem] = cnt * other
 
         self.calc_mass()
-        self.formula_from_dict(self.atoms)
+        self.formula_from_dict(self._atoms)
         self.isotope = self.isotope * other
 
     def __mul__(self, other):
@@ -227,7 +230,7 @@ def __mul__(self, other):
 
         new_atoms = defaultdict(int)
 
-        for elem, cnt in iteritems(self.atoms):
+        for elem, cnt in iteritems(self._atoms):
 
             new_atoms[elem] = cnt * other
 
@@ -254,7 +257,7 @@ def as_mass(self):
         Returns this ``Formula`` instance as ``mass.MassBase`` object.
         """
 
-        return MassBase(self.formula, self.charge, self.isotope)
+        return mass.MassBase(self.formula, self.charge, self.isotope)
 
 
     def add(self, formula):
@@ -268,7 +271,7 @@ def add(self, formula):
         """
 
         for elem, cnt in mass._re_form.findall(formula):
-            self.atoms[elem] += int(cnt or '1')
+            self._atoms[elem] += int(cnt or '1')
 
         self.update()
 
@@ -284,9 +287,9 @@ def sub(self, formula):
         """
 
         for elem, cnt in mass._re_form.findall(formula):
-            self.atoms[elem] -= int(cnt or '1')
+            self._atoms[elem] -= int(cnt or '1')
 
-            if self.atoms[elem] < 0:
+            if self._atoms[elem] < 0:
 
                 raise ValueError('Can not remove %s from %s: '
                     'too few %s atoms!' % (formula, self.formula, elem))
@@ -300,10 +303,10 @@ def update(self):
         re-calculates the mass.
         """
 
-        if len(self.atoms):
+        if len(self._atoms):
 
-            self.formula = ''.join('%s%u' % (elem, self.atoms[elem])
-                                    for elem in sorted(self.atoms.keys()))
+            self.formula = ''.join('%s%u' % (elem, self._atoms[elem])
+                                    for elem in sorted(self._atoms.keys()))
             self.calc_mass()
 
 

src/lipyd/mass.py

@@ -572,7 +572,7 @@ def calc_mass(self):
                 )
                 m = 0.0
                 for element, count in atoms:
-                    count = int(count or '1')
+                    count = int('1' if count == '' else count)
                     m += self.exmass[element] * count
 
                 if self.isotope: