Replace is_numeric with isinstance to speed up parse

atomium/structures/atoms.py

@@ -2,7 +2,7 @@
 
 import weakref
 from math import sqrt, acos, degrees
-from points import Vector, is_numeric
+from points import Vector
 
 class Atom:
     """Represents an atom in three dimensional space. Every atom has an element
@@ -31,19 +31,19 @@ def __init__(self, element, x, y, z, atom_id=None, name=None, charge=0,
             raise TypeError("Element '{}' is not str".format(element))
         if not 0 < len(element) < 3:
             raise ValueError("Element {} is not 1 or 2 chars".format(element))
-        if not is_numeric(x):
+        if not isinstance(x, (float, int)):
             raise TypeError("x coordinate '{}' is not numeric".format(x))
-        if not is_numeric(y):
+        if not isinstance(y, (float, int)):
             raise TypeError("y coordinate '{}' is not numeric".format(y))
-        if not is_numeric(z):
+        if not isinstance(z, (float, int)):
             raise TypeError("z coordinate '{}' is not numeric".format(z))
         if atom_id is not None and not isinstance(atom_id, int):
             raise TypeError("ID {} is not an integer".format(atom_id))
         if name is not None and not isinstance(name, str):
             raise TypeError("name {} is not a string".format(name))
-        if not is_numeric(charge):
+        if not isinstance(charge, (float, int)):
             raise TypeError("charge '{}' is not numeric".format(charge))
-        if not is_numeric(bfactor):
+        if not isinstance(bfactor, (float, int)):
             raise TypeError("bfactor '{}' is not numeric".format(bfactor))
         self._element = element
         self._x = x
@@ -96,7 +96,7 @@ def x(self, x=None):
         if x is None:
             return self._x
         else:
-            if not is_numeric(x):
+            if not isinstance(x, (float, int)):
                 raise TypeError("x coordinate '{}' is not numeric".format(x))
             self._x = x
 
@@ -112,7 +112,7 @@ def y(self, y=None):
         if y is None:
             return self._y
         else:
-            if not is_numeric(y):
+            if not isinstance(y, (float, int)):
                 raise TypeError("y coordinate '{}' is not numeric".format(y))
             self._y = y
 
@@ -128,7 +128,7 @@ def z(self, z=None):
         if z is None:
             return self._z
         else:
-            if not is_numeric(z):
+            if not isinstance(z, (float, int)):
                 raise TypeError("z coordinate '{}' is not numeric".format(z))
             self._z = z
 
@@ -211,7 +211,7 @@ def charge(self, charge=None):
         if charge is None:
             return self._charge
         else:
-            if not is_numeric(charge):
+            if not isinstance(charge, (float, int)):
                 raise TypeError("charge '{}' is not numeric".format(charge))
             self._charge = charge
 
@@ -227,7 +227,7 @@ def bfactor(self, bfactor=None):
         if bfactor is None:
             return self._bfactor
         else:
-            if not is_numeric(bfactor):
+            if not isinstance(bfactor, (float, int)):
                 raise TypeError("bfactor '{}' is not numeric".format(bfactor))
             self._bfactor = bfactor
 

tests/unit/structure_tests/test_chains.py

@@ -17,8 +17,8 @@ def setUp(self):
         self.mock_residues = self.patcher2.start()
         self.mock_residues.return_value = (self.residue1, self.residue2)
         def mock_init(obj, *args, **kwargs):
-            obj._atoms = set()
-            obj._id_atoms = {}
+            obj._atoms = set(args[:1])
+            obj._id_atoms = {i: arg for i, arg in enumerate(args[1:])}
         self.mock_init = mock_init
 
 

tests/unit/structure_tests/test_molecules.py

@@ -9,8 +9,8 @@ def setUp(self):
         self.atom1, self.atom2, self.atom3 = Mock(Atom), Mock(Atom), Mock(Atom)
         self.atoms = [self.atom1, self.atom2, self.atom3]
         def mock_init(obj, *args, **kwargs):
-            obj._atoms = set()
-            obj._id_atoms = {}
+            obj._atoms = set(args[:1])
+            obj._id_atoms = {i: arg for i, arg in enumerate(args[1:])}
         self.mock_init = mock_init
 
 

tests/unit/structure_tests/test_residues.py

@@ -11,8 +11,8 @@ def setUp(self):
         for index, atom in enumerate(self.atoms, start=1):
             atom.atom_id.return_value = index
         def mock_init(obj, *args, **kwargs):
-            obj._atoms = set()
-            obj._id_atoms = {}
+            obj._atoms = set(args[:1])
+            obj._id_atoms = {i: arg for i, arg in enumerate(args[1:])}
         self.mock_init = mock_init