PEP8 and cleaning

pycgtool/bondset.py

@@ -13,7 +13,6 @@ class Bond:
         self.values = []
 
     def boltzmann_invert(self, temp=310):
-        # TODO needs tests
         mean, var = stat_moments(self.values)
 
         rt = 8.314 * temp / 1000.
@@ -60,9 +59,9 @@ class BondSet:
     def _populate_atom_numbers(self, mapping):
         for mol in self._molecules:
             molmap = mapping[mol]
+            index = [bead.name for bead in molmap]
             for bond in self._molecules[mol]:
-                ind = lambda name: [bead.name for bead in molmap].index(name)
-                bond.atom_numbers = [ind(atom) for atom in bond.atoms]
+                bond.atom_numbers = [index.index(atom) for atom in bond.atoms]
 
     def write_itp(self, filename, mapping):
         self._populate_atom_numbers(mapping)
@@ -173,4 +172,3 @@ class BondSet:
 
     def __iter__(self):
         return iter(self._molecules)
-

pycgtool/forcefield.py

 import os
 
+# Python 3.2 doesn't have FileExistsError
 try:
     raise FileExistsError
 except NameError:
@@ -22,4 +23,3 @@ class ForceField:
 
     def write_rtp(self, mapping, bonds):
         pass
-

pycgtool/mapping.py

@@ -90,4 +90,3 @@ class Mapping:
 
             cgframe.residues.append(res)
         return cgframe
-

pycgtool/parsers/cfg.py

 import os
 
+
 class Section:
     __slots__ = ["name", "_lines"]
 
@@ -33,18 +34,18 @@ class CFG:
         with open(self.filename) as f:
             curr_section = None
             for line in f:
-                line = line.strip("\n")
-                if line == "":
-                    continue
-                elif line[0] == ";":
+                line = line.strip(" \t\n")
+                if not line or line.startswith(";"):
                     continue
+
                 elif line.startswith("#include"):
                     cfg2 = CFG(os.path.join(os.path.dirname(self.filename),
                                             line.split()[1]))
                     self._sections.update(cfg2._sections)
                     self._section_names += cfg2._section_names
                     continue
-                elif line[0] == "[":
+
+                elif line.startswith("["):
                     curr_section = line.strip("[ ]")
                     if curr_section in self._sections:
                         raise DuplicateSectionError(curr_section, self.filename)
@@ -84,4 +85,3 @@ class CFG:
 
     def __getitem__(self, item):
         return self._sections[item]
-

pycgtool/util.py

@@ -25,6 +25,12 @@ def stat_moments(vals):
 
 
 def sliding(vals):
+    """
+    Yield three values in a sliding window along an iterable.
+
+    :param vals: Iterable to iterate over
+    :return: Iterable of tuples
+    """
     it = iter(vals)
     prev = None
     current = next(it)
@@ -33,5 +39,3 @@ def sliding(vals):
         prev = current
         current = nxt
     yield (prev, current, None)
-
-