Remove TODO comments (#876)

* remove todo, see issue #875

* see #877

* see #878

* see #879

* see #880

* see #881

* see #882

* see #883

* see #884

* see #885

* see #886

mosdef_gomc/coarse_graining.py

@@ -180,7 +180,6 @@ def _create_proxy_labels(real_thing, memo):
     if not is_leaf(real_thing):
         for label, part in real_thing.labels.items():
             if isinstance(part, list):
-                # TODO support lists with labels
                 continue
             if part in memo:
                 memo[real_thing].labels[label] = memo[part]

mosdef_gomc/compound.py

@@ -302,7 +302,7 @@ def particles_by_element(self, element):
         Parameters
         ----------
         name : str or ele.Element
-            element abbreviation or element 
+            element abbreviation or element
 
         Yields
         ------
@@ -983,7 +983,6 @@ def box(self, box):
             raise TypeError("box must be specified as an mbuild.Box")
         if self.port_particle and box is not None:
             raise ValueError("Ports cannot have a box")
-        # TODO: Fix this for non-orthogonal boxes
         # Make sure the box is bigger than the bounding box
         if box is not None:
             if (box.lengths < self.boundingbox.lengths).any():
@@ -997,7 +996,7 @@ def box(self, box):
     @property
     def element(self):
         return self._element
-    
+
     @element.setter
     def element(self, element):
         if element is None:

mosdef_gomc/conversion.py

@@ -768,9 +768,6 @@ def from_pybel(pybel_mol,
     else:
         if not ignore_box_warn:
             warn("No unitcell detected for pybel.Molecule {}".format(pybel_mol))
-#       TODO: Decide how to gather PBC information from openbabel. Options may
-#             include storing it in .periodicity or writing a separate function
-#             that returns the box.
     return compound
 
 

mosdef_gomc/coordinate_transform.py

@@ -326,7 +326,6 @@ def _create_equivalence_transform(equiv):
                 "and pair[1] is a {1}".format(type(pair[0]), type(pair[1]))
             )
 
-        # TODO: vstack is slow, replace with list concatenation
         if not pair[0].children:
             self_points = np.vstack([self_points, pair[0].pos])
             other_points = np.vstack([other_points, pair[1].pos])
@@ -381,7 +380,6 @@ def equivalence_transform(compound, from_positions, to_positions, add_bond=True)
     if add_bond:
         if isinstance(from_positions, Port) and isinstance(to_positions, Port):
             if not from_positions.anchor or not to_positions.anchor:
-                # TODO: I think warnings is undefined here
                 warn("Attempting to form bond from port that has no anchor")
             else:
                 from_positions.anchor.parent.add_bond(
@@ -400,10 +398,6 @@ def _choose_correct_port(from_port, to_port):
     chooses the set of 4 atoms that makes the anchor atoms not overlap which is
     the intended behavior for most use-cases.
 
-    TODO: -Increase robustness for cases where the anchors are a different
-           distance from their respective ports.
-          -Provide options in `force_overlap` to override this behavior.
-
     Parameters
     ----------
     from_port : mb.Port

mosdef_gomc/formats/compound.proto

@@ -29,8 +29,6 @@ message Compound {
     int64 id = 6; // this is simply a unique number for this compound
     repeated Vec2 bonds = 7;  // a list of 2-tuples
     Element element = 8;
-
-    // Todo: Maybe need something for port particles
 }
 
 

mosdef_gomc/formats/lammpsdata.py

@@ -24,16 +24,16 @@ def _check_minsmaxs(mins, maxs):
     else:
         return False
 
-def write_lammpsdata(structure, filename, atom_style='full', 
+def write_lammpsdata(structure, filename, atom_style='full',
                     unit_style='real',
                     mins=None,
                     maxs=None,
                     detect_forcefield_style=True, nbfix_in_data_file=True,
                     use_urey_bradleys=False,
                     use_rb_torsions=True, use_dihedrals=False):
     """Output a LAMMPS data file.
-    
-    Outputs a LAMMPS data file in the 'full' atom style format. Default units are 
+
+    Outputs a LAMMPS data file in the 'full' atom style format. Default units are
     'real' units. See http://lammps.sandia.gov/doc/atom_style.html for
     more information on atom styles.
 
@@ -58,7 +58,7 @@ def write_lammpsdata(structure, filename, atom_style='full',
     maxs : list
         maximum box dimension in x, y, z directions
     detect_forcefield_style: boolean
-        If True, format lammpsdata parameters based on the contents of 
+        If True, format lammpsdata parameters based on the contents of
         the parmed Structure
     use_urey_bradleys: boolean
         If True, will treat angles as CHARMM-style angles with urey bradley terms
@@ -67,7 +67,7 @@ def write_lammpsdata(structure, filename, atom_style='full',
         If True, will treat dihedrals OPLS-style torsions while looking for
         `structure.rb_torsions`
     use_dihedrals:
-        If True, will treat dihedrals as CHARMM-style dihedrals while looking for 
+        If True, will treat dihedrals as CHARMM-style dihedrals while looking for
         `structure.dihedrals`
 
     Notes
@@ -89,7 +89,7 @@ def write_lammpsdata(structure, filename, atom_style='full',
     # Check if structure is paramterized
     if unit_style == 'lj':
         if any([atom.sigma for atom in structure.atoms]) is None:
-           raise ValueError('LJ units specified but one or more atoms has undefined LJ parameters.') 
+           raise ValueError('LJ units specified but one or more atoms has undefined LJ parameters.')
 
     xyz = np.array([[atom.xx,atom.xy,atom.xz] for atom in structure.atoms])
 
@@ -149,8 +149,7 @@ def write_lammpsdata(structure, filename, atom_style='full',
         xyz = xyz / sigma_conversion_factor
         charges = (charges*1.6021e-19) / np.sqrt(4*np.pi*(sigma_conversion_factor*1e-10)*
           (epsilon_conversion_factor*4184)*epsilon_0)
-        charges[np.isinf(charges)] = 0 
-        # TODO: FIX CHARGE UNIT CONVERSION
+        charges[np.isinf(charges)] = 0
     else:
         sigma_conversion_factor = 1
         epsilon_conversion_factor = 1
@@ -170,7 +169,7 @@ def write_lammpsdata(structure, filename, atom_style='full',
         warn('Explicit box bounds (i.e., mins and maxs) were not provided. Box bounds are assumed to be min = 0 and max = length in each direction. This may not produce a system with the expected spatial location and may cause non-periodic systems to fail. Bounds can be defined explicitly by passing the them to the write_lammpsdata function or by passing box info to the save function.')
     # Divide by conversion factor
     box.maxs /= sigma_conversion_factor
-    
+
     # Lammps syntax depends on the functional form
     # Infer functional form based on the properties of the structure
     if detect_forcefield_style:
@@ -242,11 +241,11 @@ def write_lammpsdata(structure, filename, atom_style='full',
         dihedral_types, unique_dihedral_types = _get_dihedral_types(
                 structure, use_rb_torsions, use_dihedrals,
                 epsilon_conversion_factor)
-            
+
     if impropers:
         improper_types, unique_improper_types = _get_impropers(structure,
                 epsilon_conversion_factor)
-    
+
 
     with open(filename, 'w') as data:
         data.write(filename+' - created by mBuild; units = {}\n\n'.format(
@@ -324,7 +323,7 @@ def write_lammpsdata(structure, filename, atom_style='full',
             epsilon_dict = dict([(unique_types.index(atom_type)+1,epsilon) for atom_type,epsilon in zip(types,epsilons)])
             sigma_dict = dict([(unique_types.index(atom_type)+1,sigma) for atom_type,sigma in zip(types,sigmas)])
             forcefield_dict = dict([(unique_types.index(atom_type)+1,forcefield) for atom_type,forcefield in zip(types,forcefields)])
-            
+
 
 
             # Modified cross-interactions
@@ -543,7 +542,7 @@ def _get_angle_types(structure, use_urey_bradleys,
                     ub_k = ub.type.k
                     ub_req = ub.type.req
             charmm_angle_types.append((round(angle.type.k*(
-                sigma_conversion_factor**2/epsilon_conversion_factor),3), 
+                sigma_conversion_factor**2/epsilon_conversion_factor),3),
                                        round(angle.type.theteq,3),
                                        round(ub_k/epsilon_conversion_factor, 3),
                                        round(ub_req, 3),

mosdef_gomc/formats/protobuf.py

@@ -12,14 +12,9 @@ def write_pb2(cmpd, filename, binary=True):
     ---------
     cmpd : mb.Compound
     filename : str
-    binary: bool, default True 
+    binary: bool, default True
         If True, will print a binary file
         If False, will print to a text file
-        Todo: This could be more elegantly detected
-
-    Notes
-    ----
-    Todo: Handle Ports in the protocol buffer (.proto) and in this writer/reader
     """
     cmpd_to_proto = {}
 
@@ -29,7 +24,7 @@ def write_pb2(cmpd, filename, binary=True):
 
     for sub_cmpd in cmpd.successors():
         parent_cmpd = sub_cmpd.parent
-        sub_proto = cmpd_to_proto[parent_cmpd].children.add() 
+        sub_proto = cmpd_to_proto[parent_cmpd].children.add()
         sub_proto = _mb_to_proto(sub_cmpd, sub_proto)
         cmpd_to_proto[sub_cmpd] = sub_proto
 
@@ -49,10 +44,9 @@ def read_pb2(filename, binary=True):
     Parameters
     ---------
     filename : str
-    binary: bool, default True 
+    binary: bool, default True
         If True, will print a binary file
         If False, will print to a text file
-        Todo: This could be more elegantly detected
 
     Returns
     ------
@@ -99,7 +93,7 @@ def _mb_to_proto(cmpd, proto):
         proto.element.symbol = cmpd.element.symbol
         proto.element.atomic_number = cmpd.element.atomic_number
         proto.element.mass  = cmpd.element.mass
-   
+
     return proto
 
 def _add_proto_bonds(cmpd, proto):
@@ -126,7 +120,7 @@ def _proto_successors(proto):
 
     Notes
     -----
-    Base Case: there are no children to the proto, just return 
+    Base Case: there are no children to the proto, just return
     Recursion: First look at proto's children and return these children (sub_proto)
         Then make the recursive call to look at all the sub_proto's successors
     This is similar to mb.Compound().successors()
@@ -140,12 +134,12 @@ def _proto_successors(proto):
             yield (sub_sub_proto, parent_proto)
 
 def _proto_to_mb(proto):
-    """ Given compound_pb2.Compound, create mb.Compound 
-    
+    """ Given compound_pb2.Compound, create mb.Compound
+
     Parameters
     ----------
     proto: compound_pb2.Compound()
-    
+
     """
     if proto.element.symbol is '':
         elem = None
@@ -154,7 +148,7 @@ def _proto_to_mb(proto):
     return  mb.Compound(name=proto.name,
                 pos=[proto.pos.x, proto.pos.y, proto.pos.z],
                 charge=proto.charge,
-                periodicity=[proto.periodicity.x, proto.periodicity.y, 
+                periodicity=[proto.periodicity.x, proto.periodicity.y,
                             proto.periodicity.z],
                 element=elem)
 

mosdef_gomc/lib/surfaces/amorphous_silica_surface.py

@@ -9,7 +9,6 @@ def __init__(self, surface_roughness=1.0):
         super(AmorphousSilicaSurface, self).__init__()
 
         if surface_roughness == 1.0:
-            # TODO: description of how this surface was generated/citation
             mb.load('amorphous_silica_sr1.0.pdb', compound=self,
                     relative_to_module=self.__module__)
             self.periodicity = np.array([5.4366, 4.7082, 0.0])

mosdef_gomc/pattern.py

@@ -32,7 +32,7 @@ def __init__(self, points, orientations=None, scale=None, **kwargs):
         self.points = points
         if orientations is None:
             orientations = dict()
-        self.orientations = orientations  # TODO: implement for more patterns
+        self.orientations = orientations
         if scale is not None:
             self.scale(scale)
 

mosdef_gomc/tests/test_compound.py

@@ -1162,17 +1162,12 @@ def test_from_pybel_molecule(self, extension):
         pybel = import_('pybel')
         chol = list(pybel.readfile(extension,
             get_fn('cholesterol.{}'.format(extension))))[0]
-        # TODO: Actually store the box information
         cmpd = mb.Compound()
         cmpd.from_pybel(chol)
         assert chol.OBMol.NumAtoms() == cmpd.n_particles
         assert chol.OBMol.NumBonds() == cmpd.n_bonds
         first_atom = chol.OBMol.GetAtom(1)
         assert np.allclose(cmpd[0].pos, [first_atom.GetX()/10, first_atom.GetY()/10, first_atom.GetZ()/10])
-        #assert np.allclose(box.lengths,
-        #        [chol.unitcell.GetA()/10, chol.unitcell.GetB()/10,
-        #            chol.unitcell.GetC()/10],
-        #        rtol=1e-3)
 
     @pytest.mark.parametrize('test_smiles', [
         "CCO",