cleanup/docs, additional test, renamed post_remove to _remove

mbuild/compound.py

@@ -132,8 +132,8 @@ def referenced_ports(self):
         from mbuild.port import Port
         return [port for port in self.labels.values() if isinstance(port, Port)]
 
-    def post_remove(self, removed_part):
-        super(Compound, self).post_remove(removed_part)
+    def _remove(self, removed_part):
+        super(Compound, self)._remove(removed_part)
 
         # If removing an atom, make sure to remove the bonds it's part of.
         if isinstance(removed_part, Atom):

mbuild/has_parts_mixin.py

@@ -115,14 +115,14 @@ def remove(self, objs_to_remove):
         objs_to_remove.difference_update(intersection)
 
         for removed_part in intersection:
-            self.post_remove(removed_part)
+            self._remove(removed_part)
 
         # Remove the part recursively from sub-components.
         for part in self.parts:
             if isinstance(part, HasPartsMixin) and len(objs_to_remove) > 0:
                 part.remove(objs_to_remove)
 
-    def post_remove(self, removed_part):
+    def _remove(self, removed_part):
         removed_part.parent = None
         # Remove labels in the hierarchy pointing to this part.
         referrers_to_remove = set()

mbuild/tests/test_compound.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """Tests for `mbuild.compound` module. """
+import pytest
 
 from mbuild.compound import Compound
 from mbuild.examples.ethane.methyl import Methyl
@@ -11,14 +12,30 @@
 class TestCompound:
 
     def test_load_and_create(self):
-        methyl = Compound.load(get_fn('methyl.pdb'))
+        Compound.load(get_fn('methyl.pdb'))
 
     def test_update_from_file(self):
         methyl = Methyl()
         methyl.update_from_file(get_fn("methyl.pdb"))
 
-    def test_write(self):
+    def test_save(self):
         methyl = Compound.load(get_fn('methyl.pdb'))
         methyl.save(filename='methyl_out.pdb')
 
+    @pytest.fixture
+    def ethane(self):
+        from mbuild.examples.ethane.ethane import Ethane
+        return Ethane()
+
+    def test_atom_list_by_kind(self, ethane):
+        non_ports = ethane.atom_list_by_kind(excludeG=True)
+        assert sum([1 for x in non_ports if x.kind != 'G']) == 8
+
+        with_G = ethane.atom_list_by_kind()
+        assert len(with_G) == 24
+
+        only_H = ethane.atom_list_by_kind('H')
+        assert sum([1 for x in only_H if x.kind == 'H']) == 6
 
+        only_G = ethane.atom_list_by_kind('G')
+        assert sum([1 for x in only_G if x.kind == 'G']) == 16

mbuild/tests/test_examples_methane.py

@@ -10,7 +10,7 @@ def methane(self):
         from mbuild.examples.methane.methane import Methane
         return Methane()
 
-    def test_n_atoms(self, methane):
+    def test_numbers(self, methane):
         assert methane.n_atoms == 5
         assert methane.n_bonds == 4
 

mbuild/treeview.py

@@ -1,11 +1,11 @@
-# import os
-# import glob
 import Tkinter
 import ttk
-from compound import *
+from compound import Compound
+from atom import Atom
+from bond import Bond
 
-class TreeView(object):
 
+class TreeView(object):
     def __init__(self, compound, **kwargs):
         self.compound = compound
         self.nodemap = {"root": compound}
@@ -15,50 +15,42 @@ def populate_tree(self, tree, node):
         if tree.set(node, "type") != 'compound':
             return
 
-        # path = tree.set(node, "fullpath")
-        # tree.delete(*tree.get_children(node))
-
-        parent = tree.parent(node)
-
         compound = self.nodemap[node]
 
-
         for child in tree.get_children(node):
-            # print tree.item(child)
             if tree.item(child)['text'] == 'dummy':
                 tree.delete(child)
 
         for v in compound.parts:
             ptype = None
-            if isinstance(v,Compound):
+            if isinstance(v, Compound):
                 ptype = "compound"
-            if isinstance(v,Atom):
+            if isinstance(v, Atom):
                 ptype = "atom"
-            if isinstance(v,Bond):
+            if isinstance(v, Bond):
                 ptype = "bond"
 
             if not v in self.nodemap.values():
-                # find a reference to the object
+                # Find a reference to the object.
                 k = 'na'
-                for rk,rv in compound.labels.iteritems():
+                for rk, rv in compound.labels.iteritems():
                     if v is rv:
                         k = rk
                         break
-
-                id = tree.insert(node, "end", text=k, values=[k, ptype, v.__str__(), str(v.__class__)])
+                id = tree.insert(node, "end", text=k,
+                                 values=[k, ptype, v.__str__(),
+                                         str(v.__class__)])
                 self.nodemap[id] = v
-
                 if ptype == 'compound':
                     tree.insert(id, "end", text="dummy")
 
-
     def populate_roots(self, tree):
         k = ""
         ptype = "compound"
         v = self.compound
-        node = tree.insert("", "end", text="root", values=[k, ptype, v.kind, str(v.__class__)])
+        node = tree.insert("", "end", text="root",
+                           values=[k, ptype, v.kind, str(v.__class__)])
 
-        # node = tree.insert('', 'end', text=str(self.compound.__class__), values=[str(self.compound.__class__), "compound"])
         self.nodemap[node] = self.compound
         self.populate_tree(tree, node)
 
@@ -91,12 +83,11 @@ def show(self):
         hsb = ttk.Scrollbar(orient="horizontal")
 
         tree = ttk.Treeview(columns=("label", "type", "kind", "class"),
-            displaycolumns=("label", "kind", "class"), yscrollcommand=lambda f, l: self.autoscroll(vsb, f, l),
-            xscrollcommand=lambda f, l: self.autoscroll(hsb, f, l))
-
+                            displaycolumns=("label", "kind", "class"),
+                            yscrollcommand=lambda f, l: self.autoscroll(vsb, f, l),
+                            xscrollcommand=lambda f, l: self.autoscroll(hsb, f, l))
         tree.compoundTreeView = self
 
-
         vsb['command'] = tree.yview
         hsb['command'] = tree.xview
 
@@ -110,10 +101,9 @@ def show(self):
         tree.bind('<<TreeviewOpen>>', self.update_tree)
         tree.bind('<Double-Button-1>', self.change_dir)
 
-
         self.populate_roots(tree)
 
-        # Arrange the tree and its scrollbars in the toplevel
+        # Arrange the tree and its scrollbars in the toplevel.
         tree.grid(column=0, row=0, sticky='nswe')
         vsb.grid(column=1, row=0, sticky='ns')
         hsb.grid(column=0, row=1, sticky='ew')
@@ -122,7 +112,9 @@ def show(self):
 
         root.mainloop()
 
+
 if __name__ == "__main__":
-    from ethane import Ethane
+    from mbuild.examples.ethane.ethane import Ethane
+
     ethane = Ethane()
     TreeView(ethane).show()

mbuild/version.py

@@ -1,4 +1,4 @@
 __author__ = 'sallai'
 
-short_version="0.4.2"
+short_version = "0.4.2"
 version = short_version + "beta"