Polymer class revamp (#851)

* added a couple new functions, moved existing code into build function

* added some doc strings

* added a default value to the port labels

* reworked the _add_port function

* saving my progress with the add_end_groups function

* made progress with end group funcitonality

* removing a couple print statements

* added 2 new attributes to port class

* removed changes from port.py, commented out orientation and separation lines

* changed method of removing hydrogens, added n_monomers var for finding last monomer

* adding to the doc strings

* added update_separation function

* update orientation func; separation property func

* added the up subports to the rotations

* fixed the change_orientation function

* fix handling when their is no anchor particle

* fix typo

* docstring: separation is None when port has no anchor

* added 3 unit tests

* remove the port updating stuff I was trying to use

* updating port separations for end groups

* fix the way clone is being called

* added some doc strings and comments

* updated doc strings

* including jupyter notebook example and walk through

* example notebook ready

* added to recipe examples

* expanded end_group options

* update alkane recipe to make tests pass

* cleaned up if statements when updating head/tail ports

* remove trailing whitespace

* allow use of compound with existing ports to be specified in init

whitespace/formatting

* update alkane to new schema

* update tests

* blacked, changed how head/tail port work

* remove debug print

* update notebook

* update notebook

* clear nb

* add back add_hydrogens

* add add_hydrogens=False

* add_hydrogens=False, all tests pass

* changed orientation of down port to face opposite direction of up port

* Few more examples added to show new functionality

* adding a few unit tests

* removing the example notebook from the PR

* test for errors, and manually passing in end group compounds

* expanded doc strings with more detailed explanations, and some examples

* fix a conflict that was sticking around in the port doc strings

* fix formatting in the doc strings

* Doc strings to explain implementation of sequence in the build function

* add unit test for value of n < 1

* 2 new tests to test for errors

* remove unused imports

* oops, typo

Co-authored-by: chrisjonesBSU <[email protected]>
Co-authored-by: Jenny <[email protected]>
Co-authored-by: Jenny Fothergill <[email protected]>

mbuild/lib/moieties/ch2.py

@@ -19,7 +19,7 @@ def __init__(self):
         self.add(mb.Port(anchor=self[0]), "up")
         self["up"].translate([0, 0.07, 0])
 
-        self.add(mb.Port(anchor=self[0]), "down")
+        self.add(mb.Port(anchor=self[0], orientation=[0, -1, 0]), "down")
         self["down"].translate([0, -0.07, 0])
 
 

mbuild/lib/recipes/alkane.py

@@ -71,33 +71,21 @@ def __init__(self, n=3, cap_front=True, cap_end=True):
 
         # Handle general case of n >= 3
         else:
+            end_groups = [None, None]
             # Adjust length of Polmyer for absence of methyl terminations.
-            if not cap_front:
-                n += 1
-            if not cap_end:
-                n += 1
-            chain = mb.recipes.Polymer(
-                CH2(), n=n - 2, port_labels=("up", "down")
-            )
-            self.add(chain, "chain")
             if cap_front:
-                self.add(CH3(), "methyl_front")
-                mb.force_overlap(
-                    move_this=self["chain"],
-                    from_positions=self["chain"]["up"],
-                    to_positions=self["methyl_front"]["up"],
-                )
-            else:
-                # Hoist port label to Alkane level.
-                self.add(chain["up"], "up", containment=False)
-
+                n -= 1
+                end_groups[0] = CH3()
             if cap_end:
-                self.add(CH3(), "methyl_end")
-                mb.force_overlap(
-                    self["methyl_end"],
-                    self["methyl_end"]["up"],
-                    self["chain"]["down"],
-                )
-            else:
+                n -= 1
+                end_groups[1] = CH3()
+
+            chain = mb.recipes.Polymer(monomers=[CH2()], end_groups=end_groups)
+            chain.build(n, add_hydrogens=False)
+            self.add(chain, "chain")
+            if not cap_front:
+                # Hoist port label to Alkane level.
+                self.add(self["chain"]["up"], "up", containment=False)
+            if not cap_end:
                 # Hoist port label to Alkane level.
-                self.add(chain["down"], "down", containment=False)
+                self.add(self["chain"]["down"], "down", containment=False)