add more side chain option, switch H cap with CH2 cap (#37)

surface_coatings/chains/nbdac_polymer.py

@@ -11,6 +11,12 @@
 from surface_coatings.monomers.mnbdac.side_chains import AminoPropyl
 from surface_coatings.monomers.mnbdac.terminal_groups import Acetaldehyde
 
+# Create custom ch2 cap for the polymer
+# clone this when provided to the polymer
+ch2_cap = CH2()
+ch2_cap.remove(
+    ch2_cap["down"]
+)
 
 class O(mb.Compound):
     """An oxygen with two ports attached."""
@@ -91,7 +97,7 @@ class pNBDAC(mb.Compound):
     terminal_groups: mb.Compound or list of Compounds (len 2)
         Terminal groups which will be matched with side chains
     cap_front : bool, optional, default=True
-        Cap the front of the polymer (NBDAC end)
+        Cap the front of the polymer (NBDAC end) with a CH2
     cap_end : bool, optional, default=False
         Cap the end of the polymer (Silane end)
     buffer : str, optional, default=None
@@ -185,15 +191,15 @@ def __init__(
             self.labels["down"] = self["Polymer"]["down"]
 
         if cap_front:
-            front_cap = H()
+            front_cap = mb.clone(ch2_cap)
             self.add(front_cap, "front_cap")
             mb.force_overlap(
                 move_this=front_cap,
                 from_positions=front_cap["up"],
                 to_positions=self["up"],
             )
         if cap_end:
-            end_cap = H()
+            end_cap = mb.clone(ch2_cap)
             self.add(end_cap, "end_cap")
             mb.force_overlap(
                 move_this=end_cap,

surface_coatings/monomers/mnbdac/side_chains/__init__.py

@@ -1,6 +1,10 @@
 """__init__ file for mNBDAC side chains."""
+from .nh import NH
+from .amino_methyl import AminoMethyl
 from .amino_ethyl import AminoEthyl
 from .amino_propyl import AminoPropyl
+from .o import O
+from .methanol import Methanol
 from .cresol import Cresol
 from .propanol import Propanol
 from .toluidine import Toluidine

surface_coatings/monomers/mnbdac/side_chains/amino_methane.mol2

@@ -0,0 +1,24 @@
+@<TRIPOS>MOLECULE
+RES
+7 6 1 0 1
+SMALL
+NO_CHARGES
+@<TRIPOS>CRYSIN
+    7.4607     6.9693     6.6397    90.0000    90.0000    90.0000 1 1
+@<TRIPOS>ATOM
+       1 C           -0.5716     0.0451    -0.0118 C             1 RES     
+       2 N            0.8404    -0.0115    -0.3628 N             1 RES     
+       3 H           -0.7036    -0.1026     1.0824 H             1 RES     
+       4 H           -0.9886     1.0330    -0.3004 H             1 RES     
+       5 H           -1.1240    -0.7488    -0.5574 H             1 RES     
+       6 H            1.2108    -0.9362    -0.0445 H             1 RES     
+       7 H            1.3367     0.7211     0.1945 H             1 RES     
+@<TRIPOS>BOND
+       1        1        2 1
+       2        1        3 1
+       3        1        4 1
+       4        1        5 1
+       5        2        6 1
+       6        2        7 1
+@<TRIPOS>SUBSTRUCTURE
+       1 RES             1 RESIDUE    0 **** ROOT      0

surface_coatings/monomers/mnbdac/side_chains/amino_methyl.py

@@ -0,0 +1,23 @@
+"""AminoMethyl side chain class."""
+import mbuild as mb
+
+
+class AminoMethyl(mb.Compound):
+    """AminoEthyl side chain class."""
+
+    def __init__(self):
+        super().__init__()
+        mb.load(
+            "amino_methane.mol2",
+            compound=self,
+            backend="gmso",
+            relative_to_module=self.__module__,
+            infer_hierarchy=False,
+        )
+
+        to_remove = [self[4], self[6]]
+        for part in to_remove:
+            self.remove(part)
+
+        self.labels["terminal"] = self["Compound[0]"].labels.pop("port[1]")
+        self.labels["side"] = self["Compound[0]"].labels.pop("port[3]")

surface_coatings/monomers/mnbdac/side_chains/methanol.mol2

@@ -0,0 +1,22 @@
+@<TRIPOS>MOLECULE
+RES
+6 5 1 0 1
+SMALL
+NO_CHARGES
+@<TRIPOS>CRYSIN
+    7.5955     6.7325     6.5627    90.0000    90.0000    90.0000 1 1
+@<TRIPOS>ATOM
+       1 C           -0.3566    -0.0316    -0.0168 C             1 RES     
+       2 O            0.9584    -0.4372    -0.2657 O             1 RES     
+       3 H           -0.5386     0.0288     1.0783 H             1 RES     
+       4 H           -1.0555    -0.7739    -0.4544 H             1 RES     
+       5 H           -0.5477     0.9586    -0.4845 H             1 RES     
+       6 H            1.5400     0.2553     0.1430 H             1 RES     
+@<TRIPOS>BOND
+       1        1        2 1
+       2        1        3 1
+       3        1        4 1
+       4        1        5 1
+       5        2        6 1
+@<TRIPOS>SUBSTRUCTURE
+       1 RES             1 RESIDUE    0 **** ROOT      0

surface_coatings/monomers/mnbdac/side_chains/methanol.py

@@ -0,0 +1,23 @@
+"""Methanol side chain class."""
+import mbuild as mb
+
+
+class Methanol(mb.Compound):
+    """Methanol side chain class."""
+
+    def __init__(self):
+        super().__init__()
+        mb.load(
+            "methanol.mol2",
+            compound=self,
+            backend="gmso",
+            relative_to_module=self.__module__,
+            infer_hierarchy=False,
+        )
+
+        to_remove = [self[3], self[5]]
+        for part in to_remove:
+            self.remove(part)
+
+        self.labels["terminal"] = self["Compound[0]"].labels.pop("port[1]")
+        self.labels["side"] = self["Compound[0]"].labels.pop("port[3]")

surface_coatings/monomers/mnbdac/side_chains/nh.py

@@ -0,0 +1,21 @@
+"""A NH with 2 ports."""
+
+import numpy as np
+
+import mbuild as mb
+
+
+class NH(mb.Compound):
+    """A NH with 2 ports."""
+
+    def __init__(self):
+        super().__init__()
+
+        self.add(mb.load("N", smiles=True))
+
+        h_to_remove = [self[2], self[3]]
+        for h in h_to_remove:
+            self.remove(h)
+
+        self.labels["side"] = self["Compound[0]"].labels.pop("port[1]")
+        self.labels["terminal"] = self["Compound[0]"].labels.pop("port[3]")

surface_coatings/monomers/mnbdac/side_chains/o.py

@@ -0,0 +1,19 @@
+"""An oxygen with 2 ports."""
+
+import numpy as np
+
+import mbuild as mb
+
+
+class O(mb.Compound):
+    """A oxygen with 2 ports."""
+
+    def __init__(self):
+        super().__init__()
+        self.add(mb.Particle(name="O", element="O"))
+
+        self.add(mb.Port(anchor=self[0]), "side")
+        self["side"].translate(np.array([0, 0.07, 0]))
+
+        self.add(mb.Port(anchor=self[0]), "terminal")
+        self["terminal"].translate(np.array([0, -0.07, 0]))