From 783baf3bd8d32ef0535f351c6bc07122ed7b3078 Mon Sep 17 00:00:00 2001
From: Co Quach <43968221+daico007@users.noreply.github.com>
Date: Mon, 11 Mar 2024 07:08:21 -0500
Subject: [PATCH] add more side chain option, switch H cap with CH2 cap (#37)
---
surface_coatings/chains/nbdac_polymer.py | 12 +++++++---
.../monomers/mnbdac/side_chains/__init__.py | 4 ++++
.../mnbdac/side_chains/amino_methane.mol2 | 24 +++++++++++++++++++
.../mnbdac/side_chains/amino_methyl.py | 23 ++++++++++++++++++
.../monomers/mnbdac/side_chains/methanol.mol2 | 22 +++++++++++++++++
.../monomers/mnbdac/side_chains/methanol.py | 23 ++++++++++++++++++
.../monomers/mnbdac/side_chains/nh.py | 21 ++++++++++++++++
.../monomers/mnbdac/side_chains/o.py | 19 +++++++++++++++
8 files changed, 145 insertions(+), 3 deletions(-)
create mode 100644 surface_coatings/monomers/mnbdac/side_chains/amino_methane.mol2
create mode 100644 surface_coatings/monomers/mnbdac/side_chains/amino_methyl.py
create mode 100644 surface_coatings/monomers/mnbdac/side_chains/methanol.mol2
create mode 100644 surface_coatings/monomers/mnbdac/side_chains/methanol.py
create mode 100644 surface_coatings/monomers/mnbdac/side_chains/nh.py
create mode 100644 surface_coatings/monomers/mnbdac/side_chains/o.py
diff --git a/surface_coatings/chains/nbdac_polymer.py b/surface_coatings/chains/nbdac_polymer.py
index 8b1789e..7f206ca 100644
--- a/surface_coatings/chains/nbdac_polymer.py
+++ b/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
@@ -185,7 +191,7 @@ 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,
@@ -193,7 +199,7 @@ def __init__(
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,
diff --git a/surface_coatings/monomers/mnbdac/side_chains/__init__.py b/surface_coatings/monomers/mnbdac/side_chains/__init__.py
index c6d603f..ed14e57 100644
--- a/surface_coatings/monomers/mnbdac/side_chains/__init__.py
+++ b/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
diff --git a/surface_coatings/monomers/mnbdac/side_chains/amino_methane.mol2 b/surface_coatings/monomers/mnbdac/side_chains/amino_methane.mol2
new file mode 100644
index 0000000..28c9829
--- /dev/null
+++ b/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
diff --git a/surface_coatings/monomers/mnbdac/side_chains/amino_methyl.py b/surface_coatings/monomers/mnbdac/side_chains/amino_methyl.py
new file mode 100644
index 0000000..676c62f
--- /dev/null
+++ b/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]")
diff --git a/surface_coatings/monomers/mnbdac/side_chains/methanol.mol2 b/surface_coatings/monomers/mnbdac/side_chains/methanol.mol2
new file mode 100644
index 0000000..4af1b66
--- /dev/null
+++ b/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
diff --git a/surface_coatings/monomers/mnbdac/side_chains/methanol.py b/surface_coatings/monomers/mnbdac/side_chains/methanol.py
new file mode 100644
index 0000000..7e74dbb
--- /dev/null
+++ b/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]")
diff --git a/surface_coatings/monomers/mnbdac/side_chains/nh.py b/surface_coatings/monomers/mnbdac/side_chains/nh.py
new file mode 100644
index 0000000..1150c04
--- /dev/null
+++ b/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]")
diff --git a/surface_coatings/monomers/mnbdac/side_chains/o.py b/surface_coatings/monomers/mnbdac/side_chains/o.py
new file mode 100644
index 0000000..b9eda93
--- /dev/null
+++ b/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]))