Skip to content

Implement tetra-PEG #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
clpetix wants to merge 1 commit into
base: main
Choose a base branch
from
Draft

Implement tetra-PEG #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
79 changes: 78 additions & 1 deletion compounds/molecule.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,83 @@ class Butanol(Alcohol):
def __init__(self):
super().__init__(n=4)

class TetraPEGcenter(mb.Compound):
"""Center of the tetraPEG polymer.

This is a carbon with four CO groups attached, each of which can
be used to attach a PEG chain.

"""

def __init__(self):
super().__init__()

# carbon at origin
c = mb.Particle(name='C', element='C', pos=[0,0,0])
self.add(c,'C')

# place carbon arms and hydrogens
c1 = mb.Particle(name='C1', element='C', pos=[0.107911, 0.095853, 0.057694])
c1h1 = mb.Particle(name="C1H1", element="H", pos=[0.06053, 0.17198, 0.12032])
c1h2 = mb.Particle(name="C1H2", element="H", pos=[0.15933, 0.14676, -0.02429])

c2 = mb.Particle(name='C2', element='C', pos=[0.07170, -0.10494, -0.09039])
c2h1 = mb.Particle(name="C2H1", element="H", pos=[0.11844, -0.05440, -0.17532])
c2h2 = mb.Particle(name="C2H2", element="H", pos=[0.15039, -0.15501, -0.03337])

c3 = mb.Particle(name='C3', element='C', pos=[-0.07549, -0.07157, 0.11575])
c3h1 = mb.Particle(name="C3H1", element="H", pos=[-0.15319, -0.13690, 0.07510])
c3h2 = mb.Particle(name="C3H2", element="H", pos=[-0.00565, -0.13355, 0.17261])

c4 = mb.Particle(name='C4', element='C', pos=[-0.09778, 0.08787, -0.08377])
c4h1 = mb.Particle(name="C4H1", element="H", pos=[-0.13560, 0.16946, -0.02154])
c4h2 = mb.Particle(name="C4H2", element="H", pos=[-0.04421, 0.13187, -0.16830])

o1 = mb.Particle(name='O_1', element='O', pos=[0.20502, 0.02589, 0.13608])
o2 = mb.Particle(name='O_2', element='O', pos=[-0.01703, -0.20568, -0.13953])
o3 = mb.Particle(name='O_3', element='O', pos=[-0.13654, 0.02285, 0.20438])
o4 = mb.Particle(name='O_4', element='O', pos=[-0.20989, 0.01454, -0.13365])

# add atoms to the compound
self.add(c1, 'C1')
self.add(c1h1, 'C1H1')
self.add(c1h2, 'C1H2')
self.add(c2, 'C2')
self.add(c2h1, 'C2H1')
self.add(c2h2, 'C2H2')
self.add(c3, 'C3')
self.add(c3h1, 'C3H1')
self.add(c3h2, 'C3H2')
self.add(c4, 'C4')
self.add(c4h1, 'C4H1')
self.add(c4h2, 'C4H2')
self.add(o1, 'O_1')
self.add(o2, 'O_2')
self.add(o3, 'O_3')
self.add(o4, 'O_4')

# bonds to central carbon
self.add_bond((c, c1))
self.add_bond((c, c2))
self.add_bond((c, c3))
self.add_bond((c, c4))

# bond c's to hydrogens
self.add_bond((c1, c1h1))
self.add_bond((c1, c1h2))
self.add_bond((c2, c2h1))
self.add_bond((c2, c2h2))
self.add_bond((c3, c3h1))
self.add_bond((c3, c3h2))
self.add_bond((c4, c4h1))
self.add_bond((c4, c4h2))

# add CO groups
self.add_bond((c1, o1))
self.add_bond((c2, o2))
self.add_bond((c3, o3))
self.add_bond((c4, o4))

class Implicit4SiteWater(mb.Compound):
pass

Expand All @@ -90,7 +167,7 @@ class OPCWater(Implicit4SiteWater):

"""
def __init__(self):
super().__init__()
super().__init__(name="SOL")

# OPC parameters (Table 2)
b = 0.08724 # nm
Expand Down
85 changes: 85 additions & 0 deletions compounds/polymer.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@

from . import geometry
from . import moiety
from . import molecule
from .tools import spin

class CrosslinkedPEGDA(mb.Compound):
Expand Down Expand Up @@ -231,3 +232,87 @@ def __init__(self, n):

def Ree(self):
return self['monomer'][-1]['C2']['C'].pos-self['monomer'][0]['O'].pos

class TetraPEG(mb.Compound):
def __init__(self, n):
super().__init__(name="PEG")

bc = geometry.bond['CT','CT']
bo = geometry.bond['CT','OS']
bh = geometry.bond['HO','OH']

# # create central atom
center = molecule.TetraPEGcenter()
self.add(center)

# create PEG chains
# PEG chain 1 (good)
peg_1 = PolyethyleneOxide(n)
peg_1.translate(center['O_1'].pos)
spin(peg_1, 0, [0,0,1], center['O_1'].pos)
spin(peg_1, -np.pi/4, [0,1,0], center['O_1'].pos)
self.add(peg_1, 'peg_1')
self.remove(peg_1['monomer'][0]['O'])
self.add_bond((center['O_1'], peg_1['monomer'][0]['C1']['C']))

# PEGend 1
O1 = mb.Particle(name='O', element='O', pos=peg_1['monomer'][-1]['C2']['C'].pos + bo*np.array([1,0,0]))
H1 = mb.Particle(name='H', element='H', pos=O1.pos + bh*np.array([1,0,0]))
self.add(O1, 'O1')
self.add(H1, 'H1')
self.add_bond((peg_1['monomer'][-1]['C2']['C'], O1))
self.add_bond((O1, H1))

# PEG chain 2 (good)
peg_2 = PolyethyleneOxide(n)
peg_2.translate(center['O_2'].pos)
spin(peg_2, 3*np.pi/2, [0,0,1], center['O_2'].pos)
spin(peg_2, np.pi/4, [1,0,0], center['O_2'].pos)
self.add(peg_2, 'peg_2')
self.remove(peg_2['monomer'][0]['O'])
self.add_bond((center['O_2'], peg_2['monomer'][0]['C1']['C']))

# PEGend 2
O2 = mb.Particle(name='O', element='O', pos=peg_2['monomer'][-1]['C2']['C'].pos + bo*np.array([-1,0,0]))
H2 = mb.Particle(name='H', element='H', pos=O2.pos + bh*np.array([-1,0,0]))
self.add(O2, 'O2')
self.add(H2, 'H2')
self.add_bond((peg_2['monomer'][-1]['C2']['C'], O2))
self.add_bond((O2, H2))

# PEG chain 3 (good)
peg_3 = PolyethyleneOxide(n)
peg_3.translate(center['O_3'].pos)
spin(peg_3, 3*np.pi/4, [0,0,1], center['O_3'].pos)
spin(peg_3, np.pi/4, [0,1,0], center['O_3'].pos)
self.add(peg_3, 'peg_3')
self.remove(peg_3['monomer'][0]['O'])
self.add_bond((center['O_3'], peg_3['monomer'][0]['C1']['C']))

# PEGend 3
O3 = mb.Particle(name='O', element='O', pos=peg_3['monomer'][-1]['C2']['C'].pos + bo*np.array([0,1,0]))
H3 = mb.Particle(name='H', element='H', pos=O3.pos + bh*np.array([0,1,0]))
self.add(O3, 'O3')
self.add(H3, 'H3')
self.add_bond((peg_3['monomer'][-1]['C2']['C'], O3))
self.add_bond((O3, H3))

# PEG chain 4
peg_4 = PolyethyleneOxide(n)
peg_4.translate(center['O_4'].pos)
spin(peg_4, np.pi, [0,0,1], center['O_4'].pos)
spin(peg_4, -np.pi/4, [0,1,0], center['O_4'].pos)
self.add(peg_4, 'peg_4')
self.remove(peg_4['monomer'][0]['O'])
self.add_bond((center['O_4'], peg_4['monomer'][0]['C1']['C']))

# PEGend 4
O4 = mb.Particle(name='O', element='O', pos=peg_4['monomer'][-1]['C2']['C'].pos + bo*np.array([0,-1,0]))
H4 = mb.Particle(name='H', element='H', pos=O4.pos + bh*np.array([0,-1,0]))
self.add(O4, 'O4')
self.add(H4, 'H4')
self.add_bond((peg_4['monomer'][-1]['C2']['C'], O4))
self.add_bond((O4, H4))

# try to shift polymer to keep it mostly in the bounding box
self.translate(-np.amin(self.xyz,axis=0))