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r_classes.py
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import mbuild as mb
import warnings
import numpy
import ipywidgets as widgets
warnings.filterwarnings('ignore')
class c11_bo(mb.Compound):
def __init__(self):
super(c11_bo, self).__init__()
self.add(mb.load("CCCCCCCCCCCC(CCCC)CCCCCC",smiles=True))
carbon1 = list(self.particles_by_name('C'))[0]
self.add(mb.Port(anchor=carbon1, orientation=[1, -1, -1], separation=0.08), "p1")
H1 = list(self.particles_by_name('H'))[0]
self.remove(H1)
class HD(mb.Compound):
def __init__(self):
super(HD, self).__init__()
self.add(mb.load("CC(CCCCCC)CCCCCCCC",smiles=True))
carbon1 = list(self.particles_by_name('C'))[0]
self.add(mb.Port(anchor=carbon1, orientation=[1, 1, 1], separation=0.08), "p1")
H1 = list(self.particles_by_name('H'))[0]
self.remove(H1)
class ODD(mb.Compound):
def __init__(self):
super(ODD, self).__init__()
self.add(mb.load("CC(CCCCCCCCCC)CCCCCCCC",smiles=True))
carbon1 = list(self.particles_by_name('C'))[0]
self.add(mb.Port(anchor=carbon1, orientation=[-1, -1, -1], separation=0.08), "p1")
H1 = list(self.particles_by_name('H'))[0]
self.remove(H1)
class C1BO(mb.Compound):
def __init__(self):
super(C1BO, self).__init__()
self.add(mb.load("CC(CCCC)CCCCCC",smiles=True))
carbon1 = list(self.particles_by_name('C'))[0]
self.add(mb.Port(anchor=carbon1, orientation=[-1, -1, -1], separation=0.08), "p1")
H1 = list(self.particles_by_name('H'))[0]
self.remove(H1)
class C3BO(mb.Compound):
def __init__(self):
super(C3BO, self).__init__()
self.add(mb.load("CCCC(CCCC)CCCCCC",smiles=True))
carbon1 = list(self.particles_by_name('C'))[0]
self.add(mb.Port(anchor=carbon1, orientation=[-1, -1, -1], separation=0.08), "p1")
H1 = list(self.particles_by_name('H'))[0]
self.remove(H1)
class C4BO(mb.Compound):
def __init__(self):
super(C4BO, self).__init__()
self.add(mb.load("CCCCC(CCCC)CCCCCC",smiles=True))
carbon1 = list(self.particles_by_name('C'))[0]
self.add(mb.Port(anchor=carbon1, orientation=[-1, -1, -1], separation=0.08), "p1")
H1 = list(self.particles_by_name('H'))[0]
self.remove(H1)
class C5BO(mb.Compound):
def __init__(self):
super(C5BO, self).__init__()
self.add(mb.load("CCCCCC(CCCC)CCCCCC",smiles=True))
carbon1 = list(self.particles_by_name('C'))[0]
self.add(mb.Port(anchor=carbon1, orientation=[1, 1, 1], separation=0.08), "p1")
H1 = list(self.particles_by_name('H'))[0]
self.remove(H1)
class C16(mb.Compound):
def __init__(self):
super(C16, self).__init__()
self.add(mb.load("CCCCCCCCCCCCCCCC",smiles=True))
carbon1 = list(self.particles_by_name('C'))[0]
self.add(mb.Port(anchor=carbon1, orientation=[1, 1, 1], separation=0.08), "p1")
H1 = list(self.particles_by_name('H'))[0]
self.remove(H1)
class ene_ODD(mb.Compound):
def __init__(self):
super(ene_ODD, self).__init__()
self.add(mb.load("CCCCCCCCCCC(CCCCCCCC)CCCC(CCCCCCCC)CCCCCCCCCC",smiles=True))
carbon1 = self[20]
self.add(mb.Port(anchor=carbon1, orientation=[1, -1, 1], separation=0.08), "p1")
self.add(mb.Port(anchor=carbon1, orientation=[1, -2, 1], separation=0.08), "p2")
H1 = self[82]
H2 = self[83]
self.remove(H1)
self.remove(H2)
class ene_HD(mb.Compound):
def __init__(self):
super(ene_HD, self).__init__()
self.add(mb.load("CCCCCCCCC(CCCCCC)CCCC(CCCCCC)CCCCCCCC",smiles=True))
carbon1 = self[16]
self.add(mb.Port(anchor=carbon1, orientation=[0, 1, -1], separation=0.08), "p1")
self.add(mb.Port(anchor=carbon1, orientation=[-1, -1, -1], separation=0.08), "p2")
H1 = self[66]
H2 = self[67]
self.remove(H1)
self.remove(H2)