def monomer():
try:
s = system.read_pubchem_smiles('CC')
except:
import os
s = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, 'CC.mol'))
f = forcefield.Gaff()
s.apply_forcefield(f)
c1 = s.particles[1]
c2 = s.particles[2]
c1.linker = 'head'
c2.linker = 'tail'
for b in c1.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c1 else b.b
s.particles.remove(pb.tag, update=False)
break
for b in c2.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c2 else b.b
s.particles.remove(pb.tag, update=False)
break
s.remove_spare_bonding()
lmps.quick_min(s, min_style='fire')
s.add_particle_bonding()
return s
def monomer():
try:
s = system.read_pubchem_smiles('CCC(OCCSSCCO)=O')
except:
import os
s = system.read_mol(os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, 'CC(C)C(=O)OC.mol'))
f = forcefield.Gaff()
s.apply_forcefield(f)
c3 = s.particles[8]
c4 = s.particles[11]
for b in c3.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c3 else b.b
s.particles.remove(pb.tag, update=False)
break
for b in c4.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c4 else b.b
s.particles.remove(pb.tag, update=False)
break
s.remove_spare_bonding()
c3.linker = 'head'
c4.linker = 'tail'
lmps.quick_min(s, min_style='cg')
s.add_particle_bonding()
return s
def monomer():
try:
import os
s = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, 'disGde.mol'))
# s = system.read_pubchem_smiles('O=C(OCCSSCCC(O)=O)CC')
except:
import os
s = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, 'CC(C)C(=O)OC.mol'))
f = forcefield.Gaff()
s.apply_forcefield(f)
c3 = s.particles[1]
c4 = s.particles[2]
for b in c3.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c3 else b.b
s.particles.remove(pb.tag, update=False)
break
for b in c4.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c4 else b.b
s.particles.remove(pb.tag, update=False)
break
s.remove_spare_bonding()
c3.linker = 'head'
c4.linker = 'tail'
lmps.quick_min(s, min_style='cg')
s.add_particle_bonding()
s.apply_charges(f, charges='gasteiger')
signal = 0
for pb in s.particles:
if pb.elem == 'O' and 1 in pb.bond_orders and len(set(
pb.bond_orders)) == 1:
signal += 1
if signal == 2 and pb.elem == 'O' and 1 in pb.bond_orders and len(
set(pb.bond_orders)) == 1:
pb.charge = pb.charge - 1
return s
def monomer():
try:
s = system.read_pubchem_smiles('CCc1=cc=cc=c1')
except:
import os
s = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, 'CCc1=cc=cc=c1.mol'))
m = s.molecules[1]
f = forcefield.Gaff()
for b in s.bonds:
if b.a.bonds.count == 3 and b.b.bonds.count == 3:
b.order = 4
s.apply_forcefield(f)
c1 = s.particles[1]
c5 = s.particles[5]
for b in c1.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c1 else b.b
s.particles.remove(pb.tag, update=False)
break
for b in c5.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c5 else b.b
s.particles.remove(pb.tag, update=False)
break
s.remove_spare_bonding()
s.set_box(padding=10)
c1.linker = 'head'
c5.linker = 'tail'
lmps.quick_min(s, min_style='fire')
s.add_particle_bonding()
return s
from pysimm import system, lmps, forcefield, gasteiger
# create empty system
s = system.System()
# create new molecule in our system
m = s.molecules.add(system.Molecule())
# retrieve GAFF parameters
f = forcefield.Gaff()
# get a copy of the c3 particle type object from GAFF
# get method returns a list, we need the first element
gaff_c3 = f.particle_types.get('c3')[0].copy()
# now we need to add this particle type to our system
s.particle_types.add(gaff_c3)
# we'll first make the carbon atom at the origin
# we'll include gasteiger charges later
c1 = s.particles.add(
system.Particle(type=gaff_c3, x=0, y=0, z=0, charge=0, molecule=m))
# get hc particle type object from GAFF
gaff_hc = f.particle_types.get('hc')[0].copy()
# add hc particle type to system
s.particle_types.add(gaff_hc)
# now we'll add 4 hydrogen atoms bonded to our carbon atom
# these atoms will be placed randomly 1.5 angstroms from the carbon atom
def polymer_chain(length):
mon = monomer()
polym = random_walk(mon, length, forcefield=forcefield.Gaff())
return polym