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.Pcff()
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()
s.pair_style = 'lj/cut'
lmps.quick_min(s, min_style='fire')
s.add_particle_bonding()
return s
def monomer():
try:
s = system.read_pubchem_smiles('O=C(OCCCC)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.Pcff()
s.apply_forcefield(f)
c3 = s.particles[7]
c4 = s.particles[9]
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='fire')
s.add_particle_bonding()
return s
def setUp(self):
self.sst = system.read_pubchem_cid(6360)
self.sst.dim = system.Dimension(xlo=-10,
ylo=-10,
zlo=-10,
xhi=10,
yhi=10,
zhi=10)
self.sst.apply_forcefield(forcefield.Pcff(), charges='gasteiger')
self.fname_temp = 'testfile.output.{}'
self.fname = ''
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.Pcff()
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
def get_types():
types = []
desc = []
molfile = request.form['mol']
ff = request.form['ff']
typer = request.form['typer']
s = system.read_mol(molfile)
try:
if ff == 'Dreiding':
f = forcefield.Dreiding()
s.apply_forcefield(f)
elif ff == 'Polymer Consistent Force Field (PCFF)':
f = forcefield.Pcff()
s.apply_forcefield(f)
elif ff == 'Generalized Amber Force Field (GAFF)':
f = forcefield.Gaff2()
if typer == 'pysimm':
s.apply_forcefield(f)
elif typer == 'antechamber':
cwd = os.getcwd()
tempdir = tempfile.mkdtemp()
print(tempdir)
os.chdir(tempdir)
amber.get_forcefield_types(s, f=f)
os.chdir(cwd)
shutil.rmtree(tempdir)
types = [p.type.name for p in s.particles]
desc = [p.type.desc for p in s.particles]
except:
print('error typing occurred')
p_elems = set(p.elem for p in s.particles)
possible_types = {e: [] for e in p_elems}
possible_types_desc = {e: [] for e in p_elems}
for pt in f.particle_types:
if pt.elem in p_elems:
possible_types[pt.elem].append(pt.name)
possible_types_desc[pt.elem].append(pt.desc)
return jsonify(types=types,
desc=desc,
possible_types=possible_types,
possible_types_desc=possible_types_desc)
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.Pcff()
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:
import os
s = system.read_mol(os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, 'disIpro.mol'))
# s = system.read_pubchem_smiles('CCC(OCCSSCCN)=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.Pcff()
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')
for pb in s.particles:
if pb.elem == 'N':
pb.charge = pb.charge + 1.0
return s
def get_lmps():
molfile = request.form['mol']
type_names = map(lambda x: x.split()[-1],
request.form.getlist('typeNames[]'))
ff = request.form['ff']
if ff == 'Dreiding':
f = forcefield.Dreiding()
elif ff == 'Polymer Consistent Force Field (PCFF)':
f = forcefield.Pcff()
elif ff == 'Generalized Amber Force Field (GAFF)':
f = forcefield.Gaff2()
s = system.read_mol(molfile)
types = {
name: s.particle_types.add(f.particle_types.get(name)[0].copy())
for name in set(type_names)
}
for p, pname in zip(s.particles, type_names):
p.type = types[pname]
s.apply_forcefield(f, skip_ptypes=True)
s.pair_style = f.pair_style
return jsonify(lmpsData=s.write_lammps('string'))
'This is no more than a python2.7 interactive shell with certain pySIMM modules imported for your convenience'
)
print('Importing modules now...')
from pysimm import system, amber, lmps, forcefield
if args.lammps_data:
s = system.read_lammps(args.lammps_data)
elif args.molfile:
s = system.read_mol(args.molfile)
if args.forcefield and args.forcefield in supported_forcefields:
if args.forcefield.lower() == 'dreiding':
print('typing with %s' % args.forcefield)
s.apply_forcefield(forcefield.Dreiding())
elif args.forcefield.lower() == 'pcff':
s.apply_forcefield(forcefield.Pcff())
elif args.forcefield:
print('forcefield %s is not supported in '
'command line interface at this time')
elif args.cml_file:
s = system.read_cml(args.cml_file)
elif args.yaml_file:
s = system.read_yaml(args.yaml_file)
elif args.lmps2xyz:
s = system.read_lammps(args.lmps2xyz[0])
if args.unwrap:
print(
'unwrapping system so bonds do no cross simulation boundaries...'
'this may take a while if your system is large')
s.unwrap()
s.write_xyz(args.lmps2xyz[1])
def run(test=False):
# we'll make a polyethylene monomer and a polystyrene monomer from the pysimm models database
pe = pe_monomer()
ps = ps_monomer()
ba = ba_monomer()
H20 = water_water()
dise = dise_monomer()
disg = disg_monomer()
disi = disi_monomer()
amide = amide_monomer()
peg = peg_monomer()
Na = pos_salt()
Cl = neg_salt()
# we'll instantiate a Dreiding forcefield object for use later
f = forcefield.Pcff()
# the monomers do not have any charges, so we will derive partial charges using the gasteiger algorithm
pe.apply_charges(f, charges='gasteiger')
ps.apply_charges(f, charges='gasteiger')
#H20.apply_charges(f,charges = 'gasteiger')
ba.apply_charges(f,charges = 'gasteiger')
peg.apply_charges(f,charges = 'gasteiger')
amide.apply_charges(f,charges = 'gasteiger')
dise.apply_charges(f,charges='gasteiger')
# the buckingham potential isn't great at small distances, and therefore we use the LJ potential while growing the polymer
pe.pair_style = 'lj/cut'
ps.pair_style = 'lj/cut'
H20.pair_style = 'lj/cut'
ba.pair_style = 'lj/cut'
dise.pair_style = 'lj/cut'
disg.pair_style = 'lj/cut'
peg.pair_style = 'lj/cut'
amide.pair_style = 'lj/cut'
disi.pair_style = 'lj/cut'
Na.pair_style = 'lj/cut'
Cl.pair_style = 'lj/cut'
##### Specifiy What Monomer that you are going to use and the frequency of each Monomer
polist = [ba, amide, disg,disi,dise]
monlist = [2,2,1,1,1]
n_molecules = 10000 # Number of Water Molecules Try to keep it at 10,000
##Current Monomers available
# PEG5 : peg
# Butyl Acrylate : ba
# amide monomer: amide
# Ethelyne: pa
# Polystyrene: ps
# MethylAcrylate: pmma
# disulfideG: disg
# disulfideI: disi
# disulfideE: dise
####################################################################################
pattern = shuffle(monlist, polist)
# run the copolymer random walk method with 10 total repeat units, using an alternating pattern
z = np.ones(len(pattern))
setter = []
for elem in range(0, len(z)):
setter.append(int(z[elem]))
print(setter)
polymer = copolymer(pattern, len(pattern), pattern=setter, forcefield=f)
polymer.write_xyz('polymernonsolvated.xyz')
charge = 0
for pb in polymer.particles:
charge = charge + pb.charge
print("The System has: " + str(charge) + " charge")
numSa = round(charge)
if charge<0:
salt = 'Na'
charg = +1
else:
salt = 'Cl'
charg = -1
partition = n_molecules/(abs(numSa)+1)
if round(charge) == 0:
system.replicate([H20], n_molecules, s_=polymer, density=0.6)
else:
for iters in range(0, abs(numSa)+1):
system.replicate([H20], abs(int(partition)),s_ = polymer, density=0.6)
if iters == abs(numSa):
lmps.quick_min(polymer, min_style='sd')
break
m = polymer.molecules.add(system.Molecule())
dreiding_salt_ = polymer.particle_types.add(f.particle_types.get(salt)[0].copy())
polymer.particles.add(system.Particle(type=dreiding_salt_, x=polymer.dim.dx/2, y=polymer.dim.dy/2, z=polymer.dim.dz/2, charge=charg, molecule=m))
lmps.quick_min(polymer, min_style='sd')
charge = 0
for pb in polymer.particles:
charge = charge + pb.charge
print("The System has: " + str(charge) + " charge")
# write a few different file formats
polymer.write_xyz('polymersolvated.xyz')
# polymer.write_yaml('polymer.yaml')
polymer.write_lammps('polymer.lmps')
