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 run(test=False):
# use a smiles string to query the pubchem search database and read the mol file returned from the http request
# if cannot get to internet, read local cached response from pubchem
try:
s = system.read_pubchem_smiles('c1=cc=cc=c1')
except:
import os
s = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, 'c1=cc=cc=c1.mol'))
# the resulting system (benzene) has alternating double bonds
# we want pysimm to recognize the ring as aromatic, so we define each bond in the ring to be bond order 'A'
for b in s.bonds:
if b.a.elem == 'C' and b.b.elem == 'C':
b.order = 'A'
# the resulting system has sufficient information to type with a forcefield, here we will use the Dreiding force field
# we will also determine partial charges using the gasteiger algorithm
s.apply_forcefield(forcefield.Dreiding(), charges='gasteiger')
# we'll perform a 2 step energy minimization using the steepest decent and conjugate gradient algorithms in LAMMPS
lmps.quick_min(s, min_style='sd', name='min_sd')
lmps.quick_min(s, min_style='cg', name='min_cg')
# write a few different file formats
s.write_xyz('benzene.xyz')
s.write_yaml('benzene.yaml')
s.write_lammps('benzene.lmps')
s.write_chemdoodle_json('benzene.json')
def monomer():
try:
s = system.read_pubchem_smiles('CC(C)C(=O)OC')
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.Dreiding()
s.apply_forcefield(f)
c3 = s.particles[3]
c4 = s.particles[4]
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 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 test_read_v3000mol(self):
# check the v2000 format mol file
file_path = os.path.join(self.TEST_DATA_PATH,
'testfile.molv3000_input.mol')
test_sst = system.read_mol(file_path, version='V3000')
self.assertGreater(len(test_sst.particles), 0)
self.assertGreater(len(test_sst.bonds), 0)
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.Dreiding()
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 monomer(**kwargs):
isomer = kwargs.get('isomer', {})
try:
import os
if isomer == 'endo':
s = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, 'NbTMS_H2_endo.mol'))
elif isomer == 'exo_endo':
s = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, 'NbTMS_H2_exo_endo.mol'))
else:
s = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, 'NbTMS_H2_exo_exo.mol'))
except:
print("!!!could not read mol!!!")
raise
f = forcefield.Dreiding()
for b in s.bonds:
if b.a.bonds.count == 3 and b.b.bonds.count == 3:
b.order = 4
s.apply_forcefield(f)
h = s.particles[7]
t = s.particles[8]
m = s.particles[32]
s.remove_spare_bonding()
s.set_box(padding=10)
h.linker = 'head'
t.linker = 'tail'
m.linker = 'mirror'
# lmps.quick_min(s, min_style='fire')
s.add_particle_bonding()
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
def SPC():
try:
s = system.read_pubchem_smiles('[H]O[H]')
except:
import os
s = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, 'CC.mol'))
f = forcefield.Dreiding()
s.apply_forcefield(f)
for pb in s.particles:
if pb.elem == 'H':
pb.charge = 0.4238
elif pb.elem == 'O':
pb.charge = -0.8476
lmps.quick_min(s, min_style='fire')
return s
def run(test=False):
# use a smiles string to query the pubchem search database and read the mol file returned from the http request
try:
s = system.read_pubchem_smiles('CO')
except:
import os
s = system.read_mol(os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, 'CO.mol'))
# the resulting system has sufficient information to type with a forcefield, here we will use the GAFF2 force field
s.apply_forcefield(forcefield.Gaff2())
# we'll perform energy minimization using the fire algorithm in LAMMPS
lmps.quick_min(s, min_style='fire')
# write a few different file formats
s.write_xyz('methanol.xyz')
s.write_yaml('methanol.yaml')
s.write_lammps('methanol.lmps')
s.write_chemdoodle_json('methanol.json')
def monomer(ff, is_capped=False):
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, 'topologies', 'CCc1=cc=cc=c1.mol'))
for b in s.bonds:
if b.a.bonds.count == 3 and b.b.bonds.count == 3:
b.order = 4
c1 = s.particles[1]
c5 = s.particles[5]
c1.linker = 'head'
c5.linker = 'tail'
if not is_capped:
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.apply_forcefield(ff, charges='gasteiger')
s.set_box(padding=10)
sim = lmps.Simulation(s, print_to_screen=False, log='ps_mon_relax.log')
sim.add(lmps.Init())
sim.add_min(min_style='fire')
sim.run()
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 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'))
def run(test=False):
try:
ethanol = system.read_pubchem_smiles('CCO')
except:
import os
ethanol = system.read_mol(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'CCO.mol'))
try:
acetone = system.read_pubchem_smiles('CC(=O)C')
except:
import os
acetone = system.read_mol(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'CC(=O)C.mol'))
f = forcefield.Gaff2()
ethanol.apply_forcefield(f, charges='gasteiger')
acetone.apply_forcefield(f, charges='gasteiger')
# amber.calc_charges(ethanol)
# amber.calc_charges(acetone)
lmps.quick_min(ethanol, min_style='fire')
lmps.quick_min(acetone, min_style='fire')
molecule_list = [ethanol, acetone]
if test:
n_molecules = [20, 20]
else:
n_molecules = [200, 200]
s = system.replicate(molecule_list, n_molecules, density=0.3)
min_settings = {
'name': 'cg_min',
'min_style': 'cg',
'maxiter': int(5e+5),
'maxeval': int(5e+6),
}
nvt_settings = {
'name': 'nvt_md',
'print_to_screen': True,
'ensemble': 'nvt',
'temperature': {
'start': 100,
'stop': 300
},
'new_v': True,
'length': 2500
}
npt_settings = {
'name': 'npt_md',
'print_to_screen': True,
'ensemble': 'npt',
'temperature': 300,
'new_v': True,
'pressure': {
'start': 1000,
'stop': 1
},
'length': 5000,
}
npt_settings_add = {
'name': 'npt_md',
'print_to_screen': True,
'ensemble': 'npt',
'temperature': 300,
'new_v': True,
'pressure': {
'start': 1,
'stop': 1
},
'length': 5000,
}
if test:
nvt_settings['length'] = 2000
npt_settings['length'] = 2000
sim = lmps.Simulation(s)
sim.add_min(**min_settings)
sim.add(lmps.OutputSettings(thermo={'freq': 500,
'style': 'custom',
'args': ['step', 'temp', 'etotal', 'press', 'density']}))
sim.add_md(**nvt_settings)
sim.add_md(**npt_settings)
sim.add_md(**npt_settings_add)
sim.run()
s.write_yaml('mixture.yaml')
s.write_lammps('mixture.lmps')
import numpy
from pysimm import lmps
from pysimm import system
from pysimm import forcefield
sst = system.read_mol('ethylpropylether.mol')
# decorate the system read from a simple .mol file and type it with CHARMM FF parameters and simple gasteiger charges
for b in sst.bonds:
b.order = 1
ff = forcefield.Charmm()
sst.apply_forcefield(ff, charges='gasteiger')
sst.set_charge()
# also expand the system to a minimal size at which the periodic image convention is held
bxSize = 25.0
sst.dim.dx = bxSize
sst.dim.dy = bxSize
sst.dim.dz = bxSize
sst.center('box', [0.0, 0.0, 0.0], True)
# read a water molecule from .lmps file that already contains all details
solvnt = system.read_lammps('tipS3P.lmps', angle_style='charmm')
# knowing volume of the box let's find out how many water molecules are needed to feet at each side of a cubic box:
solvnt.set_mass()
ngrid = numpy.floor(((bxSize ** 3) * 0.6022 / solvnt.mass) ** (1.0 / 3.0))
# put water molecules in the nodes of a regular grid
rng = numpy.linspace(sst.dim.xlo, sst.dim.xhi, int(ngrid) + 1)
count = 0
def run(test=False):
try:
ethanol = system.read_pubchem_smiles('CCO')
except:
import os
ethanol = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'CCO.mol'))
try:
acetone = system.read_pubchem_smiles('CC(=O)C')
except:
import os
acetone = system.read_mol(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'CC(=O)C.mol'))
f = forcefield.Gaff2()
ethanol.apply_forcefield(f, charges='gasteiger')
acetone.apply_forcefield(f, charges='gasteiger')
# amber.calc_charges(ethanol)
# amber.calc_charges(acetone)
lmps.quick_min(ethanol, min_style='fire')
lmps.quick_min(acetone, min_style='fire')
molecule_list = [ethanol, acetone]
if test:
n_molecules = [30, 20]
else:
n_molecules = [300, 200]
s = system.replicate(molecule_list, n_molecules, density=0.3)
min_settings = {
'name': 'fire_min',
'min_style': 'fire',
'print_to_screen': True
}
nvt_settings = {
'name': 'nvt_md',
'print_to_screen': True,
'ensemble': 'nvt',
'temperature': {
'start': 100,
'stop': 300
},
'new_v': True,
'length': 10000
}
npt_settings = {
'name': 'npt_md',
'print_to_screen': True,
'ensemble': 'npt',
'temperature': 300,
'new_v': True,
'pressure': {
'start': 1000,
'stop': 1
},
'length': 100000,
'thermo_style': 'custom step temp press density'
}
if test:
nvt_settings['length'] = 2000
npt_settings['length'] = 2000
lmps.quick_min(s, **min_settings)
lmps.quick_md(s, **nvt_settings)
lmps.quick_md(s, **npt_settings)
s.write_xyz('mixture.xyz')
s.write_yaml('mixture.yaml')
s.write_lammps('mixture.lmps')
s.write_chemdoodle_json('mixture.json')
'PySIMM:', *a) if pysimm.verbose else lambda *a, **k: None
pysimm.debug_print = lambda *a, **k: print(
'(debug) PySIMM:', *a) if pysimm.debug else lambda *a, **k: None
print('\nWelcome to the pySIMM command line interface\n')
print(
'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])
