Source code for pysimm.models.monomers.gaff.ps

from pysimm import system, lmps, forcefield
from pysimm.apps.random_walk import random_walk

[docs]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 c1 else b.b s.particles.remove(pb.tag, update=False) break s.remove_spare_bonding() c1.linker = 'head' c5.linker = 'tail' lmps.quick_min(s, min_style='fire') s.add_particle_bonding() return s
[docs]def polymer_chain(length): mon = monomer() polym = random_walk(mon, length, forcefield=forcefield.Gaff()) return polym