def remove_clashes(self):
""" Remove clashes from modeled glycans
"""
dihe_parameters = self.myGlycosylator.builder.Parameters.parameters[
'DIHEDRALS']
vwd_parameters = self.myGlycosylator.builder.Parameters.parameters[
'NONBONDED']
static_glycans = None
for k in self.original_glycanMolecules:
if k not in self.linked_glycanMolecules:
if static_glycans is not None:
static_glycans += self.original_glycanMolecules[
k].atom_group
else:
static_glycans = self.original_glycanMolecules[
k].atom_group.copy()
environment = self.myGlycosylator.protein.copy()
environment += static_glycans
#Build topology
self.myGlycosylator.build_glycan_topology(
glycanMolecules=self.linked_glycanMolecules, build_all=False)
sampler = glc.Sampler(self.linked_glycanMolecules.values(),
environment, dihe_parameters, vwd_parameters)
sampler.remove_clashes_GA()
myGlycosylator = gl.Glycosylator(
os.path.join(gl.GLYCOSYLATOR_PATH,
'support/toppar_charmm/carbohydrates.rtf'),
os.path.join(gl.GLYCOSYLATOR_PATH,
'support/toppar_charmm/carbohydrates.prm'))
myGlycosylator.builder.Topology.read_topology(
os.path.join(gl.GLYCOSYLATOR_PATH, 'support/topology/DUMMY.top'))
#Load topology information about glycans
myGlycosylator.read_connectivity_topology(
os.path.join(gl.GLYCOSYLATOR_PATH, 'support/topology/mannose.top'))
################################################################################
# 2. Load HIV-1 Env trimer
myGlycosylator.load_glycoprotein(
os.path.join(gl.GLYCOSYLATOR_PATH, 'support/examples/env_4tvp.pdb'))
myGlycosylator.build_glycan_topology(patch='NGLB')
################################################################################
# 3. Remove clashes with genetic algorithm
dihe_parameters = myGlycosylator.builder.Parameters.parameters['DIHEDRALS']
vwd_parameters = myGlycosylator.builder.Parameters.parameters['NONBONDED']
# 4. Consider all glycans in HIV-1 Env trimer
mySampler = gl.Sampler(myGlycosylator.glycanMolecules.values(),
myGlycosylator.protein, dihe_parameters, vwd_parameters)
#mySampler.remove_clashes_GA(n_generation = 20, pop_size=30, mutation_rate=0.01)
mySampler.remove_clashes_GA_iterative(n_iter=5,
n_individues=3,
n_generation=30,
pop_size=30,
mutation_rate=0.01)
myGlycosylator.write_glycoprotein('HIV_optimized.pdb')
myGlycosylator = gl.Glycosylator(os.path.join(gl.GLYCOSYLATOR_PATH, 'support/toppar_charmm/carbohydrates.rtf'), os.path.join(gl.GLYCOSYLATOR_PATH, 'support/toppar_charmm/carbohydrates.prm'))
myGlycosylator.builder.Topology.read_topology(os.path.join(gl.GLYCOSYLATOR_PATH, 'support/topology/DUMMY.top'))
#Load topology information about glycans
myGlycosylator.read_connectivity_topology(os.path.join(gl.GLYCOSYLATOR_PATH, 'support/topology/mannose.top'))
################################################################################
# 2. Build a mannose 9 ab initio
man9, bonds = myGlycosylator.glycosylate('MAN9_3;4,2')
myMan9 = gl.Molecule('mannose9')
myMan9.set_AtomGroup(man9, bonds = bonds, update_bonds = False)
myMan9.update_connectivity(update_bonds = False)
myGlycosylator.assign_patches(myMan9)
################################################################################
# 3. Atom type and initialize from AtomGroup
atom_type = myGlycosylator.assign_atom_type(myMan9)
myMan9.set_atom_type(atom_type)
# 4. Do not consider torsional angles invovling terminal hydrogen
myMan9.define_torsionals(hydrogens = False)
################################################################################
# 5. Remove clashes with genetic algorithm
dihe_parameters = myGlycosylator.builder.Parameters.parameters['DIHEDRALS']
vwd_parameters = myGlycosylator.builder.Parameters.parameters['NONBONDED']
mySampler = gl.Sampler([myMan9], None, dihe_parameters, vwd_parameters)
mySampler.remove_clashes_GA_iterative(n_iter = 1, n_generation = 30, pop_size=30, mutation_rate=0.01)
myMan9.writePDB('Man9_optimized.pdb')
