def _construct_traj(self):
logger.debug('Loading Trajectory object for model {0} ({1}/{2})'.format(self.df.templateid.iloc[0], 0, len(self.df.model_filepath)))
traj = mdtraj.load_pdb(self.df.model_filepath[0])
remove_disulfide_bonds_from_topology(traj.topology)
self.traj = traj
for m, model_filepath in enumerate(self.df.model_filepath[1:]):
logger.debug('Loading Trajectory object for model {0} ({1}/{2})'.format(self.df.templateid.iloc[m+1], m+1, len(self.df.model_filepath)))
traj = mdtraj.load_pdb(model_filepath)
remove_disulfide_bonds_from_topology(traj.topology)
self.traj += traj
def _construct_traj(self):
logger.debug(
'Loading Trajectory object for model {0} ({1}/{2})'.format(
self.df.templateid.iloc[0], 0, len(self.df.model_filepath)))
traj = mdtraj.load_pdb(self.df.model_filepath[0])
remove_disulfide_bonds_from_topology(traj.topology)
self.traj = traj
for m, model_filepath in enumerate(self.df.model_filepath[1:]):
logger.debug(
'Loading Trajectory object for model {0} ({1}/{2})'.format(
self.df.templateid.iloc[m + 1], m + 1,
len(self.df.model_filepath)))
traj = mdtraj.load_pdb(model_filepath)
remove_disulfide_bonds_from_topology(traj.topology)
self.traj += traj
def _gen_implicit_start_models(self,
ff='amber99sbildn.xml',
implicit_water_model='amber99_obc.xml',
ph=8.0):
self.ph = ph
from simtk.openmm import app
valid_model_templateids = [
templateid for templateid in self.templateids if os.path.exists(
os.path.join(
self.models_target_dir, templateid, ensembler.core.
model_filenames_by_ensembler_stage['refine_implicit_md']))
]
gen_model_templateids = [
templateid for templateid in valid_model_templateids
if not os.path.exists(
os.path.join(self.models_target_dir, templateid,
self.model_filename))
]
# make reference model
forcefield = app.ForceField(ff, implicit_water_model)
reference_model_id = get_highest_seqid_existing_model(
models_target_dir=self.models_target_dir)
logger.debug('Using {0} as reference model'.format(reference_model_id))
reference_model_path = os.path.join(
self.models_target_dir, reference_model_id,
model_filenames_by_ensembler_stage['build_models'])
with gzip.open(reference_model_path) as reference_pdb_file:
reference_pdb = app.PDBFile(reference_pdb_file)
remove_disulfide_bonds_from_topology(reference_pdb.topology)
reference_topology = reference_pdb.topology
reference_modeller = app.Modeller(reference_pdb.topology,
reference_pdb.positions)
reference_variants = reference_modeller.addHydrogens(forcefield,
pH=self.ph)
for template_index in range(mpistate.rank, len(gen_model_templateids),
mpistate.size):
templateid = gen_model_templateids[template_index]
logger.debug(
'Generating implicit-start model for {0}'.format(templateid))
try:
input_model_filepath = os.path.join(
self.models_target_dir, templateid,
model_filenames_by_ensembler_stage['build_models'])
output_model_filepath = os.path.join(self.models_target_dir,
templateid,
self.model_filename)
with gzip.open(input_model_filepath) as pdb_file:
pdb = app.PDBFile(pdb_file)
remove_disulfide_bonds_from_topology(pdb.topology)
modeller = app.Modeller(reference_topology, pdb.positions)
modeller.addHydrogens(forcefield,
pH=self.ph,
variants=reference_variants)
topology = modeller.getTopology()
positions = modeller.getPositions()
with gzip.open(output_model_filepath,
'wt') as output_model_file:
app.PDBFile.writeHeader(topology, file=output_model_file)
app.PDBFile.writeFile(topology,
positions,
file=output_model_file)
app.PDBFile.writeFooter(topology, file=output_model_file)
except Exception as e:
print('Error for model {0}: {1}'.format(templateid, e))
continue
def _gen_implicit_start_models(
self,
ff='amber99sbildn.xml', implicit_water_model='amber99_obc.xml',
ph=8.0):
self.ph = ph
from simtk.openmm import app
valid_model_templateids = [
templateid for templateid in self.templateids
if os.path.exists(
os.path.join(
self.models_target_dir, templateid,
ensembler.core.model_filenames_by_ensembler_stage['refine_implicit_md']
)
)
]
gen_model_templateids = [
templateid for templateid in valid_model_templateids
if not os.path.exists(
os.path.join(self.models_target_dir, templateid, self.model_filename)
)
]
# make reference model
forcefield = app.ForceField(ff, implicit_water_model)
reference_model_id = get_highest_seqid_existing_model(models_target_dir=self.models_target_dir)
logger.debug('Using {0} as reference model'.format(reference_model_id))
reference_model_path = os.path.join(self.models_target_dir, reference_model_id, model_filenames_by_ensembler_stage['build_models'])
with gzip.open(reference_model_path) as reference_pdb_file:
reference_pdb = app.PDBFile(reference_pdb_file)
remove_disulfide_bonds_from_topology(reference_pdb.topology)
reference_topology = reference_pdb.topology
reference_modeller = app.Modeller(reference_pdb.topology, reference_pdb.positions)
reference_variants = reference_modeller.addHydrogens(forcefield, pH=self.ph)
for template_index in range(mpistate.rank, len(gen_model_templateids), mpistate.size):
templateid = gen_model_templateids[template_index]
logger.debug('Generating implicit-start model for {0}'.format(templateid))
try:
input_model_filepath = os.path.join(self.models_target_dir, templateid, model_filenames_by_ensembler_stage['build_models'])
output_model_filepath = os.path.join(self.models_target_dir, templateid, self.model_filename)
with gzip.open(input_model_filepath) as pdb_file:
pdb = app.PDBFile(pdb_file)
remove_disulfide_bonds_from_topology(pdb.topology)
modeller = app.Modeller(reference_topology, pdb.positions)
modeller.addHydrogens(forcefield, pH=self.ph, variants=reference_variants)
topology = modeller.getTopology()
positions = modeller.getPositions()
with gzip.open(output_model_filepath, 'wt') as output_model_file:
app.PDBFile.writeHeader(topology, file=output_model_file)
app.PDBFile.writeFile(topology, positions, file=output_model_file)
app.PDBFile.writeFooter(topology, file=output_model_file)
except Exception as e:
print('Error for model {0}: {1}'.format(templateid, e))
continue
