def wrapper(*args, **kwargs):
""" Wraps a python function so that it will be executed remotely using a compute engine
Note:
At runtime, this documentation should be replaced with that of the wrapped function
"""
# If the wrapper is not enabled, just run the wrapped function as normal.
f = func # keeps a reference to the original function in this closure
if not wrapper.enabled:
return f(*args, **kwargs)
wait = kwargs.get('wait', True)
# Bind instance methods to their objects
if self.is_imethod:
f, args = _bind_instance_method(f, args)
# Submit job to remote engine
python_call = bpy.PythonCall(f, *args, **kwargs)
image = utils.if_not_none(self.image, configuration.config.default_python_image)
engine = utils.if_not_none(self.engine, mdt.compute.get_engine())
job = bpy.PythonJob(engine,
image,
python_call,
name=self.jobname,
sendsource=self.sendsource)
if self.display:
uibase.display_log(job.get_display_object(), title=f.__name__)
if wait:
job.wait()
return job.result
else:
return job
def am1_bcc_charges(mol, minsteps=None, wait=True):
""" Doesn't work yet ..."""
charge = utils.if_not_none(mol.charge, 0)
engine = mdt.compute.get_engine()
image = compute.get_image_path(IMAGE, engine)
command = 'antechamber -fi pdb -i mol.pdb -fo mol2 -o out.mol2 -c bcc -an n'
if charge != 0: command += ' -nc %d' % charge
if minsteps is not None: command += ' -ek "maxcyc=%d"' % minsteps
def parse_mol2(job):
"""Callback to complete the job"""
atom_info = utils.DotDict(job=job)
lines = iter(job.get_output('out.mol2').read().split('\n'))
while True:
line = lines.next()
fields = line.split()
if fields[0] == 'ATOM':
idx = int(fields[1]) - 1
name = fields[2]
assert mol.atoms[idx].name == name
atom_info[mol.atoms[idx]] = utils.DotDict(partialcharge=u.q_e *
float(fields[-2]),
atomtype=fields[-1])
return atom_info
job = engine.launch(image,
command=command,
name="am1-bcc, %s" % mol.name,
inputs={'mol.pdb': mol.write(format='pdb')},
when_finished=parse_mol2)
uibase.display_log(job.get_display_object(), job.name)
if not wait: return job()
else: job.wait()
def show_parameterization_results(errormessages, molin, molout=None):
if uibase.widgets_enabled:
report = ParameterizationDisplay(errormessages, molin, molout)
uibase.display_log(report, title='ERRORS/WARNINGS', show=True)
else:
print 'Forcefield assignment: %s' % ('Success' if molout is not None else 'Failure')
for err in errormessages:
print utils.html_to_text(err.desc)
def show_parameterization_results(errormessages, molin, molout=None):
if uibase.widgets_enabled:
report = ParameterizationDisplay(errormessages, molin, molout)
uibase.display_log(report, title='ERRORS/WARNINGS', show=True)
else:
print 'Forcefield assignment: %s' % ('Success' if molout is not None else 'Failure')
for err in errormessages:
print utils.html_to_text(err.desc)
def assign_forcefield(mol, **kwargs):
""" see run_tleap docstring """
from moldesign.widgets.parameterization import ParameterizationDisplay
job = run_tleap(mol, **kwargs)
if 'output.inpcrd' in job.get_output():
prmtop = job.get_output('output.prmtop')
inpcrd = job.get_output('output.inpcrd')
params = AmberParameters(prmtop, inpcrd, job)
newmol = mdt.read_amber(params.prmtop, params.inpcrd)
newmol.ff.amber_params = params
else:
newmol = None
report = ParameterizationDisplay(job, mol, molout=newmol)
uibase.display_log(report, title='ERRORS/WARNINGS', show=True)
if newmol is not None:
return newmol
else:
raise ParameterizationError(
'TLeap failed to assign force field parameters for %s' % mol, job)
def get_gaff_parameters(mol, charges, image=IMAGE, engine=None):
""" Doesn't work yet"""
inputs = {}
# Add charges to molecule
inputs['mol.charges'] = '\n'.join(map(str, charges))
inputs['mol.mol2'] = mol.write(format='mol2')
# Creates a mol2 file with the passed charges
cmds.append(
'antechamber -i mol.mol2 -fi mol2 -o mol_charged.mol2 -fo mol2 -c rc -cf mol.charges'
)
# Add missing parameters, write out library and parameter files
cmds.append('parmchk -i mol_charged.mol2 -f mol2 -o mol.frcmod')
# Create the lib file
cmds.append('tleap -f lea.in')
inputs['leap.in'] = '\n'.join([
"source leaprc.%s" % ff, "source leaprc.gaff",
"LIG = loadmol2 mol_charged.mol2", "fmod = loadamberparams mol.frcmod",
"check LIG", "saveoff LIG mol.lib",
"saveamberparm LIG mol.prmtop mol.inpcrd", "quit\n"
])
# Submit the job and wait
job = engine.launch(imagename,
' && '.join(cmds),
inputs=inputs,
name="GAFF assignments" % mol.name)
uibase.display_log(job.get_display_object(), "tleap, %s" % mol.name)
job.wait()
param = GAFFParameters(job.get_output('mol.lib'),
job.get_output('mol.frcmod'), job)
return param