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 pull():
from moldesign import compute
streams = []
for img in DOCKER_IMAGES:
imgurl = compute.get_image_path(img)
print 'Pulling %s' % imgurl
streams.append(compute.get_engine().client.pull(imgurl))
for s in streams:
for line in s.split('\n'):
print line
def run_tleap(mol, forcefields=None, parameters=None, **kwargs):
"""
Drives tleap to create a prmtop and inpcrd file. Specifically uses the AmberTools 16
tleap distribution.
Defaults are as recommended in the ambertools manual.
Args:
mol (moldesign.Molecule): Molecule to set up
forcefields (List[str]): list of the names of forcefields to use
(see AmberTools manual for descriptions)
parameters (List[ExtraAmberParameters]): (optional) list of amber parameters
for non-standard residues
**kwargs: keyword arguments to :meth:`compute.run_job`
References:
Ambertools Manual, http://ambermd.org/doc12/Amber16.pdf. See page 33 for forcefield
recommendations.
"""
# Prepare input for tleap
if forcefields is None:
forcefields = mdt.forcefields.ffdefaults.values()
leapstr = ['source %s' % LEAPRCFILES[ff] for ff in forcefields]
inputs = {'input.pdb': mol.write(format='pdb')}
if parameters:
if hasattr(parameters, 'lib') or hasattr(parameters, 'frcmod'):
parameters = [parameters]
for ipmtr, p in enumerate(parameters):
frcname = 'res%d.frcmod' % ipmtr
libname = 'res%d.lib' % ipmtr
inputs[frcname] = p.frcmod
inputs[libname] = p.lib
leapstr.append('loadAmberParams %s' % frcname)
leapstr.append('loadoff %s' % libname)
leapstr.append('mol = loadpdb input.pdb\n'
"check mol\n"
"saveamberparm mol output.prmtop output.inpcrd\n"
"savepdb mol output.pdb\n"
"quit\n")
inputs['input.leap'] = '\n'.join(leapstr)
job = pyccc.Job(image=compute.get_image_path(IMAGE),
command='tleap -f input.leap',
inputs=inputs,
name="tleap, %s" % mol.name)
return compute.run_job(job, **kwargs)
def run_tleap(mol, forcefields=None, parameters=None, **kwargs):
"""
Drives tleap to create a prmtop and inpcrd file. Specifically uses the AmberTools 16
tleap distribution.
Defaults are as recommended in the ambertools manual.
Args:
mol (moldesign.Molecule): Molecule to set up
forcefields (List[str]): list of the names of forcefields to use
(see AmberTools manual for descriptions)
parameters (List[ExtraAmberParameters]): (optional) list of amber parameters
for non-standard residues
**kwargs: keyword arguments to :meth:`compute.run_job`
References:
Ambertools Manual, http://ambermd.org/doc12/Amber16.pdf. See page 33 for forcefield
recommendations.
"""
# Prepare input for tleap
if forcefields is None:
forcefields = mdt.forcefields.ffdefaults.values()
leapstr = ['source %s' % LEAPRCFILES[ff] for ff in forcefields]
inputs = {'input.pdb': mol.write(format='pdb')}
if parameters:
if hasattr(parameters, 'lib') or hasattr(parameters, 'frcmod'):
parameters = [parameters]
for ipmtr, p in enumerate(parameters):
frcname = 'res%d.frcmod' % ipmtr
libname = 'res%d.lib' % ipmtr
inputs[frcname] = p.frcmod
inputs[libname] = p.lib
leapstr.append('loadAmberParams %s' % frcname)
leapstr.append('loadoff %s' % libname)
leapstr.append('mol = loadpdb input.pdb\n'
"check mol\n"
"saveamberparm mol output.prmtop output.inpcrd\n"
"savepdb mol output.pdb\n"
"quit\n")
inputs['input.leap'] = '\n'.join(leapstr)
job = pyccc.Job(image=compute.get_image_path(IMAGE),
command='tleap -f input.leap',
inputs=inputs,
name="tleap, %s" % mol.name)
return compute.run_job(job, **kwargs)
def init_config():
"""Called at the end of package import to read initial configuration and setup cloud computing.
"""
config.update(CONFIG_DEFAULTS)
path = _get_config_path()
if os.path.exists(path):
with open(path, 'r') as infile:
print 'Reading configuration from %s' % path
config.update(yaml.load(infile))
if config.default_python_image is None:
config.default_python_image = compute.get_image_path('moldesign_complete')
def init_config():
"""Called at the end of package import to read initial configuration and setup cloud computing.
"""
config.update(CONFIG_DEFAULTS)
path = _get_config_path()
if os.path.exists(path):
with open(path, 'r') as infile:
print 'Reading configuration from %s' % path
config.update(yaml.load(infile))
if config.default_python_image is None:
config.default_python_image = compute.get_image_path(
'moldesign_complete')
def calculate(self, requests=None, guess=None, wait=True):
inputfile = [
'SQM input for %s' % self.mol.name, ' &qmmm',
" qm_theory='%s' qmcharge=%d, printcharges=1, maxcyc=0" %
(self.params.theory, self.get_formal_charge()), '/'
]
for atom in self.mol.atoms:
inputfile.append(
' {atom.atnum} {atom.name} {pos[0]:.8f} {pos[1]:.8f} {pos[2]:.8f}'
.format(atom=atom, pos=atom.position.value_in(u.angstrom)))
engine = mdt.compute.get_engine()
image = compute.get_image_path(IMAGE)
job = engine.launch(image,
'sqm -i mol.in -o mol.out',
inputs={'mol.in': '\n'.join(inputfile)},
name="sqm single point, %s" % self.mol.name)
if not wait: return job
else: return self._parse_results(job)
def run_tleap(mol,
protein='ff14SB',
dna='OL15',
rna='OL3',
carbohydrate='GLYCAM_06j-1',
lipid='lipid14',
water='tip3p',
organic='gaff2',
off_files=(),
frcmod_files=(),
**kwargs):
"""
Drives tleap to create a prmtop and inpcrd file. Specifically uses the AmberTools 16
tleap distribution.
Defaults are as recommended in the ambertools manual.
Args:
mol (moldesign.Molecule): Molecule to set up
protein (str): protein forcefield name (default:ff14SB)
dna (str): dna forcefield name (default: OL15)
rna (str): rna forcefield name (default: OL3)
carbohydrate (str): carbohydrate forcefield name (default: GLYCAM_06j)
lipid (str): lipid forcefield name (default: lipid14)
water (str): water forcefield name (default: tip3p)
organic (str): organic forcefield name (default: gaff2)
off_files (List[batch.FileContainer]):
frcmod_files (List[batch.FileContainer]):
**kwargs: keyword arguments to :meth:`compute.run_job`
References:
Ambertools Manual, http://ambermd.org/doc12/Amber16.pdf. See page 33 for forcefield
recommendations.
"""
# Prepare input for tleap
leapstr = [
'source %s' % LEAPRCFILES[ff]
for ff in (protein, dna, rna, carbohydrate, lipid, water, organic)
]
for frcmod in frcmod_files:
fname = frcmod.dumphere()
leapstr.append('loadamberparam %s' % fname)
for off in off_files:
fname = off.dumphere()
leapstr.append('loadoff %s' % fname)
leapstr.append('mol = loadpdb input.pdb\n'
"check mol\n"
"saveamberparm mol output.prmtop output.inpcrd\n"
"quit\n")
# Launch the job
inputs = {
'input.pdb': mol.write(format='pdb'),
'input.leap': '\n'.join(leapstr)
}
job = pyccc.Job(image=compute.get_image_path(IMAGE),
command='tleap -f input.leap',
inputs=inputs,
name="tleap, %s" % mol.name)
return compute.run_job(job, **kwargs)