def _antechamber_calc_charges(mol, ambname, chargename, kwargs):
charge = utils.if_not_none(mol.charge, 0)
command = 'antechamber -fi mol2 -i mol.mol2 -fo mol2 -o out.mol2 -c %s -an n'%ambname
if charge != 0:
command += ' -nc %d' % charge.value_in(u.q_e)
def finish_job(job):
"""Callback to complete the job"""
lines = iter(job.get_output('out.mol2').read().split('\n'))
charges = utils.DotDict(type='atomic')
line = lines.next()
while line.strip()[:len('@<TRIPOS>ATOM')] != '@<TRIPOS>ATOM':
line = lines.next()
line = lines.next()
while line.strip()[:len('@<TRIPOS>BOND')] != '@<TRIPOS>BOND':
fields = line.split()
idx = int(fields[0])-1
assert mol.atoms[idx].name == fields[1]
charges[mol.atoms[idx]] = u.q_e*float(fields[-1])
line = lines.next()
mol.properties[chargename] = charges
return charges
job = pyccc.Job(image=mdt.compute.get_image_path(IMAGE),
command=command,
name="%s, %s" % (chargename, mol.name),
inputs={'mol.mol2': mol.write(format='mol2')},
when_finished=finish_job)
return compute.run_job(job, _return_result=True, **kwargs)
def _antechamber_calc_charges(mol, ambname, chargename, kwargs):
charge = utils.if_not_none(mol.charge, 0)
command = 'antechamber -fi mol2 -i mol.mol2 -fo mol2 -o out.mol2 -c %s -an n' % ambname
if charge != 0:
command += ' -nc %d' % charge.value_in(u.q_e)
def finish_job(job):
"""Callback to complete the job"""
lines = iter(job.get_output('out.mol2').read().split('\n'))
charges = utils.DotDict(type='atomic')
line = lines.next()
while line.strip()[:len('@<TRIPOS>ATOM')] != '@<TRIPOS>ATOM':
line = lines.next()
line = lines.next()
while line.strip()[:len('@<TRIPOS>BOND')] != '@<TRIPOS>BOND':
fields = line.split()
idx = int(fields[0]) - 1
assert mol.atoms[idx].name == fields[1]
charges[mol.atoms[idx]] = u.q_e * float(fields[-1])
line = lines.next()
mol.properties[chargename] = charges
return charges
job = pyccc.Job(image=mdt.compute.get_image_path(IMAGE),
command=command,
name="%s, %s" % (chargename, mol.name),
inputs={'mol.mol2': mol.write(format='mol2')},
when_finished=finish_job)
return compute.run_job(job, _return_result=True, **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 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,
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)