def __init__(self,
targets=None,
forcefields=('amber99sbildn.xml', ),
auto_parametrize=None,
parameters=None,
platform=None,
*args,
**kwargs):
if kwargs.get('precision', 6) < 6:
kwargs['precision'] = 6
ObjectiveProvider.__init__(self, **kwargs)
self.auto_parametrize = auto_parametrize
self._targets = targets
self._parameters = parameters
self.platform = platform
self.topology = None
self._simulation = None
additional_ffxml = []
if parameters:
additional_ffxml.append(create_ffxml_file(*zip(*parameters)))
if auto_parametrize:
filenames = [
g.path for m in auto_parametrize
for g in self.environment.cfg.genes if g.name == m
]
additional_ffxml.append(self._gaff2xml(*filenames))
self._forcefields = tuple(forcefields) + tuple(additional_ffxml)
self.forcefield = openmm_app.ForceField(*self._forcefields)
def oemols_to_ffxml(molecules, base_molecule_name="lig"):
"""Generate an OpenMM ffxml object and MDTraj trajectories from multiple OEMols
Parameters
----------
molecules : list(OEMole)
Molecules WITH CHARGES. Each can have multiple conformations.
WILL GIVE UNDEFINED RESULTS IF NOT CHARGED.
base_molecule_name : str, optional, default='lig'
Base name of molecule to use inside parameter files.
Returns
-------
trajectories : list(mdtraj.Trajectory)
List of MDTraj Trajectories for molecule. May contain multiple frames
ffxml : StringIO
StringIO representation of ffxml file.
Notes
-----
We allow multiple different molecules at once so that they can all be
included in a single ffxml file, which is currently the only recommended
way to simulate multiple GAFF molecules in a single simulation. For most
applications, you will have just a single molecule:
e.g. molecules = [my_oemol]
The resulting ffxml StringIO object can be directly input to OpenMM e.g.
`forcefield = app.ForceField(ffxml)`
This will generate a lot of temporary files, so you may want to use
utils.enter_temp_directory() to avoid clutter.
"""
all_trajectories = []
gaff_mol2_filenames = []
frcmod_filenames = []
print(os.getcwd())
for i, molecule in enumerate(molecules):
trajectories = []
for j in range(molecule.NumConfs()):
molecule_name = "%s-%d-%d" % (base_molecule_name, i, j)
mol2_filename = "./%s.mol2" % molecule_name
_unused = molecule_to_mol2(molecule, mol2_filename, conformer=j)
gaff_mol2_filename, frcmod_filename = run_antechamber(
molecule_name, mol2_filename, charge_method=None
) # It's redundant to run antechamber on each frame, fix me later.
traj = md.load(gaff_mol2_filename)
trajectories.append(traj)
if j == 0: # Only need 1 frame of forcefield files
gaff_mol2_filenames.append(gaff_mol2_filename)
frcmod_filenames.append(frcmod_filename)
# Create a trajectory with all frames of the current molecule
traj = trajectories[0].join(trajectories[1:])
all_trajectories.append(traj)
ffxml = create_ffxml_file(gaff_mol2_filenames, frcmod_filenames, override_mol2_residue_name=base_molecule_name)
return all_trajectories, ffxml
def oemols_to_ffxml(molecules, base_molecule_name="lig"):
"""Generate an OpenMM ffxml object and MDTraj trajectories from multiple OEMols
Parameters
----------
molecules : list(OEMole)
Molecules WITH CHARGES. Each can have multiple conformations.
WILL GIVE UNDEFINED RESULTS IF NOT CHARGED.
base_molecule_name : str, optional, default='lig'
Base name of molecule to use inside parameter files.
Returns
-------
trajectories : list(mdtraj.Trajectory)
List of MDTraj Trajectories for molecule. May contain multiple frames
ffxml : StringIO
StringIO representation of ffxml file.
Notes
-----
We allow multiple different molecules at once so that they can all be
included in a single ffxml file, which is currently the only recommended
way to simulate multiple GAFF molecules in a single simulation. For most
applications, you will have just a single molecule:
e.g. molecules = [my_oemol]
The resulting ffxml StringIO object can be directly input to OpenMM e.g.
`forcefield = app.ForceField(ffxml)`
This will generate a lot of temporary files, so you may want to use
utils.enter_temp_directory() to avoid clutter.
"""
all_trajectories = []
gaff_mol2_filenames = []
frcmod_filenames = []
print(os.getcwd())
for i, molecule in enumerate(molecules):
trajectories = []
for j in range(molecule.NumConfs()):
molecule_name = "%s-%d-%d" % (base_molecule_name, i, j)
mol2_filename = "./%s.mol2" % molecule_name
_unused = molecule_to_mol2(molecule, mol2_filename, conformer=j)
gaff_mol2_filename, frcmod_filename = run_antechamber(molecule_name, mol2_filename, charge_method=None) # It's redundant to run antechamber on each frame, fix me later.
traj = md.load(gaff_mol2_filename)
trajectories.append(traj)
if j == 0: # Only need 1 frame of forcefield files
gaff_mol2_filenames.append(gaff_mol2_filename)
frcmod_filenames.append(frcmod_filename)
# Create a trajectory with all frames of the current molecule
traj = trajectories[0].join(trajectories[1:])
all_trajectories.append(traj)
ffxml = create_ffxml_file(gaff_mol2_filenames, frcmod_filenames, override_mol2_residue_name=base_molecule_name)
return all_trajectories, ffxml
def process_forcefield(*forcefields):
"""
Given a list of filenames, check which ones are `frcmods`. If so,
convert them to ffxml. Else, just return them.
"""
for forcefield in forcefields:
if forcefield.endswith('.frcmod'):
yield create_ffxml_file(forcefield)
else:
yield forcefield
def process_forcefield(*forcefields):
"""
Given a list of filenames, check which ones are `frcmods`. If so,
convert them to ffxml. Else, just return them.
"""
for forcefield in forcefields:
if forcefield.endswith('.frcmod'):
gaffmol2 = os.path.splitext(forcefield)[0] + '.gaff.mol2'
yield create_ffxml_file([gaffmol2], [forcefield])
else:
yield forcefield
def _gaff2xml(*filenames, **kwargs):
"""
Use OpenMolTools wrapper to run antechamber programatically
and auto parametrize requested molecules.
Parameters
----------
filenames: list of str
List of the filenames of the molecules to parametrize
Returns
-------
ffxmls : StringIO
Compiled ffxml file produced by antechamber and openmoltools converter
"""
frcmods, gaffmol2s = [], []
for filename in filenames:
name = '.'.join(filename.split('.')[:-1])
gaffmol2, frcmod = run_antechamber(name, filename, **kwargs)
frcmods.append(frcmod)
gaffmol2s.append(gaffmol2)
return create_ffxml_file(gaffmol2s, frcmods)
def _process_forcefield(forcefield):
if forcefield.endswith('.frcmod'):
return create_ffxml_file(forcefield)
return forcefield
