def run(job, runner=None, path=None, folder=None, **kwargs):
"""
Pickup a runner and initialize it.
:params job: computation to run
:type job: Promise Object
:param runner: Type of runner to use
:type runner: String
"""
initialize = False
try:
config = builtins.config
if path and os.path.abspath(path) != config.jm.path or \
folder and folder != config.jm.folder:
msg = "Reinitializing Plams with new path and/or folder name.\n"
warn(msg)
plams.finish()
plams.init(path=path, folder=folder)
except AttributeError:
plams.init(path=path, folder=folder)
initialize = True
builtins.config.log.stdout = 0
builtins.config.jobmanager.jobfolder_exists = 'rename'
if runner is None:
ret = call_default(job, **kwargs)
# elif runner.lower() == 'xenon':
# ret = call_xenon(job, **kwargs)
else:
raise "Don't know runner: {}".format(runner)
if initialize:
plams.finish()
return ret
def wrapper(*args, **kwargs):
if not plams.config:
plams.init()
plams.config.log.stdout = 0
result = fun(*args, **kwargs)
plams.finish()
return result
def wrapper(*args, **kwargs):
try:
builtins.config
except AttributeError:
plams.init()
builtins.config.log.stdout = 0
result = fun(*args, **kwargs)
plams.finish()
return result
def run(self):
folder = time.strftime("[%H:%M](%d-%m-%Y)", time.localtime())
plams.init(path=self.run_path, folder=folder)
kffiles = []
for job in self.jobs:
res = job.run(False)
kffiles.append(res.KFPATH)
plams.finish()
return kffiles
def run(job, runner=None, path=None, folder=None, **kwargs):
"""
Pickup a runner and initialize it.
:params job: computation to run
:type job: Promise Object
:param runner: Type of runner to use
:type runner: String
"""
plams.init(path=path, folder=folder)
plams.config.log.stdout = 0
if runner is None:
ret = call_default(job, kwargs.get('n_processes', 1))
else:
raise "Don't know runner: {}".format(runner)
plams.finish()
return ret
def test_restart_init() -> None:
"""Tests for :func:`restart_init` and :class:`RestartInit`."""
workdir = PATH / 'plams_workdir'
try:
init(PATH)
finish()
assertion.isdir(workdir)
init_restart(PATH)
assertion.isdir(workdir)
assertion.isdir(f'{workdir}.002', invert=True)
finish()
with InitRestart(PATH):
assertion.isdir(workdir)
assertion.isdir(f'{workdir}.002', invert=True)
finally:
shutil.rmtree(workdir) if isdir(workdir) else None
shutil.rmtree(f'{workdir}.002') if isdir(f'{workdir}.002') else None
def run(job, runner=None, path=None, folder=None, **kwargs):
"""
Pickup a runner and initialize it.
:params job: computation to run
:type job: Promise Object
:param runner: Type of runner to use
:type runner: String
"""
plams.init(path=path, folder=folder)
plams.config.log.stdout = 0
if runner is None:
ret = call_default(job, kwargs.get('n_processes', 1),
kwargs.get('always_cache', True))
else:
raise "Don't know runner: {}".format(runner)
plams.finish()
return ret
def run(self, init=True, path=None):
'''
Method that runs this job
'''
if init:
if path is None:
plams.init(path=os.getcwd() + r'\RUNS',
folder=time.strftime("[%H:%M](%d-%m-%Y)",
time.localtime()))
else:
plams.init(path=path)
s = self.settings
job = plams.ADFJob(molecule=self.mol, name=self.job_name, settings=s)
results = job.run()
results.dir = '\\'.join(results._kfpath().split('\\')[:-2])
results.KFPATH = results._kfpath()
if init: plams.finish()
return results._kfpath()
def run(job, runner=None, path=None, folder=None, **kwargs):
"""
Pickup a runner and initialize it.
:params job: computation to run
:type job: Promise Object
:param runner: Type of runner to use
:type runner: String
"""
plams.init(path=path, folder=folder)
plams.config.log.stdout = 0
if runner is None:
ret = call_default(job, **kwargs)
# elif runner.lower() == 'xenon':
# ret = call_xenon(job, **kwargs)
else:
raise "Don't know runner: {}".format(runner)
plams.finish()
return ret
def main():
"""
Main interface that reads the file and retrieve all useful geoms etc.
Then rewrite geometries in a usable formatter_class
Prep all NBO computations
Run ADF on each computation
"""
# Retrieve command line values
args = get_input_arguments()
input_file = args['input_file']
output_file = args['output_file']
# Init PLAMS, Setting up a plams.$PID directory in the working dir
init()
# Retrieve settings from input file
settings = get_settings(args)
geometries = IRC_coordinates_from_t21(input_file)
natoms = number_of_atoms(input_file)
# Prep a bunch of NBO computations
NBO_jobs = [prepare_NBO_computation(geom, settings) for geom in geometries]
# Run each job in parallel as managed by plams
for job in NBO_jobs:
job.run()
# NBO_values is a list of list of charges
NBO_values = [
extract_NBO_charges(job._filenames.get('out'), natoms)
for job in NBO_jobs
]
# Write NBO data
print_NBO_charges_to_file(NBO_values, output_file)
# Close plams session
finish()
def __exit__(self, exc_type, exc_value, traceback) -> None:
"""Exit the context manager, call :func:`finish<scm.plams.core.functions.finish>`."""
finish(self.otherJM)
def __exit__(self, exc_type, exc_value, traceback) -> None:
"""Exit the context manager; call |plams.finish|."""
finish()
# Retrieve the gradients and dipoles
grad_less = np.asarray(jobres.readkf('GeoOpt', 'Gradients_InputOrder'))
pol_less = np.asarray(jobres.readkf('Properties', 'Polarizability'))
### CONVERSIONS ###
bohr_to_ang = 0.529177
# Saves derivative of gradients in numHess
polTens[:, mode] = (
(pol_plus - pol_less) /
(2 * scaling)) * bohr_to_ang #bohr to ang conv included
numHess[:, mode] = (
(grad_plus - grad_less) /
(2 * scaling)) * bohr_to_ang #bohr to ang conv included
plams.finish()
################## END OF PLAMS ########################
# Same as in change of basis for a range of spectral region
smallHess = (np.dot(np.transpose(V), (numHess)))
numFreq, numMode = CalcNormalModes(smallHess)
smallPol = np.dot(numMode, np.transpose(polTens))
newNumMode = np.transpose(np.dot(V, np.transpose(numMode)))
print("smallPol_before transpose", smallPol)
smallPol = np.transpose(smallPol)
print("smallPol_after transpose", smallPol)
# rotStrengths[1], dipStrengths[1] = rotatStr(numFreq, newNumMode, rkfFiles[0].get_APTs(), rkfFiles[0].get_AATs())
# dipStrengths[1] = dipoleStrength(numFreq,newNumMode,smallPol)
# export_peaks("modeselection",rotStrengths[1], dipStrengths[1])
def get_lig_charge(ligand: Molecule,
desired_charge: float,
ligand_idx: Union[None, int, Iterable[int], slice] = None,
invert_idx: bool = False,
settings: Optional[Settings] = None,
path: Union[None, str, PathLike] = None,
folder: Union[None, str, PathLike] = None) -> pd.Series:
"""Calculate and rescale the **ligand** charges using MATCH_.
The atomic charges in **ligand_idx** wil be altered such that the molecular
charge of **ligand** is equal to **desired_charge**.
.. _MATCH: http://brooks.chem.lsa.umich.edu/index.php?page=match&subdir=articles/resources/software
Examples
--------
.. code:: python
>>> import pandas as pd
>>> from scm.plams import Molecule
>>> from CAT.recipes import get_lig_charge
>>> ligand = Molecule(...)
>>> desired_charge = 0.66
>>> ligand_idx = 0, 1, 2, 3, 4
>>> charge_series: pd.Series = get_lig_charge(
... ligand, desired_charge, ligand_idx
... )
>>> charge_series.sum() == desired_charge
True
Parameters
----------
ligand : :class:`~scm.plams.core.mol.molecule.Molecule`
The input ligand.
desired_charge : :class:`float`
The desired molecular charge of the ligand.
ligand_idx : :class:`int` or :class:`~collections.abc.Iterable` [:class:`int`], optional
An integer or iterable of integers representing atomic indices.
The charges of these atoms will be rescaled;
all others will be frozen with respect to the MATCH output.
Setting this value to ``None`` means that *all* atomic charges are considered variable.
Indices should be 0-based.
invert_idx : :class:`bool`
If ``True`` invert **ligand_idx**, *i.e.* all atoms specified therein are
now threated as constants and the rest as variables,
rather than the other way around.
settings : :class:`~scm.plams.core.settings.Settings`, optional
The input settings for :class:`~nanoCAT.ff.match_job.MatchJob`.
Will default to the ``"top_all36_cgenff_new"`` forcefield if not specified.
path : :class:`str` or :class:`~os.PathLike`, optional
The path to the PLAMS workdir as passed to :func:`~scm.plams.core.functions.init`.
Will default to the current working directory if ``None``.
folder : :class:`str` or :class:`~os.PathLike`, optional
The name of the to-be created to the PLAMS working directory
as passed to :func:`~scm.plams.core.functions.init`.
Will default to ``"plams_workdir"`` if ``None``.
Returns
-------
:class:`pd.Series` [:class:`str`, :class:`float`]
A Series with the atom types of **ligand** as keys and atomic charges as values.
See Also
--------
:class:`MatchJob`
A :class:`~scm.plams.core.basejob.Job` subclass for interfacing with MATCH_:
Multipurpose Atom-Typer for CHARMM.
""" # noqa
if settings is None:
settings = Settings()
settings.input.forcefield = 'top_all36_cgenff_new'
# Run the MATCH Job
init(path, folder)
ligand = ligand.copy()
run_match_job(ligand, settings, action='raise')
finish()
# Extract the charges and new atom types
count = len(ligand)
charge = np.fromiter((at.properties.charge_float for at in ligand), count=count, dtype=float)
symbol = np.fromiter((at.properties.symbol for at in ligand), count=count, dtype='<U4')
# Identify the atom subset
idx = _parse_ligand_idx(ligand_idx)
if invert_idx:
idx = _invert_idx(idx, count)
try:
idx_len = len(idx) # type: ignore
except TypeError: # idx is a slice object
idx_len = len(charge[idx])
# Correct the charges and return
charge[idx] -= (charge.sum() - desired_charge) / idx_len
return pd.Series(charge, index=symbol, name='charge')
