schrodinger.application.matsci.crest module¶
Utilities for Crest.
Copyright Schrodinger, LLC. All rights reserved.
- class schrodinger.application.matsci.crest.CrestJob(cmd, subdir)¶
Bases:
schrodinger.application.matsci.jobutils.LoggingSubprocessJob
Manage a raw Crest job.
- __init__(cmd, subdir)¶
See parent class for documentation.
- update()¶
See parent class for documentation.
- class schrodinger.application.matsci.crest.CrestCSearchJob(*args, **kwargs)¶
Bases:
schrodinger.application.matsci.crest.CrestJob
Manage a raw Crest conformational search job.
- CONFORMERS_XYZ_OUT = 'crest_conformers.xyz'¶
- __init__(*args, **kwargs)¶
See parent class for documentation.
- update()¶
See parent class for documentation.
- class schrodinger.application.matsci.crest.CrestTOML(toml_fn=None, toml_dict=None)¶
Bases:
object
Manage a Crest TOML file.
- INPUT = 'input'¶
- THREADS = 'threads'¶
- CONSTRAINTS = 'constraints'¶
- CALCULATION = 'calculation'¶
- LEVEL = 'level'¶
- CHARGE = 'charge'¶
- UHF = 'uhf'¶
- __init__(toml_fn=None, toml_dict=None)¶
- Parameters
toml_fn (str) – the TOML input file
toml_dict (str) – the TOML input dictionary
- getCalculationDict(create=True)¶
Return the calculation dictionary and optionally create one if it is missing.
- Parameters
create (bool) – if True and the calculation dictionary is missing then create one
- Return type
dict
- Returns
the calculation dictionary
- getLevelDicts(create=True)¶
Return the level dictionaries and optionally create one if they are missing.
- Parameters
create (bool) – if True and the level dictionaries are missing then create one
- Return type
list
- Returns
the level dictionaries
- setInput(ainput)¶
Set the input.
- Parameters
ainput (str) – the input
- setThreads(threads)¶
Set the threads.
- Parameters
threads (int) – the threads
- setConstraints(constraints)¶
Set the constraints.
- Parameters
constraints (str) – the constraints
- setCharge(charge)¶
Set the charge in the TOML dictionary.
- Parameters
charge (int) – the charge
- setUhf(uhf)¶
Set the uhf in the TOML dictionary.
- Parameters
uhf (int) – the uhf
- write(toml_fn)¶
Write the TOML dictionary to the given TOML file.
- Parameters
toml_fn (str) – the TOML file
- exception schrodinger.application.matsci.crest.CrestException¶
Bases:
Exception
- class schrodinger.application.matsci.crest.Crest(mae_fn, cmd=None, toml_fn=None, constraints_fn=None, other_fns=None, tpp=1, logger=None)¶
Bases:
object
Wrapper class for managing a Crest job.
- JOB_CLASS¶
- INPUT_FLAG = '--input'¶
- THREAD_FLAG = '-T'¶
- __init__(mae_fn, cmd=None, toml_fn=None, constraints_fn=None, other_fns=None, tpp=1, logger=None)¶
- Parameters
mae_fn (str) – the input Maestro file
cmd (str) – the command line
toml_fn (str) – the TOML input Crest file
constraints_fn (str) – the constraints input Crest file
other_fns (list) – any other input Crest files
tpp (int) – the number of threads
logger (logging.Logger) – output logger
- static validate(mae_fn=None, options=None)¶
Validate input.
- Parameters
mae_fn (str) – the input Maestro file
options (argparse.Namespace) – the options
- Raises
CrestException – if there is an issue
- getCmd(cmd=None)¶
Return the command line.
- Parameters
cmd (str) – the command line
- Return type
list[str]
- Returns
the command line
- writeInputXYZs(xyz_fn)¶
Write input xyzs.
- Parameters
xyz_fn (str) – the file name to write
- writeInputTOML()¶
Write input toml.
- getConstraintsRefXYZFileName()¶
Return the constraints reference xyz file name.
- Return type
str or None
- Returns
the constraints reference xyz file name if there is one
- writeInput()¶
Write input files.
- writeOutput()¶
Write output files.
- run()¶
Run a Crest job.
- Raises
CrestException – if there is an issue
- class schrodinger.application.matsci.crest.CrestCSearch(mae_fn, cmd=None, constraints_fn=None, tpp=1, logger=None)¶
Bases:
schrodinger.application.matsci.crest.Crest
Wrapper class for managing a Crest conformational search job.
- JOB_CLASS¶
alias of
schrodinger.application.matsci.crest.CrestCSearchJob
- TOML_DICT = {'calculation': {'elog': 'energies.log', 'eprint': True, 'hess_update': 'bfgs', 'level': [{'method': 'tblite', 'tblite_level': 'gfn2', 'charge': None, 'uhf': None}], 'type': 1}, 'input': None, 'threads': None}¶
- __init__(mae_fn, cmd=None, constraints_fn=None, tpp=1, logger=None)¶
- Parameters
mae_fn (str) – the input Maestro file
cmd (str) – the command line
constraints_fn (str) – the constraints input Crest file
tpp (int) – the number of threads
logger (logging.Logger) – output logger
- getCmd(cmd=None)¶
See parent class for documentation.
- writeInputTOML()¶
See parent class for documentation.
- getConformers()¶
Return the conformers.
- Return type
- Returns
the conformers
- writeOutput()¶
See parent class for documentation.
- schrodinger.application.matsci.crest.write_substructure_constraints_file(in_fn, natoms, restrain_idxs, out_fn, force_constant=0.5)¶
Write a substructure constraints file. This is how to constrain atoms in Crest.
- Parameters
in_fn (str) – the input xyz file name
natoms (int) – the number of atoms in the input xyz file
restrain_idxs (list[int]) – the indices of the atoms to restrain
out_fn (str) – the output constraints file name
force_constant (float) – the force constant in Hartree/Bohr^2
- schrodinger.application.matsci.crest.validate_platform()¶
Validate platform.
- Raises
CrestException – if there is an issue