schrodinger.application.matsci.crest module¶

Utilities for Crest.

class schrodinger.application.matsci.crest.CrestJob(cmd, subdir)¶

Bases: 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: 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'¶

CONSTRAINT = 'constraint'¶

CONSTRAINTS = 'constraints'¶

CALCULATION = 'calculation'¶

LEVEL = 'level'¶

CHARGE = 'charge'¶

UHF = 'uhf'¶

CONSTRAINT_FC = 'fc'¶

__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

getConstraintDict(create=True)¶

Return the constraint dictionary and optionally create one if it is missing.

Parameters:: create (bool) – if True and the constraint dictionary is missing then create one
Return type:: dict
Returns:: the constraint dictionary

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

setConstraintFc(fc)¶

Set the constraint force constant in the TOML dictionary.

Parameters:: fc (float) – the force constant (Hartree/Bohr^2)

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, fc=None, other_fns=None, tpp=1, logger=None)¶

Bases: object

Wrapper class for managing a Crest job.

JOB_CLASS¶: alias of CrestJob

INPUT_FLAG = '--input'¶

THREAD_FLAG = '-T'¶

__init__(mae_fn, cmd=None, toml_fn=None, constraints_fn=None, fc=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
fc (float) – the constraint force constant (Hartree/Bohr^2)
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, fc=None, tpp=1, logger=None)¶

Bases: Crest

Wrapper class for managing a Crest conformational search job.

JOB_CLASS¶: alias of 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}¶

SUB_RMSD_FLAG = '--subrmsd'¶

NO_REF_TOPO_FLAG = '--noreftopo'¶

EWIN_FLAG = '--ewin'¶

ETHR_FLAG = '--ethr'¶

RTHR_FLAG = '--rthr'¶

BTHR_FLAG = '--bthr'¶

NCI_FLAG = '--nci'¶

WSCAL_FLAG = '--wscal'¶

NO_TOPO_FLAG = '--notopo'¶

NO_CROSS_FLAG = '--nocross'¶

__init__(mae_fn, cmd=None, constraints_fn=None, fc=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.

isValidConformer(conformer)¶

Return True if the given conformer is valid, False otherwise.

Parameters:: conformer (schrodinger.structure.Structure) – the conformer
Return type:: bool
Returns:: True if the given conformer is valid, False otherwise

getConformers()¶

Return the conformers dictionary sorted by increasing energy.

Raises:: CrestException – if there is an issue
Return type:: dict[float]=list[schrodinger.structure.Structure]
Returns:: dict with keys as energies (units Hartree), and values as lists of structure.Structure, sorted by increasing energy

getConformerList()¶

Return a list of conformers sorted by increasing energy.

Return type:: list[schrodinger.structure.Structure]
Returns:: conformers sorted by increasing energy

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