schrodinger.application.matsci.crest module¶

Utilities for Crest.

class schrodinger.application.matsci.crest.CrestHostValidatorMixin¶

Bases: object

Validate the job host for GUI panels that can launch CREST.

validateCrestHost()¶

Reject CREST jobs assigned to an unsupported localhost.

Return type:: bool or (bool, str)
Returns:: Whether the selected host is compatible, and an error message if it is not

class schrodinger.application.matsci.crest.CrestOutputFileLoc(filename, sub_subdir)¶

Bases: tuple

filename¶: Alias for field number 0

sub_subdir¶: Alias for field number 1

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.ValidatedCrestJob(*args, **kwargs)¶

Bases: CrestJob

Base class for validated Crest jobs.

__init__(*args, **kwargs)¶: See parent class for documentation.

property xyz_out¶

Return the output xyz file name for the given job type.

Return type:: CrestOutputFileLoc
Returns:: the output xyz file as CrestOutputFileLoc

update()¶: See parent class for documentation.

class schrodinger.application.matsci.crest.CrestCSearchJob(*args, **kwargs)¶

Bases: ValidatedCrestJob

Manage a raw Crest conformational search job.

property xyz_out¶

Return the output xyz file name for Crest conformational search.

Return type:: CrestOutputFileLoc
Returns:: the output xyz file as CrestOutputFileLoc

class schrodinger.application.matsci.crest.CrestQCGJob(*args, **kwargs)¶

Bases: ValidatedCrestJob

Manage a raw Crest Quantum Cluster Growth job.

property xyz_out¶

Return the output xyz file name for Crest QCG.

Return type:: CrestOutputFileLoc
Returns:: the output xyz file as CrestOutputFileLoc

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'¶

METHOD = 'method'¶

TBLITE_LEVEL = 'tblite_level'¶

CHARGE = 'charge'¶

UHF = 'uhf'¶

CONSTRAINT_FC = 'fc'¶

CALCULATION_TYPE = 'type'¶

ENERGY_PRINT = 'eprint'¶

ENERGY_LOG = 'elog'¶

HESSIAN_UPDATE = 'hess_update'¶

EXACT_RF = 'exact_rf'¶

METHOD_TBLITE = 'tblite'¶

METHOD_GFNFF = 'gfnff'¶

TBLITE_LEVEL_GFN1 = 'gfn1'¶

TBLITE_LEVEL_GFN2 = 'gfn2'¶

ENERGY_LOG_FILENAME = 'energies.log'¶

HESSIAN_UPDATE_BFGS = 'bfgs'¶

__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'¶

GFN1_FLAG = '--gfn1'¶

GFN2_FLAG = '--gfn2'¶

GFNFF_FLAG = '--gfnff'¶

__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.

getBondingTemplate(st)¶

Return a structure with the input bonding, atom-ordered like the given Crest output structure.

Parameters:: st (Structure) – the Crest output structure
Return type:: Structure
Returns:: the bonding template

transferBonding(st)¶

Return a copy of the bonding template with the coordinates of the given Crest output structure. Bonds, including zero-order bonds, bond orders, and formal charges are taken from the input.

Parameters:: st (Structure) – the Crest output structure
Return type:: Structure
Returns:: the structure with the input bonding and output coordinates

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

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'¶

THEORY_FLAGS = ('--gfn1', '--gfn2', '--gfnff')¶

DEFAULT_THEORY_FLAG = '--gfn2'¶

TBLITE_LEVELS = {'--gfn1': 'gfn1', '--gfn2': 'gfn2'}¶

__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.

classmethod getTheoryFlag(cmd)¶

Return the theory flag selected by the command line.

Parameters:: cmd (list(str)) – the command line
Return type:: str
Returns:: the selected theory flag
Raises:: CrestException – if multiple theory flags are present

getTOMLDict()¶

Return the TOML dictionary for the selected theory level.

Return type:: dict
Returns:: the TOML dictionary

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

doBonding(st)¶

Assign bonds and bond orders on the given structure.

Parameters:: st (schrodinger.structure.Structure) – the structure
Return type:: schrodinger.structure.Structure
Returns:: the structure with bonds and bond orders assigned

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.

class schrodinger.application.matsci.crest.CrestQCG(mae_fn, solv_mae_fn, cmd=None, other_fns=None, tpp=1, logger=None)¶

Bases: Crest

Wrapper class for managing a Crest Quantum Cluster Growth job.

JOB_CLASS¶: alias of CrestQCGJob

QCG_FLAG = '--qcg'¶

GROW_FLAG = '--grow'¶

ENSEMBLE_FLAG = '--ensemble'¶

GSOLV_FLAG = '--gsolv'¶

NSOLV_FLAG = '--nsolv'¶

NOPREOPT_FLAG = '--nopreopt'¶

FIXSOLUTE_FLAG = '--fixsolute'¶

NOFIXSOLUTE_FLAG = '--nofix'¶

ENSEMBLE_LVL_FLAG = '--enslvl'¶

SIM_LEN_FLAG = '--mdtime'¶

NCLUS_FLAG = '--nclus'¶

FREQ_LVL_FLAG = '--freqlvl'¶

DIRECTED_FLAG = '--directed'¶

SOLVENT_FN = 'solvent.xyz'¶

__init__(mae_fn, solv_mae_fn, cmd=None, other_fns=None, tpp=1, logger=None)¶

Parameters:

mae_fn (str) – the input solute Maestro file
solv_mae_fn (str) – the input solvent Maestro file
cmd (str) – the command line
other_fns (list[str]) – the other input filenames (directed docking)
tpp (int) – the number of threads
logger (logging.Logger) – output logger

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

writeInputXYZs(xyz_fn)¶

Write input xyzs for solute and solvent.

Parameters:: xyz_fn (str) – the file name to write

getCmd(cmd=None)¶

Get the command line arguments for the job.

Parameters:: cmd (str) – the command line
Return type:: list[str]
Returns:: the command line

getBondingTemplate(st)¶

See parent class for documentation. The Crest QCG output cluster contains the solute atoms followed by the solvent molecules, each in input atom order.

Raises:: CrestException – if the output atoms can not be partitioned into the solute and solvent molecules or do not match the template

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