stko.XTBCREST

class stko.XTBCREST(crest_path, xtb_path, gfn_version=2, output_dir=None, opt_level='normal', md_len=None, ewin=5, speed_setting=None, keepdir=False, num_cores=4, cross=True, charge=0, electronic_temperature=300, solvent_model='gbsa', solvent=None, num_unpaired_electrons=0, unlimited_memory=False)[source]

Bases: Optimizer

Uses GFN-n to run CREST on molecules.

See also

Parameters:

  • crest_path (str) – The path to the CREST executable.

  • xtb_path (str) – The path to the xTB executable. Version >6.3.0 is required.

  • gfn_version (int) – Parameterization of GFN to use in xTB. For details see https://xtb-docs.readthedocs.io/en/latest/basics.html.

  • output_dir (str | None) – The name of the directory into which files generated during the optimization are written, if None then uuid.uuid4() is used.

  • opt_level (str) – Optimization level to use. Can be one of 'crude', 'sloppy', 'loose', 'lax', 'normal', 'tight', 'vtight' or 'extreme'. For details see https://xtb-docs.readthedocs.io/en/latest/optimization.html .

  • md_len (float | None) – Set length of the meta-dynamics simulations (MTD) in ps. Default is chosen based on size and flexibility of the system.

  • ewin (float) – Set the energy threshold in kcal/mol for conformer selection. Double this is used in crude optimization. Defaults ot 5 kcal/mol and is overridden by speed_setting.

  • speed_setting (None | str) – Conformer search speed setting. Fast methods turn off parts of the calculations and alter MD run times. Defaults to no modification of iMTD-GC algorithm: None. Can be one of 'norotmd', 'quick', 'squick' or 'mquick'. Overrides ewin with chosen parameters. For details see https://xtb-docs.readthedocs.io/en/latest/crestcmd.html.

  • keepdir (bool) – True to keep subdirectories from MD runs. Defaults to False. For details see https://xtb-docs.readthedocs.io/en/latest/crestcmd.html.

  • num_cores (int) – The number of cores CREST should use.

  • charge (int) – Formal molecular charge.

  • electronic_temperature (float) – Electronic temperature in Kelvin.

  • solvent_model (str) – Solvent model to use out of older gbsa and newer alpb. gbsa is default for backwards compatability, but alpb is recommended. For details see https://xtb-docs.readthedocs.io/en/latest/gbsa.html.

  • solvent (str | None) – Solvent to use in GBSA implicit solvation method. For details see https://xtb-docs.readthedocs.io/en/latest/gbsa.html.

  • num_unpaired_electrons (int) – Number of unpaired electrons.

  • cross (bool) – Whether or not structure crossing is performed.

  • unlimited_memory (bool) – If True optimize() will be run without constraints on the stack size. If memory issues are encountered, this should be True, however this may raise issues on clusters.

Notes

Requires version > 6.2 of xtb.

When running optimize(), this calculator changes the present working directory with os.chdir(). The original working directory will be restored even if an error is raised, so unless multi-threading is being used this implementation detail should not matter.

Restrictions to iMTD-GC Algorithm Z-matrix sorting is forced to be off because stk.Molecules cannot have their atom ordering changed by an external program at this stage.

Examples

Note that for ConstructedMolecule objects constructed by stk, XTBCREST should usually be used in a OptimizerSequence. This is because xTB only uses xyz coordinates as input and so will not recognize the long bonds created during construction. An optimizer which can minimize these bonds should be used before XTBCREST. Further, CREST runs best on an input structure optimized at the same level used throughout the algorithm (i.e. XTB).

import stk
import stko

bb1 = stk.BuildingBlock('NCCNCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock('O=CCCC=O', [stk.AldehydeFactory()])
polymer = stk.ConstructedMolecule(
    stk.polymer.Linear(
        building_blocks=(bb1, bb2),
        repeating_unit="AB",
        orientations=[0, 0],
        num_repeating_units=1
    )
)

xtb = stko.OptimizerSequence(
    stko.UFF(),
    stko.XTB(
        xtb_path='/opt/gfnxtb/xtb',
        unlimited_memory=True,
    ),
    # Perform quick conformer search.
    stko.XTBCREST(
        crest_path='/opt/crest/crest',
        xtb_path='/opt/gfnxtb/xtb',
        opt_level='normal',
        speed_setting='quick',
        unlimited_memory=True,
    ),
)
polymer = xtb.optimize(polymer)

While most auxiliary and MD run files will be deleted if keepdir is False, the files listed below are kept in output_dir and could be useful for further analysis!

crest_best.xyz: Structure of the lowest energy conformer.
This structure is output by optimize().
crest_conformers.xyz: Structure of all conformers.
All conformers with RMSD and energy threshold of the
lowest energy conformer.
crest_rotamers.xyz: Structure of all rotamers.
All unique rotamers explored by CREST.
crest.energies: Relative conformer energies in a.u..
gfn_topo: GFN-FF binary topology file.
Defines the molecules force field topology.

Methods

optimize

Optimize mol.
optimize(mol)[source]

Optimize mol.

Parameters:

mol (MoleculeT) – The molecule to be optimized.

Returns:

The optimized molecule.

Return type:

MoleculeT