md

class isicle.md.RDKitWrapper[source]

Wrapper for RDKit functionality.

Implements WrapperInterface to ensure required methods are exposed.

geom

Internal molecule representation.

Type:

isicle.geometry.Geometry

method

Method of RDKit conformer generation specified.

Type:

str

numConfs

The number of conformers to generate.

Type:

int

result

Dictionary containing simulation results.

Type:

dict

_abc_impl = <_abc._abc_data object>
_configure_distance_geometry(pruneRmsThresh: float = -1.0, forceTol: float = 0.001, randomSeed: int = -1)[source]

Set parameters for distance geometry based conformer generation. :param pruneRmsThresh: Greedy pruning mainting conformers are <float> apart based upon RMSD of heavy atoms.

Default: no pruning, -1.0

Parameters:

  • forceTol (float) – Tolerance to be used in force-field minimizations

  • randomSeed (int) – provide a seed for the random number generator -1 causes RNG to not be seeded

_configure_etdg()[source]

Set parameters for ETDG conformer generation.

_configure_etkdg1()[source]

Set parameters for ETKDG conformer generation, based on work by Riniker and Landrum. Version 1: RDKit default

_configure_etkdg2()[source]

Set parameters for ETKDG conformer generation, based on work by Riniker and Landrum. Version 2: (default) 2016 release, updated torsion angle potentials

_configure_etkdg3(variant=True)[source]

Set parameters for ETKDG conformer generation, based on work by Riniker and Landrum. Version 3: Updated sampling small rings AND macrocycles

_configure_etkdg3_variant()[source]

Set parameters for ETKDG conformer generation, based on work by Riniker and Landrum. Version 3 variant: Updated sampling for small rings, NOT macrocycles

_default_value = None
_defaults = ['geom', 'method', 'numConfs', 'result']
configure(method: str = 'etkdgv3', numConfs: int = 10, **kwargs)[source]

Set conformer generation parameters. :param method: distance for distance geometry method (default)

etkdg for ETKDG method etkdgv2 for ETKDG method etkdgv3 for ETKDG method sretkdgv3 for ETKDG method

Parameters:

  • numConfs (int) – the number of conformers to generate

  • **kwargs – Keyword arguments to configure the simulation See _configure_distance_geometry()

finish()[source]

Parse RDKit conformers generated.

parse()[source]
run(geom, **kwargs)[source]

Generate conformers using RKDit and supplied parameters.

Parameters:

  • geom (Geometry) – Molecule representation.

  • **kwargs – Keyword arguments to configure the simulation. See configure().

Returns:

Wrapper object containing relevant outputs from the simulation.

Return type:

RDKitWrapper

set_geometry(geom)[source]

Set Geometry instance for simulation.

Parameters:

geom (Geometry) – Molecule representation.

submit()[source]

Execute conformer generation with user-specifed method, parameters.

class isicle.md.XTBWrapper[source]

Wrapper for xtb functionality.

Implements WrapperInterface to ensure required methods are exposed.

temp_dir

Path to temporary directory used for simulation.

Type:

str

geom

Internal molecule representation.

Type:

isicle.geometry.Geometry

result

Dictionary containing simulation results.

Type:

dict

_abc_impl = <_abc._abc_data object>
_configure_crest(ewin=6, optlevel='Normal', forcefield='gfn2', protonate=False, deprotonate=False, tautomerize=False, ion=None, dryrun=False, processes=1, solvation=None, ignore_topology=False)[source]

Set command line for crest simulations.

Parameters:

  • ewin (int) – Energy window (kcal/mol) for conformer, (de)protomer, or tautomer search. Default : 6

  • optlevel (str) – Optimization convergence level Default : normal Supported : crude, sloppy, loose, lax, normal, tight, vtight extreme

  • forcefield (str) – GFN forcefield for the optimization Default: gff Supported forcefields: gfn2, gfn1, gff

  • protonate (bool) – Signal to initiate protomer search. Suggested ewin = 30. Default : False

  • deprotonate (bool) – Signal to initiate deprotonated conformers. Suggesting ewin = 30. Default : False

  • tautomer (bool) – Signal to initiate tautomer search. Default : False

  • ion (str) – Keyword to couple with protonate to ionize molecule with an ion other than a proton. See parse_ion for list of ion options.

_configure_xtb(forcefield='gfn2', optlevel='normal', solvation=None)[source]

Set command line for xtb simulations.

Parameters:

  • forcefield (str) – GFN forcefield for the optimization Default: gff Supported forcefields: gfn2, gfn1, gff

  • optlevel (str) – Optimization convergence level Default : normal Supported : crude, sloppy, loose, lax, normal, tight, vtight extreme

_default_value = None
_defaults = ['geom', 'result', 'temp_dir']
configure(task='optimize', forcefield='gfn2', ewin=6, ion=None, optlevel='Normal', dryrun=False, processes=1, solvation=None, ignore_topology=False)[source]

Generate command line

Parameters:

  • tasks (str) – Set task to “optimize”, “conformer”, “protonate”, “deprotonate”, or “tautomerize”. Default : “optimize”

  • forcefield (str) – GFN forcefield for the optimization Default: gff Supported forcefields: gfn2, gfn1, gff

  • ewin (int) – Energy window (kcal/mol) for conformer(set to 6), (de)protomer(set to 30), or tautomer(set to 30) search. Default : 6

  • ion (str) – Ion for protomer calculation.

  • optlevel (str or list of str) – Set optimization level. Supply globally or per task.

  • ion – Keyword to couple with protonate to ionize molecule with an ion other than a proton. See parse_ion for list of ion options.

finish()[source]

Parse results, save xtb output files, and clean temporary directory

parse()[source]

Parse xTB simulation results.

Returns:

Dictionary containing parsed outputs from the simulation.

Return type:

dict

run(geom, **kwargs)[source]

Optimize geometry via density functional theory using supplied functional and basis set.

Parameters:

  • geom (Geometry) – Molecule representation.

  • **kwargs – Keyword arguments to configure the simulation. See configure().

Returns:

Wrapper object containing relevant outputs from the simulation.

Return type:

XTBWrapper

save_geometry(fmt='xyz')[source]

Save internal Geometry representation to file.

Parameters:

fmt (str) – Filetype used by xtb. Must be “xyz”, “smi”, “.inchi”, “.mol”, “.xyz”, “.pdb”, “.pkl”.

set_geometry(geom)[source]

Set Geometry instance for simulation.

Parameters:

geom (Geometry) – Molecule representation.

submit()[source]

Run xtb or crest simulation according to configured inputs.

isicle.md._backend_selector(backend)[source]

Selects a supported molecular dynamics backend for associated simulation. Currently only NWChem has been implemented.

Parameters:

backend (str) – Alias for backend selection (xtb).

Returns:

Wrapped functionality of the selected backend. Must implement WrapperInterface.

Return type:

backend

isicle.md.md(geom, backend='xtb', **kwargs)[source]

Optimize geometry via molecular dyanmics using supplied forcefield and basis set.

Parameters:

backend (str) – Alias for backend selection (xtb).

Returns:

Object containing relevant outputs from the simulation.

Return type:

result