autosolvate.autosolvate.solventBoxBuilder

class autosolvate.autosolvate.solventBoxBuilder(xyzfile: str, slu_netcharge=0, slu_spinmult=1, charge_method='resp', slu_count=1, solvent='water', solvent_frcmod='', solvent_off='', solvent_box_name='SLVBOX', slv_generate=False, slv_xyz='', slv_count=1680, cube_size=54, closeness=0.8, folder='/home/docs/checkouts/readthedocs.org/user_builds/autosolvate/checkouts/py312/docs/', outputFile='', **kwargs)[source]

Solvated molecule in specified solvent.

Parameters:

  • solvent (str, Optional, default: ‘water’) – Currently implemented solvents are: ‘water’, ‘methanol’, ‘chloroform’, ‘nma’, ‘acetonitrile’

  • slu_netcharge (int, Optional, default 0) – Charge of solute, the solvent box will be neutralized with Cl- and Na+ ions

  • cube_size (float, Optional, default: 54) – Size of MM solvent box

  • charge_method (str, Optional, default: “resp”) – Use ‘resp’ (quantum mechanical calculation needed) or ‘bcc’ to estimate partial charges

  • slu_spinmult (int, Optional, default: 1) – Spinmultiplicity of solute

  • outputFile (str, Optional, default=’water_solvated’) – Filename-prefix for outputfiles

  • srun_use (bool, Optional, default=’False) – Run all commands with a srun prefix

Returns:

To run solvation, call build function.

Return type:

None

__init__(xyzfile: str, slu_netcharge=0, slu_spinmult=1, charge_method='resp', slu_count=1, solvent='water', solvent_frcmod='', solvent_off='', solvent_box_name='SLVBOX', slv_generate=False, slv_xyz='', slv_count=1680, cube_size=54, closeness=0.8, folder='/home/docs/checkouts/readthedocs.org/user_builds/autosolvate/checkouts/py312/docs/', outputFile='', **kwargs)[source]

Methods

__init__(xyzfile[, slu_netcharge, ...])

build()

Build the solvated system

get_solvent(solvent[, slv_xyz, ...])