autosolvate.multicomponent.MixtureBuilder

class autosolvate.multicomponent.MixtureBuilder(folder='/home/docs/checkouts/readthedocs.org/user_builds/autosolvate/checkouts/py312/docs/', cube_size=54, closeness=2.0, charge_method='bcc', prefix=None, amberhome: str = None, water_model: str = 'tip3p', qm_program: str = 'gaussian', qm_exe: str = None, qm_dir: str = None)

Create amber parameter files for a single solute with mixed solvents

Use ‘add_solute’ to add solute and ‘add_solvent’ to add solvent.

Parameters:

• folder (str, Optional, default: current working directory) – working directory

• cube_size (int, Optional, default: 54) – size of solvent cube in angstroms

• closeness (float, Optional, default: 2.0) – Solute-solvent closeness setting, corresponding to the tolerance parameter in packmol in Å,

• charge_method (str, Optional, default: “bcc”) – name of charge fitting method (bcc, resp)

• prefix (str, Optional, default: None) – prefix of the output file names. Default will be <solute_name>_<solvent_name_1>_…-<solvent_name_n>

__init__(folder='/home/docs/checkouts/readthedocs.org/user_builds/autosolvate/checkouts/py312/docs/', cube_size=54, closeness=2.0, charge_method='bcc', prefix=None, amberhome: str = None, water_model: str = 'tip3p', qm_program: str = 'gaussian', qm_exe: str = None, qm_dir: str = None)

Methods

__init__([folder, cube_size, closeness, ...])
add_complex_solute(xyzfile[, ...])	add a molecular complex as the solute.
add_solute(xyzfile[, name, residue_name, ...])	add a solute molecule
add_solvent([xyzfile, name, residue_name, ...])	add a type of solvent
add_transition_metal_complex_solute(xyzfile)	add a transition metal complex as the solute.
build()	Start to build the mixed solvent box.
get_solvent_type([xyzfile, name])