Solvation

Solvation#

class bindflow.preparation.solvent.Solvate(water_model_code: str, builder_dir: PathLike | str | bytes = '.solvate', load_dependencies: List[str] | None = None)[source]#
__call__(structure: parmed.Structure, bt: str = 'triclinic', box: list[float] | None = None, angles: list[float] | None = None, d: float | None = None, c: bool = False, pname: str = 'NA', nname: str = 'CL', ion_conc: float = 0.15, rmin: float = 1.0, exclusion_list: list | None = None, out_dir: PathLike | str | bytes = '.', out_name: str = 'solvated', f_xyz: tuple = (2500, 2500, 2500), settles_to_constraints_on: PathLike | str | bytes | None = None) → None[source]#

Call self as a function.

__init__(water_model_code: str, builder_dir: PathLike | str | bytes = '.solvate', load_dependencies: List[str] | None = None) → None[source]#

Class to solvate GMX systems. Force fields were extracted from GMX topologies.

Remember to cite properly the main references if you use any of the water models in your work.

Available water models:
  • amber:

    • amber/spc

    • amber/spce

    • amber/tip3p

    • amber/tip4p

    • amber/tip4pew

    • amber/tip5p

  • charmm

    • charmm/spc

    • charmm/spce

    • charmm/tip3p

    • charmm/tips3p

    • charmm/tip4p

    • charmm/tip5p

  • oplsaa

    • oplsaa/spc

    • oplsaa/spce

    • oplsaa/tip3p

    • oplsaa/tip4p

    • oplsaa/tip4pew

    • oplsaa/tip5p

    • oplsaa/tip5pe

Parameters:

  • water_model_code (str) – Water model code in the form: “{force field family}/{water model}”

  • builder_dir (tools.PathLik, optional) – Where the temporal files will be written.

  • load_dependencies (List[str], optional) – It is used in case some previous loading steps are needed for GROMACS commands; e.g: [‘source /groups/CBG/opt/spack-0.18.1/shared.bash’, ‘module load sandybridge/gromacs/2025.4’], by default None

Raises:

  • ValueError – Invalid force field family

  • ValueError – Invalid water model for the selected force field

clean(directory: None | PathLike | str | bytes = None) → None[source]#

Used to delete self.builder_dir or directory if provided

Danger

Use it wisely (when directory is provided), you may ended up deleting your computer :-)

Parameters:

directory (Union[None, tools.PathLike], optional) – Directory to delete, by default None

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