a3fe.analyse.waters

Functions to analyse binding site waters.

Functions

get_av_waters_lambda_window(simulations, ...)

Calculate average number of waters within given distance of an atom (or two atoms) with given index over the specified percentage of the end of the trajectory, for all simulations for all runs for all lambda windows supplied.

get_av_waters_simulation(input_dir, ...[, ...])

Calculate average number of waters within given distance of an atom (or two atoms) with given index over the specified percentage of the end of the trajectory.

get_av_waters_stage(lam_windows, ...[, ...])

Calculate average number of waters within given distance of an atom (or two atoms) with given index over the specified percentage of the end of the trajectory, for all simulations for all runs for all lambda windows supplied.
a3fe.analyse.waters.get_av_waters_lambda_window(simulations: ~typing.List[Simulation], percent_traj: float, lam_val: float, index: int, length: float, run_nos: ~typing.List[int], index2: int | None = None, length2: float | None = None, print_fn: ~typing.Callable[[str], None] = <built-in function print>) → ndarray[source]

Calculate average number of waters within given distance of an atom (or two atoms) with given index over the specified percentage of the end of the trajectory, for all simulations for all runs for all lambda windows supplied.

Parameters:

  • simulations (List[LamWindow]) – List of Simulatino objects for which to calculate average number of waters

  • percent_traj (float) – percentage of trajectory (beginning from end) over which to average

  • lam_val (float) – Current value of lambda. Used for printing output.

  • index (int) – Atom from which distance is calculated

  • length (float) – Distance in Angstrom

  • run_nos (List[int]) – List of run numbers to include in the analysis.

  • index2 (int, optional, default=None) – Optional. Index of second atom from which water must be within a specified distance

  • length2 (float, optional, default=None) – Optional. Distance (Angstrom) from second atom which water must be within

  • print_fn (Optional[Callable[[str], None]], default=print) – Optional. Function to use for printing output.

Returns:

avg_close_waters – Average number of waters within the specified distance(s) of the specified atom(s) for each lambda window for each run. Shape is (n_runs).

Return type:

_np.ndarray

a3fe.analyse.waters.get_av_waters_simulation(input_dir: str, percent_traj: float, index: int, length: float, index2: int | None = None, length2: float | None = None) → float[source]

Calculate average number of waters within given distance of an atom (or two atoms) with given index over the specified percentage of the end of the trajectory.

Parameters:

  • input_dir (str) – Absolute path to the input directory containing the trajectory information and the topology files.

  • percent_traj (float) – percentage of trajectory (beginning from end) over which to average

  • index (int) – Atom from which distance is calculated

  • length (float) – Distance in Angstrom

  • index2 (int, optional, default=None) – Optional. Index of second atom from which water must be within a specified distance

  • length2 (float, optional, default=None) – Optional. Distance (Angstrom) from second atom which water must be within

Returns:

avg_close_waters – Average number of waters within the specified distance(s) of the specified atom(s)

Return type:

float

a3fe.analyse.waters.get_av_waters_stage(lam_windows: ~typing.List[LamWindow], percent_traj: float, index: int, length: float, index2: int | None = None, length2: float | None = None, run_nos: ~typing.List[int] | None = None, print_fn: ~typing.Callable[[str], None] | None = <built-in function print>) → ndarray[source]

Calculate average number of waters within given distance of an atom (or two atoms) with given index over the specified percentage of the end of the trajectory, for all simulations for all runs for all lambda windows supplied.

Parameters:

  • lam_windows (List[LamWindow]) – List of LamWindow objects for which to calculate average number of waters

  • percent_traj (float) – percentage of trajectory (beginning from end) over which to average

  • index (int) – Atom from which distance is calculated

  • length (float) – Distance in Angstrom

  • index2 (int, optional, default=None) – Optional. Index of second atom from which water must be within a specified distance

  • length2 (float, optional, default=None) – Optional. Distance (Angstrom) from second atom which water must be within

  • run_nos (Optional[List[int]], default=None) – Optional. List of run numbers to include in the analysis. If None, all runs will be included.

  • print_fn (Optional[Callable[[str], None]], default=print) – Optional. Function to use for printing output.

Returns:

avg_close_waters – Average number of waters within the specified distance(s) of the specified atom(s) for each lambda window for each run. Shape is (n_runs, n_lam_windows).

Return type:

_np.ndarray