ectoolkits.analysis.proton_transfer_cv module

class ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV(atomgroup, idxs_type1_o: List[int], idxs_type2_o: List[int], num_bridge: int = 0, verbose=True, **kwargs)

Bases: AnalysisBase

Class for analyzing Proton Transfer Collective Variables (CVs) in molecular dynamics simulations.

This class extends the MDAnalysis AnalysisBase class and provides methods to analyze proton transfer events between donor and acceptor atoms, potentially mediated by bridge water molecules.

u

The MDAnalysis Universe object containing the atomgroup and trajectory.

Type:

Universe

idxs_type1_o

List of indices for type 1 oxygen atoms (donors).

Type:

List[int]

idxs_type2_o

List of indices for type 2 oxygen atoms (acceptors).

Type:

List[int]

num_bridge

The number of bridge water molecules between the donor and acceptor.

Type:

int

idxs_water_o

List of indices for bridge water oxygen atoms.

Type:

List[int]

ag_O

AtomGroup of oxygen atoms.

Type:

AtomGroup

ag_H

AtomGroup of hydrogen atoms.

Type:

AtomGroup

n_results

Number of results to store for each frame.

Type:

int

results

Array to store the results of the analysis.

Type:

ndarray

extra_detail

Whether to include detailed results in the analysis. Defaults to True.

Type:

bool

_prepare()

Prepares the results array for storing analysis results.

_single_frame()

Analyzes a single frame of the trajectory.

_conclude()

Finalizes the analysis by calculating averages and transforming results into a DataFrame.

_gen_connectivity()

Generates the connectivity between oxygen and hydrogen atoms.

_get_candidates_hbonds()

Identifies candidate hydrogen bonds based on donor, acceptor, and bridge atoms.

_get_proton_transfer_cv()

Calculates the proton transfer collective variables for candidate hydrogen bonds.