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)[source]#
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
- _conclude()[source]#
Finalizes the analysis by calculating averages and transforming results into a DataFrame.