rgpycrumbs.eon.con_splitter

Attributes

ira_mod
CONSOLE

Classes

AlignMode	Defines structural alignment strategies.
SplitMode	Defines trajectory validation strictness.

Functions

align_path(frames, mode, iraconf)	Applies the selected alignment strategy to the image sequence.
con_splitter(neb_trajectory_file, mode, output_dir, ...)	Splits a multi-step trajectory file (.traj, .con, etc.) into

Module Contents

rgpycrumbs.eon.con_splitter.ira_mod

rgpycrumbs.eon.con_splitter.CONSOLE

class rgpycrumbs.eon.con_splitter.AlignMode(*args, **kwds)

Bases: enum.Enum

Defines structural alignment strategies.

NONE = 'none'

ALL = 'all'

ENDPOINTS = 'endpoints'

class rgpycrumbs.eon.con_splitter.SplitMode(*args, **kwds)

Bases: enum.Enum

Defines trajectory validation strictness.

NEB = 'neb'

FLEX = 'flex'

rgpycrumbs.eon.con_splitter.align_path(frames, mode: AlignMode, iraconf: rgpycrumbs.geom.api.alignment.IRAConfig)

Applies the selected alignment strategy to the image sequence.

rgpycrumbs.eon.con_splitter.con_splitter(neb_trajectory_file: pathlib.Path, mode: str, output_dir: pathlib.Path | None, images_per_path: int, path_index: int, center: bool, box_diagonal: tuple[float, float, float], align_type: str, use_ira: bool, ira_kmax: float, path_list_filename: str)

Splits a multi-step trajectory file (.traj, .con, etc.) into individual .con files for a single specified path.

This script reads a trajectory file, which may contain multiple NEB optimization steps (paths), and extracts only the frames corresponding to a single specified path.

It writes each frame of that path into a separate .con file (e.g., ipath_000.con, ipath_001.con, …).

It also generates a text file (default: ‘ipath.dat’) that lists the absolute paths of all created .con files.

This utility extracts specific optimization steps and applies physical chemistry refinements such as centering, cell overrides, and structural alignment (RMSD minimization).