iphasimulator.trajectory_centering

Index-file helpers for reusable GROMACS centering groups.

Attributes

`GROUP_HEADER_PATTERN`
`DEFAULT_CENTER_GROUP`
`WORKFLOW_CENTER_SOURCES`

Classes

`GromacsIndex`	Parsed GROMACS index groups, preserving group order.
`CenterIndexResult`	Result from creating or reusing a dedicated centering index.

Functions

`read_index`(→ GromacsIndex)	Read a GROMACS `.ndx` file into named atom groups.
`write_index`(→ pathlib.Path)	Write a GROMACS index file with stable 15-atom line wrapping.
`resolve_center_source_groups`(→ tuple[str, ...])	Return source groups for a workflow, filtering to groups present in the index.
`merged_group_atoms`(→ tuple[int, ...])	Merge one or more index groups into a sorted unique atom list.
`ensure_center_index`(→ CenterIndexResult)	Create or reuse a GROMACS index file containing a dedicated `center` group.

Module Contents

iphasimulator.trajectory_centering.GROUP_HEADER_PATTERN

iphasimulator.trajectory_centering.DEFAULT_CENTER_GROUP = 'center'

iphasimulator.trajectory_centering.WORKFLOW_CENTER_SOURCES: dict[str, tuple[str, ...]]

class iphasimulator.trajectory_centering.GromacsIndex

Parsed GROMACS index groups, preserving group order.

groups: dict[str, tuple[int, ...]]

property names: tuple[str, ...]

has_group(name: str) → bool

group(name: str) → tuple[int, ...]

class iphasimulator.trajectory_centering.CenterIndexResult

Result from creating or reusing a dedicated centering index.

index_path: pathlib.Path

center_group: str

source_groups: tuple[str, ...]

created: bool

reused_existing_center: bool

iphasimulator.trajectory_centering.read_index(index_path: str | pathlib.Path) → GromacsIndex: Read a GROMACS .ndx file into named atom groups.

iphasimulator.trajectory_centering.write_index(index: GromacsIndex, index_path: str | pathlib.Path) → pathlib.Path: Write a GROMACS index file with stable 15-atom line wrapping.

iphasimulator.trajectory_centering.resolve_center_source_groups(index: GromacsIndex, *, workflow_type: str = 'polymer', source_groups: tuple[str, ...] | list[str] | None = None) → tuple[str, ...]: Return source groups for a workflow, filtering to groups present in the index.

iphasimulator.trajectory_centering.merged_group_atoms(index: GromacsIndex, group_names: tuple[str, ...]) → tuple[int, ...]: Merge one or more index groups into a sorted unique atom list.

iphasimulator.trajectory_centering.ensure_center_index(source_index: str | pathlib.Path, output_index: str | pathlib.Path | None = None, *, workflow_type: str = 'polymer', source_groups: tuple[str, ...] | list[str] | None = None, center_group: str = DEFAULT_CENTER_GROUP) → CenterIndexResult

Create or reuse a GROMACS index file containing a dedicated center group.

Existing [ center ] groups are reused. Otherwise the group is generated from the workflow source groups, currently PHA for polymer-only systems.