iphasimulator.trajectory_processing

Configuration-driven, streaming GROMACS XTC processing for enzyme–PHA systems.

Run python -m iphasimulator.trajectory_processing instrcution.txt --dry-run. Paths in YAML are relative to that file. No simulation or viewer is launched.

Attributes

WORKFLOW

Classes

ProcessingConfig

Validated settings; all filesystem paths are absolute after loading.

Functions

`load_config`(→ ProcessingConfig)	Read strict YAML, rejecting unknown/duplicate keys and invalid values.
`resolved_settings`(→ dict)	Return JSON/YAML-serialisable settings, including resolved paths.
`check_output_safety`(→ None)	Refuse raw-input containment and replacement of unowned output folders.
`preflight`(cfg)	Validate files/tools, topology, named selections and the first XTC frame.
`command_plan`(→ list[dict])	Construct separate preparation and optional fitting trjconv operations.
`process_trajectory`(→ dict)	Load, validate and run once; a dry run reads only metadata/first frame.
`main`([argv])	CLI entry point shared with the notebook.

Module Contents

iphasimulator.trajectory_processing.WORKFLOW = 'iphasimulator.trajectory_processing.v1'

class iphasimulator.trajectory_processing.ProcessingConfig

Validated settings; all filesystem paths are absolute after loading.

instruction_file: pathlib.Path

input_trajectory: pathlib.Path

structure: pathlib.Path

index: pathlib.Path

output_dir: pathlib.Path

schema_version: int = 1

stride: int = 100

pbc: str = 'none'

center: bool = False

center_group: str | None = None

fit: str = 'none'

fit_group: str | None = None

output_group: str = 'SYSTEM'

prepare_vmd: bool = True

overwrite: bool = False

dry_run: bool = False

gmx: str = 'gmx'

custom_groups: dict[str, str]

iphasimulator.trajectory_processing.load_config(path: str | pathlib.Path) → ProcessingConfig: Read strict YAML, rejecting unknown/duplicate keys and invalid values.

iphasimulator.trajectory_processing.resolved_settings(cfg: ProcessingConfig) → dict: Return JSON/YAML-serialisable settings, including resolved paths.

iphasimulator.trajectory_processing.check_output_safety(cfg: ProcessingConfig) → None: Refuse raw-input containment and replacement of unowned output folders.

iphasimulator.trajectory_processing.preflight(cfg: ProcessingConfig)

Validate files/tools, topology, named selections and the first XTC frame.

This is read-only, including in dry-run mode. XTC contains no atom identities: its atom count can be checked, but provenance/order must be supplied correctly.

iphasimulator.trajectory_processing.command_plan(cfg: ProcessingConfig, executable: str, directory: pathlib.Path | None = None) → list[dict]: Construct separate preparation and optional fitting trjconv operations.

iphasimulator.trajectory_processing.process_trajectory(instruction_file: str | pathlib.Path, *, dry_run: bool | None = None) → dict

Load, validate and run once; a dry run reads only metadata/first frame.

Results are assembled in a staging directory and published locally only after streaming verification. Explicit overwrite archives the previous owned result. Failures retain logs in the staging directory and leave previous results intact.

iphasimulator.trajectory_processing.main(argv=None): CLI entry point shared with the notebook.