Grain Segmentation

Parameters

Parameter	Type	Default	Description
`rmsd`	`float`	`0.1`	RMSD threshold for PTM structure identification.
`minGrainAtomCount`	`int`	`100`	Minimum number of atoms required to keep a grain.
`adoptOrphanAtoms`	`bool`	`true`	Exposed in the interface, but the current implementation does not visibly perform a dedicated orphan-adoption phase.
`handleCoherentInterfaces`	`bool`	`true`	Handle coherent interfaces between compatible structures.
`outputBonds`	`bool`	`false`	Exposed parameter; bond output is not currently surfaced as a documented result file.

Output

`{outputBase}_grains.msgpack`

type Vec3 = [float, float, float];
type Quaternion = [float, float, float, float];

interface Grain {
    id: int;
    size: int;
    orientation: Quaternion;
    pos: Vec3;
}

interface GrainSegmentationOutput {
    main_listing: {
        total_grains: int;
        merging_threshold: float;
    };
    sub_listings: {
        grains: Grain[];
    };
}

`{outputBase}_atoms.msgpack`

Atoms grouped by identified structure family for downstream visualization.

Grain Segmentation

Parameters

Output

`{outputBase}_grains.msgpack`

`{outputBase}_atoms.msgpack`

See Also

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