jbrowse-plugin-protein3d

WIP for displaying 3D protein structure alongside the genome browser

LaunchView-ProteinView extension point

This plugin registers a LaunchView-ProteinView extension point that allows
programmatic launching of a ProteinView. This can be used via the JBrowse 2
session spec URL parameters (see
https://jbrowse.org/jb2/docs/urlparams/#session-spec).

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| Parameter | Required | Description |
| -------------------------------- | -------- | ---------------------------------------------------- |
| url | Yes | Structure file URL (PDB, mmCIF, etc.) |
| userProvidedTranscriptSequence | No | Protein sequence for alignment |
| feature | No | Genomic feature for cross-linking |
| connectedViewId | No | ID of connected LinearGenomeView |
| alignmentAlgorithm | No | 'emboss_matcher', 'emboss_needle', or 'emboss_water' |
| displayName | No | Custom view display name |
| height | No | View height in pixels (default: 650) |
| showControls | No | Show Mol\* controls panel |
| showHighlight | No | Show alignment highlight on structure |
| zoomToBaseLevel | No | Zoom to base level on click (default: true) |

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``
https://jbrowse.org/code/jb2/main/?config=config.json&session=spec-{"views":[{"type":"ProteinView","url":"https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v4.cif"}]}
`

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`typescript
pluginManager.evaluateExtensionPoint('LaunchView-ProteinView', {
session,
url: 'https://alphafold.ebi.ac.uk/files/AF-P12345-F1-model_v4.cif',
userProvidedTranscriptSequence: 'MKTLLLTLVVV...',
displayName: 'AlphaFold - P12345',
})
``