Feature/v2 bloodplasma

[rugeli]

Problem

per an external user’s request, we are providing a v2 version of the blood plasma recipe as an example of using pdb representations

Solution

• added a v2 blood plasma recipe converted from the existing v1 recipe
• added color normalization in the migration script
• updated the validation schema to accept both float and int for priority

Type of change

• New feature (non-breaking change which adds functionality)

Steps to Verify:

1. pack -r examples/recipes/v2/BloodPlasma-no-HIV_fv2.1.json
   note: packing this recipe for the first time takes more than 30 minutes. The progress bar stopped at 61%, but packing completed successfully. We'll need to fix it separately.

2. view the result in Simularium

[github-actions]

Packing analysis report

Analysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST

Ingredient name	Encapsulating radius	Average number packed
ext_A	25	236.0

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key	Pairwise distance distribution
ext_A

[rugeli]

One example object that includes a PDB atomic representation:

"dLDL": {
            "jitter_attempts": 5,
            "rotation_range": 6.2831,
            "color": [
                0.5607843137254902,
                0.396078431372549,
                0.6784313725490196
            ],
            "max_jitter": [
                1,
                1,
                0
            ],
            "principal_vector": [
                1,
                0,
                0
            ],
            "perturb_axis_amplitude": 0.1,
            "is_attractor": false,
            "packing_mode": "random",
            "type": "multi_sphere",
            "rejection_threshold": 30,
            "place_method": "jitter",
            "rotation_axis": null,
            "use_rotation_axis": false,
            "orient_bias_range": [
                3.141592607179586,
                3.141592607179586
            ],
            "representations": {
                "atomic": {
                    "id": "EMD-5239.map",
                    "format": ".pdb"
                },
                "packing": {
                    "path": "github:collisionTrees",
                    "name": "EMDB_5239.sph",
                    "format": ".sph"
                },
                "mesh": {
                    "path": "github:geometries",
                    "name": "dLDL_1.dae",
                    "format": ".dae",
                    "coordinate_system": "left"
                }
            }
        },

[builab]

THank you