ecoli.library.test_rnap_initialization

Tests for RNAP initialization edge cases fixed in PR #359. Specifically: 1. RNAPs are assigned to chromosome domains based on their actual coordinates,

not just their transcription unit (TU) start positions

2. RNAPs cannot be initialized at the same location (collision detection)

class ecoli.library.test_rnap_initialization.TestRNAPCollisionDetection

Bases: object

Test that RNAPs cannot be initialized at the same location.

class ecoli.library.test_rnap_initialization.TestRNAPDomainAssignment

Bases: object

Test that RNAPs are correctly assigned to chromosome domains.

ecoli.library.test_rnap_initialization.check_domain_boundaries(unique_mols)

ecoli.library.test_rnap_initialization.check_no_duplicates(active_rnaps)

ecoli.library.test_rnap_initialization.mock_bulk_state()

Create mock bulk state with inactive RNAPs.

ecoli.library.test_rnap_initialization.mock_sim_data()

Create a minimal mock sim_data object for testing.

ecoli.library.test_rnap_initialization.mock_unique_molecules_double_replicating()

Create mock unique molecules with 2 rounds replication in progress: - Domain 0 (mother domain) - Domain 1 and 2 (daughter domains created by 1st fork) - Domain 3 and 4 (daughter domains created by 2nd fork) - 4 active replisomes creating the forks - Promoters distributed across domains