Convert v0 to v1¶

cremdb_convert migrates a legacy v0 database to the deduplicated v1 schema. The old freq column becomes a named fragment set in the new database.

Basic conversion¶

cremdb_convert -i old.db -o fragments.db --set-name chembl

This creates fragments.db with the v1 tables (envs, frags, frags_h, radiusN) and one fragment-set column (chembl) populated from the v0 freq values.

Option	Default	Description
-i, --input	— (required)	Existing v0 database
-o, --output	— (required)	New v1 database (created)
--set-name	undefined	Name of the set column to create and fill from the old freq
--radii	1 2 3 4 5	Radii to convert
--batch-size	10000	Rows processed per batch
--verify	off	Verify the conversion after completion
--quiet	off	Suppress progress output

Convert selected radii¶

cremdb_convert -i old.db -o fragments.db --radii 1 2 3 --set-name chembl

Verify the conversion¶

cremdb_convert -i old.db -o fragments.db --set-name chembl --verify

--verify samples rows from each radius and checks that the reconstructed environment, core, and SMARTS match the source database.

What is preserved¶

• Environment, core SMILES, and dist2 information.
• The old freq values, mapped into the new --set-name column.
• Additional non-standard fragment columns from the old database are carried over into the frags table where possible.

New radiusN tables also gain an is_ring_closure column (default 0); v0 databases contain only acyclic-cut fragments, so converted rows are all acyclic. To obtain ring-closure rows, build with cremdb_create --frag-mode.

Naming and safety¶

• --set-name must be a valid SQLite identifier and cannot be env_id or core_smi_id.
• If the output file already exists, cremdb_convert asks for confirmation before overwriting it.