Phase Database Structure

The database is stored in a directory, dbName.phdb, which contains all the files associated with the database. The files and directories that are standard parts of the database are described in Table 1. You should not generally need to modify these files, but you may find it useful to examine them. In addition to these files, the database can contain subset files, named subset_phase.inp.

You should not create or store other databases inside the database directory, as this is likely to lead to job failure.

Table 1. Database files and directories
File or Directory	Description
`database.sqlite`	An SQLite database with tables that hold global information about the database: `dprop_name_table`—Holds the name of the property used to detect and eliminate duplicates, `s_phase_Unique_SMILES`. `dprop_values_table`—Holds `mol_id` and `s_phase_Unique_SMILES` for each database record. `props_table`—Holds `mol_id`, `title`, `num_confs`, `has_sites`, plus all imported and computed properties for each database record. This table does not exist unless an "extract" job has been run, and it must be regenerated when changes to the database are made. `props_map_table`—Mappings of the column names in `props_table` to the CT property names in the block database files stored in `database_ligands`/. This table always exists, but is empty if properties have not been extracted. `summary_table` —Holds `mol_id`, `title`, `num_confs`, and `has_sites` for each database record. `has_sites` is 1 or 0, depending on whether or not sites are stored for a given record.
`database_dbversion`	Version file. Holds the Phase version number, the method of creation (always "CL"), and the storage format ("SQLite").
`database_feature.ini`	Feature definitions.
`database_history.log`	History of changes to the database, containing the date and the command issued.
`database_info.log`	Detailed information about changes to the database.
`database_master_phase.inp`	Master subset file.
`database_props.csv`	Copy of the data in `props_table` in CSV format. This file is only present if an `extract` job has been run.
`database_props_map.csv`	Copy of the mappings in `props_map_table` in CSV format. This file is only present if an `extract` job has been run with `-map`.
`database_props_stats.csv`	Statistics for the properties in `props_table`: `count`, `min`, `max` `avg`. `count` is the number of records for which the property exists. For string properties, `avg` is an empty value. This file is only present if an `extract` job has been run with `-stats`.
`database_summary.csv`	Copy of the data in `summary_table` in CSV format.
`database_ligands`	All block data is held under this directory. There is one SQLite file for each block of 5000 records, e.g., `database_ligands/block_1/block_struct_1.sqlite`. Structures, sites, CT-level properties, and 2D/3D indexes are stored in this file. When an `extract` job is run, the properties in these block files are extracted and written to the top-level file `database.sqlite`.
`database_restart`	This directory contains files that are required to restart a `phase_database` job. The files in this directory are updated as a job progresses. When the job and all of its subjobs finish normally, this directory is removed automatically.