kripodb.db

Fragments and fingerprints sqlite based data storage.

Registers BitMap and molblockgz data types in sqlite.

class kripodb.db.FastInserter(cursor)

Use with to make inserting faster, but less safe

By setting journal mode to WAL and turn synchronous off.

Parameters:cursor (sqlite3.Cursor) – Sqlite cursor

Examples

>>> with FastInserter(cursor):
        cursor.executemany('INSERT INTO table VALUES (?), rows))

class kripodb.db.FingerprintsDb(filename)

Fingerprints database

as_dict(number_of_bits=None)

Returns a dict-like object to query and alter fingerprints db

Parameters:number_of_bits (Optional[int]) – Number of bits that all fingerprints have Returns:BitMapDict

create_tables()

Abstract method which is called after connecting to database so tables can be created.

Use CREATE TABLE IF NOT EXISTS … in method to prevent duplicate create errors.

class kripodb.db.FragmentsDb(filename)

Fragments database

add_fragment(frag_id, pdb_code, prot_chain, het_code, frag_nr, atom_codes, hash_code, het_chain, het_seq_nr, nr_r_groups)

Add fragment to database

Parameters:

• frag_id (str) – Fragment identifier
• pdb_code (str) – Protein databank identifier
• prot_chain (str) – Major chain of pdb on which pharmacophore is based
• het_code (str) – Ligand/Hetero code
• frag_nr (int) – Fragment number, whole ligand has number 1, fragments are >1
• atom_codes (str) – Comma separated list of HETATOM atom names which make up the fragment (hydrogens are excluded)
• hash_code (str) – Unique identifier for fragment
• het_chain (str) – Chain ligand is part of
• het_seq_nr (int) – Residue sequence number of ligand the fragment is a part of
• nr_r_groups (int) – Number of R groups in fragment

add_fragments_from_shelve(myshelve, skipdups=False)

Adds fragments from shelve to fragments table.

Also creates index on pdb_code column.

Parameters:

• myshelve (Dict[Fragment]) – Dictionary with fragment identifier as key and fragment as value.
• skipdups (bool) – Skip duplicates, instead of dieing one first duplicate

add_molecule(mol)

Adds molecule to molecules table

Uses the name of the molecule as the primary key.

Parameters:mol (rdkit.Chem.AllChem.Mol) – the rdkit molecule

add_molecules(mols)

Adds molecules to to molecules table.

Parameters:mols (list[rdkit.Chem.Mol]) – List of molecules

add_pdbs(pdbs)

Adds pdb meta data to to pdbs table.

Parameters:pdbs (Iterable[Dict]) – List of pdb meta data

by_pdb_code(pdb_code)

Retrieve fragments which are part of a PDB structure.

Parameters:pdb_code (str) – PDB code Returns:List of fragments Return type:List[Fragment] Raises:LookupError – When pdb_code could not be found

create_tables()

Create tables if they don’t exist

id2label()

Lookup table of fragments from an number to a label.

Returns:SqliteDict

is_ligand_stored(pdb_code, het_code)

Check whether ligand is already in database

Parameters:

• pdb_code (str) – Protein databank identifier
• het_code (str) – Ligand/hetero identifier

Returns:

bool

label2id()

Lookup table of fragments from an label to a number.

Returns:SqliteDict

class kripodb.db.IntbitsetDict(db, number_of_bits=None)

Dictionary of BitMaps with sqlite3 backend.

Parameters:

• db (FingerprintsDb) – Fingerprints db
• number_of_bits (int) – Number of bits

number_of_bits

int – Number of bits the bitsets consist of

update([E, ]**F) → None. Update D from mapping/iterable E and F.

If E present and has a .keys() method, does: for k in E: D[k] = E[k] If E present and lacks .keys() method, does: for (k, v) in E: D[k] = v In either case, this is followed by: for k, v in F.items(): D[k] = v

class kripodb.db.SqliteDb(filename)

Wrapper around a sqlite database connection

Database is created if it does not exist.

Parameters:filename (str) – Sqlite filename

connection

sqlite3.Connection – Sqlite connection

cursor

sqlite3.Cursor – Sqlite cursor

close()

Close database

commit()

Commit pending changes

create_tables()

Abstract method which is called after connecting to database so tables can be created.

Use CREATE TABLE IF NOT EXISTS … in method to prevent duplicate create errors.

class kripodb.db.SqliteDict(connection, table_name, key_column, value_column)

Dict-like object of 2 columns of a sqlite table.

Can be used to query and alter the table.

Parameters:

• connection (sqlite3.Connection) – Sqlite connection
• table_name (str) – Table name
• key_column (str) – Column name used as key
• value_column (str) – Column name used as value

connection

sqlite3.Connection – Sqlite connection

cursor

sqlite3.Cursor – Sqlite cursor

items() → list of D's (key, value) pairs, as 2-tuples

iteritems() → an iterator over the (key, value) items of D

iteritems_startswith(prefix)

item iterator over keys with prefix

Parameters:prefix (str) – Prefix of key

Examples

All items with key starting with letter ‘a’ are returned.

>>> for frag_id, fragment in fragments.iteritems_startswith('a'):
        # do something with frag_id and fragment

Returns:List[Tuple[key, value]]

itervalues() → an iterator over the values of D

materialize()

Fetches all kev/value pairs from the sqlite database.

Useful when dictionary is iterated multiple times and the cost of fetching is to high.

Returns:Dictionary with all kev/value pairs Return type:Dict

values() → list of D's values

kripodb.db.adapt_BitMap(ibs)

Convert BitMap to it’s serialized format

Parameters:ibs (BitMap) – bitset

Examples

Serialize BitMap

>>> adapt_BitMap(BitMap([1, 2, 3, 4]))
'xœ“c@
ð'

Returns:serialized BitMap Return type:str

kripodb.db.adapt_molblockgz(mol)

Convert RDKit molecule to compressed molblock

Parameters:mol (rdkit.Chem.Mol) – molecule Returns:Compressed molblock Return type:str

kripodb.db.convert_BitMap(s)

Convert serialized BitMap to BitMap

Parameters:s (str) – serialized BitMap

Examples

Deserialize BitMap

>>> ibs = convert_BitMap('xœ“c@
ð')
BitMap([1, 2, 3, 4])

Returns:bitset Return type:BitMap

kripodb.db.convert_molblockgz(molgz)

Convert compressed molblock to RDKit molecule

Parameters:molgz – (str) zlib compressed molblock Returns:molecule Return type:rdkit.Chem.Mol