rdkit.Dbase.StorageUtils module

Various storage (molecular and otherwise) functionality

rdkit.Dbase.StorageUtils.GetNextId(conn, table, idColName='Id')

returns the next available Id in the database

see RegisterItem for testing/documentation

rdkit.Dbase.StorageUtils.GetNextRDId(conn, table, idColName='Id', leadText='')

returns the next available RDId in the database

see RegisterItem for testing/documentation

rdkit.Dbase.StorageUtils.IndexToRDId(idx, leadText='RDCmpd')

Converts an integer index into an RDId

The format of the ID is:

leadText-xxx-xxx-xxx-y

The number blocks are zero padded and the final digit (y) is a checksum:

>>> str(IndexToRDId(9))
'RDCmpd-000-009-9'
>>> str(IndexToRDId(9009))
'RDCmpd-009-009-8'

A millions block is included if it’s nonzero:

>>> str(IndexToRDId(9000009))
'RDCmpd-009-000-009-8'

The text at the beginning can be altered:

>>> str(IndexToRDId(9,leadText='RDAlt'))
'RDAlt-000-009-9'

Negative indices are errors:

>>> try:
...   IndexToRDId(-1)
... except ValueError:
...   print('ok')
... else:
...   print('failed')
ok

rdkit.Dbase.StorageUtils.RDIdToInt(ID, validate=1)

Returns the integer index for a given RDId Throws a ValueError on error

>>> RDIdToInt('RDCmpd-000-009-9')
9
>>> RDIdToInt('RDCmpd-009-000-009-8')
9000009
>>> RDIdToInt('RDData_000_009_9')
9
>>> try:
...   RDIdToInt('RDCmpd-009-000-109-8')
... except ValueError:
...   print('ok')
... else:
...   print('failed')
ok
>>> try:
...   RDIdToInt('bogus')
... except ValueError:
...   print('ok')
... else:
...   print('failed')
ok

rdkit.Dbase.StorageUtils.RegisterItem(conn, table, value, columnName, data=None, id='', idColName='Id', leadText='RDCmpd')

>>> from rdkit.Dbase.DbConnection import DbConnect
>>> conn = DbConnect(tempDbName)
>>> tblName = 'StorageTest'
>>> conn.AddTable(tblName,'id varchar(32) not null primary key,label varchar(40),val int')
>>> RegisterItem(conn,tblName,'label1','label',['label1',1])==(1, 'RDCmpd-000-001-1')
True
>>> RegisterItem(conn,tblName,'label2','label',['label2',1])==(1, 'RDCmpd-000-002-2')
True
>>> RegisterItem(conn,tblName,'label1','label',['label1',1])==(0, 'RDCmpd-000-001-1')
True
>>> str(GetNextRDId(conn,tblName))
'RDCmpd-000-003-3'
>>> tuple(conn.GetData(table=tblName)[0])==('RDCmpd-000-001-1', 'label1', 1)
True

It’s also possible to provide ids by hand:

>>> RegisterItem(conn,tblName,'label10','label',['label10',1],
...              id='RDCmpd-000-010-1')==(1, 'RDCmpd-000-010-1')
True
>>> str(GetNextRDId(conn,tblName))
'RDCmpd-000-011-2'

rdkit.Dbase.StorageUtils.RegisterItems(conn, table, values, columnName, rows, startId='', idColName='Id', leadText='RDCmpd')

rdkit.Dbase.StorageUtils.ValidateRDId(ID)

returns whether or not an RDId is valid

>>> ValidateRDId('RDCmpd-000-009-9')
1
>>> ValidateRDId('RDCmpd-009-000-009-8')
1
>>> ValidateRDId('RDCmpd-009-000-109-8')
0
>>> ValidateRDId('bogus')
0