rdkit.Dbase.DbUtils module

a set of functions for interacting with databases

When possible, it’s probably preferable to use a _DbConnection.DbConnect_ object

rdkit.Dbase.DbUtils.DatabaseToDatabase(fromDb, fromTbl, toDb, toTbl, fields='*', join='', where='', user='sysdba', password='masterkey', keyCol=None, nullMarker='None')

FIX: at the moment this is a hack

rdkit.Dbase.DbUtils.DatabaseToText(dBase, table, fields='*', join='', where='', user='sysdba', password='masterkey', delim=',', cn=None)

Pulls the contents of a database and makes a deliminted text file from them

Arguments

  • dBase: the name of the DB file to be used

  • table: the name of the table to query

  • fields: the fields to select with the SQL query

  • join: the join clause of the SQL query (e.g. ‘join foo on foo.bar=base.bar’)

  • where: the where clause of the SQL query (e.g. ‘where foo = 2’ or ‘where bar > 17.6’)

  • user: the username for DB access

  • password: the password to be used for DB access

Returns

  • the CSV data (as text)

rdkit.Dbase.DbUtils.GetColumns(dBase, table, fieldString, user='sysdba', password='masterkey', join='', cn=None)

gets a set of data from a table

Arguments

  • dBase: database name

  • table: table name

  • fieldString: a string with the names of the fields to be extracted,

    this should be a comma delimited list

  • user and password:

  • join: a join clause (omit the verb ‘join’)

Returns

  • a list of the data

rdkit.Dbase.DbUtils.GetData(dBase, table, fieldString='*', whereString='', user='sysdba', password='masterkey', removeDups=-1, join='', forceList=0, transform=None, randomAccess=1, extras=None, cn=None)

a more flexible method to get a set of data from a table

Arguments

  • fields: a string with the names of the fields to be extracted,

    this should be a comma delimited list

  • where: the SQL where clause to be used with the DB query

  • removeDups indicates the column which should be used to screen

    out duplicates. Only the first appearance of a duplicate will be left in the dataset.

Returns

  • a list of the data

Notes

  • EFF: this isn’t particularly efficient

rdkit.Dbase.DbUtils.GetTypeStrings(colHeadings, colTypes, keyCol=None)

returns a list of SQL type strings

rdkit.Dbase.DbUtils.TextFileToDatabase(dBase, table, inF, delim=',', user='sysdba', password='masterkey', maxColLabelLen=31, keyCol=None, nullMarker=None)

loads the contents of the text file into a database.

Arguments

  • dBase: the name of the DB to use

  • table: the name of the table to create/overwrite

  • inF: the file like object from which the data should be pulled (must support readline())

  • delim: the delimiter used to separate fields

  • user: the user name to use in connecting to the DB

  • password: the password to use in connecting to the DB

  • maxColLabelLen: the maximum length a column label should be allowed to have (truncation otherwise)

  • keyCol: the column to be used as an index for the db

Notes

  • if _table_ already exists, it is destroyed before we write the new data

  • we assume that the first row of the file contains the column names

rdkit.Dbase.DbUtils.TypeFinder(data, nRows, nCols, nullMarker=None)

finds the types of the columns in _data_

if nullMarker is not None, elements of the data table which are

equal to nullMarker will not count towards setting the type of their columns.