Bingo Changelog¶

Bingo 1.9.1¶

13 September 2020

We are glad to announce a new version for Bingo cartridges. Installation artifacts can be found at Downloads

PostgreSQL 11 and 12 versions support was added and tested
Bug was fixed with tautomer fingerprints
Indigo-core changes and bugfixes.

Bingo 1.8.0 beta¶

12 January 2018

We are glad to announce a new version for Bingo cartridges. As always, installation artifacts can be found at Downloads

General changes:

Indigo-core changes and bugfixes.
New configuration option was added ingore_bad_valence. Together with ignore-stereochemistry-errors this option allows to ignore almost all existing errors for the molecular databases. This caused the significant changes for the internal indexation and search engines to be able work with ‘incorrect’ structures
Add timeout support for utility functions
getMass() precision was changed to double
Standardize method was added. Standardization description can be found here
Add stabilizations for bingo-core search engine. Add reject-invalid-structures for general methods.

Bingo engine-specific changes:

PostgreSQL 9.5, 9.6 and 10.1 versions support was added and tested
Microsoft SQL Server 2017 was added and tested

Roadmap to a stable version:

Document and add descriptions with examples for all the changes and new options
Create more regression tests for the new functionallity
Resolve current Bingo bug requests from GitHub repo

Bingo 1.7.10 dev6¶

28 December 2014

General changes:

Indigo now understands aromatic rings with external double bonds such as O=C1C=CC=CC=C1.
Either cis/trans bond marked is preserved during molfile loading even if substitutes are collinear.
Fixed an issue in the SMILES loader module that set invalid number of implicit hydrogens: https://groups.google.com/d/msg/indigo-bugs/i7g3hoSXxhI/XaXsEOVJ8_cJ
New method to get stereocenter pyramid. Thanks to Daniel for the feature request: https://groups.google.com/d/msg/indigo-dev/z0a1QwRMrx4/0s-KEtPBB_EJ
Fingerprints computation now works 30% faster.
All stereocenter exceptions now includes also atom index: https://groups.google.com/d/msg/indigo-bugs/nZOmFCEsNqk/S92lgH5zjvwJ

Bingo PostgreSQL-specific changes:

PostgreSQL 9.3 and PostgreSQL 9.4 versions support was added
Bug with join queries was fixed
Multithread option was implemented for the index create procedure
Other bugfixes and improvements

Bingo 1.7.9¶

3 April 2013

General changes:

Fingerprints now include information about single-atom fragments. This resolved an issue with empty fingerprints for single-atom molecules. Also this change makes substructure search more efficient in case of rare atoms in a query.
Timeout parameter for exact search method for a single structure. Default value is 1 min.
Smiles saver doesn’t throw exception about implicit hydrogens if they are not saving in SMILES

Bingo PostgreSQL-specific changes:

bug with similarity search for null structures was fixed
performance was improved for join queries
bug with exact join query (windows) was fixed
bitmap scan feature was turned off by default for bingo

Bingo 1.7.8b2¶

15 February 2013

General changes for Bingo Oracle, SQL Server and PostgreSQL:

all the bug fixes from the Indigo branch (AAM cancellation timeout, aromatization bug fixed and others)

Bingo PostgreSQL-specific changes:

import sdf bug was fixed (throw error on incorrect format)
bug with the rescan queries was fixed (join queries now work properly)
errors while binary matching were fixed
multi-threading was implemented for index building (creating index performance was improved)

Bingo 1.7.7¶

29 January 2013

This is a stable Bingo release for the all three databases: Oracle, MS SQL Server, and PostgreSQL. It includes all the bug fixes from the Indigo branch.

New methods for Bingo Oracle, SQL Server and PostgreSQL:

bingo.InChI(molecule, options) method to compute InChI identifier. You can pass any options that are supported by InChI library via options argument. For example you can provide options in the following way:
```
bingo.InChI(molecule, '/DoNotAddH /SUU /SLUUD')
```
bingo.InChIKey(inchi) method to compute InChI Key. To get an InChI key from a molecule with a default options use the following syntax:
```
select bingo.InChIKey(bingo.InChI(molecule, ''))
```
bingo.fingerprint(molecule, options) and bingo.rfingerprint(reaction, options) methods to compute fingerprints. The options are the same as we have for the IndigoObject.fingerprint method in Indigo:
sim - “Similarity fingerprint”, useful for calculating similarity measures (the default)
sub - “Substructure fingerprint”, useful for substructure screening
sub-res - “Resonance substructure fingerprint”, useful for resonance substructure screening
sub-tau - “Tautomer substructure fingerprint”, useful for tautomer substructure screening
full - “Full fingerprint”, which has all the mentioned fingerprint types included

Bingo PostgreSQL-specific changes:

PostgreSQL 9.2 support was added
Bug with cost estimation engine was fixed
bingo.compactMolecule(molecule, xyz) and bingo.compactReaction(reaction, xyz) methods were added
All utility methods now return text (not cstring)
All utility methods now accept binary byte parameter for input structures(returned by bingo.compactMolecule() and bingo.compactReaction())

Bingo Oracle-specific changes:

rowid is included into the message in case of exceptions

Bingo SQL Server-specific changes:

primary keys are added to the Bingo-specific table to support replication procedure.
more details in the diagnostics log: thread id, process id, and etc.
better support for query cancellation

Also we switch to a continues version numbering like we are doing with Indigo releases.

Bingo 1.7 beta4¶

24 April 2012

All the improvements have been merged from the Indigo branch (versions above 1.1 beta6), including:

Better handling of molecules with invalid valence.
Molecule serialization with more than 8 R-groups
incorrect empty R-Group logic loading attachment points loading from molfile was fixed

The new release contains bingo-specific changes including critical bugfixes for PostgreSQL:

Bug with inserting to a table contained more than 64k molecules was fixed.
Build and search queries now support cancel requests.
Bug with possible dead lock for PostgreSQL hang queries was fixed.
Binary data storing was fixed.
Possible segmentation fault during raising exceptions was fixed.
The issue with queries contained several bingo functions was resolved.

Also, bug with Oracle 11.2 on Windows 7 x64 was fixed.

Bingo 1.7 beta3¶

28 December 2011

All the bugfixes and improvements from the Indigo branch have been merged into the Bingo branch including:

Cis-trans issues has been fixed.
More accurate query fingerprints for SMARTS queries.

Bingo-specific changes:

Support of the PostgreSQL 9.1
Now binary files for Oracle are available for download, because we eliminated a linkage with OCI libraries. No building from source is required any more for getting Bingo for Oracle on Windows.

Bingo 1.7 beta2¶

30 November 2011 (no public announcement)

Bugfix release.

Bingo 1.7 beta1¶

29 September 2011

First Bingo version for PostgreSQL. The cartridge is covered almost all the functionality taken from the Bingo Oracle and the Bingo Sql Server parts.

The Bingo library for the PostgreSQL supports index building for molecules and reactions. The algorithm for the index search includes both the basic Bingo search engine principles and the unique heuristic algorithms for the PostgreSQL database. Thus the PostgreSQL Bingo cartridge can show a great performance comparable to or greater than other Bingo implementations.

Bingo 1.6.0¶

17 June 2011

The stable Bingo release.