After 18 years, pgchem::tigress retires

To whom it may concern.

Today I will retire pgchem::tigress, the PostgreSQL chemoinformatics extension based on OpenBabel, after 18 years of service. This decision is based on three main reasons:

1. I have not touched the GIST-Index Code for at least eight years, but beginning with PostgreSQL 14.x it started to cause SIGSEVs when building the index on molecules, and I'm unable to find the cause.
2. OpenBabel 3.x made changes in their API that would require me to rewrite functions or to disable them. And those changes are not very well documented.
3. Since my recent brush with death, I have decided that there are better ways to spend my time, than chasing Signal 11s. Especially since the RDKit cartridge has come a long way, and is more powerful than pgchem::tigress ever was.

This decision was not easy, since building pgchem::tigress was a part of my life. It was the first open source ever released by Bayer AG (at least in Germany). It also is the foundation of my PhD thesis. 

The code will remain public as long as there is a way to publish it.

It looks like pgchem::tigress just got a major upgrade

With the Release of PostgreSQL 12.x and OpenBabel 3.x, I decided to see if pgchem::tigress would still compile. Well, it took some minor changes, but YES, it does!

And - it seems like OpenBabel now handles E/Z and enantiomer stereochemistry correctly, at least in SMILES notation. This is a major step forward, but I have to do some more checks before the next release...

pgchem::tigress 4.0 released

pgchem::tigress 4.0 is finally out!

• This builds against PostgreSQL >= 9.4.x and OpenBabel 4.2.x on Linux.
• It contains all fixes and contributions of the previous versions.
• Support for building with Indigo has been removed
• A lot of dead code has been removed
• All palloc calls have been replaced by palloc0
• MOLECULE is not binary compatible and needs to be recreated when you upgrade from 3.2 to 4.0!
• MS spectrum creation has been removed. You may use enviPat instead for much more accurate spectra 

So: CREATE EXTENSION pgchem_tigress;

pgchem::tigress vs. OpenBabel 2.4.0

OpenBabel 2.4.0 is released, the build process worked flawlessly, 100% tests passed.

Now I have to see if the Tigress still likes it...

Well, pgchem::tigress builds against OpenBabel 2.4.0 without errors, but will it work?

Yes, pgchem::tigress works with OpenBabel 2.4.0 without any notable alterations, except changing:

OPENBABEL_SOURCE=openbabel-2.3.2

in the Makefile to:

OPENBABEL_SOURCE=openbabel-2.4.0

As always with .0 releases, subtle issues might be lurking below the surface, though.

pgchem::tigress - bugfix release

I recently discovered a bug in the fingerprinter code of pgchem::tigress which led to the following undesirable behaviour:

select 'ClC1=CC=C(CN2CCN\C2=N\N(=O)=O)C=N1'::molecule = '[O-][N+](=O)N=C1NCCN1Cc1ccc(Cl)nc1'::molecule

true

but:

select fp2string('ClC1=CC=C(CN2CCN\C2=N\N(=O)=O)C=N1'::molecule) = fp2string('[O-][N+](=O)N=C1NCCN1Cc1ccc(Cl)nc1'::molecule)

false

I.e. the fingerprinter code regards the two differently drawn nitro groups as chemically different while the exact matcher correctly recognizes them as chemically equal. So, whenever an index is used for exact match searching, it was overselective, possibly filtering out correct hits.

This has been fixed.

Also, the add_hydrogens() function now accepts a fourth parameter to specify the PH value for protonation. If unspecified, it has a default of 7.4 so existing code using this function won't break.