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CHANGELOG

mmpdb 2.2 - 2019-11-01

This minor release contains improvements that help reducing the database size. MAny transformations and associated statistics inside the database are unlikely to ever be used, since there are other transformations that will yield the same compounds. To accomplish this, three new options have been introduced:

  • max-radius: The maximum radius can now be set on the command line during indexing. This was hardcoded in previous versions.

  • smallest-transformation-only: Some transformation scan be reduced to smaller transformations, for example p-Fluoro-phenyl >> p-Chloro-phenyl to Fluoro >> Chloro. If this flag is set during indexing, reducible transformations will not be written to the database. Note that this only setting reduces the number of transformations for a given pair. It does not completely remove a pair.

  • min-heavies-per-const-frag: For double- and triple-cuts, fragmentations are created where the constant parts can be very small down to a single atom. For example, if the fragmentation algorithm can generate a single-cut where the variable fragment is p-Fluorophenyl, it will also generate a double cut with phenyl as variable fragment and F as one of the constant pieces. The 'min-heavies-per-const-frag' option can be used during fragmentation to eliminate multiple cuts where one of the constant fragments is very small. If this is set to 3 or 4, double- and triple cuts only happen at positions that would be considered real scaffolds changes in the middle of molecules. Note that in principle this option only reduces the number of pairs for a given transformation, effectively removing multiple-cuts where possible. There may be edge cases where pairs are completely removed, because the single cut transfers too many atoms. If you use this option, you may want to adjust the --max-variable-heavies option during indexing.

    The last '--smalles-transformation-only' and '--min-heavies-per-const 3' options together typically reduce the database size by ~ 70%.

mmpdb 2.1 - 2018-04-27

  • RDKit 2018_03_1 changed the SMILES output so wildcard atoms are represented with a * instead of [*]. mmpdb works with SMILES strings at the syntax level. Parts of the code expected only the old RDKit behavior and crashed or gave the wrong output for the new behavior. For example, the fragmentation algorithm raised an AssertionError saying:
  File "mmpdblib/fragment_algorithm.py", line 368, in make_single_cut
    constant_smiles_with_H = replace_wildcard_with_H(constant_smiles)
  File "mmpdblib/fragment_algorithm.py", line 302, in replace_wildcard_with_H
    assert smiles.count("[*]") == 1, smiles
AssertionError: *O

Version 2.1 now supports both ways of representing the wildcard atom and will work with RDKit releases from 2017 and 2018.

  • The tests are now included as part of the distribution.

  • mmpdb is available from PyPI using "pip install mmpdb"

  • A preprint of our paper is available from ChemRxiv. We received word today that JCIM has accepted it (after minor changes).

mmpdb 2.0 - 2017-08-15

First public release of mmpdb, an open-source matched molecular pair package designed to create and query MMP databases for big-pharma sized ADMET datasets.