Lomap Change Log#

v3.3.0#

This release offers a series of usability improvements and prepares Lomap for its next major release.

Changed:

  • Changed the default charge_changes_score from 0.0 to 0.1 in the gufe bindings to enable connected networks for ligands of different net charge by default (PR #83).

  • By default generate_lomap_network (gufe bindings) now fails if it cannot create a network where all the nodes are at least indirectly connected to each other. This behaviour can be controlled using the allow_disconnected keyword (PR #154).

  • The gufe package is now an optional dependency of Lomap (PR #134).

  • Minimum tested Python version has been raised to Python 3.11 and gufe raised to v1.0 (PR #124).

  • The seed argument to LomapAtomMapper and MCS is now None by default, which has the same behaviour as the previous default "" (an empty string - which means no seed). This is purely an aesthetic change to make the code more Pythonic. (PR #156).

Deprecated:

  • The dbmol CLI is deprecated and will be removed in the next major release of Lomap (Issue #138).

  • The fp module and associated Figureprint class are deprecated and will be removed in the next release of Lomap (Issue #129).

  • Deprecated the use of str(None) as an input to the hub keyword argument in graphgen.GraphGen.pick_lead. This option will be removed in the next release of Lomap, please use None instead (PR #125).

Removed:

  • Testing code which was available by directly calling mcs.py has been removed (PR #137).

Fixed:

  • The gufe bindings for the MNCAR score, which encodes the “minimum number of common atoms rule”, incorrectly compared the common atoms threshold ths as > instead of >=. This is now fixed. (Issue #147).

  • Improvements to the optional pygraphviz dependency (PR #141).

  • Various historical typing issues, including modernizing various rdkit.Chem.AllChem calls (PR #125).

v3.2.1#

Fixed:

  • Fixed bug where generate_lomap_network() would throw an error if molecules was passed in instead of ligands.

v3.2.0#

Deprecated:

  • Replaced the molecules argument with ligands in generate_lomap_network(). Argument name molecules will be deprecated.

v2.3.0#

Added:

  • Added shift option to MCS and cli (-s or –shift), this defaults to True. In combination with threed/-3 this option controls if the two structures are shifted on top of each other (using only translation and no rotation) before geometric mismatch is judged. This was always used as default until now. In cases where bad symmetric options are being chosen, using shift=False might resolve issues (Issue #26).

v2.2.0#

Added:

  • Added use_common_core option to DBMolecules and -C / --common-core option to CLI. This is on by default and speeds up network creation by 10-50x (PR #25).

Fixed:

  • Fixed DBMolecules iteration in Python v3 (PR #18).

v2.1.0#

Added:

  • Added element_change keyword to MCS class. This toggles if elemental changes are allowed within a mapping. Defaults to True (this was the previous behaviour).

  • Added -L switch command line usage to toggle element changes.

v2.0.0#

Added:

  • Added regression tests for MCS class.

Changed:

  • Replaced usage of argparse.Namespace as input to class inits (e.g. MCS) in favour of dicts.

  • Renamed various dunderscore variables to single underscore.

  • Rewrote tests in pytest, using fixtures to iterate over cases.

Fixed:

  • Fixed bug in explicit hydrogen atom mappings.

v1.0.0#

Added:

  • Added versioning.

  • Support for Python 3.5 and networkx v2.

  • Improved visualization of output networks.

Fixed:

  • Better enforcement of PEP8 style.

Removed:

  • Support for Python v2.7.

v0.0.x#

This is an internal Alpha version.

Added:

  • Basic functionality for preparing a Perturbation map for alchemical free energy calculations.