v4.3.0

• standalone mol-to-graph conversion from command line.
• minor fixes

v4.2.2

What's Changed

• New symmetry detection algorithm
• New mutation that adds fused rings
• Fixed tournament selection
• Upgrade all dependencies

v4.2.0

What's Changed

• new add ring mutation
• add timeout for fragment isomorphism inspector
• fix APClass-controlled mapping of APs
• fix error on large SDF files
• fix xover with APClass compatibility
• add informative msg for JSOM version mismatch
• refactored ring-closing machinery

Full Changelog: v4.1.3...v4.2.0

v4.1.3

• add possibility to save population at end of each generation.
• removed dependency on JAVA_HOME for package installations on Unix.
• added noarch package.

v4.1.2

• debug detection of symmetry upon mol-to-graph conversion

v4.1.1

• Introduced fast communication via sockets to retrieve descriptor scores/fitness from external tools (e.g., python servers)
• Conversion of molecular representation into DENOPTIM graphs by on-the-fly fragmentation (via GUI or in GA run)
• Extended the functionality of the genetic algorithm by adding optional behavior.
• Generalized SUS selection strategy
• GUI can now handle also settings not directly defined in GUI's forms.
• Minor debugs.

v4.0.0

Main differences with version 3.x:

• AP identifiers are guaranteed to be unique only within a graph, thus there is no more limit on the number of APs that can be generated by a single run (used to be Integer.MAX_VALUE, i.e., ca. 2 billions)
• The JSON format for reporting symmetric sets of attachment points and vertexes has been simplified. Use the format conversion scriptto convert JSON and .sdf files generated by version<4 to the new format.
• It is now possible to control the maximum size of the subgraphs that the crossover operation can swap. See keyword GA-MaxXoverSubGraphSixe.

v3.2.6

adds visualization of molecular fragments as 2D structures even for 0D fragments.

v3.2.4

Minor bug fixes:

• GUI now reads shape of probability functions
• GA does not accept invalid parent selection scheme, but points out the problem.

v3.2.3

• debug counting of possible ring when using RCA of same type
• re-allow FSE to run without fitness provider