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NEWS.md

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NEWS

v0.17.2

  • Fixed rem_vertex (#114)
  • The default destination path of the compiled package is now /usr/local/moleculargraphjl
  • The behavior of stereocenters with an unnecessarily high number of wedges has been clarified.
  • Fixed serialization of molecules with invalid stereochemistry.

v0.17.1

  • The library builder (built with PackageCompiler) is now Julia v1.11 compatible
  • Fixed inappropriate size of atom indices and highlights when exporting very large PNG structure images.

v0.17

  • valence and aromaticity
    • pi_delocalized and hybridization_delocalized are deprecated. pi_electron and hybridization always consider contribution of N, O, S lone pairs to the adjacent conjugation system.
    • valence works with non-organic atoms and hypervalent atoms, and hybridization may better explain molecular geometry (e.g. -SO2-).
    • Aromaticity determination algorithm has been improved, allowing more reasonable detection in many cases even for fused rings (e.g. azulene).
    • (sub)structure match functions matches atom_symbol and hybridization of each atoms by default. hybridization may better explain molecular geometry.
  • metadata behavior (e.g. option block in SDFile)
    • metadata function would be deprecated (too general and easy to conflict with other packages).
    • get_prop(mol::MolGraph, key::String) returns the value of the metadata field.
    • set_prop! should work similarly.
    • Still get_prop(mol::MolGraph, key::Symbol) returns other graph properties (e.g. stereochem) but in many cases these should be automatically generated and should not be modified.
    • Molecules built from SMILES should be able to have manually curated metadata fields.
    • convenient metadata setter/getters (e.g. mol["compound_id"] = "ABC00001")

v0.16

Toward version 0.16.0, I have been working on 2D structure images export to PNG (with Cairo) and building binary packages for C and Python.

  • html_fixed_size and html_grid now takes MolGraph objects, not SVG.
  • Some molecule parameter methods for 2D drawing (e. g. is_atom_visible, double_bond_style) are no longer exposed.
  • Added Cairo.jl to the dependencies

v0.15

This release contains significant performance improvements in maximum common substructure (MCS) methods. Here are some API changes:

  • tcmcis/tcmces are renamed to tdmcis/tdmces (Abbreviation of Topologically-constrained Disconnected MCS in the original literature)
  • libinchi was updated based on InChI version 1.06. Now inchi and inchikey can take InChI options as optional arguments.
  • pi_electron and hybridization now do not consider delocalization of lone pairs on N, O and S. Default subgraph isomorphism matcher functions use pi_electron to consider bond orders, so the matching behavior would change a bit.
  • pi_delocalized and hybridization_delocalized, which consider the delocalization, are also available (maybe slightly expensive).
  • MCS calculation methods (disconnected_mcis/mces, connected_mcis/mces and tdmcis/mces), and clique detection methods called from them now return Tuple{Dict{T,T},Symbol}. The dict is the mapping of matched vertices/edges, and the symbol is the status (:done, :targetreached or :timedout)