MolecularGraph.jl

MolecularGraph v0.17.1

Diff since v0.17.0

• 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.

MolecularGraph v0.17.0

Diff since v0.16.1

• Improved valence and aromaticity determination algorithms
• Improved molecule metadata access (e.g. SDFIle option block)

Merged pull requests:

• CompatHelper: bump compat for MakieCore to 0.8, (keep existing compat) (#108) (@github-actions[bot])
• Create NEWS.md (#109) (@timholy)

Closed issues:

• API changes in v0.15.0 (#98)

MolecularGraph v0.16.1

Diff since v0.16.0

• Fixed wrong stereochemistry of SMILES molecules
• SDFile reader error logs can be stored in gprops instead of standard output

MolecularGraph v0.16.0

Diff since v0.15.2

Breaking changes

• 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

MolecularGraph v0.15.2

Diff since v0.15.1

Merged pull requests:

• CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat) (#103) (@github-actions[bot])
• CompatHelper: bump compat for MakieCore to 0.7, (keep existing compat) (#104) (@github-actions[bot])

Closed issues:

• Coulomb matrices calculation (#99)
• Merging edgemincyclebasis into Graphs.jl (#101)
• Will has_exact_match care about trivial hydrogens or chiral centers? (#102)

MolecularGraph v0.15.1

Diff since v0.15.0

MolecularGraph v0.15.0

Diff since v0.14.3

Closed issues:

• coordgen does not work with Julia 1.9 (#93)

Merged pull requests:

• CompatHelper: add new compat entry for DelimitedFiles at version 1, (keep existing compat) (#94) (@github-actions[bot])
• Support sdf and mol generation from inchi string (#95) (@hhaensel)

MolecularGraph v0.14.3

Diff since v0.14.2

MolecularGraph v0.14.2

Diff since v0.14.1

Closed issues:

• name clash with Base.VERSION (#92)

MolecularGraph v0.14.1

Diff since v0.14.0

Closed issues:

• Erroneous catching of diasteromers (#91)

MolecularGraph v0.14.0

Diff since v0.13.0

Closed issues:

• structure image grid (#24)
• Atom color set (#49)
• Breaking changes in v0.10.0 (#58)
• V3000 format (#60)
• UndefVarError: libcoordgen not defined when drawing a molecule (#68)
• RDKit GetMolFrags equivalent? (#73)
• How does one go about generating the 3D visualization? (#74)
• bond aromaticity not stored in SmilesBond (#75)
• Bump minimum Julia requirement to 1.6 (#80)
• MolecularGraph.Graph -> Graphs.jl (#81)
• sethighlight! doesn't work on single carbon atoms in skeletal notation (#82)
• How are SMILES atoms parsed to the indices used in MolecularGraph? (#84)
• How can I add a bond between two fragments, given their fragment indices? (#85)
• precalculate! doesn't cache isaromatic(mol::MolGraph) property. (#86)
• Update and expand 3D display functions? (#88)

Merged pull requests:

• Commented checks for atom visibility (issues/82) (#83) (@Boxylmer)
• Expand 3D drawing utilities (#90) (@tmcgrath325)

MolecularGraph v0.13.0

Diff since v0.12.0

MolecularGraph v0.12.0

Diff since v0.11.0

Closed issues:

• Integrating MolecularGraph.jl with Gtk (#65)

Merged pull requests:

• Base.multimedia.display(mol) (#77) (@eahenle)
• Delete Manifest.toml (#78) (@eahenle)

MolecularGraph v0.11.0

Diff since v0.10.0

Closed issues:

• Add reactions (#61)

Merged pull requests:

• add support for V3000 format and rxn files (#62) (@hhaensel)
• Corrections for extended molfile support and rdfilereader support of bare rxn files (#63) (@hhaensel)

MolecularGraph v0.10.0

Diff since v0.9.0

Closed issues:

• No charge on carbon chain SVG (#25)
• Gaps in allene-like double bonds (#26)
• outerplanarity test failure on Julia 1.6 (#44)
• Re-design of MCS calculation functions (#57)

Merged pull requests:

• Generalize exception type (#59) (@timholy)

MolecularGraph v0.9.0

Diff since v0.8.0

Closed issues:

• Tidy up structure matching functions (#33)
• Monomorphism mapping algorithm and its performance (#48)
• New release? (#51)
• Parse % symbols for ring closures in SMILES (#56)

Merged pull requests:

• MassInstallAction: Install the TagBot workflow on this repository (#53) (@mojaie)
• MassInstallAction: Install the Documenter workflow on this repository (#54) (@mojaie)

MolecularGraph v0.8.0

Diff since v0.7.1

Closed issues:

• Duplicate detection in functional groups (#31)
• sdfilewriter should be closed (#35)
• Add a few more topics? (#36)
• Format of return from edgesubgraphmatches? (#39)
• Bridges depend on starting node (#42)
• Any interest in 3d display? (#46)

Merged pull requests:

• modified sdfilewriter to use filename (#32) (@richardskim111)
• Support multiline attributes (#37) (@timholy)
• Activate CI (#38) (@timholy)
• Make subgraph operations more generic (#40) (@timholy)
• Add outer constructors for "state" types (#41) (@timholy)
• Don't specialize connectedcomponents for subgraphs (#43) (@timholy)
• Add substructure 1:1 node matching (#45) (@timholy)
• Add covalent radii and 3d drawing utilities (#47) (@timholy)

MolecularGraph v0.7.1

Diff since v0.7.0

Closed issues:

• default preprocessing (#20)
• refactor molecular property methods (#21)
• Get rid of too many descriptor caches (#22)

MolecularGraph v0.7.0

Diff since v0.6.0

Closed issues:

• Topics and destructive changes in v0.6.0 (#14)
• Serialization (#17)
• InChI (#18)

Changes

• setdiastereo!, setstereocenter!(SDFile) and kekulize!(SMILES) are called by default when molecule data are loaded (#20)
• Many functions renamed (see #21)
• Fixed unexpected behavior in planarity tests
• Isotope table expanded
• Descriptor caching mechanism improved (#22)

MolecularGraph v0.6.0

Diff since v0.5.0

Closed issues:

• Working on stereochemistry (#11)
• Information about simulatemassspec (#15)
• Render svg to Gtk (#16)