Release 3.0.0

Changes:

• Add overload to editing::substitute to specify which sides are substituted
• Add BondDiscretizationOption::RoundToNearest to IO::split to be consistent with IO::read

Release 2.0.1

Changes:

• Update address in license

Release 2.0.0

Changes:

• Cleaving graphs always returns Cleave object including ComponentMap
• Changed C++ standard from C++14 to C++17
• BondStereopermutator update on atom deletion
• Dependency handling for Boost versions >1.70
• BondStereoPermutator determination on eta bonds
• Nitrogen thermalization in cyclic systems
• Feasible stereopermutations consistency between serialization and deserialization
• The gradient target for the conformer optimization is now passed correctly

Release 1.2.1

Changes:

• Include the shape position groups into the serialization to ensure the correct reconstruction of site to vertex maps. This should make the molecule serialization and deserialization more consistent (and less error prone).
• DirectedConformerGenerator::binMidpointIntegers deprecated because it returns dihedral angles that are defined differently from DirectedConformerGenerator::Relabeler::add.

Release 1.2.0

Changes:

• Increase flatness threshold for rings (from 0.05 to 0.07)
• Symmetry reduced dihedral calculation in conformer and decision list generation
• Decision list: random atom choice in dihedral representation, now: fixed choice

Release 1.1.0

Added

• Molecule:

  • Bond stereopermutator addition and removal functions
  • Manual atom stereopermutator thermalization control

• Graph: Added modifying functions to the interface for stand-alone class use

• Graph algorithms

  • Ranking equivalent groups and ranking distinct atoms algorithms exploiting ranking results to classify chemical equivalence.
  • Shortest path generator between vertices in the graph
  • Edit distance. Algorithm to calculate minimal set of vertex and edge alterations to transform one graph into another.
  • Reaction edit distance. Variation of the graph edit distance algorithm that conserves element types. Also adds an associated function that plots the edits.

• Conformer deduplication: More Relabeler-related functions

• Experimental SMILES emitter: IO/SmilesEmitter.h

• Limited support for periodic boundary conditions via Utils::PeriodicSystem. Periodic systems can be interpreted, canonicalized and serialized, but not conformer generated. Ranking across boundaries is yet unsupported.

• Python bindings:

  • Added modifying functions to Graph
  • Direct copying support for Molecule instead of via pickling
  • Added build-time generation of typing stubs with pybind11-stubgen

Changed

• Graph and Molecule are now implementations of a common interface for graph information and modification. This interface might be expanded in the future.

• More colorful graphviz rendering for elements

• Conan: Better integration with community packages. No longer require full CMake from all dependencies but follow conan packaging philosophy <https://github.com/conan-io/conan-center-index/blob/master/docs/faqs.md#why-are-cmake-findconfig-files-and-pkg-config-files-not-packaged>_.

• CMake: option MOLASSEMBLER_PARALLELIZE is now SCINE_PARALLELIZE to follow SCINE convention.

• Interpretations without bond orders infer bond orders in binary fashion from Utils' BondDetector instead of from UFF parameters

• Bond stereopermutator alignment:
  BondStereopermutator::Alignment::BetweenEclipsedAndStaggered now generates the same amount of alignments as BondStereopermutator::Alignment::Eclipsed, not twice as many.

• Auxiliary library Temple

  • Refactor map to be able to apply it to tuples and arrays, too.
  • Clean up ContainerTraits.h

• SMILES parser

  • Parsing errors as part of exception string, not written to stdout
  • Perfect matching of aromatic subgraphs, error reporting
  • Fix valence filling bug for atom types with multiple valid valences

• Python bindings

  • Altered name of ChiralStatePreservation enum member from None to DoNotPreserve (the former is a reserved keyword)
  • Better automatic type signature annotations in docstrings

Deprecated

• Graph properties N and B for the number of atoms and the number of bonds have been deprecated in favor of new V and E properties in order to match complexity annotations and single-letter object properties
• StereopermutatorList method try_remove is deprecated in favor of remove, which now behaves as try_remove would (no throwing).
• Several AtomStereopermutator methods have been deprecated in favor of refactors with other function arguments not tightly coupled to the Graph class, permitting stand-alone class use

Removed

• Several constant global data variables in the private API have been replaced with stateless functions or function-local caches.
• Constexpr shape property generation: It was clang-only and provided no tangible performance benefits. Best code is no code. Got rid of a few global variables in the process.

Fixed

• Conformer generation: Removed an incorrect check for non-terminal vertices without an atom stereopermutator failing in some haptic cases

• Permutator propagation:

  • Fixed missing propagation of atom stereopermutator placement and re-keying the atom stereopermutator map in StereopermutatorList
  • Add missing propagation of bond stereopermutator state on vertex removal
  • Trial stereopermutation vertex links weren't permuted along with the site indices

• Directed conformer generation: Fixed incorrect precondition check with unassigned stereopermutators

• Python bindings' interpret.interpret has been renamed to an interpret.molecules overload as originally intended.

• Shape mapping generator between the same two shapes did not return the identity mapping

Release 1.0.0

Added

• Add Conan support

• Explicit definition of which headers make up the public API in the
  tutorial-like documentation

• Molecule canonicalization: After canonicalization, isomorphism checks reduce
  to an identity comparison.

• GraphAlgorithms.h for public graph algorithms. Currently contains only a
  graph distance BFS algorithm

• A doc target that builds the Doxygen documentation, which is now more
  extensive and contains the beginnings of a tutorial

• Many parameters of Distance Geometry can now be altered by passing a
  non-defaulted Configuration object.

• Isomer predicate and generator header Isomers.h

• Higher-level editing functionality in Editing.h

• More shapes up to icosahedron and cuboctahedron (size 12)

• Continuous symmetry, shape measures

• Experimental SMILES Parser

• Python bindings

  • Molecule instances integrate nicely with notebooks using _repr_svg_
  • Doctested examples

Changed

• The PRNG Engine is seeded directly instead of a wrapper object that helps
  with generating random numbers. The PRNG engine is part of molassembler's
  public interface instead of the sublibrary temple. The engine is constructed
  on first use.
• Molassembler's validation and analysis binaries are no longer built by
  default (see CMake options)
• Add BSD-3 license marker to all files and a checker script
• Adopt Scine code conventions regarding namespace formatting
• Enclose temple, shapes, and stereopermutation sub-libraries in molassembler
  namespace