qcscine/molassembler: 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