Summary:

Introduces the core computational engine for DREIDING atom typing and the final builder module for generating a complete MolecularTopology. It includes an iterative, relaxation-based typing engine that applies a prioritized rule set to an annotated molecular graph. After successful typing, a new builder module constructs the final topological representation, including atoms, bonds, angles, and both proper and improper dihedrals.

Changes:

• Developed the Iterative Atom Typing Engine:

  • Created a TyperEngine (processor::typer) that iteratively applies rules until a stable set of atom types is achieved.
  • The engine uses a relaxation algorithm: it runs multiple rounds, allowing atom types to be updated based on the types of their neighbors, which resolves dependencies (e.g., typing an acidic hydrogen requires its oxygen neighbor to be typed first).
  • Rules are sorted and applied based on priority, ensuring that specific, high-priority rules are matched before general, low-priority ones.
  • Implemented robust error handling for cases where atoms remain untyped, providing diagnostics for debugging rule sets.

• Implemented the Final Topology Builder:

  • Created a builder module to translate the annotated graph and assigned atom types into the final MolecularTopology output format.
  • Atom & Bond Generation: Directly translates the typed atoms and initial bonds into the final structure.
  • Angle Perception: Implemented an algorithm to systematically find all unique bond angles (i-j-k triplets) from the graph's adjacency list.
  • Proper Dihedral Perception: Developed a graph traversal algorithm to identify all unique proper dihedral angles (i-j-k-l chains).
  • Improper Dihedral Perception: Implemented logic to generate improper dihedrals for planar centers (e.g., SP2 or Resonant atoms with degree 3), which are crucial for maintaining planarity in force fields.

• Enhanced Test Infrastructure:

  • Added comprehensive unit tests for the topology builder, covering various molecules from simple alkanes to complex aromatic systems like benzene.
  • Developed a test harness (TestMolecule) to simplify the construction of test cases with pre-defined atom properties.
  • Added extensive integration tests for the TyperEngine to validate its logic on molecules requiring iterative relaxation (e.g., acetic acid) and special cases (e.g., diborane).