Class: Chemicalml::Convention::Molecular::Constraints::BondMustReferenceAtomsInSameMolecule

Inherits:
Constraint::DocumentConstraint show all
Defined in:
lib/chemicalml/convention/molecular/constraints/bond_must_reference_atoms_in_same_molecule.rb

Overview

Bonds MUST reference atoms within the same parent molecule per the molecular convention.

Instance Method Summary collapse

Instance Method Details

#check(document) ⇒ Object 



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# File 'lib/chemicalml/convention/molecular/constraints/bond_must_reference_atoms_in_same_molecule.rb', line 10

def check(document)
  violations = []
  walk_nodes(document) do |node, path|
    next unless molecule?(node)

    known = atom_ids_within(node).to_set
    bonds_within(node).each do |bond|
      missing = atom_refs_of(bond).reject { |r| known.include?(r) }
      next if missing.empty?

      violations << violation(
        path: path.empty? ? "molecule[#{node.id}]" : path.join("/"),
        message: "bond #{bond.id.inspect} references atoms not in the same molecule: #{missing.inspect}"
      )
    end
  end
  violations
end