Module: Chemicalml::Cml::Visitable

Included in:
Schema24::Abundance, Schema24::Action, Schema24::ActionList, Schema24::Alternative, Schema24::Amount, Schema24::Angle, Schema24::Annotation, Schema24::AnyCml, Schema24::Appinfo, Schema24::Arg, Schema24::Array, Schema24::ArrayList, Schema24::Atom, Schema24::AtomArray, Schema24::AtomParity, Schema24::AtomSet, Schema24::AtomType, Schema24::AtomTypeList, Schema24::AtomicBasisFunction, Schema24::Band, Schema24::BandList, Schema24::BasisSet, Schema24::Bond, Schema24::BondArray, Schema24::BondSet, Schema24::BondStereo, Schema24::BondType, Schema24::BondTypeList, Schema24::CellParameter, Schema24::ComplexObject, Schema24::ConditionList, Schema24::Crystal, Schema24::Definition, Schema24::Description, Schema24::Dictionary, Schema24::DictionaryEntry, Schema24::Dimension, Schema24::Document, Schema24::Documentation, Schema24::Eigen, Schema24::Electron, Schema24::Enumeration, Schema24::Expression, Schema24::Float, Schema24::FloatArray, Schema24::Formula, Schema24::Fragment, Schema24::FragmentList, Schema24::Gradient, Schema24::Identifier, Schema24::Integer, Schema24::IntegerArray, Schema24::Isotope, Schema24::IsotopeList, Schema24::Join, Schema24::Kpoint, Schema24::KpointList, Schema24::Label, Schema24::Lattice, Schema24::LatticeVector, Schema24::Length, Schema24::Line3, Schema24::Link, Schema24::List, Schema24::Map, Schema24::Matrix, Schema24::Mechanism, Schema24::MechanismComponent, Schema24::Metadata, Schema24::MetadataList, Schema24::Module, Schema24::Molecule, Schema24::MoleculeList, Schema24::Name, Schema24::Object, Schema24::Observation, Schema24::Operator, Schema24::Parameter, Schema24::ParameterList, Schema24::Particle, Schema24::Peak, Schema24::PeakGroup, Schema24::PeakList, Schema24::PeakStructure, Schema24::Plane3, Schema24::Point3, Schema24::Potential, Schema24::PotentialForm, Schema24::PotentialList, Schema24::Product, Schema24::ProductList, Schema24::Property, Schema24::PropertyList, Schema24::Reactant, Schema24::ReactantList, Schema24::Reaction, Schema24::ReactionList, Schema24::ReactionScheme, Schema24::ReactionStep, Schema24::ReactionStepList, Schema24::ReactiveCentre, Schema24::Region, Schema24::RelatedEntry, Schema24::Sample, Schema24::Scalar, Schema24::Spectator, Schema24::SpectatorList, Schema24::Spectrum, Schema24::SpectrumData, Schema24::SpectrumList, Schema24::Sphere3, Schema24::Stmml, Schema24::String, Schema24::StringArray, Schema24::Substance, Schema24::SubstanceList, Schema24::Symmetry, Schema24::System, Schema24::Table, Schema24::TableCell, Schema24::TableContent, Schema24::TableHeader, Schema24::TableHeaderCell, Schema24::TableRow, Schema24::TableRowList, Schema24::Tcell, Schema24::Torsion, Schema24::Transform3, Schema24::TransitionState, Schema24::Trow, Schema24::Unit, Schema24::UnitList, Schema24::UnitType, Schema24::UnitTypeList, Schema24::Vector3, Schema24::Xaxis, Schema24::Yaxis, Schema24::ZMatrix, Schema3::Abundance, Schema3::Action, Schema3::ActionList, Schema3::Amount, Schema3::Angle, Schema3::AnyCml, Schema3::Array, Schema3::ArrayList, Schema3::Atom, Schema3::AtomArray, Schema3::AtomParity, Schema3::AtomSet, Schema3::AtomType, Schema3::AtomTypeList, Schema3::AtomicBasisFunction, Schema3::Band, Schema3::BandList, Schema3::BasisSet, Schema3::Bond, Schema3::BondArray, Schema3::BondSet, Schema3::BondStereo, Schema3::BondType, Schema3::BondTypeList, Schema3::CellParameter, Schema3::ConditionList, Schema3::Crystal, Schema3::Definition, Schema3::Description, Schema3::Dictionary, Schema3::DictionaryEntry, Schema3::Dimension, Schema3::Document, Schema3::Documentation, Schema3::Eigen, Schema3::Electron, Schema3::Formula, Schema3::Fragment, Schema3::FragmentList, Schema3::Gradient, Schema3::Identifier, Schema3::Isotope, Schema3::IsotopeList, Schema3::Join, Schema3::Kpoint, Schema3::KpointList, Schema3::Label, Schema3::Lattice, Schema3::LatticeVector, Schema3::Length, Schema3::Line3, Schema3::Link, Schema3::List, Schema3::Map, Schema3::Matrix, Schema3::Mechanism, Schema3::MechanismComponent, Schema3::Metadata, Schema3::MetadataList, Schema3::Module, Schema3::Molecule, Schema3::MoleculeList, Schema3::Name, Schema3::Object, Schema3::Observation, Schema3::Parameter, Schema3::ParameterList, Schema3::Particle, Schema3::Peak, Schema3::PeakGroup, Schema3::PeakList, Schema3::PeakStructure, Schema3::Plane3, Schema3::Point3, Schema3::Potential, Schema3::PotentialForm, Schema3::PotentialList, Schema3::Product, Schema3::ProductList, Schema3::Property, Schema3::PropertyList, Schema3::Reactant, Schema3::ReactantList, Schema3::Reaction, Schema3::ReactionList, Schema3::ReactionScheme, Schema3::ReactionStep, Schema3::ReactionStepList, Schema3::ReactiveCentre, Schema3::Region, Schema3::Sample, Schema3::Scalar, Schema3::Spectator, Schema3::SpectatorList, Schema3::Spectrum, Schema3::SpectrumData, Schema3::SpectrumList, Schema3::Sphere3, Schema3::Stmml, Schema3::Substance, Schema3::SubstanceList, Schema3::Symmetry, Schema3::System, Schema3::Table, Schema3::TableCell, Schema3::TableContent, Schema3::TableHeader, Schema3::TableHeaderCell, Schema3::TableRow, Schema3::TableRowList, Schema3::Torsion, Schema3::Transform3, Schema3::TransitionState, Schema3::Unit, Schema3::UnitList, Schema3::UnitType, Schema3::UnitTypeList, Schema3::Vector3, Schema3::Xaxis, Schema3::Yaxis, Schema3::ZMatrix
Defined in:
lib/chemicalml/cml/visitable.rb

Overview

Marker mixin included by every wire class. Provides a uniform interface the convention-constraint walker relies on:

- `wire_children` returns the child wire nodes
- `node_id` returns the id attribute or `nil`
- `element_name` returns the XML tag name

All three use lutaml-model's attribute registry — no duck typing. A wire class that doesn't declare an :id attribute simply has node_id return nil.

Instance Method Summary collapse

Instance Method Details

#atom_count ⇒ Object

Count of every Atom in the subtree.



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# File 'lib/chemicalml/cml/visitable.rb', line 113

def atom_count
  each_atom.count
end

#bond_count ⇒ Object

Count of every Bond in the subtree.



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# File 'lib/chemicalml/cml/visitable.rb', line 118

def bond_count
  each_bond.count
end

#collect_wire_nodes(value) ⇒ Object 



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# File 'lib/chemicalml/cml/visitable.rb', line 36

def collect_wire_nodes(value)
  return [] if value.nil?

  if value.is_a?(::Array)
    value.select { |v| wire_node?(v) }
  elsif wire_node?(value)
    [value]
  else
    []
  end
end

#declared_attribute?(name) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/chemicalml/cml/visitable.rb', line 58

def declared_attribute?(name)
  self.class.model.attributes.key?(name)
rescue StandardError
  false
end

#declared_attribute_names ⇒ Object 



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# File 'lib/chemicalml/cml/visitable.rb', line 52

def declared_attribute_names
  self.class.model.attributes.keys
rescue StandardError
  []
end

#each_atom ⇒ Object

Iterate every Atom in the subtree.



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# File 'lib/chemicalml/cml/visitable.rb', line 77

def each_atom(&)
  return to_enum(:each_atom) unless block_given?

  each_wire_node { |n| yield(n) if n.is_a?(Chemicalml::Cml::Role::Atom) }
end

#each_bond ⇒ Object

Iterate every Bond in the subtree.



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# File 'lib/chemicalml/cml/visitable.rb', line 84

def each_bond(&)
  return to_enum(:each_bond) unless block_given?

  each_wire_node { |n| yield(n) if n.is_a?(Chemicalml::Cml::Role::Bond) }
end

#each_molecule ⇒ Object

Iterate every Molecule in the subtree (top-level + nested).



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# File 'lib/chemicalml/cml/visitable.rb', line 91

def each_molecule(&)
  return to_enum(:each_molecule) unless block_given?

  each_wire_node { |n| yield(n) if n.is_a?(Chemicalml::Cml::Role::Molecule) }
end

#each_wire_node {|Lutaml::Model::Serializable| ... } ⇒ Enumerator

Walk the entire subtree from this node, yielding each wire instance. DFS pre-order. Useful for find-style queries and aggregate counts.

Yields:

  • (Lutaml::Model::Serializable) —

    each wire node.

Returns:

  • (Enumerator) —

    without a block.



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# File 'lib/chemicalml/cml/visitable.rb', line 70

def each_wire_node(&)
  return to_enum(:each_wire_node) unless block_given?

  walk(self, &)
end

#element_name ⇒ Object 



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# File 'lib/chemicalml/cml/visitable.rb', line 28

def element_name
  xml_mapping = self.class.mappings[:xml]
  root = xml_mapping&.root
  root&.name || self.class.name.split('::').last
rescue StandardError
  self.class.name.split('::').last
end

#find_atom(id) ⇒ Object

Find the first atom in the subtree with the given id, or nil.



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# File 'lib/chemicalml/cml/visitable.rb', line 98

def find_atom(id)
  each_atom.find { |a| a.node_id == id }
end

#find_bond(id) ⇒ Object

Find the first bond in the subtree with the given id, or nil.



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# File 'lib/chemicalml/cml/visitable.rb', line 103

def find_bond(id)
  each_bond.find { |b| b.node_id == id }
end

#find_molecule(id) ⇒ Object

Find the first molecule in the subtree with the given id.



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# File 'lib/chemicalml/cml/visitable.rb', line 108

def find_molecule(id)
  each_molecule.find { |m| m.node_id == id }
end

#molecule_count ⇒ Object

Count of every Molecule in the subtree (recursive).



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# File 'lib/chemicalml/cml/visitable.rb', line 123

def molecule_count
  each_molecule.count
end

#node_id ⇒ Object 



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# File 'lib/chemicalml/cml/visitable.rb', line 22

def node_id
  return id if declared_attribute?(:id)

  nil
end

#wire_children ⇒ Object 



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# File 'lib/chemicalml/cml/visitable.rb', line 16

def wire_children
  declared_attribute_names.flat_map do |name|
    collect_wire_nodes(public_send(name))
  end
end

#wire_node?(value) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/chemicalml/cml/visitable.rb', line 48

def wire_node?(value)
  value.is_a?(Lutaml::Model::Serializable)
end