class Chem::Structure::Builder

• Chem::Structure::Builder
• Reference
• Object

Defined in:

Constructors

• .new(guess_bonds : Bool = false, guess_names : Bool = false, use_templates : Bool = false, **options)

Instance Method Summary

• #atom(name : String, serial : Int32, coords : Spatial::Vec3, element : Element, **options) : Atom
• #atom(name : String, serial : Int32, coords : Spatial::Vec3, **options) : Atom
• #atom(element : Element | Symbol, coords : Spatial::Vec3, **options) : Atom

  Creates an Atom of element at the given coordinates.

• #atom(name : String, coords : Spatial::Vec3, **options) : Atom
• #atom(index : Int) : Atom
• #atom(coords : Spatial::Vec3, **options) : Atom
• #atom?(index : Int) : Atom | Nil
• #bond(name : String, other : String, order : BondOrder = :single) : Bond
• #bond(i : Int, j : Int, order : BondOrder = :single, aromatic : Bool = false) : Bond
• #bonds(bond_table : Hash(Tuple(Int32, Int32), BondOrder)) : Nil
• #build : Structure
• #cell(a : Spatial::Vec3, b : Spatial::Vec3, c : Spatial::Vec3) : Spatial::Parallelepiped
• #cell(a : Float64, b : Float64, c : Float64) : Spatial::Parallelepiped
• #cell(cell : Spatial::Parallelepiped | Nil)
• #cell : Spatial::Parallelepiped | Nil
• #cell! : Spatial::Parallelepiped
• #chain(id : Char) : Chain
• #chain : Chain
• #chain(id : Char, & : self -> ) : Nil
• #chain(& : self -> ) : Nil
• #current_chain : Chain | Nil
• #current_residue : Residue | Nil
• #expt(expt : Structure::Experiment | Nil)
• #residue(name : String, number : Int32, inscode : Char | Nil = nil) : Residue
• #residue(name : String) : Residue
• #residue : Residue
• #residue(name : String, number : Int32, inscode : Char | Nil = nil, & : self -> ) : Nil
• #residue(name : String, & : self -> ) : Nil
• #secondary_structure(i : Tuple(Char, Int32, Char | Nil), j : Tuple(Char, Int32, Char | Nil), type : Protein::SecondaryStructure) : Nil
• #secondary_structure(ri : Residue, rj : Residue, type : Protein::SecondaryStructure)
• #title(title : String)

Constructor Detail

Instance Method Detail

structure = Chem::Structure.build do |builder|
  builder.residue
  builder.atom Chem::PeriodicTable::H, Chem::Spatial::Vec3.zero
  builder.atom Chem::PeriodicTable::C, Chem::Spatial::Vec3.zero
  builder.atom Chem::PeriodicTable::H, Chem::Spatial::Vec3.zero
  builder.atom Chem::PeriodicTable::H, Chem::Spatial::Vec3.zero
  builder.atom Chem::PeriodicTable::C, Chem::Spatial::Vec3.zero
  builder.residue
  builder.atom Chem::PeriodicTable::H, Chem::Spatial::Vec3.zero
  builder.atom Chem::PeriodicTable::C, Chem::Spatial::Vec3.zero
  builder.atom Chem::PeriodicTable::N, Chem::Spatial::Vec3.zero
end
structure.atoms.map(&.name) # => ["H1", "C1", "H2", "H3", "C2", "H1", "C1", "N1"]