class Chem::Chain

• Chem::Chain
• Reference
• Object

Defined in:

Constructors

• .new(structure : Structure, id : Char)

Instance Method Summary

• #<=>(rhs : self) : Int32

  The comparison operator.

• #[](number : Int32, insertion_code : Char | Nil = nil) : Residue
• #[]?(number : Int32, insertion_code : Char | Nil = nil) : Residue | Nil
• #atoms : AtomView
• #clear : self
• #delete(residue : Residue) : Residue | Nil
• #dig(number : Int32, insertion_code : Char | Nil) : Residue
• #dig(number : Int32, insertion_code : Char | Nil, *subindexes)
• #dig(number : Int32) : Residue
• #dig(number : Int32, *subindexes)
• #dig?(number : Int32, insertion_code : Char | Nil) : Residue | Nil
• #dig?(number : Int32, insertion_code : Char | Nil, *subindexes)
• #dig?(number : Int32) : Residue | Nil
• #dig?(number : Int32, *subindexes)
• #id : Char
• #inspect(io : IO) : Nil

  Appends a String representation of this object which includes its class name, its object address and the values of all instance variables.

• #matches?(id : Char) : Bool

  Returns true if the chain id equals the given character, else false.

• #matches?(ids : Enumerable(Char)) : Bool

  Returns true if the chain id is included in the given characters, else false.

• #polymer? : Bool
• #renumber_residues_by(& : Residue -> _) : Nil

  Renumber residues based on the order by the output value of the block.

• #renumber_residues_by_connectivity : Nil

  Renumber residues based on bond information.

• #reset_cache : Nil
• #residues : ResidueView
• #spec(io : IO) : Nil

  Writes the chain specification to the given IO.

• #spec : String

  Returns the chain specification.

• #structure : Structure
• #structure(*args, **options)

  TODO remove this nonsensical line

• #structure(*args, **options, &)

  TODO remove this nonsensical line

• #to_gen(fractional : Bool = false) : String

  Returns a string representation of the chain using the Chem::Gen file format.

• #to_gen(output : IO | Path | String, fractional : Bool = false) : Nil

  Writes the chain to output using the Chem::Gen file format.

• #to_mol(variant : Chem::Mol::Variant = :v2000) : String

  Returns a string representation of the chain using the Chem::Mol file format.

• #to_mol(output : IO | Path | String, variant : Chem::Mol::Variant = :v2000) : Nil

  Writes the chain to output using the Chem::Mol file format.

• #to_mol2(output : IO | Path | String) : Nil

  Writes the chain to output using the Chem::Mol2 file format.

• #to_mol2 : String

  Returns a string representation of the chain using the Chem::Mol2 file format.

• #to_pdb(bonds : Chem::PDB::Writer::BondOptions = Chem::PDB::Writer::BondOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false) : String

  Returns a string representation of the chain using the Chem::PDB file format.

• #to_pdb(output : IO | Path | String, bonds : Chem::PDB::Writer::BondOptions = Chem::PDB::Writer::BondOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false) : Nil

  Writes the chain to output using the Chem::PDB file format.

• #to_s(io : IO)

  Appends a short String representation of this object which includes its class name and its object address.

• #to_xyz(extended : Bool = false, fields : Array(String) = [] of String) : String

  Returns a string representation of the chain using the Chem::XYZ file format.

• #to_xyz(output : IO | Path | String, extended : Bool = false, fields : Array(String) = [] of String) : Nil

  Writes the chain to output using the Chem::XYZ file format.

• #write(output : IO | Path | String, format : Chem::Format | String) : Nil

  Writes the chain to output using format.

• #write(path : Path | String) : Nil

  Writes the chain to the specified file.

Constructor Detail

Instance Method Detail

chains = Structure.read("peptide.pdb").chains

chains[0] <=> chains[1] # => -1
chains[1] <=> chains[1] # => 0
chains[2] <=> chains[1] # => 1

class Person
  def initialize(@name : String, @age : Int32)
  end
end

Person.new("John", 32).inspect # => #<Person:0x10fd31f20 @name="John", @age=32>

class Person
  def initialize(@name : String, @age : Int32)
  end
end

Person.new("John", 32).to_s # => #<Person:0x10a199f20>