class

Chem::Templates::Residue

Inherits Reference / Object

Constructors

build
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build(residue : Chem::Residue, description : String | Nil = nil, link_bond : Bond | Nil = nil, symmetric_atom_groups : Array(Array(Tuple(String, String))) | Nil = nil) : self

Creates a new residue template from an existing residue.

Every atom and bond is converted to a template, which are then passed down to the constructor along with the optional arguments. Information such as name, code, etc. is obtained from the residue.

If link_bond is nil, it will be obtained from the associated residue template if exists. Otherwise, it will be guessed from the connectivity. If the residue is connected to two other residues by equivalent bonds, one of them will be chosen. The sense of the link bond will be infered from the residue numbering.

Raises Error if there is missing connectivity (no bonds).

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new(names : Array(String), code : Char | Nil, type : ResidueType, description : String | Nil, atoms : Array(Atom), bonds : Array(Bond), root root_name : String, link_bond : Bond | Nil = nil, symmetric_atom_groups : Array(Array(Tuple(String, String))) | Nil = nil)
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Instance methods

[](atom_t : Atom, other : Atom) : Bond

Returns the bond template between the given atoms. Raises KeyError if the bond does not exist.

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[](name : String, other : String) : Bond

Returns the bond template between the given atoms. Raises KeyError if the bond does not exist.

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[](name : String) : Atom
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[]?(atom_t : Atom, other : Atom) : Bond | Nil

Returns the bond template between the given atoms if exists, else nil.

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[]?(name : String, other : String) : Bond | Nil

Returns the bond template between the given atoms if exists, else nil.

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[]?(name : String) : Atom | Nil
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atoms
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bonds
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code
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description
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formal_charge
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name

Returns the designated residue name.

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names
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polymer?
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root
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symmetric_atom_groups
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to_s(io : IO) : Nil

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

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

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