class Chem::Atom

• Chem::Atom
• Reference
• Object

Overview

TODO rename charge to #formal_charge

TODO add partial_charge : Float64 = 0.0

TODO add residue_index that starts from 0 and does not reset per chain

Defined in:

Constructors

• .new(name : String, serial : Int32, coords : Spatial::Vector, residue : Residue, element : Element | Nil = nil, formal_charge : Int32 = 0, mass : Number | Nil = nil, occupancy : Float64 = 1, partial_charge : Float64 = 0.0, temperature_factor : Float64 = 0, vdw_radius : Number | Nil = nil)

Instance Method Summary

• #<=>(rhs : self) : Int32

  The comparison operator.

• #===(element : Element) : Bool

  Case equality.

• #===(atom_t : Topology::AtomType) : Bool

  Case equality.

• #atomic_number(*args, **options)
• #atomic_number(*args, **options, &)
• #bonded?(to other : self) : Bool
• #bonded_atoms : Array(Atom)
• #bonds : BondArray
• #chain(*args, **options)
• #chain(*args, **options, &)
• #constraint : Constraint | Nil
• #constraint=(constraint : Constraint | Nil)
• #coords : Spatial::Vector
• #coords=(coords : Spatial::Vector)
• #covalent_radius(*args, **options)
• #covalent_radius(*args, **options, &)
• #each_bonded_atom : Iterator(Atom)
• #each_bonded_atom(& : self -> ) : Nil
• #element : Element
• #element=(element : Element)
• #formal_charge : Int32
• #formal_charge=(formal_charge : Int32)
• #inspect(io : ::IO)
• #mass : Float64
• #mass=(mass : Float64)
• #match?(atom_t : Topology::AtomType) : Bool

  Matches self against atom_t.

• #max_valency(*args, **options)
• #max_valency(*args, **options, &)
• #missing_valency : Int32
• #name : String
• #name=(name : String)
• #nominal_valency : Int32
• #occupancy : Float64
• #occupancy=(occupancy : Float64)
• #partial_charge : Float64
• #partial_charge=(partial_charge : Float64)
• #residue : Residue
• #residue=(new_res : Residue) : Residue
• #serial : Int32
• #serial=(serial : Int32)
• #temperature_factor : Float64
• #temperature_factor=(temperature_factor : Float64)
• #to_s(io : ::IO)
• #valency : Int32
• #vdw_radius : Float64
• #vdw_radius=(vdw_radius : Float64)
• #within_covalent_distance?(rhs : self) : Bool
• #x(*args, **options)
• #x(*args, **options, &)
• #y(*args, **options)
• #y(*args, **options, &)
• #z(*args, **options)
• #z(*args, **options, &)

Constructor Detail

Instance Method Detail

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

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

structure = Structure.read "peptide.pdb"
desc = case structure.dig('A', 5, "CK")
       when Topology::AtomType("C")  then "carbonyl carbon"
       when Topology::AtomType("CA") then "alpha carbon"
       when Topology::AtomType("CB") then "beta carbon"
       when Topology::AtomType("CG") then "gamma carbon"
       when Topology::AtomType("CD") then "delta carbon"
       when PeriodicTable::C         then "carbon"
       else                               "non-carbon"
       end
desc # => "non-carbon"

structure = Structure.read "peptide.pdb"
desc = case structure.dig('A', 5, "CA")
       when Topology::AtomType("C")  then "carbonyl carbon"
       when Topology::AtomType("CA") then "alpha carbon"
       when Topology::AtomType("CB") then "beta carbon"
       when Topology::AtomType("CG") then "gamma carbon"
       when Topology::AtomType("CD") then "delta carbon"
       when PeriodicTable::C         then "carbon"
       else                               "non-carbon"
       end
desc # => "alpha carbon"

atom = Structure.read("peptide.pdb").dig 'A', 1, "CA"
atom.match?(Topology::AtomType.new("CA"))               # => true
atom.match?(Topology::AtomType.new("CA", element: "N")) # => false
atom.match?(Topology::AtomType.new("ND2"))              # => false