class Chem::Atom

Chem::Atom
Reference
Object

Included Modules

Comparable(Chem::Atom)

Defined in:

chem/core/atom.cr

Constructors

.new(structure : Structure, element : Element, pos : Spatial::Vec3, *, name : String | Nil = nil, number : Int32 | Nil = nil, residue : Residue | Nil = nil, typename : String | Nil = nil, formal_charge : Int32 = 0, mass : Float64 = element.mass, occupancy : Float64 = 1, partial_charge : Float64 = 0.0, temperature_factor : Float64 = 0, vdw_radius : Float64 = element.vdw_radius)
Creates an atom in structure with the given element and coordinates.
.new(residue : Residue, name : String, pos : Spatial::Vec3, element : Element | Nil = nil, **options) : self
Creates an atom in residue (and its parent structure).

Instance Method Summary

#<=>(other : self) : Int32
The comparison operator.
#==(rhs : self) : Bool
Returns true if self and rhs are the same atom, else false.
#actinium?
Returns true if the atom's element is "Actinium", else false.
#aluminum?
Returns true if the atom's element is "Aluminum", else false.
#americium?
Returns true if the atom's element is "Americium", else false.
#antimony?
Returns true if the atom's element is "Antimony", else false.
#argon?
Returns true if the atom's element is "Argon", else false.
#arsenic?
Returns true if the atom's element is "Arsenic", else false.
#astatine?
Returns true if the atom's element is "Astatine", else false.
#atomic_number(*args, **options)
#atomic_number(*args, **options, &)
#barium?
Returns true if the atom's element is "Barium", else false.
#berkelium?
Returns true if the atom's element is "Berkelium", else false.
#beryllium?
Returns true if the atom's element is "Beryllium", else false.
#bismuth?
Returns true if the atom's element is "Bismuth", else false.
#bohrium?
Returns true if the atom's element is "Bohrium", else false.
#bonded?(to other : self) : Bool
#bonded_atoms : Array(Atom)
#bonds : BondArray
#boron?
Returns true if the atom's element is "Boron", else false.
#bromine?
Returns true if the atom's element is "Bromine", else false.
#cadmium?
Returns true if the atom's element is "Cadmium", else false.
#calcium?
Returns true if the atom's element is "Calcium", else false.
#californium?
Returns true if the atom's element is "Californium", else false.
#carbon?
Returns true if the atom's element is "Carbon", else false.
#cerium?
Returns true if the atom's element is "Cerium", else false.
#cesium?
Returns true if the atom's element is "Cesium", else false.
#chain : Chain
Returns the parent chain.
#chain? : Chain | Nil
Returns the parent chain, or nil if the atom has no residue.
#chlorine?
Returns true if the atom's element is "Chlorine", else false.
#chromium?
Returns true if the atom's element is "Chromium", else false.
#cobalt?
Returns true if the atom's element is "Cobalt", else false.
#constraint : Spatial::Direction | Nil
#constraint=(constraint : Spatial::Direction | Nil)
#copernicium?
Returns true if the atom's element is "Copernicium", else false.
#copper?
Returns true if the atom's element is "Copper", else false.
#covalent_radius(*args, **options)
#covalent_radius(*args, **options, &)
#curium?
Returns true if the atom's element is "Curium", else false.
#darmstadtium?
Returns true if the atom's element is "Darmstadtium", else false.
#degree : Int32
Returns the number of bonds.
#delete : Nil
Removes the atom from its parent structure and residue, and deletes its bonds.
#dna? : Bool
Returns true if the atom belongs to a dna residue, else false.
#dubnium?
Returns true if the atom's element is "Dubnium", else false.
#dysprosium?
Returns true if the atom's element is "Dysprosium", else false.
#each_bonded_atom : Iterator(Atom)
#each_bonded_atom(& : self -> ) : Nil
#einsteinium?
Returns true if the atom's element is "Einsteinium", else false.
#element : Element
#element=(element : Element)
#erbium?
Returns true if the atom's element is "Erbium", else false.
#europium?
Returns true if the atom's element is "Europium", else false.
#fermium?
Returns true if the atom's element is "Fermium", else false.
#flerovium?
Returns true if the atom's element is "Flerovium", else false.
#fluorine?
Returns true if the atom's element is "Fluorine", else false.
#formal_charge : Int32
#formal_charge=(formal_charge : Int32)
#francium?
Returns true if the atom's element is "Francium", else false.
#gadolinium?
Returns true if the atom's element is "Gadolinium", else false.
#gallium?
Returns true if the atom's element is "Gallium", else false.
#germanium?
Returns true if the atom's element is "Germanium", else false.
#gold?
Returns true if the atom's element is "Gold", else false.
#hafnium?
Returns true if the atom's element is "Hafnium", else false.
#hassium?
Returns true if the atom's element is "Hassium", else false.
#heavy?(*args, **options)
#heavy?(*args, **options, &)
#helium?
Returns true if the atom's element is "Helium", else false.
#het? : Bool
Returns true if the atom belongs to a non-standard (HET) residue, else false.
#holmium?
Returns true if the atom's element is "Holmium", else false.
#hydrogen?
Returns true if the atom's element is "Hydrogen", else false.
#indium?
Returns true if the atom's element is "Indium", else false.
#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.
#iodine?
Returns true if the atom's element is "Iodine", else false.
#ion? : Bool
Returns true if the atom belongs to a ion residue, else false.
#iridium?
Returns true if the atom's element is "Iridium", else false.
#iron?
Returns true if the atom's element is "Iron", else false.
#krypton?
Returns true if the atom's element is "Krypton", else false.
#lanthanum?
Returns true if the atom's element is "Lanthanum", else false.
#lawrencium?
Returns true if the atom's element is "Lawrencium", else false.
#lead?
Returns true if the atom's element is "Lead", else false.
#lithium?
Returns true if the atom's element is "Lithium", else false.
#livermorium?
Returns true if the atom's element is "Livermorium", else false.
#lutetium?
Returns true if the atom's element is "Lutetium", else false.
#magnesium?
Returns true if the atom's element is "Magnesium", else false.
#manganese?
Returns true if the atom's element is "Manganese", else false.
#mass : Float64
#mass=(mass : Float64)
#matches?(number : Int) : Bool
Returns true if the atom number equals the given number, else false.
#matches?(str : String) : Bool
Returns true if the atom name equals the given name, else false.
#matches?(pattern : Regex) : Bool
Returns true if the atom name matches the given pattern, else false.
#matches?(numbers : Range(Int, Int) | Range(Nil, Int) | Range(Int, Nil) | Range(Nil, Nil)) : Bool
Returns true if the atom number is included in the given range, else false.
#matches?(numbers : Enumerable(Int)) : Bool
Returns true if the atom number is included in the given numbers, else false.
#matches?(names : Enumerable(String)) : Bool
Returns true if the atom name is included in the given names, else false.
#matches?(element : Element) : Bool
Returns true if the atom's element equals the given element, else false.
#matches?(atom_t : Templates::Atom) : Bool
Returns true if the atom matches the given template, else false.
#max_valence(*args, **options)
#max_valence(*args, **options, &)
#meitnerium?
Returns true if the atom's element is "Meitnerium", else false.
#membrane? : Bool
Returns true if the atom belongs to a membrane residue, else false.
#mendelevium?
Returns true if the atom's element is "Mendelevium", else false.
#mercury?
Returns true if the atom's element is "Mercury", else false.
#metadata : Metadata
Hash-like container that stores the atom's additional properties as key (string)-value pairs.
#missing_valence : Int32
#molybdenum?
Returns true if the atom's element is "Molybdenum", else false.
#moscovium?
Returns true if the atom's element is "Moscovium", else false.
#name : String
Atom name.
#name=(name : String | Nil) : String | Nil
Assigns the atom name.
#name? : String | Nil
Atom name.
#neodymium?
Returns true if the atom's element is "Neodymium", else false.
#neon?
Returns true if the atom's element is "Neon", else false.
#neptunium?
Returns true if the atom's element is "Neptunium", else false.
#nickel?
Returns true if the atom's element is "Nickel", else false.
#nihonium?
Returns true if the atom's element is "Nihonium", else false.
#niobium?
Returns true if the atom's element is "Niobium", else false.
#nitrogen?
Returns true if the atom's element is "Nitrogen", else false.
#nobelium?
Returns true if the atom's element is "Nobelium", else false.
#number : Int32
Serial number (PDB-style id).
#number=(number : Int32)
Serial number (PDB-style id).
#occupancy : Float64
#occupancy=(occupancy : Float64)
#oganesson?
Returns true if the atom's element is "Oganesson", else false.
#osmium?
Returns true if the atom's element is "Osmium", else false.
#other? : Bool
Returns true if the atom belongs to a other residue, else false.
#oxygen?
Returns true if the atom's element is "Oxygen", else false.
#palladium?
Returns true if the atom's element is "Palladium", else false.
#partial_charge : Float64
#partial_charge=(partial_charge : Float64)
#phosphorus?
Returns true if the atom's element is "Phosphorus", else false.
#platinum?
Returns true if the atom's element is "Platinum", else false.
#plutonium?
Returns true if the atom's element is "Plutonium", else false.
#polonium?
Returns true if the atom's element is "Polonium", else false.
#pos : Spatial::Vec3
#pos=(pos : Spatial::Vec3)
#potassium?
Returns true if the atom's element is "Potassium", else false.
#praseodymium?
Returns true if the atom's element is "Praseodymium", else false.
#proactinium?
Returns true if the atom's element is "Proactinium", else false.
#promethium?
Returns true if the atom's element is "Promethium", else false.
#protein? : Bool
Returns true if the atom belongs to a protein residue, else false.
#radium?
Returns true if the atom's element is "Radium", else false.
#radon?
Returns true if the atom's element is "Radon", else false.
#residue : Residue
Parent residue.
#residue=(new_res : Residue) : Residue
Assigns the parent residue.
#residue? : Residue | Nil
Parent residue.
#rhenium?
Returns true if the atom's element is "Rhenium", else false.
#rhodium?
Returns true if the atom's element is "Rhodium", else false.
#roentgenium?
Returns true if the atom's element is "Roentgenium", else false.
#rubidium?
Returns true if the atom's element is "Rubidium", else false.
#ruthenium?
Returns true if the atom's element is "Ruthenium", else false.
#rutherfordium?
Returns true if the atom's element is "Rutherfordium", else false.
#samarium?
Returns true if the atom's element is "Samarium", else false.
#scandium?
Returns true if the atom's element is "Scandium", else false.
#seaborgium?
Returns true if the atom's element is "Seaborgium", else false.
#selenium?
Returns true if the atom's element is "Selenium", else false.
#silicon?
Returns true if the atom's element is "Silicon", else false.
#silver?
Returns true if the atom's element is "Silver", else false.
#sodium?
Returns true if the atom's element is "Sodium", else false.
#solvent? : Bool
Returns true if the atom belongs to a solvent residue, else false.
#spec(io : IO) : Nil
Writes the atom specification to the given IO.
#spec : String
Returns the atom specification.
#strontium?
Returns true if the atom's element is "Strontium", else false.
#structure : Structure
Parent structure.
#sulfur?
Returns true if the atom's element is "Sulfur", else false.
#tantalum?
Returns true if the atom's element is "Tantalum", else false.
#target_valence : Int32
Returns the target valence based on the effective valence.
#technetium?
Returns true if the atom's element is "Technetium", else false.
#tellurium?
Returns true if the atom's element is "Tellurium", else false.
#temperature_factor : Float64
#temperature_factor=(temperature_factor : Float64)
#tennessine?
Returns true if the atom's element is "Tennessine", else false.
#terbium?
Returns true if the atom's element is "Terbium", else false.
#terminal? : Bool
Returns true if the atom is connected to one heavy atom (hydrogens are ignored), else false.
#thallium?
Returns true if the atom's element is "Thallium", else false.
#thorium?
Returns true if the atom's element is "Thorium", else false.
#thulium?
Returns true if the atom's element is "Thulium", else false.
#tin?
Returns true if the atom's element is "Tin", else false.
#titanium?
Returns true if the atom's element is "Titanium", else false.
#to_s(io : IO)
Appends a short String representation of this object which includes its class name and its object address.
#tungsten?
Returns true if the atom's element is "Tungsten", else false.
#typename : String | Nil
Atom typename.
#typename=(typename : String | Nil)
Atom typename.
#uranium?
Returns true if the atom's element is "Uranium", else false.
#valence : Int32
Returns the effective valence.
#valence_electrons(*args, **options)
#valence_electrons(*args, **options, &)
#vanadium?
Returns true if the atom's element is "Vanadium", else false.
#vdw_radius : Float64
#vdw_radius=(vdw_radius : Float64)
#water? : Bool
Returns true if the atom belongs to a water residue, else false.
#within_covalent_distance?(rhs : self) : Bool
#x(*args, **options)
#x(*args, **options, &)
#xenon?
Returns true if the atom's element is "Xenon", else false.
#y(*args, **options)
#y(*args, **options, &)
#ytterbium?
Returns true if the atom's element is "Ytterbium", else false.
#yttrium?
Returns true if the atom's element is "Yttrium", else false.
#z(*args, **options)
#z(*args, **options, &)
#zinc?
Returns true if the atom's element is "Zinc", else false.
#zirconium?
Returns true if the atom's element is "Zirconium", else false.

Constructor Detail

def self.new(structure : Structure, element : Element, pos : Spatial::Vec3, *, name : String | Nil = nil, number : Int32 | Nil = nil, residue : Residue | Nil = nil, typename : String | Nil = nil, formal_charge : Int32 = 0, mass : Float64 = element.mass, occupancy : Float64 = 1, partial_charge : Float64 = 0.0, temperature_factor : Float64 = 0, vdw_radius : Float64 = element.vdw_radius) #

Creates an atom in structure with the given element and coordinates.

name belongs with topology: pass it together with residue. number defaults to the next 1-based insertion index.

[View source]

def self.new(residue : Residue, name : String, pos : Spatial::Vec3, element : Element | Nil = nil, **options) : self #

Creates an atom in residue (and its parent structure). The element is guessed from name unless element is given.

[View source]

Instance Method Detail

def <=>(other : self) : Int32 #

The comparison operator.

Returns -1, 0 or 1 depending on whether self precedes rhs, equals to rhs or comes after rhs. The comparison is done based on atom number.

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

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

[View source]

def ==(rhs : self) : Bool #

Returns true if self and rhs are the same atom, else false.

NOTE overrides the equality operator included by Comparable, which uses the <=> operator thus returning true for two different atoms that have the same number.

[View source]

def actinium? #

Returns true if the atom's element is "Actinium", else false.

[View source]

def aluminum? #

Returns true if the atom's element is "Aluminum", else false.

[View source]

def americium? #

Returns true if the atom's element is "Americium", else false.

[View source]

def antimony? #

Returns true if the atom's element is "Antimony", else false.

[View source]

def argon? #

Returns true if the atom's element is "Argon", else false.

[View source]

def arsenic? #

Returns true if the atom's element is "Arsenic", else false.

[View source]

def astatine? #

Returns true if the atom's element is "Astatine", else false.

[View source]

def atomic_number(*args, **options) #

[View source]

def atomic_number(*args, **options, &) #

[View source]

def barium? #

Returns true if the atom's element is "Barium", else false.

[View source]

def berkelium? #

Returns true if the atom's element is "Berkelium", else false.

[View source]

def beryllium? #

Returns true if the atom's element is "Beryllium", else false.

[View source]

def bismuth? #

Returns true if the atom's element is "Bismuth", else false.

[View source]

def bohrium? #

Returns true if the atom's element is "Bohrium", else false.

[View source]

def bonded?(to other : self) : Bool #

[View source]

def bonded_atoms : Array(Atom) #

[View source]

def bonds : BondArray #

[View source]

def boron? #

Returns true if the atom's element is "Boron", else false.

[View source]

def bromine? #

Returns true if the atom's element is "Bromine", else false.

[View source]

def cadmium? #

Returns true if the atom's element is "Cadmium", else false.

[View source]

def calcium? #

Returns true if the atom's element is "Calcium", else false.

[View source]

def californium? #

Returns true if the atom's element is "Californium", else false.

[View source]

def carbon? #

Returns true if the atom's element is "Carbon", else false.

[View source]

def cerium? #

Returns true if the atom's element is "Cerium", else false.

[View source]

def cesium? #

Returns true if the atom's element is "Cesium", else false.

[View source]

def chain : Chain #

Returns the parent chain. Raises if the atom has no residue.

[View source]

def chain? : Chain | Nil #

Returns the parent chain, or nil if the atom has no residue.

[View source]

def chlorine? #

Returns true if the atom's element is "Chlorine", else false.

[View source]

def chromium? #

Returns true if the atom's element is "Chromium", else false.

[View source]

def cobalt? #

Returns true if the atom's element is "Cobalt", else false.

[View source]

def constraint : Spatial::Direction | Nil #

[View source]

def constraint=(constraint : Spatial::Direction | Nil) #

[View source]

def copernicium? #

Returns true if the atom's element is "Copernicium", else false.

[View source]

def copper? #

Returns true if the atom's element is "Copper", else false.

[View source]

def covalent_radius(*args, **options) #

[View source]

def covalent_radius(*args, **options, &) #

[View source]

def curium? #

Returns true if the atom's element is "Curium", else false.

[View source]

def darmstadtium? #

Returns true if the atom's element is "Darmstadtium", else false.

[View source]

def degree : Int32 #

Returns the number of bonds.

[View source]

def delete : Nil #

Removes the atom from its parent structure and residue, and deletes its bonds.

[View source]

def dna? : Bool #

Returns true if the atom belongs to a dna residue, else false.

[View source]

def dubnium? #

Returns true if the atom's element is "Dubnium", else false.

[View source]

def dysprosium? #

Returns true if the atom's element is "Dysprosium", else false.

[View source]

def each_bonded_atom : Iterator(Atom) #

[View source]

def each_bonded_atom(& : self -> ) : Nil #

[View source]

def einsteinium? #

Returns true if the atom's element is "Einsteinium", else false.

[View source]

def element : Element #

[View source]

def element=(element : Element) #

[View source]

def erbium? #

Returns true if the atom's element is "Erbium", else false.

[View source]

def europium? #

Returns true if the atom's element is "Europium", else false.

[View source]

def fermium? #

Returns true if the atom's element is "Fermium", else false.

[View source]

def flerovium? #

Returns true if the atom's element is "Flerovium", else false.

[View source]

def fluorine? #

Returns true if the atom's element is "Fluorine", else false.

[View source]

def formal_charge : Int32 #

[View source]

def formal_charge=(formal_charge : Int32) #

[View source]

def francium? #

Returns true if the atom's element is "Francium", else false.

[View source]

def gadolinium? #

Returns true if the atom's element is "Gadolinium", else false.

[View source]

def gallium? #

Returns true if the atom's element is "Gallium", else false.

[View source]

def germanium? #

Returns true if the atom's element is "Germanium", else false.

[View source]

def gold? #

Returns true if the atom's element is "Gold", else false.

[View source]

def hafnium? #

Returns true if the atom's element is "Hafnium", else false.

[View source]

def hassium? #

Returns true if the atom's element is "Hassium", else false.

[View source]

def heavy?(*args, **options) #

[View source]

def heavy?(*args, **options, &) #

[View source]

def helium? #

Returns true if the atom's element is "Helium", else false.

[View source]

def het? : Bool #

Returns true if the atom belongs to a non-standard (HET) residue, else false.

[View source]

def holmium? #

Returns true if the atom's element is "Holmium", else false.

[View source]

def hydrogen? #

Returns true if the atom's element is "Hydrogen", else false.

[View source]

def indium? #

Returns true if the atom's element is "Indium", else false.

[View source]

def inspect(io : IO) : Nil #

Description copied from class Reference

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

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

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

[View source]

def iodine? #

Returns true if the atom's element is "Iodine", else false.

[View source]

def ion? : Bool #

Returns true if the atom belongs to a ion residue, else false.

[View source]

def iridium? #

Returns true if the atom's element is "Iridium", else false.

[View source]

def iron? #

Returns true if the atom's element is "Iron", else false.

[View source]

def krypton? #

Returns true if the atom's element is "Krypton", else false.

[View source]

def lanthanum? #

Returns true if the atom's element is "Lanthanum", else false.

[View source]

def lawrencium? #

Returns true if the atom's element is "Lawrencium", else false.

[View source]

def lead? #

Returns true if the atom's element is "Lead", else false.

[View source]

def lithium? #

Returns true if the atom's element is "Lithium", else false.

[View source]

def livermorium? #

Returns true if the atom's element is "Livermorium", else false.

[View source]

def lutetium? #

Returns true if the atom's element is "Lutetium", else false.

[View source]

def magnesium? #

Returns true if the atom's element is "Magnesium", else false.

[View source]

def manganese? #

Returns true if the atom's element is "Manganese", else false.

[View source]

def mass : Float64 #

[View source]

def mass=(mass : Float64) #

[View source]

def matches?(number : Int) : Bool #

Returns true if the atom number equals the given number, else false.

[View source]

def matches?(str : String) : Bool #

Returns true if the atom name equals the given name, else false.

[View source]

def matches?(pattern : Regex) : Bool #

Returns true if the atom name matches the given pattern, else false.

[View source]

def matches?(numbers : Range(Int, Int) | Range(Nil, Int) | Range(Int, Nil) | Range(Nil, Nil)) : Bool #

Returns true if the atom number is included in the given range, else false.

[View source]

def matches?(numbers : Enumerable(Int)) : Bool #

Returns true if the atom number is included in the given numbers, else false.

[View source]

def matches?(names : Enumerable(String)) : Bool #

Returns true if the atom name is included in the given names, else false.

[View source]

def matches?(element : Element) : Bool #

Returns true if the atom's element equals the given element, else false.

[View source]

def matches?(atom_t : Templates::Atom) : Bool #

Returns true if the atom matches the given template, else false.

Checking for a match considers both atom name and element.

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

TODO compare topology via Templates::Atom#top_spec

[View source]

def max_valence(*args, **options) #

[View source]

def max_valence(*args, **options, &) #

[View source]

def meitnerium? #

Returns true if the atom's element is "Meitnerium", else false.

[View source]

def membrane? : Bool #

Returns true if the atom belongs to a membrane residue, else false.

[View source]

def mendelevium? #

Returns true if the atom's element is "Mendelevium", else false.

[View source]

def mercury? #

Returns true if the atom's element is "Mercury", else false.

[View source]

def metadata : Metadata #

Hash-like container that stores the atom's additional properties as key (string)-value pairs. A property's value can be any of the primitive types (string, integer, float, or bool), and so it's internally stored as Metadata::Any. Use the cast methods (#as_*) to convert to the desired type.

atom.metadata["foo"] = 123
atom.metadata["foo"]      # => Metadata::Any(123)
atom.metadata["foo"].as_i # => 123
atom.metadata["foo"].as_f # => 123.0
atom.metadata["foo"].as_s # raises TypeCastError

[View source]

def missing_valence : Int32 #

[View source]

def molybdenum? #

Returns true if the atom's element is "Molybdenum", else false.

[View source]

def moscovium? #

Returns true if the atom's element is "Moscovium", else false.

[View source]

def name : String #

Atom name. Raises if unset. Use #name? when the atom may have been created without a name (no topology).

[View source]

def name=(name : String | Nil) : String | Nil #

Assigns the atom name. Raises if name is nil and the atom belongs to a residue.

[View source]

def name? : String | Nil #

Atom name. Raises if unset. Use #name? when the atom may have been created without a name (no topology).

[View source]

def neodymium? #

Returns true if the atom's element is "Neodymium", else false.

[View source]

def neon? #

Returns true if the atom's element is "Neon", else false.

[View source]

def neptunium? #

Returns true if the atom's element is "Neptunium", else false.

[View source]

def nickel? #

Returns true if the atom's element is "Nickel", else false.

[View source]

def nihonium? #

Returns true if the atom's element is "Nihonium", else false.

[View source]

def niobium? #

Returns true if the atom's element is "Niobium", else false.

[View source]

def nitrogen? #

Returns true if the atom's element is "Nitrogen", else false.

[View source]

def nobelium? #

Returns true if the atom's element is "Nobelium", else false.

[View source]

def number : Int32 #

Serial number (PDB-style id). Independent of the atom's index in Structure#atoms. Assigned as 1-based insertion order when omitted.

[View source]

def number=(number : Int32) #

Serial number (PDB-style id). Independent of the atom's index in Structure#atoms. Assigned as 1-based insertion order when omitted.

[View source]

def occupancy : Float64 #

[View source]

def occupancy=(occupancy : Float64) #

[View source]

def oganesson? #

Returns true if the atom's element is "Oganesson", else false.

[View source]

def osmium? #

Returns true if the atom's element is "Osmium", else false.

[View source]

def other? : Bool #

Returns true if the atom belongs to a other residue, else false.

[View source]

def oxygen? #

Returns true if the atom's element is "Oxygen", else false.

[View source]

def palladium? #

Returns true if the atom's element is "Palladium", else false.

[View source]

def partial_charge : Float64 #

[View source]

def partial_charge=(partial_charge : Float64) #

[View source]

def phosphorus? #

Returns true if the atom's element is "Phosphorus", else false.

[View source]

def platinum? #

Returns true if the atom's element is "Platinum", else false.

[View source]

def plutonium? #

Returns true if the atom's element is "Plutonium", else false.

[View source]

def polonium? #

Returns true if the atom's element is "Polonium", else false.

[View source]

def pos : Spatial::Vec3 #

[View source]

def pos=(pos : Spatial::Vec3) #

[View source]

def potassium? #

Returns true if the atom's element is "Potassium", else false.

[View source]

def praseodymium? #

Returns true if the atom's element is "Praseodymium", else false.

[View source]

def proactinium? #

Returns true if the atom's element is "Proactinium", else false.

[View source]

def promethium? #

Returns true if the atom's element is "Promethium", else false.

[View source]

def protein? : Bool #

Returns true if the atom belongs to a protein residue, else false.

[View source]

def radium? #

Returns true if the atom's element is "Radium", else false.

[View source]

def radon? #

Returns true if the atom's element is "Radon", else false.

[View source]

def residue : Residue #

Parent residue. Raises if the atom is not in a residue. Use #residue? when hierarchy may be absent.

[View source]

def residue=(new_res : Residue) : Residue #

Assigns the parent residue. To remove the atom from the structure, use #delete.

[View source]

def residue? : Residue | Nil #

Parent residue. Raises if the atom is not in a residue. Use #residue? when hierarchy may be absent.

[View source]

def rhenium? #

Returns true if the atom's element is "Rhenium", else false.

[View source]

def rhodium? #

Returns true if the atom's element is "Rhodium", else false.

[View source]

def roentgenium? #

Returns true if the atom's element is "Roentgenium", else false.

[View source]

def rubidium? #

Returns true if the atom's element is "Rubidium", else false.

[View source]

def ruthenium? #

Returns true if the atom's element is "Ruthenium", else false.

[View source]

def rutherfordium? #

Returns true if the atom's element is "Rutherfordium", else false.

[View source]

def samarium? #

Returns true if the atom's element is "Samarium", else false.

[View source]

def scandium? #

Returns true if the atom's element is "Scandium", else false.

[View source]

def seaborgium? #

Returns true if the atom's element is "Seaborgium", else false.

[View source]

def selenium? #

Returns true if the atom's element is "Selenium", else false.

[View source]

def silicon? #

Returns true if the atom's element is "Silicon", else false.

[View source]

def silver? #

Returns true if the atom's element is "Silver", else false.

[View source]

def sodium? #

Returns true if the atom's element is "Sodium", else false.

[View source]

def solvent? : Bool #

Returns true if the atom belongs to a solvent residue, else false.

[View source]

def spec(io : IO) : Nil #

Writes the atom specification to the given IO.

Atom specification is a short string representation encoding atom information including chain, residue, atom name, and atom number.

[View source]

def spec : String #

Returns the atom specification.

Atom specification is a short string representation encoding atom information including chain, residue, atom name, and atom number.

[View source]

def strontium? #

Returns true if the atom's element is "Strontium", else false.

[View source]

def structure : Structure #

Parent structure.

[View source]

def sulfur? #

Returns true if the atom's element is "Sulfur", else false.

[View source]

def tantalum? #

Returns true if the atom's element is "Tantalum", else false.

[View source]

def target_valence : Int32 #

Returns the target valence based on the effective valence. This is useful for multi-valent elements (e.g., sulfur, phosphorus).

[View source]

def technetium? #

Returns true if the atom's element is "Technetium", else false.

[View source]

def tellurium? #

Returns true if the atom's element is "Tellurium", else false.

[View source]

def temperature_factor : Float64 #

[View source]

def temperature_factor=(temperature_factor : Float64) #

[View source]

def tennessine? #

Returns true if the atom's element is "Tennessine", else false.

[View source]

def terbium? #

Returns true if the atom's element is "Terbium", else false.

[View source]

def terminal? : Bool #

Returns true if the atom is connected to one heavy atom (hydrogens are ignored), else false. This is useful to detect terminal functional groups such as -CH₃, -NH₂, etc.

[View source]

def thallium? #

Returns true if the atom's element is "Thallium", else false.

[View source]

def thorium? #

Returns true if the atom's element is "Thorium", else false.

[View source]

def thulium? #

Returns true if the atom's element is "Thulium", else false.

[View source]

def tin? #

Returns true if the atom's element is "Tin", else false.

[View source]

def titanium? #

Returns true if the atom's element is "Titanium", else false.

[View source]

def to_s(io : IO) #

Description copied from class Reference

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>

[View source]

def tungsten? #

Returns true if the atom's element is "Tungsten", else false.

[View source]

def typename : String | Nil #

Atom typename. Usually specifies the atomic parameter set assigned to this atom within a given force field.

[View source]

def typename=(typename : String | Nil) #

Atom typename. Usually specifies the atomic parameter set assigned to this atom within a given force field.

[View source]

def uranium? #

Returns true if the atom's element is "Uranium", else false.

[View source]

def valence : Int32 #

Returns the effective valence. This is equivalent to the sum of the bond orders.

[View source]

def valence_electrons(*args, **options) #

[View source]

def valence_electrons(*args, **options, &) #

[View source]

def vanadium? #

Returns true if the atom's element is "Vanadium", else false.

[View source]

def vdw_radius : Float64 #

[View source]

def vdw_radius=(vdw_radius : Float64) #

[View source]

def water? : Bool #

Returns true if the atom belongs to a water residue, else false.

[View source]

def within_covalent_distance?(rhs : self) : Bool #

[View source]

def x(*args, **options) #

[View source]

def x(*args, **options, &) #

[View source]

def xenon? #

Returns true if the atom's element is "Xenon", else false.

[View source]

def y(*args, **options) #

[View source]

def y(*args, **options, &) #

[View source]

def ytterbium? #

Returns true if the atom's element is "Ytterbium", else false.

[View source]

def yttrium? #

Returns true if the atom's element is "Yttrium", else false.

[View source]

def z(*args, **options) #

[View source]

def z(*args, **options, &) #

[View source]

def zinc? #

Returns true if the atom's element is "Zinc", else false.

[View source]

def zirconium? #

Returns true if the atom's element is "Zirconium", else false.

[View source]

CrystalDoc.info

chem

class Chem::Atom

Included Modules

Defined in:

Constructors

Instance Method Summary

Constructor Detail

Instance Method Detail