class

Chem::Atom

Inherits Comparable / Reference / Object

Constructors

new(residue : Residue, serial : Int32, element : Element, name : String, coords : Spatial::Vec3, 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)

Instance methods

<=>(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 serial.

atoms = Structure.read(&quot;peptide.pdb&quot;).atoms

atoms[0] &lt;=&gt; atoms[1] # =&gt; -1
atoms[1] &lt;=&gt; atoms[1] # =&gt; 0
atoms[2] &lt;=&gt; atoms[1] # =&gt; 1

===(atom_t : Templates::Atom) : Bool

Case equality. This is equivalent to #matches?.

structure = Structure.read &quot;peptide.pdb&quot;
desc = case structure.dig('A', 5, &quot;CA&quot;)
       when Templates::Atom(&quot;C&quot;)  then &quot;carbonyl carbon&quot;
       when Templates::Atom(&quot;CA&quot;) then &quot;alpha carbon&quot;
       when Templates::Atom(&quot;CB&quot;) then &quot;beta carbon&quot;
       when Templates::Atom(&quot;CG&quot;) then &quot;gamma carbon&quot;
       when Templates::Atom(&quot;CD&quot;) then &quot;delta carbon&quot;
       when PeriodicTable::C         then &quot;carbon&quot;
       else                               &quot;non-carbon&quot;
       end
desc # =&gt; &quot;alpha carbon&quot;

===(element : Element) : Bool

Case equality. Returns true if atom's element is element, otherwise false.

structure = Structure.read &quot;peptide.pdb&quot;
desc = case structure.dig('A', 5, &quot;CK&quot;)
       when Templates::Atom(&quot;C&quot;)  then &quot;carbonyl carbon&quot;
       when Templates::Atom(&quot;CA&quot;) then &quot;alpha carbon&quot;
       when Templates::Atom(&quot;CB&quot;) then &quot;beta carbon&quot;
       when Templates::Atom(&quot;CG&quot;) then &quot;gamma carbon&quot;
       when Templates::Atom(&quot;CD&quot;) then &quot;delta carbon&quot;
       when PeriodicTable::C         then &quot;carbon&quot;
       else                               &quot;non-carbon&quot;
       end
desc # =&gt; &quot;non-carbon&quot;

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

bonds

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(*args, **options)

chain(*args, **options, &)

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

constraint=(constraint : Constraint | Nil)

coords

coords=(coords : Spatial::Vec3)

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

Returns the number of bonds.

dna?

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

each_bonded_atom

einsteinium?

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

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

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?

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.

iodine?

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

ion?

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

mass=(mass : Float64)

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(&quot;peptide.pdb&quot;).dig 'A', 1, &quot;CA&quot;
atom.match?(Templates::Atom.new(&quot;CA&quot;))               # =&gt; true
atom.match?(Templates::Atom.new(&quot;CA&quot;, element: &quot;N&quot;)) # =&gt; false
atom.match?(Templates::Atom.new(&quot;ND2&quot;))              # =&gt; false

TODO: compare topology via Templates::Atom#top_spec

max_valence(*args, **options)

max_valence(*args, **options, &)

meitnerium?

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

membrane?

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

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[&quot;foo&quot;] = 123
atom.metadata[&quot;foo&quot;]      # =&gt; Metadata::Any(123)
atom.metadata[&quot;foo&quot;].as_i # =&gt; 123
atom.metadata[&quot;foo&quot;].as_f # =&gt; 123.0
atom.metadata[&quot;foo&quot;].as_s # raises TypeCastError

missing_valence

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

name=(name : String)

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.

occupancy

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?

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

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.

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?

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=(new_res : Residue) : 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.

serial

serial=(serial : Int32)

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?

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

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.

spec

Returns the atom specification.

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

strontium?

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

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

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

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

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.

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.

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

Person.new(&quot;John&quot;, 32).to_s # =&gt; #&lt;Person:0x10a199f20&gt;

tungsten?

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

typename

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

typename=(typename : String | Nil)

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

uranium?

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

valence

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

valence_electrons(*args, **options)

valence_electrons(*args, **options, &)

vanadium?

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

vdw_radius

vdw_radius=(vdw_radius : Float64)

water?

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.