chemaxon.struc
Class PeriodicSystem

java.lang.Object
  chemaxon.struc.PeriodicSystem

public class PeriodicSystem
extends java.lang.Object

Periodic System of the Elements. Provides basic information of the chemical elements and their isotopes.

Information on the elements are stored at element.zip. By default this file is located at the chemaxon directory but it can be overwritten by a file having the same name at user_home/chemaxon directory.

Information on the elements are stored at isotopes.data. By default this file is located at the chemaxon directory but it can be overwritten by a file having the same name at user_home/chemaxon directory.

API usage example:

           int elementCount = PeriodicSystem.getElementCount();   // number of elements in the periodic system
           int isotopeCount = PeriodicSystem.getIsotopeCount();   // number of isotopes in the periodic system
           String symbol = PeriodicSystem.getSymbol(6);                   // element symbol of the 6th element
           String name = PeriodicSystem.getName(6);                               // element name of the 6th element
           int atomicNumber = PeriodicSystem.getAtomicNumber("C");   // atomic number of carbon
           double mass = PeriodicSystem.getMass(6);                               // elemental mass (weight) of an element
           int precision = PeriodicSystem.getMassPrecision(6);     // precision of a certain the elemental mass (weight)
           int isotopes = PeriodicSystem.getIsotopeCount(6);             // number of isotopes of carbon
           int mainIsotope = PeriodicSystem.getMostFrequentNaturalIsotope(6);   // the most frequent natural isotope of carbon
           double isotopeMass = PeriodicSystem.getMass(6, 14);     // isotopic mass (weight) of carbon 14
           int isotopePrecision = PeriodicSystem.getMassPrecision(6, 14);          // precision of a certain isotopic mass (weight)
           int deuterium = PeriodicSystem.getAtomicNumber("D");   // atomic number of Deuterium
 

Version:

Marvin 5.2.1, 03/29/2009

Author:

Gyorgy Pirok, Peter Csizmadia

Field Summary

static int	Ac
static int	Ag
static int	Al
static int	Am
static int	Ar
static int	As
static int	At
static int	Au
static int	B
static int	Ba
static int	Be
static int	Bh
static int	Bi
static int	Bk
static int	Br
static int	C
static int	Ca
static int	Cd
static int	Ce
static int	Cf
static int	Cl
static int	Cm
static int	Co
static int	Cr
static int	Cs
static int	Cu
static int	Db
static int	Ds
static int	Dy
static int	Er
static int	Es
static int	Eu
static int	F
static int	Fe
static int	Fm
static int	Fr
static int	Ga
static int	Gd
static int	Ge
static int	H
static int	He
static int	Hf
static int	Hg
static int	Ho
static int	Hs
static int	I
static int	In
static int	Ir
static int	K
static int	Kr
static int	La
static int	Li
static int	Lr
static int	Lu
static int	Md
static int	Mg
static int	Mn
static int	Mo
static int	Mt
static int	N
static int	Na
static int	Nb
static int	Nd
static int	Ne
static int	Ni
static int	No
static int	Np
static int	O
static int	Os
static int	P
static int	Pa
static int	Pb
static int	Pd
static int	Pm
static int	Po
static int	Pr
static int	Pt
static int	Pu
static int	Ra
static int	Rb
static int	Re
static int	Rf
static int	Rg
static int	Rh
static int	Rn
static int	Ru
static int	S
static int	Sb
static int	Sc
static int	Se
static int	Sg
static int	Si
static int	Sm
static int	Sn
static int	Sr
static int	Ta
static int	Tb
static int	Tc
static int	Te
static int	Th
static int	Ti
static int	Tl
static int	Tm
static int	U
static int	V
static int	W
static int	Xe
static int	Y
static int	Yb
static int	Zn
static int	Zr

Constructor Summary

PeriodicSystem()

Method Summary

static int	findAtomicNumber(java.lang.String symbol) Returns the atomic number of the element in the periodic system specified by its symbol.
static double	getAbundance(int z, int m) Natural abundance of the isotope
static int	getAtomicNumber(java.lang.String symbol) Deprecated. As of Marvin 5.9, replaced by a similar method which throws IllegalArgumentException in case of failure findAtomicNumber(String).
static double	getAtomicRadius(int z) Atomic radius of the element Angstroms.
static int	getColumn(int z) The column or group of an element in the periodic system.
static double	getCovalentRadius(int z) Covalent radius of the element in Angstroms.
static double	getCovalentRadius(int z, int t) Covalent radius of the element in specific bond type in Angstroms.
static int	getElementCount() Number of elements in the periodic system
static int	getIsotope(int z, int i) Retrieves an isotope of the element
static int	getIsotopeCount() Number of isotopes in the periodic system
static int	getIsotopeCount(int z) Number of isotopes of the element
static double	getMass(int z) Atomic weight of the element based on the natural abundance of its isotopes
static double	getMass(int z, int m) Atomic weight of an isotope
static int	getMassPrecision(int z) The precision of an elemental mass is the number of measured digits after the decimal separator.
static int	getMassPrecision(int z, int m) The precision of an isotopic mass is the number of measured digits after the decimal separator.
static int	getMostFrequentNaturalIsotope(int z) Returns the mass number of the most frequent natural isotope of the element
static java.lang.String	getName(int z) Name of the element
static int	getRow(int z) The row or or period of an element in the periodic system.
static java.lang.String	getSymbol(int z) Symbol of the element
static double	getVanDerWaalsRadius(int z) Van der Waals radius of the element in Angstroms.
static boolean	isActinideMetal(int z) Checks if the given atom is an actinide metal Actinium is included.
static boolean	isAlkaliMetal(int z) Checks if the given atom is an alkali (group I.) metal.
static boolean	isAlkalineEarthMetal(int z) Checks if the given atom is an alkaline earth (group II.) metal.
static boolean	isAtomicSymbol(java.lang.String symbol) Returns whether the given string corresponds to an atomic number of an element in the periodic system specified by its symbol.
static boolean	isHalogen(int z) Checks if the given atom is a halogen.
static boolean	isLanthanideMetal(int z) Checks if the given atom is a lanthanide metal Lanthanum is included.
static boolean	isMetal(int z) Decides whether the element is a metal.
static boolean	isMetalloid(int z) Checks if the given atom is a metalloid.
static boolean	isNobleGas(int z) Checks if the given atom is a noble gas.
static boolean	isOtherMetal(int z) Checks if the given atom is an "other metal", group IIIa-Va metal.
static boolean	isTransitionMetal(int z) Checks if the given atom is a transition metal, IB-VIIIB.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

H

public static final int H

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He

public static final int He

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Li

public static final int Li

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Be

public static final int Be

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B

public static final int B

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C

public static final int C

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N

public static final int N

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O

public static final int O

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F

public static final int F

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Ne

public static final int Ne

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Na

public static final int Na

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Mg

public static final int Mg

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Al

public static final int Al

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Si

public static final int Si

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P

public static final int P

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S

public static final int S

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Cl

public static final int Cl

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Ar

public static final int Ar

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K

public static final int K

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Ca

public static final int Ca

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Sc

public static final int Sc

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Ti

public static final int Ti

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V

public static final int V

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Cr

public static final int Cr

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Mn

public static final int Mn

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Fe

public static final int Fe

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Co

public static final int Co

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Ni

public static final int Ni

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Cu

public static final int Cu

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Zn

public static final int Zn

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Ga

public static final int Ga

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Ge

public static final int Ge

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As

public static final int As

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Se

public static final int Se

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Br

public static final int Br

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Kr

public static final int Kr

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Rb

public static final int Rb

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Sr

public static final int Sr

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Y

public static final int Y

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Zr

public static final int Zr

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Nb

public static final int Nb

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Mo

public static final int Mo

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Tc

public static final int Tc

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Ru

public static final int Ru

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Rh

public static final int Rh

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Pd

public static final int Pd

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Ag

public static final int Ag

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Cd

public static final int Cd

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In

public static final int In

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Sn

public static final int Sn

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Sb

public static final int Sb

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Te

public static final int Te

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I

public static final int I

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Xe

public static final int Xe

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Cs

public static final int Cs

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Ba

public static final int Ba

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La

public static final int La

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Ce

public static final int Ce

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Pr

public static final int Pr

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Nd

public static final int Nd

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Pm

public static final int Pm

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Sm

public static final int Sm

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Eu

public static final int Eu

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Gd

public static final int Gd

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Tb

public static final int Tb

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Dy

public static final int Dy

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Ho

public static final int Ho

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Er

public static final int Er

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Tm

public static final int Tm

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Yb

public static final int Yb

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Lu

public static final int Lu

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Hf

public static final int Hf

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Ta

public static final int Ta

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W

public static final int W

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Re

public static final int Re

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Os

public static final int Os

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Ir

public static final int Ir

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Pt

public static final int Pt

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Au

public static final int Au

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Hg

public static final int Hg

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Tl

public static final int Tl

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Pb

public static final int Pb

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Bi

public static final int Bi

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Po

public static final int Po

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At

public static final int At

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Rn

public static final int Rn

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Fr

public static final int Fr

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Ra

public static final int Ra

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Ac

public static final int Ac

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Th

public static final int Th

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Pa

public static final int Pa

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U

public static final int U

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Np

public static final int Np

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Pu

public static final int Pu

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Am

public static final int Am

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Cm

public static final int Cm

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Bk

public static final int Bk

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Cf

public static final int Cf

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Es

public static final int Es

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Fm

public static final int Fm

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Md

public static final int Md

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No

public static final int No

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Lr

public static final int Lr

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Rf

public static final int Rf

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Db

public static final int Db

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Sg

public static final int Sg

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Bh

public static final int Bh

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Hs

public static final int Hs

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Mt

public static final int Mt

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Ds

public static final int Ds

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Rg

public static final int Rg

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Constructor Detail

PeriodicSystem

public PeriodicSystem()

Method Detail

getElementCount

public static int getElementCount()

Number of elements in the periodic system

Returns:

number of element

getIsotopeCount

public static int getIsotopeCount()

Number of isotopes in the periodic system

Returns:

number of isotopes

getIsotopeCount

public static int getIsotopeCount(int z)

Number of isotopes of the element

Parameters:

z - atomic number of the element (protons)

Returns:

number of isotopes

getIsotope

public static int getIsotope(int z,
                             int i)

Retrieves an isotope of the element

Parameters:

z - atomic number of the element (protons)

i - index of the isotope (0 based)

Returns:

mass number of the isotope

getName

public static java.lang.String getName(int z)

Name of the element

Parameters:

z - atomic number (protons)

Returns:

element name

getSymbol

public static java.lang.String getSymbol(int z)

Symbol of the element

Parameters:

z - atomic number (protons)

Returns:

element symbol

getMass

public static double getMass(int z)

Atomic weight of the element based on the natural abundance of its isotopes

Parameters:

z - atomic number (protons)

Returns:

elemental mass

getMass

public static double getMass(int z,
                             int m)

Atomic weight of an isotope

Parameters:

z - atomic number of the isotope

m - mass number of the isotope (0 for element mass)

Returns:

isotope mass (0 if isotope does not exist)

getMassPrecision

public static int getMassPrecision(int z)

The precision of an elemental mass is the number of measured digits after the decimal separator. For example, the mass of Mg is 24.3050, so its precision is 4.

Parameters:

z - atomic number (protons)

Returns:

the number of significant digits after the decimal point

getMassPrecision

public static int getMassPrecision(int z,
                                   int m)

The precision of an isotopic mass is the number of measured digits after the decimal separator. For example, the mass of [4He] is 4.002603250, so its precision is 9.

Parameters:

z - atomic number (protons)

m - mass number of the isotope (0 for element mass)

Returns:

the number of significant digits after the decimal point (0 if isotope does not exists)

getAbundance

public static double getAbundance(int z,
                                  int m)

Natural abundance of the isotope

Parameters:

z - atomic number of the isotope (protons)

m - mass number of the isotope (protons + neutrons)

Returns:

natural abundance (100 for the most frequent isotope)

getMostFrequentNaturalIsotope

public static int getMostFrequentNaturalIsotope(int z)

Returns the mass number of the most frequent natural isotope of the element

Parameters:

z - atomic number (protons)

Returns:

mass number of the isotope (0 if artificial element)

getAtomicNumber

public static int getAtomicNumber(java.lang.String symbol)

Deprecated. As of Marvin 5.9, replaced by a similar method which throws IllegalArgumentException in case of failure findAtomicNumber(String).

Returns the atomic number of the element in the periodic system specified by its symbol. Case insensitive. In addition to elements of the periodic system, Deuterium and Tritium isotopes are also handled.

Parameters:

symbol - atom symbol e.g. "C", "Br", "BR".

Returns:

atomic number or -1 if not found.

findAtomicNumber

public static int findAtomicNumber(java.lang.String symbol)
                            throws java.lang.IllegalArgumentException

Returns the atomic number of the element in the periodic system specified by its symbol. Case insensitive. In addition to elements of the periodic system, Deuterium and Tritium isotopes are also handled.

Parameters:

symbol - atom symbol e.g. "C", "Br", "BR".

Returns:

atomic number

Throws:

java.lang.IllegalArgumentException - if symbol does not correspond to a chemical element in the periodic table.

isAtomicSymbol

public static boolean isAtomicSymbol(java.lang.String symbol)

Returns whether the given string corresponds to an atomic number of an element in the periodic system specified by its symbol. Case insensitive.

Parameters:

symbol - atom symbol e.g. "C", "Br", "BR".

Returns:

true if atomic number found else false.

getAtomicRadius

public static double getAtomicRadius(int z)

Atomic radius of the element Angstroms.

Parameters:

z - atomic number (protons)

Returns:

atomic radius (1.5 if unknown)

getCovalentRadius

public static double getCovalentRadius(int z)

Covalent radius of the element in Angstroms.

Parameters:

z - atomic number (protons)

Returns:

atomic radius (1.5 if unknown)

getCovalentRadius

public static double getCovalentRadius(int z,
                                       int t)

Covalent radius of the element in specific bond type in Angstroms.

Parameters:

z - atomic number (protons)

t - bond type

Returns:

atomic radius (1.5 if unknown)

getVanDerWaalsRadius

public static double getVanDerWaalsRadius(int z)

Van der Waals radius of the element in Angstroms.

Parameters:

z - atomic number (protons)

Returns:

atomic radius (2.0 if unknown)

getColumn

public static int getColumn(int z)

The column or group of an element in the periodic system.

Parameters:

z - atomic number (protons)

Returns:

column of the given element (0 for unknown)

Since:

Marvin 4.1

getRow

public static int getRow(int z)

The row or or period of an element in the periodic system.

Parameters:

z - atomic number (protons)

Returns:

column of the given element (0 for unknown)

Since:

Marvin 4.1

isMetal

public static boolean isMetal(int z)

Decides whether the element is a metal. It returns true for those elements, that are classified as different kinds of metals in Periodic System dialog of Marvin: alkali metal, alkaline earth metal, transition metal and other metals, as well as Ge, Sb and Po from the metalloids.

Parameters:

z - atomic number (protons)

Returns:

true if the element is metal

isAlkaliMetal

public static boolean isAlkaliMetal(int z)

Checks if the given atom is an alkali (group I.) metal.

Parameters:

z - atomic number of the atom.

Returns:

true if the given atom is alkali metal.

isAlkalineEarthMetal

public static boolean isAlkalineEarthMetal(int z)

Checks if the given atom is an alkaline earth (group II.) metal.

Parameters:

z - atomic number of the atom.

Returns:

true if the given atom is an alkaline earth metal.

isOtherMetal

public static boolean isOtherMetal(int z)

Checks if the given atom is an "other metal", group IIIa-Va metal.

Parameters:

z - atomic number of the atom.

Returns:

true if the given atom is an other metal.

isTransitionMetal

public static boolean isTransitionMetal(int z)

Checks if the given atom is a transition metal, IB-VIIIB. Lanthanum and Actinium are excluded.

Parameters:

z - atomic number of the atom.

Returns:

true if the given atom is a transition metal.

isLanthanideMetal

public static boolean isLanthanideMetal(int z)

Checks if the given atom is a lanthanide metal Lanthanum is included.

Parameters:

z - atomic number of the atom.

Returns:

true if the given atom is a lanthanide metal.

isActinideMetal

public static boolean isActinideMetal(int z)

Checks if the given atom is an actinide metal Actinium is included.

Parameters:

z - atomic number of the atom.

Returns:

true if the given atom is a actinide metal.

isMetalloid

public static boolean isMetalloid(int z)

Checks if the given atom is a metalloid. (B, Si, Ge, As, Sb, Te)

Parameters:

z - atomic number of the atom.

Returns:

true if the given atom is a metalloid.

isHalogen

public static boolean isHalogen(int z)

Checks if the given atom is a halogen. (F, Cl, Br, I)

Parameters:

z - atomic number of the atom.

Returns:

true if the given atom is a halogen.

isNobleGas

public static boolean isNobleGas(int z)

Checks if the given atom is a noble gas.

Parameters:

z - atomic number of the atom.

Returns:

true if the given atom is a noble gas.