Package org.jmol.util

Class Elements

java.lang.Object

org.jmol.util.Elements

public class Elements
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
static int	altElementMax	length of the altElementSymbols, altElementNames, altElementNumbers arrays
static float[]	atomicMass
static short[]	covalentMars	Default table of covalent Radii stored as a short mar ...
static java.lang.String[]	elementNames
static int	elementNumberMax	one larger than the last elementNumber, same as elementSymbols.length
static java.lang.String[]	elementSymbols	The default elementSymbols.
static int	firstIsotope	first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
static int	FORMAL_CHARGE_MAX
static int	FORMAL_CHARGE_MIN	ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7.
static java.util.Map<java.lang.String,java.lang.Integer>	htElementMap
static short[]	vanderwaalsMars	Default table of van der Waals Radii.
static java.lang.String	VdwPROBE

Constructor Summary

Constructors

Constructor	Description
Elements()

Method Summary

Modifier and Type	Method	Description
static int	altElementIndexFromNumber(int atomicAndIsotopeNumber)
static java.lang.String	altElementNameFromIndex(int i)
static short	altElementNumberFromIndex(int i)
static java.lang.String	altElementSymbolFromIndex(int i)
static java.lang.String	altIsotopeSymbolFromIndex(int i)
static java.lang.String	altIsotopeSymbolFromIndex2(int i)
static java.lang.String	elementNameFromNumber(int elementNumber)
static short	elementNumberFromSymbol(java.lang.String elementSymbol, boolean isSilent)
static java.lang.String	elementSymbolFromNumber(int elementNumber)
static float	getAllredRochowElectroNeg(int elemno)
static short	getAtomicAndIsotopeNumber(int n, int mass)
static float	getAtomicMass(int i)
static float	getBondingRadFromTable(int atomicNumber, int charge, short[] table)
static float	getBondingRadiusFloat(short atomicNumberAndIsotope, int charge)
static short	getElementNumber(short atomicAndIsotopeNumber)
static float	getHydrophobicity(int i)
static short	getIsotopeNumber(short atomicAndIsotopeNumber)
static int	getNaturalIsotope(int elementNumber)
static int	getVanderwaalsMar(int i, EnumVdw type)
static boolean	isNaturalIsotope(java.lang.String isotopeSymbol)

Methods inherited from class java.lang.Object

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

Field Detail

elementSymbols

public static final java.lang.String[] elementSymbols

The default elementSymbols. Presumably the only entry which may cause confusion is element 0, whose symbol we have defined as "Xx".

atomicMass

public static final float[] atomicMass

elementNumberMax

public static final int elementNumberMax

one larger than the last elementNumber, same as elementSymbols.length

htElementMap

public static java.util.Map<java.lang.String,java.lang.Integer> htElementMap

elementNames

public static final java.lang.String[] elementNames

firstIsotope

public static final int firstIsotope

first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays

See Also:

Constant Field Values

altElementMax

public static final int altElementMax

length of the altElementSymbols, altElementNames, altElementNumbers arrays

VdwPROBE

public static final java.lang.String VdwPROBE

See Also:

Constant Field Values

vanderwaalsMars

public static final short[] vanderwaalsMars

Default table of van der Waals Radii. values are stored as MAR -- Milli Angstrom Radius Used for spacefill rendering of atoms. Values taken from OpenBabel. Note that AUTO_JMOL, AUTO_BABEL, and AUTO_RASMOL are 4, 5, and 6, respectively, so their mod will be JMOL, BABEL, and RASMOL. AUTO is 8, so will default to Jmol

See Also:

openbabel.sourceforge.net, vdw_comparison.xls

covalentMars

public static final short[] covalentMars

Default table of covalent Radii stored as a short mar ... Milli Angstrom Radius Values taken from OpenBabel.

See Also:

openbabel.sourceforge.net

FORMAL_CHARGE_MIN

public static final int FORMAL_CHARGE_MIN

ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7. This data is from Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143 (scanned for Jmol by Phillip Barak, Jan 2004) Reorganized from two separate arrays 9/2006 by Bob Hanson, who thought it was just too hard to look these up and, if necessary, add or modify. At the same time, the table was split into cations and anions for easier retrieval. O- and N+ removed 9/2008 - BH. The problem is that the formal charge is used to determine bonding radius. But these formal charges are different than the charges used in compilation of HCP data (which is crystal ionic radii). Specifically, because O- and N+ are very common in organic compounds, I have removed their radii from the table FOR OUR PURPOSES HERE. I suppose there are some ionic compounds that have O- and N+ as isolated ions, but what they would be I have no clue. Better to be safe and go with somewhat more reasonable values. Argh. Changed for Jmol 11.6.RC15

See Also:

Constant Field Values

FORMAL_CHARGE_MAX

public static final int FORMAL_CHARGE_MAX

See Also:

Constant Field Values

Constructor Detail

Elements

public Elements()

Method Detail

getAtomicMass

public static float getAtomicMass(int i)

elementNumberFromSymbol

public static final short elementNumberFromSymbol(java.lang.String elementSymbol,
                                                  boolean isSilent)

Parameters:

elementSymbol - First char must be upper case, second char accepts upper or lower case

isSilent - TODO

Returns:

elementNumber = atomicNumber + IsotopeNumber*128

elementSymbolFromNumber

public static final java.lang.String elementSymbolFromNumber(int elementNumber)

Parameters:

elementNumber - may be atomicNumber + isotopeNumber*128

Returns:

elementSymbol

elementNameFromNumber

public static final java.lang.String elementNameFromNumber(int elementNumber)

Parameters:

elementNumber - may be atomicNumber + isotopeNumber*128

Returns:

elementName

altElementNameFromIndex

public static final java.lang.String altElementNameFromIndex(int i)

Parameters:

i - index into altElementNames

Returns:

elementName

altElementNumberFromIndex

public static final short altElementNumberFromIndex(int i)

Parameters:

i - index into altElementNumbers

Returns:

elementNumber (may be atomicNumber + isotopeNumber*128)

altElementSymbolFromIndex

public static final java.lang.String altElementSymbolFromIndex(int i)

Parameters:

i - index into altElementSymbols

Returns:

elementSymbol

altIsotopeSymbolFromIndex

public static final java.lang.String altIsotopeSymbolFromIndex(int i)

Parameters:

i - index into altElementSymbols

Returns:

2H

altIsotopeSymbolFromIndex2

public static final java.lang.String altIsotopeSymbolFromIndex2(int i)

Parameters:

i - index into altElementSymbols

Returns:

H2

getElementNumber

public static final short getElementNumber(short atomicAndIsotopeNumber)

getIsotopeNumber

public static final short getIsotopeNumber(short atomicAndIsotopeNumber)

getAtomicAndIsotopeNumber

public static final short getAtomicAndIsotopeNumber(int n,
                                                    int mass)

altElementIndexFromNumber

public static final int altElementIndexFromNumber(int atomicAndIsotopeNumber)

Parameters:

atomicAndIsotopeNumber - (may be atomicNumber + isotopeNumber*128)

Returns:

index into altElementNumbers

getNaturalIsotope

public static int getNaturalIsotope(int elementNumber)

isNaturalIsotope

public static final boolean isNaturalIsotope(java.lang.String isotopeSymbol)

getBondingRadiusFloat

public static float getBondingRadiusFloat(short atomicNumberAndIsotope,
                                          int charge)

getBondingRadFromTable

public static float getBondingRadFromTable(int atomicNumber,
                                           int charge,
                                           short[] table)

getVanderwaalsMar

public static int getVanderwaalsMar(int i,
                                    EnumVdw type)

getHydrophobicity

public static float getHydrophobicity(int i)

getAllredRochowElectroNeg

public static float getAllredRochowElectroNeg(int elemno)