Package org.jmol.util
Class Elements
java.lang.Object
org.jmol.util.Elements
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
length of the altElementSymbols, altElementNames, altElementNumbers arraysstatic final float[]
static int
static int
static final short[]
Default table of bonding radii stored as a short mar ...static final int
static final String[]
static final int
one larger than the last elementNumber, same as elementSymbols.lengthstatic final String[]
The default elementSymbols.static final int
first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arraysstatic final int
static final int
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 invalid input: '<'invalid input: '<' 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 final int
static final int
static final int[]
static final int
static final int
static final short[]
Default table of van der Waals Radii.static final String
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic final int
altElementIndexFromNumber
(int atomicAndIsotopeNumber) static final String
altElementNameFromIndex
(int i) static final int
altElementNumberFromIndex
(int i) static final String
altElementSymbolFromIndex
(int i) static final String
altIsotopeSymbolFromIndex
(int i) static final String
altIsotopeSymbolFromIndex2
(int i) static final String
elementNameFromNumber
(int elementNumber) static final int
elementNumberFromName
(String name) static final int
elementNumberFromSymbol
(String elementSymbol, boolean isSilent) static final String
elementSymbolFromNumber
(int elemNo) static float
getAllredRochowElectroNeg
(int elemno) static final int
getAtomicAndIsotopeNumber
(int n, int mass) static float
getAtomicMass
(int i) static float
getBondingRadFromTable
(int atomicNumber, int charge, short[] table) static float
getBondingRadius
(int atomicNumberAndIsotope, int charge) This method is used by: (1) the CIF reader to create molecular systems when no bonding information is present (2) Atom.getBondingRadiusFloat, used by AtomCollection.findMaxRadii and getWorkingRadius, BondCollection.deleteConnections, ModelCollection.autoBond and makeConnections (3) the MMFF minimizer for unidentified atoms In terms of bondingVersion, the critical ones are the first two.static float
getCovalentRadius
(int atomicNumberAndIsotope) Prior to Jmol 14.1.11, this was OpenBabel 1.100.1, but now it is BODRstatic final int
getElementNumber
(int atomicAndIsotopeNumber) static float
getHydrophobicity
(int i) static final int
getIsotopeNumber
(int atomicAndIsotopeNumber) static int
getNaturalIsotope
(int elementNumber) static int
getVanderwaalsMar
(int atomicAndIsotopeNumber, VDW type) static boolean
isElement
(int atomicAndIsotopeNumber, int elemNo) static final boolean
isNaturalIsotope
(String isotopeSymbol)
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Field Details
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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 -
isotopeMass
public static final int[] isotopeMass -
elementNumberMax
public static final int elementNumberMaxone larger than the last elementNumber, same as elementSymbols.length -
htElementMap
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elementNames
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ISOTOPE_NUMBER_MASK
public static final int ISOTOPE_NUMBER_MASK- See Also:
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ISOTOPE_MASS_OFFSET
public static final int ISOTOPE_MASS_OFFSET- See Also:
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ELEMENT_NUMBER_MASK
public static final int ELEMENT_NUMBER_MASK- See Also:
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firstIsotope
public static final int firstIsotopefirst entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays- See Also:
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altElementMax
public static final int altElementMaxlength of the altElementSymbols, altElementNames, altElementNumbers arrays -
VdwPROBE
- See Also:
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vanderwaalsMars
public static final short[] vanderwaalsMarsDefault 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:
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RAD_COV_IONIC_OB1_100_1
public static final int RAD_COV_IONIC_OB1_100_1- See Also:
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RAD_COV_BODR_2014_02_22
public static final int RAD_COV_BODR_2014_02_22- See Also:
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covalentVersion
public static int covalentVersion -
bondingVersion
public static int bondingVersion -
defaultBondingMars
public static final short[] defaultBondingMarsDefault table of bonding radii stored as a short mar ... milliangstrom radius Column 1 (default): Values taken from OpenBabel. http://sourceforge.net/p/openbabel /code/485/tree/openbabel/trunk/data/element.txt (dated 10/20/2004) These values are a mix of common ion (Ba2+, Na+) distances and covalent distances. They are the default for autobonding in Jmol. Column 2: Blue Obelisk Data Repository (2/22/2014) https://github.com/wadejong/bodr/blob/c7917225cad829507bdd4c8c2fe7ebd3d795c021/bodr/elements/elements.xml which is from: Pyykkö, P. and Atsumi, M. (2009), Molecular Single-Bond Covalent Radii for Elements 1–118. Chem. Eur. J., 15: 186–197. doi: 10.1002/chem.200800987 (See also http://en.wikipedia.org/wiki/Covalent_radius) These are strictly covalent numbers. The user must use "set bondingVersion 1" to set these to be used for autobonding -
FORMAL_CHARGE_MIN
public static final int FORMAL_CHARGE_MINionic 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 invalid input: '<'invalid input: '<' 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:
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FORMAL_CHARGE_MAX
public static final int FORMAL_CHARGE_MAX- See Also:
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Constructor Details
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Elements
public Elements()
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Method Details
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getNaturalIsotope
public static int getNaturalIsotope(int elementNumber) -
getAtomicMass
public static float getAtomicMass(int i) -
elementNumberFromSymbol
- Parameters:
elementSymbol
- First char must be upper case, second char accepts upper or lower caseisSilent
-- Returns:
- elementNumber = atomicNumber + IsotopeNumber*128
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elementSymbolFromNumber
- Parameters:
elemNo
- may be atomicNumber + isotopeNumber*128- Returns:
- elementSymbol
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elementNameFromNumber
- Parameters:
elementNumber
- may be atomicNumber + isotopeNumber*128- Returns:
- elementName
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elementNumberFromName
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altElementNameFromIndex
- Parameters:
i
- index into altElementNames- Returns:
- elementName
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altElementNumberFromIndex
public static final int altElementNumberFromIndex(int i) - Parameters:
i
- index into altElementNumbers- Returns:
- elementNumber (may be atomicNumber + isotopeNumber*128)
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altElementSymbolFromIndex
- Parameters:
i
- index into altElementSymbols- Returns:
- elementSymbol
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altIsotopeSymbolFromIndex
- Parameters:
i
- index into altElementSymbols- Returns:
- 2H
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altIsotopeSymbolFromIndex2
- Parameters:
i
- index into altElementSymbols- Returns:
- H2
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getElementNumber
public static final int getElementNumber(int atomicAndIsotopeNumber) -
getIsotopeNumber
public static final int getIsotopeNumber(int atomicAndIsotopeNumber) -
getAtomicAndIsotopeNumber
public static final int getAtomicAndIsotopeNumber(int n, int mass) -
altElementIndexFromNumber
public static final int altElementIndexFromNumber(int atomicAndIsotopeNumber) - Parameters:
atomicAndIsotopeNumber
- (may be atomicNumber + isotopeNumber*128)- Returns:
- index into altElementNumbers
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isNaturalIsotope
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getBondingRadius
public static float getBondingRadius(int atomicNumberAndIsotope, int charge) This method is used by: (1) the CIF reader to create molecular systems when no bonding information is present (2) Atom.getBondingRadiusFloat, used by AtomCollection.findMaxRadii and getWorkingRadius, BondCollection.deleteConnections, ModelCollection.autoBond and makeConnections (3) the MMFF minimizer for unidentified atoms In terms of bondingVersion, the critical ones are the first two. Changing the version will change the number of bonds created initially, and that would throw off any state script. So we have to do a reset after a state script to return values to defaults.- Parameters:
atomicNumberAndIsotope
-charge
-- Returns:
- a bonding radius, either ionic or covalent
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getCovalentRadius
public static float getCovalentRadius(int atomicNumberAndIsotope) Prior to Jmol 14.1.11, this was OpenBabel 1.100.1, but now it is BODR- Parameters:
atomicNumberAndIsotope
-- Returns:
- BODR covalent data, generally.
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getBondingRadFromTable
public static float getBondingRadFromTable(int atomicNumber, int charge, short[] table) -
getVanderwaalsMar
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getHydrophobicity
public static float getHydrophobicity(int i) -
getAllredRochowElectroNeg
public static float getAllredRochowElectroNeg(int elemno) -
isElement
public static boolean isElement(int atomicAndIsotopeNumber, int elemNo)
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