public class Elements
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static int |
altElementMax
length of the altElementSymbols, altElementNames, altElementNumbers arrays
|
private static java.lang.String[] |
altElementNames |
private static int[] |
altElementNumbers |
private static java.lang.String[] |
altElementSymbols |
private static short[] |
anionLookupTable |
static float[] |
atomicMass |
static int |
bondingVersion |
private static BS |
bsAnions |
private static BS |
bsCations |
private static short[] |
cationLookupTable |
static int |
covalentVersion |
static short[] |
defaultBondingMars
Default table of bonding radii stored as a short mar ...
|
private static float[] |
electroNegativities |
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 |
private static float[] |
hydrophobicities |
private static int[] |
naturalIsotopeMasses |
private static java.lang.String |
naturalIsotopes |
static int |
RAD_COV_BODR_2014_02_22 |
static int |
RAD_COV_IONIC_OB1_100_1 |
static short[] |
vanderwaalsMars
Default table of van der Waals Radii.
|
static java.lang.String |
VdwPROBE |
Constructor and Description |
---|
Elements() |
Modifier and Type | Method and Description |
---|---|
static int |
altElementIndexFromNumber(int atomicAndIsotopeNumber) |
static java.lang.String |
altElementNameFromIndex(int i) |
static int |
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 int |
elementNumberFromName(java.lang.String name) |
static int |
elementNumberFromSymbol(java.lang.String elementSymbol,
boolean isSilent) |
static java.lang.String |
elementSymbolFromNumber(int elemNo) |
static float |
getAllredRochowElectroNeg(int elemno) |
static 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 BODR
|
static int |
getElementNumber(int atomicAndIsotopeNumber) |
private static java.lang.String |
getElementSymbol(int elemNo) |
static float |
getHydrophobicity(int i) |
static int |
getIsotopeNumber(int atomicAndIsotopeNumber) |
static int |
getNaturalIsotope(int elementNumber) |
static int |
getVanderwaalsMar(int atomicAndIsotopeNumber,
VDW type) |
static boolean |
isElement(int atomicAndIsotopeNumber,
int elemNo) |
static boolean |
isNaturalIsotope(java.lang.String isotopeSymbol) |
public static final java.lang.String[] elementSymbols
public static final float[] atomicMass
public static final int elementNumberMax
public static java.util.Map<java.lang.String,java.lang.Integer> htElementMap
public static final java.lang.String[] elementNames
private static int[] naturalIsotopeMasses
private static final java.lang.String naturalIsotopes
public static final int firstIsotope
private static final int[] altElementNumbers
public static final int altElementMax
private static final java.lang.String[] altElementSymbols
private static final java.lang.String[] altElementNames
public static final java.lang.String VdwPROBE
public static final short[] vanderwaalsMars
public static final int RAD_COV_IONIC_OB1_100_1
public static final int RAD_COV_BODR_2014_02_22
public static int covalentVersion
public static int bondingVersion
public static final short[] defaultBondingMars
public static final int FORMAL_CHARGE_MIN
public static final int FORMAL_CHARGE_MAX
private static final short[] cationLookupTable
private static final short[] anionLookupTable
private static final BS bsCations
private static final BS bsAnions
private static final float[] hydrophobicities
private static float[] electroNegativities
public static float getAtomicMass(int i)
public static final int elementNumberFromSymbol(java.lang.String elementSymbol, boolean isSilent)
elementSymbol
- First char must be upper case, second char accepts upper or lower caseisSilent
- public static final java.lang.String elementSymbolFromNumber(int elemNo)
elemNo
- may be atomicNumber + isotopeNumber*128private static java.lang.String getElementSymbol(int elemNo)
public static final java.lang.String elementNameFromNumber(int elementNumber)
elementNumber
- may be atomicNumber + isotopeNumber*128public static final int elementNumberFromName(java.lang.String name)
public static final java.lang.String altElementNameFromIndex(int i)
i
- index into altElementNamespublic static final int altElementNumberFromIndex(int i)
i
- index into altElementNumberspublic static final java.lang.String altElementSymbolFromIndex(int i)
i
- index into altElementSymbolspublic static final java.lang.String altIsotopeSymbolFromIndex(int i)
i
- index into altElementSymbolspublic static final java.lang.String altIsotopeSymbolFromIndex2(int i)
i
- index into altElementSymbolspublic static final int getElementNumber(int atomicAndIsotopeNumber)
public static final int getIsotopeNumber(int atomicAndIsotopeNumber)
public static final int getAtomicAndIsotopeNumber(int n, int mass)
public static final int altElementIndexFromNumber(int atomicAndIsotopeNumber)
atomicAndIsotopeNumber
- (may be atomicNumber + isotopeNumber*128)public static int getNaturalIsotope(int elementNumber)
public static final boolean isNaturalIsotope(java.lang.String isotopeSymbol)
public static float getBondingRadius(int atomicNumberAndIsotope, int charge)
atomicNumberAndIsotope
- charge
- public static float getCovalentRadius(int atomicNumberAndIsotope)
atomicNumberAndIsotope
- public static float getBondingRadFromTable(int atomicNumber, int charge, short[] table)
public static int getVanderwaalsMar(int atomicAndIsotopeNumber, VDW type)
public static float getHydrophobicity(int i)
public static float getAllredRochowElectroNeg(int elemno)
public static boolean isElement(int atomicAndIsotopeNumber, int elemNo)