A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

absSumAllElements() - Method in class jumbo.euclid.IntArray
absolute sum of all elements
absSumAllElements() - Method in class jumbo.euclid.RealArray
absolute sum of all elements
AbstractAngle - interface org.xmlcml.cml.AbstractAngle.
 
AbstractAngleImpl - class org.xmlcml.cml.AbstractAngleImpl.
 
AbstractAngleImpl() - Constructor for class org.xmlcml.cml.AbstractAngleImpl
 
AbstractAngleImpl(Element) - Constructor for class org.xmlcml.cml.AbstractAngleImpl
 
AbstractAngleImpl(String, Document) - Constructor for class org.xmlcml.cml.AbstractAngleImpl
new Object in document context
AbstractAtom - interface org.xmlcml.cml.AbstractAtom.
 
AbstractAtomImpl - class org.xmlcml.cml.AbstractAtomImpl.
 
AbstractAtomImpl() - Constructor for class org.xmlcml.cml.AbstractAtomImpl
 
AbstractAtomImpl(Element) - Constructor for class org.xmlcml.cml.AbstractAtomImpl
 
AbstractAtomImpl(String, Document) - Constructor for class org.xmlcml.cml.AbstractAtomImpl
 
AbstractAtomRef - interface org.xmlcml.cml.AbstractAtomRef.
some Objects (Angle, Torsion...) have references to Atoms
AbstractAtomRefImpl - class org.xmlcml.cml.AbstractAtomRefImpl.
 
AbstractAtomRefImpl() - Constructor for class org.xmlcml.cml.AbstractAtomRefImpl
 
AbstractAtomRefImpl(Element) - Constructor for class org.xmlcml.cml.AbstractAtomRefImpl
 
AbstractAtomRefImpl(String, Document) - Constructor for class org.xmlcml.cml.AbstractAtomRefImpl
new Object in document context
AbstractBond - interface org.xmlcml.cml.AbstractBond.
 
AbstractBondImpl - class org.xmlcml.cml.AbstractBondImpl.
 
AbstractBondImpl() - Constructor for class org.xmlcml.cml.AbstractBondImpl
 
AbstractBondImpl(Element) - Constructor for class org.xmlcml.cml.AbstractBondImpl
 
AbstractBondImpl(String, Document) - Constructor for class org.xmlcml.cml.AbstractBondImpl
 
AbstractBuiltinContainer - interface org.xmlcml.cml.AbstractBuiltinContainer.
 
AbstractBuiltinContainerImpl - class org.xmlcml.cml.AbstractBuiltinContainerImpl.
 
AbstractBuiltinContainerImpl() - Constructor for class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
AbstractBuiltinContainerImpl(Element) - Constructor for class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
AbstractBuiltinContainerImpl(String, Document) - Constructor for class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
AbstractDocumentImpl - class uk.co.demon.ursus.dom.AbstractDocumentImpl.
DOM-based re-write of JUMBO functionality.
AbstractDocumentImpl() - Constructor for class uk.co.demon.ursus.dom.AbstractDocumentImpl
 
AbstractDocumentImpl(InputSource) - Constructor for class uk.co.demon.ursus.dom.AbstractDocumentImpl
 
AbstractDocumentImpl(String) - Constructor for class uk.co.demon.ursus.dom.AbstractDocumentImpl
 
AbstractElementImpl - class uk.co.demon.ursus.dom.AbstractElementImpl.
Xerces variant
AbstractElementImpl() - Constructor for class uk.co.demon.ursus.dom.AbstractElementImpl
should not make an isolated PMRElement
AbstractElementImpl(String, PMRDocument) - Constructor for class uk.co.demon.ursus.dom.AbstractElementImpl
have to make an element in conjunction with a document
AbstractStringVal - interface org.xmlcml.cml.AbstractStringVal.
 
AbstractStringValImpl - class org.xmlcml.cml.AbstractStringValImpl.
 
AbstractStringValImpl() - Constructor for class org.xmlcml.cml.AbstractStringValImpl
 
AbstractStringValImpl(Element) - Constructor for class org.xmlcml.cml.AbstractStringValImpl
 
AbstractStringValImpl(String, Document) - Constructor for class org.xmlcml.cml.AbstractStringValImpl
new Object in document context
AbstractStringValImpl(String, Document, String, String, String, String, String, String) - Constructor for class org.xmlcml.cml.AbstractStringValImpl
 
ACELL - Static variable in interface org.xmlcml.cml.Crystal
 
add(Atom) - Method in interface org.xmlcml.cml.AtomArray
when an Atom is added then it is split over the various StringArrays
add(Atom) - Method in class org.xmlcml.cml.AtomArrayImpl
when an Atom is added then it is split over the various StringArrays
add(Bond) - Method in interface org.xmlcml.cml.BondArray
when an Bond is added then it is split over the various StringArrays
add(Bond) - Method in class org.xmlcml.cml.BondArrayImpl
when an Bond is added then it is split over the various StringArrays
add(Choice3, double) - Method in class jumbo.euclid.Real3Range
add a single value
add(CMLValidity) - Method in interface org.xmlcml.cml.CMLValidity
 
add(CMLValidity) - Method in class org.xmlcml.cml.CMLValidityImpl
 
add(double) - Method in class jumbo.euclid.RealRange
add a value to a range
add(int) - Method in class jumbo.euclid.IntRange
add a value to a range
add(Int2) - Method in class jumbo.euclid.Int2Range
add a Int2 to a range
add(int, double) - Method in class jumbo.euclid.Real3Range
add a single value - not for general use
add(Object) - Method in interface jumbo.xml.util.XHashtable
adds an object as key with irrelevant value
add(Object) - Method in class jumbo.xml.util.XHashtableImpl
 
add(Object) - Method in interface org.xmlcml.tools.ToolHashSet
add element (cf HashSet)
add(Point3) - Method in class jumbo.euclid.Real3Range
add a Point3 to a range
add(Real2) - Method in class jumbo.euclid.Real2Range
add a Real2 to a range
addAll(Collection) - Method in interface org.xmlcml.tools.ToolHashSet
add Collection (cf HashSet)
addAngle(Angle) - Method in interface org.xmlcml.cml.Molecule
adds the Angle to the Angle content of the Molecule.
addAngle(Angle) - Method in class org.xmlcml.cml.MoleculeImpl
adds the Angle to the Angle content of the Molecule.
addArray(IntArray) - Method in class jumbo.euclid.IntArray
append elements
addArray(ObjectArray) - Method in class jumbo.euclid.ObjectArray
append elements
addArray(RealArray) - Method in class jumbo.euclid.RealArray
append elements
addAtom(Atom) - Method in interface org.xmlcml.cml.Molecule
adds the Atom to the Atom content of the Molecule.
addAtom(Atom) - Method in class org.xmlcml.cml.MoleculeImpl
adds the Atom to the Atom content of the Molecule.
addAtom(Atom) - Method in interface org.xmlcml.tools.AtomSet
add an atom.
addAtom(Atom) - Method in class org.xmlcml.tools.AtomSetImpl
add an atom.
addAtom(STElement, Atom) - Method in interface org.xmlcml.tools.SpanningTree
create new STElement (contains atom) and add to parent
addAtom(STElement, Atom) - Method in class org.xmlcml.tools.SpanningTreeImpl
 
addAtomRef(Atom) - Method in interface org.xmlcml.cml.AbstractAtomRef
 
addAtomRef(Atom) - Method in class org.xmlcml.cml.AbstractAtomRefImpl
 
addAtomRef(Atom) - Method in interface org.xmlcml.cml.AbstractBond
 
addAtomRef(Atom) - Method in class org.xmlcml.cml.AbstractBondImpl
 
addAtomRef(Atom) - Method in interface org.xmlcml.cml.HasAtomRefs
 
addAtoms() - Method in interface org.xmlcml.tools.RingNucleus
add atoms from all the rings
addAtoms() - Method in class org.xmlcml.tools.RingNucleusImpl
add atoms from all the rings
addAttributes(Element, AttributeList) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
 
addAttributes(Element, AttributeList) - Static method in class uk.co.demon.ursus.dom.SAXAdapter
 
addBond(Bond) - Method in interface org.xmlcml.cml.Molecule
adds the Bond to the Bond content of the Molecule.
addBond(Bond) - Method in class org.xmlcml.cml.MoleculeImpl
adds the Bond to the Bond content of the Molecule.
addBond(Bond) - Method in interface org.xmlcml.tools.AtomSet
adds both atoms in the bond
addBond(Bond) - Method in class org.xmlcml.tools.AtomSetImpl
adds both atoms in the bond
addBond(Bond) - Method in interface org.xmlcml.tools.BondSet
add a bond, checking for nullity and duplicates
addBond(Bond) - Method in class org.xmlcml.tools.BondSetImpl
add a bond, checking for nullity
addBond(Bond) - Method in interface org.xmlcml.tools.Ring
 
addBond(Bond) - Method in class org.xmlcml.tools.RingImpl
 
addBuiltinChildWithFloatValue(int, String[], double, boolean) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
 
addBuiltinChildWithFloatValue(int, String[], double, boolean) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
addBuiltinChildWithIntegerValue(int, String[], int, boolean) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
 
addBuiltinChildWithIntegerValue(int, String[], int, boolean) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
addBuiltinChildWithStringValue(int, String[], String, boolean) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
sets the value
addBuiltinChildWithStringValue(int, String[], String, boolean) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
creates a child with the given builtin, sets value and adds to DOM.
addChainSet(ChainSet) - Method in interface org.xmlcml.tools.SpanningTree
 
addChainSet(ChainSet) - Method in class org.xmlcml.tools.SpanningTreeImpl
this adds an *existing* chain to the vector (i.e.
addChainSet(ChainSet) - Method in interface org.xmlcml.tools.SubstituentList
 
addChainSet(ChainSet) - Method in class org.xmlcml.tools.SubstituentListImpl
 
addElectron(Electron) - Method in interface org.xmlcml.cml.Molecule
Adds a Electron to the Molecule content.
addElectron(Electron) - Method in class org.xmlcml.cml.MoleculeImpl
Adds a Electron to the Molecule content.
addElement(double) - Method in interface org.xmlcml.cml.FloatArray
 
addElement(double) - Method in class org.xmlcml.cml.FloatArrayImpl
 
addElement(double) - Method in class jumbo.euclid.RealArray
append element
addElement(FloatVal) - Method in interface org.xmlcml.cml.FloatArray
add the FloatVal.
addElement(FloatVal) - Method in class org.xmlcml.cml.FloatArrayImpl
add the FloatVal.
addElement(int) - Method in interface org.xmlcml.cml.IntegerArray
 
addElement(int) - Method in class org.xmlcml.cml.IntegerArrayImpl
 
addElement(int) - Method in class jumbo.euclid.IntArray
append element
addElement(int) - Method in class jumbo.euclid.IntSet
add integer.
addElement(Int2) - Method in class jumbo.euclid.Int2Vector
 
addElement(IntegerVal) - Method in interface org.xmlcml.cml.IntegerArray
add the IntegerVal.
addElement(IntegerVal) - Method in class org.xmlcml.cml.IntegerArrayImpl
add the IntegerVal.
addElement(IntRange) - Method in class jumbo.euclid.IntRangeVector
 
addElement(Object) - Method in class jumbo.euclid.ObjectArray
append element
addElement(Point3) - Method in class jumbo.euclid.Point3Vector
 
addElement(Real2) - Method in class jumbo.euclid.Real2Vector
 
addElement(RealRange) - Method in class jumbo.euclid.RealRangeVector
 
addElement(String) - Method in interface org.xmlcml.cml.StringArray
 
addElement(String) - Method in class org.xmlcml.cml.StringArrayImpl
 
addElement(String) - Method in class jumbo.euclid.StringSet
adds an element.
addElement(String, Object) - Method in class jumbo.euclid.HashedVector
add Object using key (default case-sensitive).
addElement(StringVal) - Method in interface org.xmlcml.cml.StringArray
add the StringVal.
addElement(StringVal) - Method in class org.xmlcml.cml.StringArrayImpl
add the StringVal.
addEnumerationToVector(Vector, Enumeration) - Static method in class jumbo.xml.util.Util
add the elements of an Enumeration to a Vector.
addFeature(Feature) - Method in interface org.xmlcml.cml.Molecule
Adds a Feature to the Molecule content.
addFeature(Feature) - Method in class org.xmlcml.cml.MoleculeImpl
Adds a Feature to the Molecule content.
addIsotope(int[], double[]) - Method in class org.xmlcml.molutil.ChemicalElement
 
addLigand(Atom) - Method in interface org.xmlcml.cml.Atom
add ligand.
addLigand(Atom) - Method in class org.xmlcml.cml.AtomImpl
add a ligand to atom, but do not create a bond.
addLink(Bond) - Method in interface org.xmlcml.tools.SpanningTree
 
addLink(Bond) - Method in class org.xmlcml.tools.SpanningTreeImpl
add link - check if bond alreay used and create vector if null
addMolecule(Molecule) - Method in interface org.xmlcml.cml.Molecule
Adds a Molecule to the Molecule content.
addMolecule(Molecule) - Method in class org.xmlcml.cml.MoleculeImpl
Adds a Molecule to the Molecule content.
addPolygonOnLine(Real2, Real2, int, int, Real2) - Static method in class jumbo.euclid.Real2
creates a polygon (returns points[]) from two points.
addProduct(Molecule) - Method in interface org.xmlcml.cml.Reaction
 
addProduct(Molecule) - Method in class org.xmlcml.cml.ReactionImpl
 
addRange(IntRange) - Method in class jumbo.euclid.IntSet
add all values from an IntRange
addReactant(Molecule) - Method in interface org.xmlcml.cml.Reaction
 
addReactant(Molecule) - Method in class org.xmlcml.cml.ReactionImpl
 
addRing(Ring) - Method in interface org.xmlcml.tools.RingNucleus
 
addRing(Ring) - Method in class org.xmlcml.tools.RingNucleusImpl
 
addRingNucleus(RingNucleus) - Method in interface org.xmlcml.tools.SubstituentList
 
addRingNucleus(RingNucleus) - Method in class org.xmlcml.tools.SubstituentListImpl
 
addRingOverlap(RingOverlap) - Method in interface org.xmlcml.tools.Ring
 
addRingOverlap(RingOverlap) - Method in class org.xmlcml.tools.RingImpl
stores knowledge of what rings are neighbours
addSequence(Sequence) - Method in interface org.xmlcml.cml.Molecule
Adds a Sequence to the Molecule content.
addSequence(Sequence) - Method in class org.xmlcml.cml.MoleculeImpl
Adds a Sequence to the Molecule content.
addSet(IntSet) - Method in class jumbo.euclid.IntSet
concatenate sets
addSet(StringSet) - Method in class jumbo.euclid.StringSet
catenates one set onto another.
addSubstituent(ChainSet) - Method in interface org.xmlcml.tools.RingNucleus
add substituent(s) in ChainSet
addSubstituent(ChainSet) - Method in class org.xmlcml.tools.RingNucleusImpl
add substituent(s) in ChainSet
addSubstituent(RingNucleus) - Method in interface org.xmlcml.tools.ChainSet
add RingNucleus substituent
addSubstituent(RingNucleus) - Method in class org.xmlcml.tools.ChainSetImpl
add RingNucleus substituent
addSubstituent(RingNucleus) - Method in interface org.xmlcml.tools.RingNucleus
add substituent(s) in RingNucleus
addSubstituent(RingNucleus) - Method in class org.xmlcml.tools.RingNucleusImpl
add substituent(s) in RingNucleus
addToClasspath(String) - Method in class jumbo.xml.util.Util
adds to the classpath and resets the system property
addTorsion(Torsion) - Method in interface org.xmlcml.cml.Molecule
adds the Torsion to the Torsion content of the Molecule.
addTorsion(Torsion) - Method in class org.xmlcml.cml.MoleculeImpl
adds the Torsion to the Torsion content of the Molecule.
addToSystemProperties(String) - Static method in class jumbo.xml.util.Util
load a file/url into the system properties,
addValidity(CMLValidity) - Method in interface org.xmlcml.cml.CMLBase
potentially subclassable to determine whether an element has valid attributes and content.
addValidity(CMLValidity) - Method in class org.xmlcml.cml.CMLBaseImpl
potentially subclassable to determine whether a node is valid.
addWarning(String) - Method in interface org.xmlcml.cml.CMLValidity
 
addWarning(String) - Method in class org.xmlcml.cml.CMLValidityImpl
 
AELFRED - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 
ALPHA - Static variable in interface org.xmlcml.cml.Crystal
 
alternativeStringTokenizer(String, char) - Static method in class jumbo.xml.util.Util
tokenize the string including adjacent delimiters (e.g.
AMP - Static variable in class jumbo.xml.util.Util
 
and(AtomSet) - Method in interface org.xmlcml.tools.AtomSet
combines this with AtomSet to find common elements, else null.
and(AtomSet) - Method in class org.xmlcml.tools.AtomSetImpl
combines this with AtomSet to find common elements, else null.
and(BondSet) - Method in interface org.xmlcml.tools.BondSet
combines this with BondSet to find common elements, else null.
and(BondSet) - Method in class org.xmlcml.tools.BondSetImpl
combines this with BondSet to find common elements, else null.
and(Hashtable, Hashtable) - Static method in class jumbo.xml.util.Util
create Hashtable with elements common to h1 and h2.
and(Ring) - Method in interface org.xmlcml.tools.Ring
create a new ring as the AND of this and ring (i.e.
and(Ring) - Method in class org.xmlcml.tools.RingImpl
create a new ring as the AND of this and ring (i.e.
and(ToolHashSet) - Method in interface org.xmlcml.tools.ToolHashSet
ToolHashSet containing elements common to this and h
and(ToolHashSet) - Method in class org.xmlcml.tools.ToolHashSetImpl
 
and(Vector, Vector) - Static method in class jumbo.xml.util.Util
create Vector with elements common to v1 and v2.
and(XHashtable) - Method in interface jumbo.xml.util.XHashtable
combines this with xHashtable to find common elements, else null.
and(XHashtable) - Method in class jumbo.xml.util.XHashtableImpl
combines this with xHashtable to find common elements, else null.
andIn(HashedVector) - Method in class jumbo.euclid.HashedVector
get elements common to both sets (crude and slow)
andTables(Hashtable, Hashtable) - Static method in class jumbo.xml.util.Util
AND 2 Hashtables - inefficient except for small tables.
andVectors(Vector, Vector) - Static method in class jumbo.xml.util.Util
finds elements common to 2 vectors.
Angle - interface org.xmlcml.cml.Angle.
 
Angle - class jumbo.euclid.Angle.
Angle - angle object
ANGLE - Static variable in interface org.xmlcml.cml.CMLBase
 
Angle() - Constructor for class jumbo.euclid.Angle
create deafult Angle (0.0)
Angle(Angle) - Constructor for class jumbo.euclid.Angle
copy constructor
Angle(double) - Constructor for class jumbo.euclid.Angle
create an angle IN RADIANS
Angle(double, AngleType) - Constructor for class jumbo.euclid.Angle
construct using degrees or radians
Angle(double, double) - Constructor for class jumbo.euclid.Angle
from X and Y components (uses atan2)
angle(int, int, int) - Method in class jumbo.euclid.Point3Vector
get angle between 3 points
angle(int, int, int) - Method in class jumbo.euclid.Real2Vector
get angle between 3 points
angle(IntSet) - Method in class jumbo.euclid.Point3Vector
get angle between 3 points
angle(IntSet) - Method in class jumbo.euclid.Real2Vector
get angle between 3 points
AngleImpl - class org.xmlcml.cml.AngleImpl.
 
AngleImpl() - Constructor for class org.xmlcml.cml.AngleImpl
 
AngleImpl(Document) - Constructor for class org.xmlcml.cml.AngleImpl
new Angle in context
AngleImpl(Element) - Constructor for class org.xmlcml.cml.AngleImpl
 
AngleType - class jumbo.euclid.AngleType.
Angle uses several switches to control its output and these are provided by this class
AngleType(int) - Constructor for class jumbo.euclid.AngleType
 
angleUnits - Variable in class org.xmlcml.cml.AbstractAngleImpl
 
AngleUnits - class org.xmlcml.cml.AngleUnits.
 
AngleUnits(String) - Constructor for class org.xmlcml.cml.AngleUnits
 
angleVector - Variable in class org.xmlcml.cml.MoleculeImpl
 
APOS - Static variable in class jumbo.xml.util.Util
 
appendColumnData(IntArray) - Method in class jumbo.euclid.IntMatrix
append data to matrix columnwise
appendColumnData(IntMatrix) - Method in class jumbo.euclid.IntMatrix
append data to matrix columnwise
appendColumnData(RealArray) - Method in class jumbo.euclid.RealMatrix
append data to matrix columnwise
appendColumnData(RealMatrix) - Method in class jumbo.euclid.RealMatrix
append data to matrix columnwise
appendRowData(IntArray) - Method in class jumbo.euclid.IntMatrix
append data to matrix rowwise
appendRowData(IntMatrix) - Method in class jumbo.euclid.IntMatrix
append data to matrix rowwise
appendRowData(RealArray) - Method in class jumbo.euclid.RealMatrix
append data to matrix rowwise
appendRowData(RealMatrix) - Method in class jumbo.euclid.RealMatrix
append data to matrix rowwise
appendTo(Node) - Method in interface uk.co.demon.ursus.dom.PMRElement
append to a parent node.
appendTo(Node) - Method in class uk.co.demon.ursus.dom.PMRElementImpl
appends this node to a parent.
applyFilter(IntArray) - Method in class jumbo.euclid.IntArray
apply filter (i.e.
applyFilter(RealArray) - Method in class jumbo.euclid.RealArray
apply filter (i.e.
AROMATIC - Static variable in interface org.xmlcml.cml.AbstractBond
aromatic bond
AROMATICITY - Static variable in interface org.xmlcml.cml.ConventionCriteria
 
ArrayDelegate - class org.xmlcml.cml.ArrayDelegate.
a delegate class to manage splitting of arrays, etc.
ArrayDelegate() - Constructor for class org.xmlcml.cml.ArrayDelegate
 
ArrayTooSmallException - exception jumbo.euclid.ArrayTooSmallException.
Array does not contain enough elems for algorithm (e.g.
ArrayTooSmallException() - Constructor for class jumbo.euclid.ArrayTooSmallException
 
ArrayTooSmallException(String) - Constructor for class jumbo.euclid.ArrayTooSmallException
 
Atom - interface org.xmlcml.cml.Atom.
 
ATOM - Static variable in interface org.xmlcml.cml.CMLBase
 
ATOM_BUILTIN_COUNT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_FLOATVAL_COUNT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_FLOATVAL_END - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_FLOATVAL_START - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_ID - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_INTEGERVAL_COUNT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_INTEGERVAL_END - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_INTEGERVAL_START - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_PARITY_FLOAT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_PARITY_INT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_STRINGVAL_COUNT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_STRINGVAL_END - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ATOM_STRINGVAL_START - Static variable in interface org.xmlcml.cml.AbstractAtom
 
atom1 - Variable in class org.xmlcml.tools.RingOverlapImpl
bridgehead atoms
atom2 - Variable in class org.xmlcml.tools.RingOverlapImpl
 
atomArray - Variable in class org.xmlcml.cml.MoleculeImpl
 
AtomArray - interface org.xmlcml.cml.AtomArray.
 
ATOMARRAY - Static variable in interface org.xmlcml.cml.CMLBase
 
AtomArrayImpl - class org.xmlcml.cml.AtomArrayImpl.
 
AtomArrayImpl() - Constructor for class org.xmlcml.cml.AtomArrayImpl
 
AtomArrayImpl(Document) - Constructor for class org.xmlcml.cml.AtomArrayImpl
new AtomArray in context
AtomArrayImpl(Element) - Constructor for class org.xmlcml.cml.AtomArrayImpl
 
atomHash(Atom, Atom) - Static method in class org.xmlcml.cml.BondImpl
 
atomIdTable - Variable in class org.xmlcml.cml.MoleculeImpl
 
AtomImpl - class org.xmlcml.cml.AtomImpl.
 
AtomImpl() - Constructor for class org.xmlcml.cml.AtomImpl
 
AtomImpl(Document) - Constructor for class org.xmlcml.cml.AtomImpl
 
AtomImpl(Element) - Constructor for class org.xmlcml.cml.AtomImpl
 
AtomImpl(Molecule, String) - Constructor for class org.xmlcml.cml.AtomImpl
create in molecule context - must have unique id.
atomList - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
general tools for input and output
atomParent - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
 
atomParity - Variable in class org.xmlcml.cml.AtomImpl
 
ATOMREF - Static variable in interface org.xmlcml.cml.AbstractBond
 
atomRefs - Variable in class org.xmlcml.cml.BondImpl
 
ATOMREFS - Static variable in interface org.xmlcml.cml.AbstractBond
 
atomRefVector - Variable in class org.xmlcml.cml.AbstractBondImpl
 
atomRefVector - Variable in class org.xmlcml.cml.AtomImpl
Vector of Objects than refer to this Atom
atomSet - Variable in class org.xmlcml.tools.BondSetImpl
 
atomSet - Variable in class org.xmlcml.tools.RingOverlapImpl
atoms in the overlap
AtomSet - interface org.xmlcml.tools.AtomSet.
a set of atoms.
AtomSetImpl - class org.xmlcml.tools.AtomSetImpl.
a set of atoms.
AtomSetImpl() - Constructor for class org.xmlcml.tools.AtomSetImpl
 
atomVector - Variable in class org.xmlcml.cml.AbstractAtomRefImpl
 
atomVector - Variable in class org.xmlcml.cml.MoleculeImpl
 
ATSIGN - Static variable in class jumbo.xml.util.Util
 
ATTRIBUTES - Static variable in interface uk.co.demon.ursus.dom.PMRNode
the attributes as a table
attributeString(AttributeList) - Static method in class uk.co.demon.ursus.dom.SAXAdapter
 

B

BACKSLASH - Static variable in class jumbo.xml.util.Util
 
BadArgumentException - exception jumbo.euclid.BadArgumentException.
Invalid arguments
BadArgumentException() - Constructor for class jumbo.euclid.BadArgumentException
 
BadArgumentException(String) - Constructor for class jumbo.euclid.BadArgumentException
 
BadSubscriptException - exception jumbo.euclid.BadSubscriptException.
checks array indices in (say) RealArray
BadSubscriptException() - Constructor for class jumbo.euclid.BadSubscriptException
 
BadSubscriptException(String) - Constructor for class jumbo.euclid.BadSubscriptException
 
BCELL - Static variable in interface org.xmlcml.cml.Crystal
 
bestPlane() - Method in class jumbo.euclid.Point3Vector
get best plane
BETA - Static variable in interface org.xmlcml.cml.Crystal
 
Bond - interface org.xmlcml.cml.Bond.
 
BOND - Static variable in interface org.xmlcml.cml.CMLBase
 
BOND_BUILTIN_COUNT - Static variable in interface org.xmlcml.cml.AbstractBond
 
BOND_FLOATVAL_COUNT - Static variable in interface org.xmlcml.cml.AbstractBond
 
BOND_FLOATVAL_END - Static variable in interface org.xmlcml.cml.AbstractBond
 
BOND_FLOATVAL_START - Static variable in interface org.xmlcml.cml.AbstractBond
 
BOND_INTEGERVAL_COUNT - Static variable in interface org.xmlcml.cml.AbstractBond
 
BOND_INTEGERVAL_END - Static variable in interface org.xmlcml.cml.AbstractBond
 
BOND_INTEGERVAL_START - Static variable in interface org.xmlcml.cml.AbstractBond
 
BOND_STRINGVAL_COUNT - Static variable in interface org.xmlcml.cml.AbstractBond
 
BOND_STRINGVAL_END - Static variable in interface org.xmlcml.cml.AbstractBond
 
BOND_STRINGVAL_START - Static variable in interface org.xmlcml.cml.AbstractBond
 
bondArray - Variable in class org.xmlcml.cml.MoleculeImpl
 
BondArray - interface org.xmlcml.cml.BondArray.
 
BONDARRAY - Static variable in interface org.xmlcml.cml.CMLBase
 
BondArrayImpl - class org.xmlcml.cml.BondArrayImpl.
 
BondArrayImpl() - Constructor for class org.xmlcml.cml.BondArrayImpl
 
BondArrayImpl(Document) - Constructor for class org.xmlcml.cml.BondArrayImpl
new BondArray in context
BondArrayImpl(Element) - Constructor for class org.xmlcml.cml.BondArrayImpl
 
bondHashTable - Variable in class org.xmlcml.cml.MoleculeImpl
 
bondIdTable - Variable in class org.xmlcml.cml.MoleculeImpl
 
BondImpl - class org.xmlcml.cml.BondImpl.
 
BondImpl() - Constructor for class org.xmlcml.cml.BondImpl
 
BondImpl(Atom, Atom) - Constructor for class org.xmlcml.cml.BondImpl
new Bond formed from atoms, in context but no other info Atoms must belong to the same non-null Molecule
BondImpl(Document) - Constructor for class org.xmlcml.cml.BondImpl
new BondImpl in context
BondImpl(Element) - Constructor for class org.xmlcml.cml.BondImpl
 
bondList - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
 
bondOrders - Static variable in interface org.xmlcml.cml.AbstractBond
 
bondParent - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
 
bondSet - Variable in class org.xmlcml.tools.RingOverlapImpl
bonds in the overlap
BondSet - interface org.xmlcml.tools.BondSet.
a set of bonds, which also counts the atoms
BondSetImpl - class org.xmlcml.tools.BondSetImpl.
a set of bonds, which also counts the atoms
BondSetImpl() - Constructor for class org.xmlcml.tools.BondSetImpl
 
bondTypeStrings - Static variable in interface org.xmlcml.cml.AbstractBond
 
bondVector - Variable in class org.xmlcml.cml.MoleculeImpl
 
BR_LOOKAHEAD - Static variable in class jumbo.xml.util.Util
lookahead for bufferedReader
bReader - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
most input requires a BufferedReader
BRIDGED - Static variable in interface org.xmlcml.tools.RingOverlap
rings are fused (two or more bonds in common)
BRIDGED - Static variable in class org.xmlcml.tools.RingOverlapImpl
rings are fused (two or more bonds in common)
bug(Exception) - Static method in class jumbo.xml.util.Util
 
bug(String) - Static method in class jumbo.xml.util.Util
record that we have hit a program bug!!!
builtin - Variable in class org.xmlcml.cml.AbstractStringValImpl
 
BUILTIN - Static variable in interface org.xmlcml.cml.CMLBase
"builtin" attribute name
builtinFloatArrays - Variable in class org.xmlcml.cml.AtomArrayImpl
 
builtinFloatArrays - Variable in class org.xmlcml.cml.BondArrayImpl
 
builtinFloatValNames - Static variable in class org.xmlcml.cml.CrystalImpl
 
builtinIntegerArrays - Variable in class org.xmlcml.cml.AtomArrayImpl
 
builtinIntegerArrays - Variable in class org.xmlcml.cml.BondArrayImpl
 
builtinIntegerValNames - Static variable in class org.xmlcml.cml.CrystalImpl
 
builtinNames - Static variable in class org.xmlcml.cml.CrystalImpl
 
builtinStringArrays - Variable in class org.xmlcml.cml.AtomArrayImpl
 
builtinStringArrays - Variable in class org.xmlcml.cml.BondArrayImpl
 
builtinStringValNames - Static variable in class org.xmlcml.cml.CrystalImpl
 
builtinValues - Variable in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 

C

calculateCoordinates() - Method in interface org.xmlcml.tools.RingNucleus
calculate coordinates for nucleus de-novo
calculateCoordinates() - Method in class org.xmlcml.tools.RingNucleusImpl
calculate coordinates for nucleus de-novo
calculateCoordinates(Real2) - Method in interface org.xmlcml.tools.Ring
calculate coordinates of a ring through two points.
calculateCoordinates(Real2) - Method in class org.xmlcml.tools.RingImpl
calculate coordinates of a ring through two points.
calculateCoordinates(Ring) - Method in interface org.xmlcml.tools.Ring
stores knowledge of what rings are neighbours ?????
calculateCoordinates(Ring) - Method in class org.xmlcml.tools.RingImpl
 
calculateTopology() - Method in interface org.xmlcml.tools.SpanningTree
 
calculateTopology() - Method in class org.xmlcml.tools.SpanningTreeImpl
get all cyclic bonds after spanning tree is created.
CANNOT - Static variable in interface org.xmlcml.cml.ConventionCriteria
 
capitalise(String) - Static method in class jumbo.xml.util.Util
capitalise a String (whatever the starting case)
CARET - Static variable in class jumbo.xml.util.Util
 
CASE - Static variable in class jumbo.xml.util.Util
case sensitivity flags - used throughout jumbo.xml
CCELL - Static variable in interface org.xmlcml.cml.Crystal
 
ChainSet - interface org.xmlcml.tools.ChainSet.
 
ChainSetImpl - class org.xmlcml.tools.ChainSetImpl.
 
ChainSetImpl() - Constructor for class org.xmlcml.tools.ChainSetImpl
 
ChainSetImpl(SpanningTree, BondSet) - Constructor for class org.xmlcml.tools.ChainSetImpl
create a Chain from a BondSet within a SpanningTree.
chainTable - Variable in class org.xmlcml.tools.SubstituentListImpl
 
characters(char[], int, int) - Method in class org.xmlcml.cml.CMLDOMSAXBuilderImpl
 
characters(char[], int, int) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive notification of character data inside an element.
characters(char[], int, int) - Method in class uk.co.demon.ursus.dom.SAXDOMBuilder
 
checkBuiltins(String[], String[], String[]) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
 
checkBuiltins(String[], String[], String[]) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
checkMatrix() - Method in class jumbo.euclid.Transform2
get new matrix type
checkMatrix() - Method in class jumbo.euclid.Transform3
get new matrix type
ChemicalElement - class org.xmlcml.molutil.ChemicalElement.
supports the elements (e.g.
ChemicalElement(String, int, double) - Constructor for class org.xmlcml.molutil.ChemicalElement
 
Choice2 - class jumbo.xml.util.Choice2.
offers the choice of 0 or 1; useful to restrict argument values (rather like enum).
Choice3 - class jumbo.xml.util.Choice3.
offers the choice of 0, 1 or 2; useful to restrict argument values (rather like enum).
CLASSNAME - Static variable in interface uk.co.demon.ursus.dom.PMRElement
 
CLASSNAME - Static variable in class uk.co.demon.ursus.dom.PMRElementImpl
 
CLASSNAME - Static variable in interface uk.co.demon.ursus.dom.Validity
 
CLASSNAME - Static variable in class uk.co.demon.ursus.dom.ValidityImpl
 
CLASSNAME - Static variable in class uk.co.demon.ursus.dom.AbstractElementImpl
 
clear() - Method in class jumbo.euclid.Int2
set to 0, 0
clear() - Method in class jumbo.euclid.Real2
set to 0, 0
clearArray() - Method in class jumbo.euclid.IntArray
clear all elements of array
clearArray() - Method in class jumbo.euclid.ObjectArray
clear all elements of array to null (or 0 or 0.0)
clearArray() - Method in class jumbo.euclid.RealArray
clear all elements of array
clearCoordinate2() - Method in interface org.xmlcml.tools.AtomSet
clear atom coordinate table
clearCoordinate2() - Method in class org.xmlcml.tools.AtomSetImpl
clear atom coordinate table
clearMatrix() - Method in class jumbo.euclid.IntMatrix
clear matrix
clearMatrix() - Method in class jumbo.euclid.RealMatrix
clear matrix
clone() - Method in class jumbo.euclid.IntArray
clones another IntArray
clone() - Method in class jumbo.euclid.RealArray
clones another RealArray
clone() - Method in interface jumbo.xml.util.XHashtable
shallow clone - return new XHashtable which contains references to objects
clone() - Method in class jumbo.xml.util.XHashtableImpl
shallow clone a new XHashtable which contains references to objects
clone() - Method in interface org.xmlcml.tools.ToolHashSet
shallow copy
clone() - Method in class org.xmlcml.tools.ToolHashSetImpl
shallow clone; errors return null
clone(Angle) - Method in class jumbo.euclid.Angle
 
clone(double[]) - Method in class jumbo.euclid.Point3
overloaded assignment from a double[] (or a RealArray)
clone(IntMatrix) - Method in class jumbo.euclid.IntMatrix
 
clone(Plane3) - Method in class jumbo.euclid.Plane3
 
clone(Point3) - Method in class jumbo.euclid.Point3
 
clone(Point3) - Method in class jumbo.euclid.Vector3
from Point3
clone(RealMatrix) - Method in class jumbo.euclid.RealMatrix
 
clone(Transform2) - Method in class jumbo.euclid.Transform2
clone
clone(Transform3) - Method in class jumbo.euclid.Transform3
clone
clone(Vector3) - Method in class jumbo.euclid.Point3
from Vector3
clone(Vector3) - Method in class jumbo.euclid.Vector3
 
CML - interface org.xmlcml.cml.CML.
do we need this?
CML - Static variable in interface org.xmlcml.cml.CMLBase
 
CMLBase - interface org.xmlcml.cml.CMLBase.
The base class for all elementObjects mentioned in the CML DTD.
CMLBaseImpl - class org.xmlcml.cml.CMLBaseImpl.
The base class for all elementObjects mentioned in the CML DTD.
CMLBaseImpl() - Constructor for class org.xmlcml.cml.CMLBaseImpl
create a Node WITHOUT tagName OR document.
CMLBaseImpl(Element) - Constructor for class org.xmlcml.cml.CMLBaseImpl
used when analysing a DOM
CMLBaseImpl(String, Document) - Constructor for class org.xmlcml.cml.CMLBaseImpl
used when creating new nodes in a DOM
CMLBaseImpl(String, Document, String, String, String, String) - Constructor for class org.xmlcml.cml.CMLBaseImpl
 
cmlBondOrder(int) - Static method in class org.xmlcml.noncml.JMEImpl
translates jme bond orders into JUMBO-MOL orders
cmlBondOrder(int) - Static method in class org.xmlcml.noncml.MDLMolImpl
translates MDL bond orders into JUMBO-MOL orders
cmlBondOrder(String) - Static method in class org.xmlcml.noncml.SMILESImpl
translates SMILES bond orders into JUMBO-MOL orders
cmlBondStereo(int) - Static method in class org.xmlcml.noncml.JMEImpl
translates jme numbers into JUMBO-MOL codes
cmlDocument - Variable in class org.xmlcml.cml.CMLDOMSAXBuilderImpl
 
CMLDocument - interface org.xmlcml.cml.CMLDocument.
The interface for any CML Document objects
CMLDocumentImpl - class org.xmlcml.cml.CMLDocumentImpl.
The base class for any CML Document objects
CMLDocumentImpl() - Constructor for class org.xmlcml.cml.CMLDocumentImpl
create an Empty Document
CMLDOMSAXBuilder - interface org.xmlcml.cml.CMLDOMSAXBuilder.
Builds a CMLDOM from SAX events
CMLDOMSAXBuilderImpl - class org.xmlcml.cml.CMLDOMSAXBuilderImpl.
Builds a CMLDOM from SAX events
CMLDOMSAXBuilderImpl() - Constructor for class org.xmlcml.cml.CMLDOMSAXBuilderImpl
default parser used
CMLDOMSAXBuilderImpl(Parser) - Constructor for class org.xmlcml.cml.CMLDOMSAXBuilderImpl
specific parser used
CMLDOMSAXBuilderImpl(String) - Constructor for class org.xmlcml.cml.CMLDOMSAXBuilderImpl
specific parser name used
CMLException - exception org.xmlcml.cml.CMLException.
 
CMLException() - Constructor for class org.xmlcml.cml.CMLException
 
CMLException(String) - Constructor for class org.xmlcml.cml.CMLException
 
CMLImpl - class org.xmlcml.cml.CMLImpl.
do we need this class?
CMLImpl() - Constructor for class org.xmlcml.cml.CMLImpl
 
CMLImpl(Document) - Constructor for class org.xmlcml.cml.CMLImpl
new CML in context
CMLImpl(Element) - Constructor for class org.xmlcml.cml.CMLImpl
 
cmlStereoBond(int) - Static method in class org.xmlcml.noncml.MDLMolImpl
translates MDL numbers into JUMBO-MOL codes
CMLValidity - interface org.xmlcml.cml.CMLValidity.
Allows node to carry its validity.
CMLValidityImpl - class org.xmlcml.cml.CMLValidityImpl.
Allows node to carry its validity.
CMLValidityImpl() - Constructor for class org.xmlcml.cml.CMLValidityImpl
 
CMLValidityImpl(String) - Constructor for class org.xmlcml.cml.CMLValidityImpl
 
COLON - Static variable in class jumbo.xml.util.Util
 
cols - Variable in class jumbo.euclid.IntMatrix
number of columns
cols - Variable in class jumbo.euclid.RealMatrix
number of columns
columnwiseDivide(RealArray) - Method in class jumbo.euclid.RealMatrix
divide each column of a matrix by a vector of scalars (i.e.
COMMA - Static variable in class jumbo.xml.util.Util
 
compareTo(Sortable) - Method in interface jumbo.euclid.Sortable
 
compareTo(Sortable) - Method in class jumbo.euclid.SortableString
 
compareTo(SortableObject) - Method in class jumbo.euclid.SortableObject
 
Complex - class jumbo.euclid.Complex.
Complex - complex number - derived from Real2
Complex() - Constructor for class jumbo.euclid.Complex
 
Complex(Complex) - Constructor for class jumbo.euclid.Complex
 
Complex(double) - Constructor for class jumbo.euclid.Complex
real component only
Complex(double, Angle) - Constructor for class jumbo.euclid.Complex
in polar coords
Complex(double, double) - Constructor for class jumbo.euclid.Complex
from components
Complex(Polar) - Constructor for class jumbo.euclid.Complex
 
Complex(Real2) - Constructor for class jumbo.euclid.Complex
from base class
concatenate(EuclidVector) - Method in class jumbo.euclid.EuclidVector
concatenate two vectors (must be of same type - hence protected)
concatenate(Transform2) - Method in class jumbo.euclid.Transform2
concatenate
concatenate(Transform3) - Method in class jumbo.euclid.Transform3
concatenate
CONSTRAINT_COUNT - Static variable in interface org.xmlcml.cml.ConventionCriteria
 
constraintNames - Static variable in interface org.xmlcml.cml.ConventionCriteria
 
contains(Atom) - Method in interface org.xmlcml.cml.Bond
true if bond contains this atom
contains(Atom) - Method in class org.xmlcml.cml.BondImpl
true if bond contains this atom
contains(double) - Method in class jumbo.euclid.RealRange
synonym for includes()
contains(int) - Method in class jumbo.euclid.IntRange
synonym for includes()
contains(int) - Method in class jumbo.euclid.IntSet
 
contains(Object) - Method in interface org.xmlcml.tools.ToolHashSet
does this contain an element?
contains(String) - Method in class jumbo.euclid.StringSet
does Set contain String? (according to case-sensitivity
containsAtom(Atom) - Method in interface org.xmlcml.tools.BondSet
does this BondSet contain a given atom?
containsAtom(Atom) - Method in class org.xmlcml.tools.BondSetImpl
does this BondSet contain a given atom?
containsKey(Object) - Method in interface jumbo.xml.util.XHashtable
from Hashtable
containsObjectWithKey(String) - Method in class jumbo.euclid.HashedVector
has key been used to store an object?
containsPoint(Point3) - Method in class jumbo.euclid.Line3
is a point on a line?
containsPoint(Point3) - Method in class jumbo.euclid.Plane3
is a point on a plane?
CONTENT - Static variable in interface uk.co.demon.ursus.dom.PMRNode
heuristically rendered content; may be subclassed
contract() - Method in class jumbo.euclid.StringSet
contract buffer to exact number of elements
Convention - class org.xmlcml.cml.Convention.
 
CONVENTION - Static variable in interface org.xmlcml.cml.HasConvention
"convention" attribute name
Convention() - Constructor for class org.xmlcml.cml.Convention
 
ConventionCriteria - interface org.xmlcml.cml.ConventionCriteria.
 
conventionName - Variable in class org.xmlcml.cml.CMLBaseImpl
 
conventionName - Variable in class org.xmlcml.cml.Coordinate3
 
conventionTable - Static variable in class org.xmlcml.cml.CMLBaseImpl
 
convertFormat(Vector, String) - Static method in class jumbo.xml.util.Util
converts character format within a Vector of Strings.
convertToSubclass(Element) - Static method in class org.xmlcml.cml.CMLBaseImpl
recursively process all nodes.
Coordinate2 - class org.xmlcml.cml.Coordinate2.
still under development - the DTD requires several attributes but it seems like overkill to start with
Coordinate2(double, double) - Constructor for class org.xmlcml.cml.Coordinate2
 
coordinate2Map - Variable in class org.xmlcml.tools.AtomSetImpl
 
Coordinate3 - class org.xmlcml.cml.Coordinate3.
still under development - the DTD requires several attributes but it seems like overkill to start with
Coordinate3(double, double, double) - Constructor for class org.xmlcml.cml.Coordinate3
 
copy(double[]) - Static method in class jumbo.euclid.RealArray
copy a double[] into a new one
copy(int[]) - Static method in class jumbo.euclid.IntArray
copy a int[] into a new one
copy(Object[]) - Static method in class jumbo.euclid.ObjectArray
copy a Object[] into a new one
copyAttributesFrom(Element, Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
 
copyFile(File, File) - Static method in class jumbo.xml.util.Util
copy one file to another (I suspect there is a better way
copyLowerToUpper() - Method in class jumbo.euclid.IntSquareMatrix
copy lower triangle into upper triangle (i.e.
copyLowerToUpper() - Method in class jumbo.euclid.RealSquareMatrix
copy lower triangle into upper triangle (i.e.
copyNode(Document, Node, boolean) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
make a copy of the Node in a different document context.
copyUpperToLower() - Method in class jumbo.euclid.IntSquareMatrix
copy upper triangle into lower triangle (i.e.
copyUpperToLower() - Method in class jumbo.euclid.RealSquareMatrix
copy upper triangle into lower triangle (i.e.
cos() - Method in class jumbo.euclid.Angle
trigonometric functions
cos(String) - Static method in class jumbo.xml.util.Util
 
count - Variable in class org.xmlcml.cml.AbstractAtomImpl
 
count - Variable in class org.xmlcml.cml.ElectronImpl
 
count - Variable in class org.xmlcml.cml.FormulaImpl
 
count - Variable in class org.xmlcml.cml.MoleculeImpl
 
COUNT - Static variable in interface org.xmlcml.cml.HasCount
"count" attribute
createArrayElement(Document) - Method in interface org.xmlcml.cml.AtomArray
 
createArrayElement(Document) - Method in class org.xmlcml.cml.AtomArrayImpl
 
createArrayElement(Document) - Method in interface org.xmlcml.cml.BondArray
 
createArrayElement(Document) - Method in class org.xmlcml.cml.BondArrayImpl
 
createArrayElement(Document) - Method in interface org.xmlcml.cml.HasBuiltinArrayNames
 
createBondToLigand(Atom) - Method in interface org.xmlcml.cml.Atom
add ligand.
createBondToLigand(Atom) - Method in class org.xmlcml.cml.AtomImpl
add ligand.
createCMLDocument(String) - Static method in class org.xmlcml.cml.CMLDocumentImpl
create from file and subclass using SAX; the default CMLDOMSAXBuilder determines the subclassing
createCMLDocument(String, CMLDOMSAXBuilder) - Static method in class org.xmlcml.cml.CMLDocumentImpl
create from file and subclass using SAX; the CMLDOMSAXBuilder determines the subclassing
createCMLElement(String, String) - Method in class org.xmlcml.noncml.NonCMLDocumentImpl
 
createCommaSeparatedStrings(Vector) - Static method in class jumbo.xml.util.Util
 
createDocument(InputSource) - Static method in class uk.co.demon.ursus.dom.PMRDocumentImpl
 
createDocument(InputSource) - Static method in class uk.co.demon.ursus.dom.AbstractDocumentImpl
 
createDocument(String) - Static method in class uk.co.demon.ursus.dom.PMRDocumentImpl
 
createDocument(String) - Static method in class uk.co.demon.ursus.dom.AbstractDocumentImpl
 
createMoleculeElement(String, String) - Method in class org.xmlcml.noncml.NonCMLDocumentImpl
 
createNewFile(String) - Static method in class jumbo.xml.util.Util
create new file, including making directory if required This seems to be a mess - f.createNewFile() doesn't seem to work A directory should have a trailing file.separator
createStringVector(StringVal) - Static method in class org.xmlcml.cml.StringArrayImpl
 
CRITERIA_COUNT - Static variable in interface org.xmlcml.cml.ConventionCriteria
 
criteriaNames - Static variable in interface org.xmlcml.cml.ConventionCriteria
 
cross(Vector3) - Method in class jumbo.euclid.Vector3
Vector product
crystal - Variable in class org.xmlcml.cml.MoleculeImpl
 
Crystal - interface org.xmlcml.cml.Crystal.
 
CRYSTAL - Static variable in interface org.xmlcml.cml.CMLBase
 
CRYSTAL_BUILTIN_COUNT - Static variable in interface org.xmlcml.cml.Crystal
 
CRYSTAL_FLOATVAL_COUNT - Static variable in interface org.xmlcml.cml.Crystal
 
CRYSTAL_FLOATVAL_END - Static variable in interface org.xmlcml.cml.Crystal
 
CRYSTAL_FLOATVAL_START - Static variable in interface org.xmlcml.cml.Crystal
 
CRYSTAL_INTEGERVAL_COUNT - Static variable in interface org.xmlcml.cml.Crystal
 
CRYSTAL_INTEGERVAL_END - Static variable in interface org.xmlcml.cml.Crystal
 
CRYSTAL_INTEGERVAL_START - Static variable in interface org.xmlcml.cml.Crystal
 
CRYSTAL_STRINGVAL_COUNT - Static variable in interface org.xmlcml.cml.Crystal
 
CRYSTAL_STRINGVAL_END - Static variable in interface org.xmlcml.cml.Crystal
 
CRYSTAL_STRINGVAL_START - Static variable in interface org.xmlcml.cml.Crystal
 
CrystalImpl - class org.xmlcml.cml.CrystalImpl.
 
CrystalImpl() - Constructor for class org.xmlcml.cml.CrystalImpl
 
CrystalImpl(Document) - Constructor for class org.xmlcml.cml.CrystalImpl
new Crystal in context
CrystalImpl(Element) - Constructor for class org.xmlcml.cml.CrystalImpl
 
cumulativeSum() - Method in class jumbo.euclid.IntArray
cumulative sum of array (new RA contains
elem[i] = sum(k = 0 to i) f[k]
cumulativeSum() - Method in class jumbo.euclid.RealArray
cumulative sum of array (new RA contains
elem[i] = sum(k = 0 to i) f[k]
currentNode - Variable in class uk.co.demon.ursus.dom.SAXDOMBuilder
 
cyclicAtomVector - Variable in class org.xmlcml.tools.RingImpl
ordered list of atoms - each element is an Atom as we traverse the Ring cyclicly.
cyclicBondVector - Variable in class org.xmlcml.tools.RingImpl
ordered list of bonds - each element is a Bond and links to the next bond in the ring cyclicly
CyclicVector - class jumbo.xml.util.CyclicVector.
a 'cyclic vector', i.e.
CyclicVector() - Constructor for class jumbo.xml.util.CyclicVector
create with an empty vector.
CyclicVector(Vector) - Constructor for class jumbo.xml.util.CyclicVector
create from a (non-empty) vector.

D

DATA_HEADER - Static variable in interface org.xmlcml.noncml.SDF
 
dataType - Variable in class org.xmlcml.cml.AbstractStringValImpl
 
debug() - Method in class jumbo.euclid.IntSet
 
debug() - Method in class jumbo.euclid.StringSet
 
debug() - Method in interface org.xmlcml.tools.ToolHashSet
 
debug() - Method in class org.xmlcml.tools.ToolHashSetImpl
 
debug(Node) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
 
debug(Writer) - Method in class org.xmlcml.cml.AtomImpl
output debug info to Writer
debug(Writer) - Method in class org.xmlcml.cml.BondImpl
output debug info to Writer
debug(Writer) - Method in interface org.xmlcml.cml.CMLBase
output debug info to Writer and return String equivalent (e.g.
debug(Writer) - Method in class org.xmlcml.cml.CMLBaseImpl
output debug info to Writer and return String equivalent (e.g.
debug(Writer) - Method in interface org.xmlcml.cml.CMLDocument
output debug info to Writer and return String equivalent (e.g.
debug(Writer) - Method in class org.xmlcml.cml.CMLDocumentImpl
output debug info to Writer and return String equivalent (e.g.
debug(Writer) - Method in class org.xmlcml.cml.MoleculeImpl
output debug info to Writer
DECREASE - Static variable in interface org.xmlcml.cml.AbstractBond
 
DEFAULT_PARSER_NAME - Static variable in class uk.co.demon.ursus.dom.AbstractDocumentImpl
 
DefaultCMLDOMSAXBuilder - class org.xmlcml.cml.DefaultCMLDOMSAXBuilder.
Builds a CMLDOM from SAX events
DefaultCMLDOMSAXBuilder() - Constructor for class org.xmlcml.cml.DefaultCMLDOMSAXBuilder
 
DefaultCMLDOMSAXBuilder(Parser) - Constructor for class org.xmlcml.cml.DefaultCMLDOMSAXBuilder
 
DefaultCMLDOMSAXBuilder(String) - Constructor for class org.xmlcml.cml.DefaultCMLDOMSAXBuilder
 
defaultParserClassName - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 
defaultParserType - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 
DEFAULTXY2LENGTH - Static variable in interface org.xmlcml.cml.AbstractBond
default screen bondlength
DEFAULTXYZ3LENGTH - Static variable in interface org.xmlcml.cml.AbstractBond
default 3d bondlength
DEGREES - Static variable in class org.xmlcml.cml.AngleUnits
 
DEGREES - Static variable in class jumbo.euclid.Angle
 
DEGREES_IN_RADIAN - Static variable in class jumbo.euclid.Angle
 
DELETE - Static variable in interface org.xmlcml.cml.AbstractBond
 
delete(Atom) - Method in interface org.xmlcml.cml.AtomArray
 
delete(Atom) - Method in class org.xmlcml.cml.AtomArrayImpl
 
delete(Bond) - Method in interface org.xmlcml.cml.BondArray
 
delete(Bond) - Method in class org.xmlcml.cml.BondArrayImpl
 
deleteAngle(Angle) - Method in interface org.xmlcml.cml.Molecule
deletes the Angle from the Angle content of the Molecule.
deleteAngle(Angle) - Method in class org.xmlcml.cml.MoleculeImpl
deletes the Angle from the Angle content of the Molecule.
deleteAtom(Atom) - Method in interface org.xmlcml.cml.Molecule
deletes the Atom from the Atom content of the Molecule.
deleteAtom(Atom) - Method in class org.xmlcml.cml.MoleculeImpl
deletes the Atom from the Atom content of the Molecule.
deleteAtom(Element) - Method in class org.xmlcml.cml.MoleculeImpl
deletes Atoms, bonds, etc.
deleteAtomRef(Atom) - Method in interface org.xmlcml.cml.AbstractAtomRef
 
deleteAtomRef(Atom) - Method in class org.xmlcml.cml.AbstractAtomRefImpl
 
deleteAtomRef(Atom) - Method in interface org.xmlcml.cml.AbstractBond
 
deleteAtomRef(Atom) - Method in class org.xmlcml.cml.AbstractBondImpl
 
deleteAtomRef(Atom) - Method in interface org.xmlcml.cml.HasAtomRefs
 
deleteAtomWithId(String) - Method in class org.xmlcml.cml.MoleculeImpl
as above but finds atom by id
deleteBond(Bond) - Method in interface org.xmlcml.cml.Molecule
deletes the Bond from the Bond content of the Molecule.
deleteBond(Bond) - Method in class org.xmlcml.cml.MoleculeImpl
deletes the Bond from the Bond content of the Molecule.
deleteColumn(int) - Method in class jumbo.euclid.IntMatrix
delete column from matrix and close up
deleteColumn(int) - Method in class jumbo.euclid.RealMatrix
delete column from matrix and close up
deleteColumns(int, int) - Method in class jumbo.euclid.IntMatrix
delete 2 or more adjacent columns (inclusive) from matrix and close up
deleteColumns(int, int) - Method in class jumbo.euclid.RealMatrix
delete 2 or more adjacent columns (inclusive) from matrix and close up
deleteElectron(Electron) - Method in interface org.xmlcml.cml.Molecule
Deletes a Electron from the Molecule content.
deleteElectron(Electron) - Method in class org.xmlcml.cml.MoleculeImpl
Deletes a Electron from the Molecule content.
deleteElement(int) - Method in class jumbo.euclid.IntArray
delete element and close up; if outside range, take no action
deleteElement(int) - Method in class jumbo.euclid.ObjectArray
delete element and close up; if outside range, take no action
deleteElement(int) - Method in class jumbo.euclid.RealArray
delete element and close up; if outside range, take no action
deleteElement(String) - Method in interface org.xmlcml.cml.StringArray
 
deleteElement(String) - Method in class org.xmlcml.cml.StringArrayImpl
 
deleteElements(double[], int, int) - Static method in class jumbo.euclid.RealArray
delete elements (lo - > hi inclusive) in a float[] and close up; if hi >= float.length hi is reset to float.length-1.
deleteElements(int[], int, int) - Static method in class jumbo.euclid.IntArray
delete elements (lo - > hi inclusive) in a float[] and close up; if hi >= float.length hi is reset to float.length-1.
deleteElements(int, int) - Method in class jumbo.euclid.IntArray
delete elements and close up; if outside range take no action
deleteElements(int, int) - Method in class jumbo.euclid.ObjectArray
delete elements and close up; if outside range take no action
deleteElements(int, int) - Method in class jumbo.euclid.RealArray
delete elements and close up; if outside range take no action
deleteFeature(Feature) - Method in interface org.xmlcml.cml.Molecule
Deletes a Feature from the Molecule content.
deleteFeature(Feature) - Method in class org.xmlcml.cml.MoleculeImpl
Deletes a Feature from the Molecule content.
deleteFile(File, boolean) - Static method in class jumbo.xml.util.Util
delete a file.
deleteHasAtomRefs(HasAtomRefs) - Method in class org.xmlcml.cml.MoleculeImpl
 
deleteMolecule(Molecule) - Method in interface org.xmlcml.cml.Molecule
Deletes a Molecule from the Molecule content.
deleteMolecule(Molecule) - Method in class org.xmlcml.cml.MoleculeImpl
Deletes a Molecule from the Molecule content.
deleteNonBuiltinArray(String) - Method in interface org.xmlcml.cml.AtomArray
 
deleteNonBuiltinArray(String) - Method in class org.xmlcml.cml.AtomArrayImpl
 
deleteNonBuiltinArray(String) - Method in interface org.xmlcml.cml.BondArray
 
deleteNonBuiltinArray(String) - Method in class org.xmlcml.cml.BondArrayImpl
 
deleteNonBuiltinArray(String) - Method in interface org.xmlcml.cml.HasBuiltinArrayNames
 
deleteNonBuiltinVal(String) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
 
deleteNonBuiltinVal(String) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
deleteNonBuiltinVal(String) - Method in interface org.xmlcml.cml.HasBuiltinNames
 
deleteProduct(Molecule) - Method in interface org.xmlcml.cml.Reaction
 
deleteProduct(Molecule) - Method in class org.xmlcml.cml.ReactionImpl
 
deleteReactant(Molecule) - Method in interface org.xmlcml.cml.Reaction
 
deleteReactant(Molecule) - Method in class org.xmlcml.cml.ReactionImpl
 
deleteRow(int) - Method in class jumbo.euclid.IntMatrix
delete row from matrix and close up
deleteRow(int) - Method in class jumbo.euclid.RealMatrix
delete row from matrix and close up
deleteRows(int, int) - Method in class jumbo.euclid.IntMatrix
delete 2 or more adjacent rows (inclusive) from matrix and close up; if (high > rows-1 high -> rows-1; or low < 0, low -> 0
deleteRows(int, int) - Method in class jumbo.euclid.RealMatrix
delete 2 or more adjacent rows (inclusive) from matrix and close up; if (high > rows-1 high -> rows-1; or low < 0, low -> 0
deleteSequence(Sequence) - Method in interface org.xmlcml.cml.Molecule
Deletes a Sequence from the Molecule content.
deleteSequence(Sequence) - Method in class org.xmlcml.cml.MoleculeImpl
Deletes a Sequence from the Molecule content.
deleteTorsion(Torsion) - Method in interface org.xmlcml.cml.Molecule
deletes the Torsion from the Torsion content of the Molecule.
deleteTorsion(Torsion) - Method in class org.xmlcml.cml.MoleculeImpl
deletes the Torsion from the Torsion content of the Molecule.
deleteWhitespaceDecsendants(Document) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
recursively removes all whitespace nodes
deleteWhitespaceDescendants(Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
recursively deletes all whitespace descendants
DELIM - Static variable in interface org.xmlcml.cml.StringArray
 
delimiter - Variable in class org.xmlcml.cml.FloatArrayImpl
 
delimiter - Variable in class org.xmlcml.cml.IntegerArrayImpl
 
delimiter - Variable in class org.xmlcml.cml.StringArrayImpl
 
depthFirstEnumeration(Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
 
depthFirstEnumeration(Node) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
iterate through whole tree
deQuote(String) - Static method in class jumbo.xml.util.Util
remove balanced quotes from ends of (trimmed) string, else no action
determinant() - Method in class jumbo.euclid.IntSquareMatrix
determinant - only goes up to order 3 at present :-(
determinant() - Method in class jumbo.euclid.RealSquareMatrix
determinant - only goes up to order 3 at present :-(
deviationsFromPlane(Plane3) - Method in class jumbo.euclid.Point3Vector
get deviations of coordinates from plane
diagonal(IntArray) - Static method in class jumbo.euclid.IntSquareMatrix
make diagonal matrix
diagonal(RealArray) - Static method in class jumbo.euclid.RealSquareMatrix
make diagonal matrix
Diagonalise - class jumbo.euclid.Diagonalise.
 
Diagonalise() - Constructor for class jumbo.euclid.Diagonalise
 
diagonaliseAndReturnRank(RealArray, RealSquareMatrix, IllCondMatrixException) - Method in class jumbo.euclid.RealSquareMatrix
diagonalisation - returns eigenvalues and vectors as MODIFIED arguments; this is NOT affected
dictRef - Variable in class org.xmlcml.cml.CMLBaseImpl
 
DICTREF - Static variable in interface org.xmlcml.cml.HasDictRef
"dictRef" attribute name
dist - Variable in class jumbo.euclid.Plane3
distance of plane from origin
distance(int, int) - Method in class jumbo.euclid.Point3Vector
get distance between 2 points
distance(int, int) - Method in class jumbo.euclid.Real2Vector
get distance between 2 points
distance(IntSet) - Method in class jumbo.euclid.Point3Vector
get distance between 2 points
distance(IntSet) - Method in class jumbo.euclid.Real2Vector
get distance between 2 points
distanceFromLine(Line3) - Method in class jumbo.euclid.Point3
 
distanceFromPlane(Plane3) - Method in class jumbo.euclid.Point3
 
divideBy(Complex) - Method in class jumbo.euclid.Complex
divide a complex by a complex
divideBy(double) - Method in class jumbo.euclid.Point3
 
divideBy(Polar) - Method in class jumbo.euclid.Polar
divide a polar by a polar
docElement - Variable in class uk.co.demon.ursus.dom.AbstractDocumentImpl
 
document - Variable in class uk.co.demon.ursus.dom.SAXDOMBuilder
 
DOLLAR - Static variable in class jumbo.xml.util.Util
 
DOMParser - class uk.co.demon.ursus.dom.DOMParser.
Wraps the Xerces DOM parser and extends NonValidatingDOMParser
DOMParser() - Constructor for class uk.co.demon.ursus.dom.DOMParser
Default constructor.
DOMParserWrapper - interface uk.co.demon.ursus.dom.DOMParserWrapper.
Encapsulates a DOM parser.
DOS - Static variable in class jumbo.xml.util.Util
 
dot(double[]) - Method in class jumbo.euclid.Vector3
dot product - protected
dot(Vector3) - Method in class jumbo.euclid.Vector3
dot product
dotProduct(Int2) - Method in class jumbo.euclid.Int2
get dot product
dotProduct(IntArray) - Method in class jumbo.euclid.IntArray
dot product of two IntArrays - if of same length - else zero
dotProduct(Real2) - Method in class jumbo.euclid.Real2
get dot product
dotProduct(RealArray) - Method in class jumbo.euclid.RealArray
dot product of two RealArrays - if of same length - else zero
DOUBLE - Static variable in interface org.xmlcml.cml.AbstractBond
double bond
dump(URL) - Static method in class jumbo.xml.util.Util
reads a stream from url and outputs it as integer values of the characters and as strings.
DXP - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 

E

Electron - interface org.xmlcml.cml.Electron.
 
ELECTRON - Static variable in interface org.xmlcml.cml.CMLBase
 
ElectronImpl - class org.xmlcml.cml.ElectronImpl.
 
ElectronImpl() - Constructor for class org.xmlcml.cml.ElectronImpl
 
ElectronImpl(Document) - Constructor for class org.xmlcml.cml.ElectronImpl
new Electron in context
ElectronImpl(Element) - Constructor for class org.xmlcml.cml.ElectronImpl
 
electronVector - Variable in class org.xmlcml.cml.MoleculeImpl
 
ELEMENT_COUNT - Static variable in interface org.xmlcml.cml.CMLBase
 
ELEMENT_NAMES - Static variable in interface org.xmlcml.cml.CMLBase
 
ELEMENT_TYPE - Static variable in interface org.xmlcml.cml.AbstractAtom
 
elementAt(int) - Method in interface org.xmlcml.cml.AtomArray
when an Atom is extracted then it is combined from the various StringArrays
elementAt(int) - Method in class org.xmlcml.cml.AtomArrayImpl
when an Atom is extracted then it is combined from the various StringArrays
elementAt(int) - Method in interface org.xmlcml.cml.BondArray
when an Bond is extracted then it is combined from the various StringArrays
elementAt(int) - Method in class org.xmlcml.cml.BondArrayImpl
when an Bond is extracted then it is combined from the various StringArrays
elementAt(int) - Method in interface org.xmlcml.cml.FloatArray
actually returns FloatVal
elementAt(int) - Method in class org.xmlcml.cml.FloatArrayImpl
actually returns FloatVal
elementAt(int) - Method in interface org.xmlcml.cml.HasSize
this will return an element of appropriate subclass
elementAt(int) - Method in interface org.xmlcml.cml.IntegerArray
return value is actually IntegerVal
elementAt(int) - Method in class org.xmlcml.cml.IntegerArrayImpl
return value is actually IntegerVal
elementAt(int) - Method in interface org.xmlcml.cml.StringArray
 
elementAt(int) - Method in class org.xmlcml.cml.StringArrayImpl
 
elementAt(int) - Method in class jumbo.euclid.Int2
get either value; counts from ZERO
elementAt(int) - Method in class jumbo.euclid.IntArray
extracts a given element from the array
elementAt(int) - Method in class jumbo.euclid.IntSet
 
elementAt(int) - Method in class jumbo.euclid.ObjectArray
extracts a given element from the array
elementAt(int) - Method in class jumbo.euclid.Point3
subscript operator counts from ZERO
elementAt(int) - Method in class jumbo.euclid.Real2
get either value; counts from ZERO
elementAt(int) - Method in class jumbo.euclid.Real2Array
 
elementAt(int) - Method in class jumbo.euclid.RealArray
extracts a given element from the array
elementAt(int) - Method in class jumbo.euclid.StringSet
return (case-sensitive) element
elementAt(int) - Method in class jumbo.euclid.Vector3
subscript operator: counts from ZERO
elementAt(Int2) - Method in class jumbo.euclid.IntMatrix
extracts a given element from the matrix
elementAt(Int2) - Method in class jumbo.euclid.RealMatrix
extracts a given element from the matrix
elementAt(int, int) - Method in class jumbo.euclid.IntMatrix
extracts a given element from the matrix
elementAt(int, int) - Method in class jumbo.euclid.RealMatrix
extracts a given element from the matrix
elementCounter() - Method in class uk.co.demon.ursus.dom.SAXAdapter
 
ELEMENTNAME - Static variable in interface uk.co.demon.ursus.dom.PMRNode
the element name as a text field
elements(int) - Method in class jumbo.xml.util.CyclicVector
creates an Enumeration starting at index.
elements(Object) - Method in class jumbo.xml.util.CyclicVector
creates an Enumeration starting with (first) element containing startObject.
elementsInRange(IntRange) - Method in class jumbo.euclid.IntMatrix
produce a mask of those elements which fall in a range (1) else (0)
elementsInRange(RealRange) - Method in class jumbo.euclid.RealMatrix
produce a mask of those elements which fall in a range (1) else (0)
elementType - Variable in class org.xmlcml.cml.AtomImpl
 
endDocument() - Method in class org.xmlcml.cml.CMLDOMSAXBuilderImpl
end of document.
endDocument() - Method in class org.xmlcml.cml.DefaultCMLDOMSAXBuilder
 
endDocument() - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive notification of the end of the document.
endDocument() - Method in class uk.co.demon.ursus.dom.SAXDOMBuilder
 
endDocument() - Method in class org.xmlcml.test.SAXAtomCounter
end of document
endElement(String) - Method in class org.xmlcml.cml.CMLDOMSAXBuilderImpl
end of Element.
endElement(String) - Method in class org.xmlcml.cml.DefaultCMLDOMSAXBuilder
 
endElement(String) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive notification of the end of an element.
endElement(String) - Method in class uk.co.demon.ursus.dom.SAXDOMBuilder
 
endElement(String) - Method in class org.xmlcml.test.SAXAtomCounter
called for each endtag
EQUALS - Static variable in class jumbo.xml.util.Util
 
equals(Angle) - Method in class jumbo.euclid.Angle
are two angles equal?
equals(double) - Method in class jumbo.euclid.Angle
are two angles equal? RADIANS
equals(Int2) - Method in class jumbo.euclid.Int2
 
equals(Int2Range) - Method in class jumbo.euclid.Int2Range
 
equals(IntArray) - Method in class jumbo.euclid.IntArray
are two arrays equal in all elements? (use epsilon as tolerance)
equals(IntMatrix) - Method in class jumbo.euclid.IntMatrix
are two matrices equal in all elements?
equals(IntRange) - Method in class jumbo.euclid.IntRange
invalid ranges return false
equals(IntSet) - Method in class jumbo.euclid.IntSet
element-by-element comparison of sets
equals(IntSquareMatrix) - Method in class jumbo.euclid.IntSquareMatrix
are two matrices identical?
equals(Line3) - Method in class jumbo.euclid.Line3
are two lines identical (coincident and parallel)?
equals(ObjectArray) - Method in class jumbo.euclid.ObjectArray
are two arrays equal in all elements?
equals(Object, Object) - Static method in class jumbo.xml.util.Util
compares tow object using equals() - allows for null objects.
equals(Plane3) - Method in class jumbo.euclid.Plane3
are two planes coincident and parllel
equals(Point3) - Method in class jumbo.euclid.Point3
are two points identical?
equals(Polar) - Method in class jumbo.euclid.Polar
are two polar equal?
equals(Real2) - Method in class jumbo.euclid.Real2
 
equals(Real2Range) - Method in class jumbo.euclid.Real2Range
 
equals(Real3Range) - Method in class jumbo.euclid.Real3Range
 
equals(RealArray) - Method in class jumbo.euclid.RealArray
are two arrays equal in all elements?
equals(RealArray, double) - Method in class jumbo.euclid.RealArray
are two arrays equal in all elements? (use epsilon as tolerance)
equals(RealMatrix) - Method in class jumbo.euclid.RealMatrix
are two matrices equal in all elements?
equals(RealRange) - Method in class jumbo.euclid.RealRange
invalid ranges return false
equals(RealSquareMatrix) - Method in class jumbo.euclid.RealSquareMatrix
are two matrices identical?
equals(String, String, int) - Static method in class jumbo.xml.util.Util
convenience function for comparing strings using Util.CASE/IGNORECASE
equals(Transform2) - Method in class jumbo.euclid.Transform2
 
equals(Transform3) - Method in class jumbo.euclid.Transform3
 
equals(Vector3) - Method in class jumbo.euclid.Vector3
are two vectors equal lengths?
error(SAXParseException) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive notification of a recoverable parser error.
error(SAXParseException) - Method in class uk.co.demon.ursus.dom.NonValidatingDOMParser
Error.
error(String) - Static method in class jumbo.xml.util.Util
Error message - nothing fancy at present.
escape(String) - Static method in class jumbo.xml.util.Util
default escape characters in an XML string (' -> ' , etc); also escape non-XML characters (e.g.
escape(String, char[], String[]) - Static method in class jumbo.xml.util.Util
escape characters in an XML string; also escape non-XML characters (e.g.
euclideanColumnLength(int) - Method in class jumbo.euclid.RealMatrix
get Euclidean length of column
euclideanColumnLengths() - Method in class jumbo.euclid.RealMatrix
get array of Euclidean column lengths
euclideanLength() - Method in class jumbo.euclid.RealArray
Euclidean length of vector
euclideanRowLength(int) - Method in class jumbo.euclid.RealMatrix
get Euclidean length of row
euclideanRowLengths() - Method in class jumbo.euclid.RealMatrix
get array of Euclidean row lengths
EuclidVector - class jumbo.euclid.EuclidVector.
an array of objects (NOT to be confused with Vector3).
EuclidVector() - Constructor for class jumbo.euclid.EuclidVector
 
EuclidVector(int) - Constructor for class jumbo.euclid.EuclidVector
 
Execute - interface org.xmlcml.cml.Execute.
Execute elements can be created by elements.
EXECUTE - Static variable in interface org.xmlcml.cml.CMLBase
 
ExecuteImpl - class org.xmlcml.cml.ExecuteImpl.
 
ExecuteImpl() - Constructor for class org.xmlcml.cml.ExecuteImpl
 
ExecuteImpl(Document) - Constructor for class org.xmlcml.cml.ExecuteImpl
new List in context
ExecuteImpl(Element) - Constructor for class org.xmlcml.cml.ExecuteImpl
 
EXPLICIT_HYDROGENS - Static variable in interface org.xmlcml.cml.ConventionCriteria
 
extractColumnData(int) - Method in class jumbo.euclid.IntMatrix
get column data from matrix
extractColumnData(int) - Method in class jumbo.euclid.RealMatrix
get column data from matrix
extractRowData(int) - Method in class jumbo.euclid.IntMatrix
get row data from matrix
extractRowData(int) - Method in class jumbo.euclid.RealMatrix
get row data from matrix
extractSubMatrixData(int, int, int, int) - Method in class jumbo.euclid.IntMatrix
extract a IntMatrix submatrix from a IntMatrix
extractSubMatrixData(int, int, int, int) - Method in class jumbo.euclid.RealMatrix
extract a RealMatrix submatrix from a RealMatrix

F

fatalError(SAXParseException) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Report a fatal XML parsing error.
fatalError(SAXParseException) - Method in class uk.co.demon.ursus.dom.NonValidatingDOMParser
Fatal error.
Feature - interface org.xmlcml.cml.Feature.
 
FEATURE - Static variable in interface org.xmlcml.cml.CMLBase
 
FeatureImpl - class org.xmlcml.cml.FeatureImpl.
 
FeatureImpl() - Constructor for class org.xmlcml.cml.FeatureImpl
 
FeatureImpl(Document) - Constructor for class org.xmlcml.cml.FeatureImpl
new Feature in context
FeatureImpl(Element) - Constructor for class org.xmlcml.cml.FeatureImpl
 
featureVector - Variable in class org.xmlcml.cml.MoleculeImpl
 
findRingNuclei() - Method in class org.xmlcml.tools.SpanningTreeImpl
 
findRings() - Method in class org.xmlcml.tools.SpanningTreeImpl
 
fitTo(Point3Vector) - Method in class jumbo.euclid.Point3Vector
fit two coordinates of same length and alignment CURRENTLY NOT VALIDATED
flarray - Variable in class jumbo.euclid.Point3
the coordinates of the point
flipAboutVector(Real2) - Static method in class jumbo.euclid.Transform2
get Transformation to mirror ('flip') across an axis NOT YET CHECKED
flmat - Variable in class jumbo.euclid.IntMatrix
the matrix
flmat - Variable in class jumbo.euclid.RealMatrix
the matrix
FLOAT - Static variable in interface org.xmlcml.cml.CMLBase
 
FLOAT_TYPE - Static variable in interface org.xmlcml.cml.CMLBase
 
FloatArray - interface org.xmlcml.cml.FloatArray.
 
FLOATARRAY - Static variable in interface org.xmlcml.cml.CMLBase
 
FloatArrayImpl - class org.xmlcml.cml.FloatArrayImpl.
 
FloatArrayImpl() - Constructor for class org.xmlcml.cml.FloatArrayImpl
 
FloatArrayImpl(Document) - Constructor for class org.xmlcml.cml.FloatArrayImpl
new FloatArray in context
FloatArrayImpl(Element) - Constructor for class org.xmlcml.cml.FloatArrayImpl
 
FloatMatrix - interface org.xmlcml.cml.FloatMatrix.
 
FLOATMATRIX - Static variable in interface org.xmlcml.cml.CMLBase
 
FloatMatrixImpl - class org.xmlcml.cml.FloatMatrixImpl.
 
FloatMatrixImpl() - Constructor for class org.xmlcml.cml.FloatMatrixImpl
 
FloatMatrixImpl(Document) - Constructor for class org.xmlcml.cml.FloatMatrixImpl
new FloatMatrix in context
FloatMatrixImpl(Element) - Constructor for class org.xmlcml.cml.FloatMatrixImpl
 
FloatVal - interface org.xmlcml.cml.FloatVal.
holds a float with max and minimum values
FloatValImpl - class org.xmlcml.cml.FloatValImpl.
holds a float with max and minimum values
FloatValImpl() - Constructor for class org.xmlcml.cml.FloatValImpl
 
FloatValImpl(Document) - Constructor for class org.xmlcml.cml.FloatValImpl
new FloatVal in context
FloatValImpl(Document, double, String, String, String, String, String, Units, double, double) - Constructor for class org.xmlcml.cml.FloatValImpl
 
FloatValImpl(Element) - Constructor for class org.xmlcml.cml.FloatValImpl
 
FloatValImpl(String, Document) - Constructor for class org.xmlcml.cml.FloatValImpl
new FloatVal in context
flush(String) - Static method in class jumbo.xml.util.Util
output String and flush()
FORMAL_CHARGE_FLOAT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
FORMAL_CHARGE_INT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
formalCharge - Variable in class org.xmlcml.cml.AtomImpl
 
FORMAT_ASCII - Static variable in class jumbo.xml.util.Util
 
FORMAT_DOS - Static variable in class jumbo.xml.util.Util
 
FORMAT_EQUALS - Static variable in class jumbo.xml.util.Util
 
FORMFEED - Static variable in class jumbo.xml.util.Util
 
Formula - interface org.xmlcml.cml.Formula.
 
FORMULA - Static variable in interface org.xmlcml.cml.CMLBase
 
FormulaImpl - class org.xmlcml.cml.FormulaImpl.
 
FormulaImpl() - Constructor for class org.xmlcml.cml.FormulaImpl
 
FormulaImpl(Document) - Constructor for class org.xmlcml.cml.FormulaImpl
new Formula in context
FormulaImpl(Element) - Constructor for class org.xmlcml.cml.FormulaImpl
 
freeMemory(long) - Static method in class jumbo.xml.util.Util
runs the garbage collector if memory drops below mem.
FUSED - Static variable in interface org.xmlcml.tools.RingOverlap
rings are fused (one bond in common)
FUSED - Static variable in class org.xmlcml.tools.RingOverlapImpl
rings are fused (one bond in common)

G

GAMMA - Static variable in interface org.xmlcml.cml.Crystal
 
generateId(int) - Method in interface org.xmlcml.cml.Atom
give each atom an ID.
generateId(int) - Method in class org.xmlcml.cml.AtomImpl
give each atom an ID.
getAcyclicAtomSet() - Method in interface org.xmlcml.tools.SpanningTree
get atoms in acyclic bonds
getAcyclicAtomSet() - Method in class org.xmlcml.tools.SpanningTreeImpl
get atoms in acyclic bonds
getAcyclicBondSet() - Method in interface org.xmlcml.tools.SpanningTree
get bonds not in rings
getAcyclicBondSet() - Method in class org.xmlcml.tools.SpanningTreeImpl
get bonds not in rings
getAncestor(Element, String) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
gets first ancestor of 'element' with tagName; [element is not its own ancestor]
getAncestors(Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
gets all ancestors of 'element' including the document Element but not Document.
getAncestorWithClass(Element, Class) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
gets first ancestor of 'element' of given class (or superclass) [element is not its ancestor]
getAngle() - Method in class jumbo.euclid.Angle
get angle in radians
getAngle() - Method in class jumbo.euclid.Real2
get angle between origin and this point (i.e polar coords) - uses atan2 (i.e.
getAngle(Point3, Point3, Point3) - Static method in class jumbo.euclid.Point3
angle (p1-p2-p3; vertex is p2)
getAngle(Real2, Real2, Real2) - Static method in class jumbo.euclid.Real2
get angle between 3 Real2s (the second is in the centre).
getAngleMadeWith(Plane3) - Method in class jumbo.euclid.Plane3
the angle between 2 planes (as an Angle)
getAngleMadeWith(Vector2) - Method in class jumbo.euclid.Vector2
I *think* I have written this so that the angle is positive as this rotates anticlockwise to v.
getAngleMadeWith(Vector3) - Method in class jumbo.euclid.Vector3
angle between two vectors
getAngleOfRotation() - Method in class jumbo.euclid.Transform2
interpret current matrix as rotation about axis NOT YET CHECKED; only worsk for orthornormal matrices
getAngleUnits() - Method in interface org.xmlcml.cml.AbstractAngle
 
getAngleUnits() - Method in class org.xmlcml.cml.AbstractAngleImpl
 
getAngleVector() - Method in interface org.xmlcml.cml.Molecule
extracts ALL the Angles as a Vector
getAngleVector() - Method in class org.xmlcml.cml.MoleculeImpl
extracts ALL the Angles as a Vector
getArray() - Method in class jumbo.euclid.IntArray
return the array as a int[]; this has to resize the array to the precise length used , or confusion will result! Note that this gives the user access to the actual array, so that they can alter its contents.
getArray() - Method in class jumbo.euclid.ObjectArray
return the array as a Object[]; this has to resize the array to the precise length used , or confusion will result! Note that this gives the user access to the actual array, so that they can alter its contents.
getArray() - Method in class jumbo.euclid.Point3
get components as double[]
getArray() - Method in class jumbo.euclid.RealArray
return the array as a double[]; this has to resize the array to the precise length used , or confusion will result! Note that this gives the user access to the actual array, so that they can alter its contents.
getArray() - Method in class jumbo.euclid.Vector3
get the vector components
getAtom() - Method in interface org.xmlcml.tools.STElement
 
getAtom() - Method in class org.xmlcml.tools.STElementImpl
 
getAtom(int) - Method in interface org.xmlcml.cml.Bond
 
getAtom(int) - Method in class org.xmlcml.cml.BondImpl
 
getAtomArray() - Method in interface org.xmlcml.cml.Molecule
packs current Atoms into an AtomArray
getAtomArray() - Method in class org.xmlcml.cml.MoleculeImpl
packs current Atoms into an AtomArray
getAtomById(String) - Method in interface org.xmlcml.cml.Molecule
 
getAtomById(String) - Method in class org.xmlcml.cml.MoleculeImpl
 
getAtomCount() - Method in interface org.xmlcml.cml.Molecule
 
getAtomCount() - Method in class org.xmlcml.cml.MoleculeImpl
 
getAtomicNumber() - Method in class org.xmlcml.molutil.ChemicalElement
 
getAtomicWeight() - Method in class org.xmlcml.molutil.ChemicalElement
 
getAtomIdTable() - Method in interface org.xmlcml.cml.Molecule
 
getAtomIdTable() - Method in class org.xmlcml.cml.MoleculeImpl
 
getAtomParity() - Method in interface org.xmlcml.cml.Atom
 
getAtomParity() - Method in class org.xmlcml.cml.AtomImpl
 
getAtomRef(int) - Method in interface org.xmlcml.cml.AbstractAtomRef
 
getAtomRef(int) - Method in class org.xmlcml.cml.AbstractAtomRefImpl
 
getAtomRef(int) - Method in interface org.xmlcml.cml.AbstractBond
 
getAtomRef(int) - Method in class org.xmlcml.cml.AbstractBondImpl
 
getAtomRef(int) - Method in interface org.xmlcml.cml.HasAtomRefs
 
getAtomRefVector() - Method in interface org.xmlcml.cml.AbstractAtomRef
 
getAtomRefVector() - Method in class org.xmlcml.cml.AbstractAtomRefImpl
 
getAtomRefVector() - Method in interface org.xmlcml.cml.AbstractBond
 
getAtomRefVector() - Method in class org.xmlcml.cml.AbstractBondImpl
 
getAtomRefVector() - Method in interface org.xmlcml.cml.Atom
Vector of elements which refer to this atom
getAtomRefVector() - Method in class org.xmlcml.cml.AtomImpl
finds all references to this atom, e.g.
getAtomRefVector() - Method in interface org.xmlcml.cml.HasAtomRefs
 
getAtomSet() - Method in interface org.xmlcml.tools.BondSet
 
getAtomSet() - Method in class org.xmlcml.tools.BondSetImpl
a BondSet always keeps count of the atoms in it
getAtomSet() - Method in interface org.xmlcml.tools.RingOverlap
get the atoms in the overlap
getAtomSet() - Method in class org.xmlcml.tools.RingOverlapImpl
get the atoms in the overlap
getAtomSet() - Method in interface org.xmlcml.tools.SpanningTree
get all atoms
getAtomSet() - Method in class org.xmlcml.tools.SpanningTreeImpl
get atoms
getAtomVector() - Method in interface org.xmlcml.cml.Molecule
extracts ALL the Atoms as a Vector
getAtomVector() - Method in class org.xmlcml.cml.MoleculeImpl
extracts ALL the Atoms as a Vector
getAttributeString(Attr) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
returns a string representing a single attribute in a start tag, e.g.
getAttributeString(Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
returns the attributes in concatenated text form (suitable for insertion to start tags).
getAxisAndAngle(Vector3, Angle) - Method in class jumbo.euclid.Transform3
returns chirality
getBond(Atom, Atom) - Method in interface org.xmlcml.cml.Molecule
get a bond from the atoms - order is irrelevant
getBond(Atom, Atom) - Method in class org.xmlcml.cml.MoleculeImpl
 
getBondArray() - Method in interface org.xmlcml.cml.Molecule
extracts ALL the bonds in a single BondArray.
getBondArray() - Method in class org.xmlcml.cml.MoleculeImpl
extracts ALL the bonds in a single BondArray.
getBondCount() - Method in interface org.xmlcml.cml.Molecule
 
getBondCount() - Method in class org.xmlcml.cml.MoleculeImpl
 
getBondLength() - Method in interface org.xmlcml.cml.Bond
 
getBondLength() - Method in class org.xmlcml.cml.BondImpl
 
getBondSet() - Method in interface org.xmlcml.tools.RingOverlap
get the bonds in the overlap
getBondSet() - Method in class org.xmlcml.tools.RingOverlapImpl
get the bonds in the overlap
getBondSet() - Method in interface org.xmlcml.tools.SpanningTree
get all bonds
getBondSet() - Method in class org.xmlcml.tools.SpanningTreeImpl
get bonds
getBondsSeparating(Atom) - Method in interface org.xmlcml.tools.ChainSet
gets bondVector separating two atoms (hence get distance)
getBondsSeparating(Atom) - Method in class org.xmlcml.tools.ChainSetImpl
gets bondVector separating two atoms (hence get distance)
getBondVector() - Method in interface org.xmlcml.cml.Molecule
extracts ALL the Bonds as a Vector
getBondVector() - Method in class org.xmlcml.cml.MoleculeImpl
extracts ALL the Bonds as a Vector
getBridgeheadAtom(int) - Method in interface org.xmlcml.tools.RingOverlap
returns atoms at end o bridgehead (i=0 or i=1)
getBridgeheadAtom(int) - Method in class org.xmlcml.tools.RingOverlapImpl
 
getBuiltin() - Method in interface org.xmlcml.cml.AbstractStringVal
 
getBuiltin() - Method in class org.xmlcml.cml.AbstractStringValImpl
 
getBuiltinArray(int) - Method in interface org.xmlcml.cml.AtomArray
this is slightly tricky/ucky since AtomArray is subclassed from Atom and StringArray from StringVal we can extract the array object as scalars and simply cast them
getBuiltinArray(int) - Method in class org.xmlcml.cml.AtomArrayImpl
this is slightly tricky/ucky since AtomArray is subclassed from Atom and StringArray from StringVal we can extract the array object as scalars and simply cast them
getBuiltinArray(int) - Method in interface org.xmlcml.cml.BondArray
this is rather trick since BondArray is subclasses from Bond and StringArray from StringVal we can extract the array object as scalars and simply cast them
getBuiltinArray(int) - Method in class org.xmlcml.cml.BondArrayImpl
this is rather trick since BondArray is subclasses from Bond and StringArray from StringVal we can extract the array object as scalars and simply cast them
getBuiltinArray(int) - Method in interface org.xmlcml.cml.HasBuiltinArrayNames
 
getBuiltinChildElements() - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
extracts all children with builtin attribute; if none empty Vector
getBuiltinChildElements() - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
extracts all children with builtin attribute; if none empty Vector
getBuiltinChildFloatValue(int, String[]) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
 
getBuiltinChildFloatValue(int, String[]) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
getBuiltinChildIntegerValue(int, String[]) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
 
getBuiltinChildIntegerValue(int, String[]) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
getBuiltinChildStringValue(int, String[]) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
returns the value of a SINGLE child with given builtin
getBuiltinChildStringValue(int, String[]) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
gets the SINGLE child with the given builtin
getBuiltinCount() - Method in class org.xmlcml.cml.AbstractAtomImpl
 
getBuiltinCount() - Method in class org.xmlcml.cml.AbstractBondImpl
 
getBuiltinCount() - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
 
getBuiltinCount() - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
getBuiltinCount() - Method in class org.xmlcml.cml.CrystalImpl
 
getBuiltinCount() - Method in interface org.xmlcml.cml.HasBuiltinNames
 
getBuiltinFloatValCount() - Static method in class org.xmlcml.cml.AbstractAtomImpl
 
getBuiltinFloatValCount() - Static method in class org.xmlcml.cml.AbstractBondImpl
 
getBuiltinFloatValCount() - Static method in class org.xmlcml.cml.CrystalImpl
 
getBuiltinFloatValNames() - Static method in class org.xmlcml.cml.AbstractAtomImpl
 
getBuiltinFloatValNames() - Static method in class org.xmlcml.cml.AbstractBondImpl
 
getBuiltinFloatValNames() - Static method in class org.xmlcml.cml.CrystalImpl
 
getBuiltinIntegerValCount() - Static method in class org.xmlcml.cml.AbstractAtomImpl
 
getBuiltinIntegerValCount() - Static method in class org.xmlcml.cml.AbstractBondImpl
 
getBuiltinIntegerValCount() - Static method in class org.xmlcml.cml.CrystalImpl
 
getBuiltinIntegerValNames() - Static method in class org.xmlcml.cml.AbstractAtomImpl
 
getBuiltinIntegerValNames() - Static method in class org.xmlcml.cml.AbstractBondImpl
 
getBuiltinIntegerValNames() - Static method in class org.xmlcml.cml.CrystalImpl
 
getBuiltinNames() - Static method in class org.xmlcml.cml.AbstractAtomImpl
 
getBuiltinNames() - Static method in class org.xmlcml.cml.AbstractBondImpl
 
getBuiltinNames() - Static method in class org.xmlcml.cml.CrystalImpl
 
getBuiltinStringValCount() - Static method in class org.xmlcml.cml.AbstractAtomImpl
 
getBuiltinStringValCount() - Static method in class org.xmlcml.cml.AbstractBondImpl
 
getBuiltinStringValCount() - Static method in class org.xmlcml.cml.CrystalImpl
 
getBuiltinStringValNames() - Static method in class org.xmlcml.cml.AbstractAtomImpl
 
getBuiltinStringValNames() - Static method in class org.xmlcml.cml.AbstractBondImpl
 
getBuiltinStringValNames() - Static method in class org.xmlcml.cml.CrystalImpl
 
getBuiltinVal(int) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
 
getBuiltinVal(int) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
getBuiltinVal(int) - Method in interface org.xmlcml.cml.HasBuiltinNames
 
getCentreOfRotation() - Method in class jumbo.euclid.Transform2
get centre of rotation
getCentreOfRotation() - Method in class jumbo.euclid.Transform3
get centre of rotation
getCentroid() - Method in class jumbo.euclid.Point3Vector
get centroid of all points
getCentroid() - Method in class jumbo.euclid.Real2Vector
get centroid of all points
getCentroid() - Method in interface org.xmlcml.tools.Ring
 
getCentroid() - Method in class org.xmlcml.tools.RingImpl
 
getChainTable() - Method in interface org.xmlcml.tools.SubstituentList
returns Hashtable of Chains.
getChainTable() - Method in class org.xmlcml.tools.SubstituentListImpl
returns Hashtable of Chains.
getChild(Element, String, String, String) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
get children with combination of tagNames, attribute names and values.
getChildElement(Element, int) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
get the index'th Element child.
getChildElementNameTable(Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
make a list of all child element names and the instances of each.
getChildElements(Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
get all Element children.
getChildrenWithElementName(Element, String) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
gets vector of XNode children with given element name (ignored if name is null or bad value of sensitivity).
getClosestPoint(Int2) - Method in class jumbo.euclid.Int2Vector
get the closest point (both ranges are assumed to have the same scales
getClosestPoint(Real2) - Method in class jumbo.euclid.Real2Vector
get the closest point (both ranges are assumed to have the same scales
getClosestPointOnLine(Line3) - Method in class jumbo.euclid.Point3
 
getClosestPointTo(Point3) - Method in class jumbo.euclid.Line3
point on line closest to another point
getClosestPointTo(Point3) - Method in class jumbo.euclid.Plane3
point on plane closest to another point
getCMLDocument() - Method in interface org.xmlcml.cml.CMLDOMSAXBuilder
 
getCMLDocument() - Method in class org.xmlcml.cml.CMLDOMSAXBuilderImpl
 
getCols() - Method in class jumbo.euclid.IntMatrix
get number of columns
getCols() - Method in class jumbo.euclid.RealMatrix
get number of columns
getColumns() - Method in interface org.xmlcml.cml.FloatMatrix
 
getColumns() - Method in class org.xmlcml.cml.FloatMatrixImpl
 
getCommaSeparatedStrings(String) - Static method in class jumbo.xml.util.Util
parse comma-separated Strings.
getConventionName() - Method in class org.xmlcml.cml.CMLBaseImpl
 
getConventionName() - Method in interface org.xmlcml.cml.HasConvention
 
getCoordinate(int, Choice2) - Method in class jumbo.euclid.Int2Vector
get a single coordinate value
getCoordinate(int, Choice2) - Method in class jumbo.euclid.Real2Vector
get a single coordinate value
getCoordinate(int, Choice3) - Method in class jumbo.euclid.Point3Vector
get a single coordinate value
getCoordinate2(Atom) - Method in interface org.xmlcml.tools.AtomSet
get coordinates for atom
getCoordinate2(Atom) - Method in class org.xmlcml.tools.AtomSetImpl
get coordinates for atom
getCount() - Method in interface org.xmlcml.cml.AbstractAtom
 
getCount() - Method in class org.xmlcml.cml.AbstractAtomImpl
 
getCount() - Method in class org.xmlcml.cml.ElectronImpl
 
getCount() - Method in interface org.xmlcml.cml.Formula
 
getCount() - Method in class org.xmlcml.cml.FormulaImpl
 
getCount() - Method in interface org.xmlcml.cml.HasCount
 
getCount() - Method in interface org.xmlcml.cml.Molecule
 
getCount() - Method in class org.xmlcml.cml.MoleculeImpl
 
getCount() - Method in interface org.xmlcml.tools.RingNucleus
get number of rings
getCount() - Method in class org.xmlcml.tools.RingNucleusImpl
 
getCount(Atom) - Method in interface org.xmlcml.tools.AtomSet
how many times has atom been added (0 means atom is not in set
getCount(Atom) - Method in class org.xmlcml.tools.AtomSetImpl
how many times has atom been added (0 means atom is not in set
getCovalentRadius() - Method in class org.xmlcml.molutil.ChemicalElement
 
getCrystal() - Method in interface org.xmlcml.cml.Molecule
extracts Crystal if present
getCrystal() - Method in class org.xmlcml.cml.MoleculeImpl
extracts Crystal if present
getCyclicAtomSet() - Method in interface org.xmlcml.tools.SpanningTree
get atoms only in rings
getCyclicAtomSet() - Method in class org.xmlcml.tools.SpanningTreeImpl
get atoms only in rings
getCyclicAtomVector() - Method in interface org.xmlcml.tools.Ring
returns an ordered list of atoms corresponding to traversal of the ring
getCyclicAtomVector() - Method in class org.xmlcml.tools.RingImpl
returns an ordered list of atoms corresponding to traversal of the ring
getCyclicBondSet() - Method in interface org.xmlcml.tools.SpanningTree
get bonds in rings
getCyclicBondSet() - Method in class org.xmlcml.tools.SpanningTreeImpl
get bonds in rings
getCyclicBondVector() - Method in interface org.xmlcml.tools.Ring
ordered cycle of bonds (e.g.
getCyclicBondVector() - Method in class org.xmlcml.tools.RingImpl
ordered cycle of bonds (e.g.
getData() - Method in interface org.xmlcml.cml.FloatMatrix
data in format [rows][cols].
getData() - Method in class org.xmlcml.cml.FloatMatrixImpl
data in format [rows][cols].
getDataType() - Method in interface org.xmlcml.cml.AbstractStringVal
String, Float, Integer all have dataType flag if required
getDataType() - Method in class org.xmlcml.cml.AbstractStringValImpl
String, Float, Integer all have dataType flag if required
getDegrees() - Method in class jumbo.euclid.Angle
get angle in degrees
getDelimiter() - Method in interface org.xmlcml.cml.FloatArray
 
getDelimiter() - Method in class org.xmlcml.cml.FloatArrayImpl
 
getDelimiter() - Method in interface org.xmlcml.cml.HasSize
 
getDelimiter() - Method in interface org.xmlcml.cml.IntegerArray
 
getDelimiter() - Method in class org.xmlcml.cml.IntegerArrayImpl
 
getDelimiter() - Method in interface org.xmlcml.cml.StringArray
 
getDelimiter() - Method in class org.xmlcml.cml.StringArrayImpl
 
getDescendants(Element, int, String) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
gets all children at given level.
getDescendantsWithClass(Node, Class) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
gets descendants of 'element' of given class (or superclass) [element is not its descendant].
getDictRef() - Method in class org.xmlcml.cml.CMLBaseImpl
 
getDictRef() - Method in interface org.xmlcml.cml.HasDictRef
 
getDistance() - Method in class jumbo.euclid.Plane3
distance from origin
getDistanceFromOrigin() - Method in class jumbo.euclid.Point3
distance of point from origin
getDistanceFromPoint(Point3) - Method in class jumbo.euclid.Line3
distance of a point from a line
getDistanceFromPoint(Point3) - Method in class jumbo.euclid.Plane3
distance of point from plane (will be a signed quantity)
getDistanceFromPoint(Point3) - Method in class jumbo.euclid.Point3
distance of point from another point
getDistanceMatrix() - Method in class jumbo.euclid.Point3Vector
distance matrix
getDocument() - Method in class uk.co.demon.ursus.dom.SAXDOMBuilder
 
getDocument() - Method in class uk.co.demon.ursus.dom.NonValidatingDOMParser
 
getElectronVector() - Method in interface org.xmlcml.cml.Molecule
extracts ALL the Electrons as a Vector
getElectronVector() - Method in class org.xmlcml.cml.MoleculeImpl
extracts ALL the Electrons as a Vector
getElement(int) - Static method in class org.xmlcml.molutil.ChemicalElement
get the element corresponding to atomic number; else returns null.
getElement(String) - Static method in class org.xmlcml.molutil.ChemicalElement
get the element corresponding to a (case-insensitive) symbol; else returns null.
getElements() - Method in class jumbo.euclid.IntSet
 
getElements() - Method in class jumbo.euclid.StringSet
return all members (case sensitive by default)
getElementType() - Method in interface org.xmlcml.cml.Atom
 
getElementType() - Method in class org.xmlcml.cml.AtomImpl
get elementType from builtin child
getEpsilon() - Static method in class jumbo.euclid.Real
get current version of epsilon
getErrorMessage(SAXParseException) - Method in class uk.co.demon.ursus.dom.SAXAdapter
get an error message string from a SAXParseException
getFeature() - Method in interface org.xmlcml.cml.Molecule
extracts the FIRST Feature if any present
getFeature() - Method in class org.xmlcml.cml.MoleculeImpl
extracts the FIRST Feature if any present
getFeatureVector() - Method in interface org.xmlcml.cml.Molecule
extracts ALL the Features as a Vector
getFeatureVector() - Method in class org.xmlcml.cml.MoleculeImpl
extracts ALL the Features as a Vector
getFileOutputStream(String) - Static method in class jumbo.xml.util.Util
get an OutputStream from a file or URL.
getFirstChildWithElementName(Element, String) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
gets first child with given element name (ignored if name is null).
getFloat(int) - Method in interface org.xmlcml.cml.FloatArray
 
getFloat(int) - Method in class org.xmlcml.cml.FloatArrayImpl
 
getFormalCharge() - Method in interface org.xmlcml.cml.Atom
 
getFormalCharge() - Method in class org.xmlcml.cml.AtomImpl
 
getHRef() - Method in interface org.xmlcml.cml.Link
 
getHRef() - Method in class org.xmlcml.cml.LinkImpl
 
getHybridization() - Method in interface org.xmlcml.cml.Atom
 
getHybridization() - Method in class org.xmlcml.cml.AtomImpl
 
getHydrogenCount() - Method in interface org.xmlcml.cml.Atom
 
getHydrogenCount() - Method in class org.xmlcml.cml.AtomImpl
 
getId() - Method in class org.xmlcml.cml.AtomImpl
if ID attribute is missing, returns atomId biltin child value and sets ID attribute to this value
getId() - Method in class org.xmlcml.cml.CMLBaseImpl
 
getId() - Method in interface org.xmlcml.cml.HasId
 
getId() - Method in interface org.xmlcml.tools.Ring
 
getId() - Method in class org.xmlcml.tools.RingImpl
 
getIgnoreCase() - Method in class jumbo.euclid.StringSet
state of case-sensitivity
getInt2(int) - Method in class jumbo.euclid.Int2Vector
get the i'th Int2
getIntArray() - Method in class jumbo.euclid.IntSet
 
getIntArray() - Method in class jumbo.euclid.ObjectArray
return contents as a IntArray if INT, else null
getInteger(int) - Method in interface org.xmlcml.cml.IntegerArray
 
getInteger(int) - Method in class org.xmlcml.cml.IntegerArrayImpl
 
getIntegerFromRoman(String) - Static method in class jumbo.xml.util.Util
translate Roman Numerals up to 50 (!!!) Some normalisation is performed.
getIntersectionWith(Line3) - Method in class jumbo.euclid.Plane3
point of intersection of plane and line
getIntersectionWith(Plane3) - Method in class jumbo.euclid.Line3
point of intersection of line and plane
getIntersectionWith(Plane3) - Method in class jumbo.euclid.Plane3
line as intersection of two planes
getIntersectionWith(Plane3, Plane3) - Method in class jumbo.euclid.Plane3
point where three planes intersect
getIntFromHex(String) - Static method in class jumbo.xml.util.Util
Translates a Hex number to its int equivalent.
getIntValue() - Method in interface org.xmlcml.cml.IntegerVal
 
getIntValue() - Method in class org.xmlcml.cml.IntegerValImpl
 
getInverse() - Method in class jumbo.euclid.RealSquareMatrix
inversion of matrix - creates NEW matrix
getIsotope() - Method in interface org.xmlcml.cml.Atom
 
getIsotope() - Method in class org.xmlcml.cml.AtomImpl
 
getIsotopeAbundances() - Method in class org.xmlcml.molutil.ChemicalElement
 
getIsotopeMasses() - Method in class org.xmlcml.molutil.ChemicalElement
 
getLength() - Method in class jumbo.euclid.Real2
get length of Real2 if centered on origin
getLength() - Method in class jumbo.euclid.Vector3
return vector length
getLigand(int) - Method in interface org.xmlcml.cml.Atom
convenience method to get element of ligand vector
getLigand(int) - Method in class org.xmlcml.cml.AtomImpl
 
getLigandCount() - Method in interface org.xmlcml.cml.Atom
get ligand count
getLigandCount() - Method in class org.xmlcml.cml.AtomImpl
get ligand count
getLigandVector() - Method in interface org.xmlcml.cml.Atom
 
getLigandVector() - Method in class org.xmlcml.cml.AtomImpl
get vector of ligands
getLine(int, int) - Method in class jumbo.euclid.Point3Vector
get the line between two points
getLinkVector() - Method in interface org.xmlcml.tools.SpanningTree
 
getLinkVector() - Method in class org.xmlcml.tools.SpanningTreeImpl
 
getMainIsotope() - Method in class org.xmlcml.molutil.ChemicalElement
get the mass of the most abundant isotope
getMatrix() - Method in class jumbo.euclid.IntMatrix
 
getMatrix() - Method in class jumbo.euclid.RealMatrix
 
getMatrixAsArray() - Method in class jumbo.euclid.IntMatrix
get matrix as int[] (in C order: m(0,0), m(0,1) ...)
getMatrixAsArray() - Method in class jumbo.euclid.RealMatrix
get matrix as double[] (in C order: m(0,0), m(0,1) ...)
getMax() - Method in class jumbo.euclid.IntRange
get maximum value (MIN_VALUE if inValid)
getMax() - Method in class jumbo.euclid.RealRange
get maximum value (NEGATIVE_INFINITY if inValid)
getMaximum() - Method in interface org.xmlcml.cml.FloatVal
maximum value, set by default to Double.MAX_VALUE
getMaximum() - Method in class org.xmlcml.cml.FloatValImpl
maximum value, set by default to Double.MAX_VALUE
getMaximum() - Method in interface org.xmlcml.cml.IntegerVal
maximum value, set by default to Integer.MAX_VALUE (2147483647)
getMaximum() - Method in class org.xmlcml.cml.IntegerValImpl
maximum value, set by default to Integer.MAX_VALUE (2147483647)
getMidPoint(Int2) - Method in class jumbo.euclid.Int2
point midway between 'this' and 'p'
getMidPoint(Point3) - Method in class jumbo.euclid.Point3
mid-point of two points
getMidPoint(Real2) - Method in class jumbo.euclid.Real2
point midway between 'this' and 'p'
getMin() - Method in class jumbo.euclid.IntRange
get minimum value (MAX_VALUE if inValid)
getMin() - Method in class jumbo.euclid.RealRange
get minimum value (POSITIVE_INFINITY if inValid)
getMinimum() - Method in interface org.xmlcml.cml.FloatVal
minimum value, set by default to Double.MIN_VALUE
getMinimum() - Method in class org.xmlcml.cml.FloatValImpl
minimum value, set by default to Double.MIN_VALUE
getMinimum() - Method in interface org.xmlcml.cml.IntegerVal
minimum value, set by default to Integer.MIN_VALUE (-2147483648)
getMinimum() - Method in class org.xmlcml.cml.IntegerValImpl
minimum value, set by default to Integer.MIN_VALUE (-2147483648)
getMolecule() - Method in interface org.xmlcml.cml.Atom
an atom may be associated with one Molecule (or none)
getMolecule() - Method in class org.xmlcml.cml.AtomImpl
 
getMolecule() - Method in interface org.xmlcml.cml.Bond
 
getMolecule() - Method in class org.xmlcml.cml.BondImpl
every Bond should be associated with one molecule
getMolecule() - Method in interface org.xmlcml.cml.CMLDocument
returns the first Molecule in the document or null if none
getMolecule() - Method in class org.xmlcml.cml.CMLDocumentImpl
 
getMolecule() - Method in class org.xmlcml.noncml.SDFImpl
 
getMolecule() - Method in interface org.xmlcml.tools.SpanningTree
 
getMolecule() - Method in class org.xmlcml.tools.SpanningTreeImpl
 
getMoleculeVector() - Method in interface org.xmlcml.cml.Molecule
extracts ALL the Molecules as a Vector
getMoleculeVector() - Method in class org.xmlcml.cml.MoleculeImpl
extracts ALL the Molecules as a Vector
getName() - Method in class org.xmlcml.cml.Units
 
getNewInstance(String) - Static method in class jumbo.xml.util.Util
gets a new instance of a class from a hashtable because normal methods are very slow
getNonBuiltinArray(String) - Method in interface org.xmlcml.cml.AtomArray
 
getNonBuiltinArray(String) - Method in class org.xmlcml.cml.AtomArrayImpl
 
getNonBuiltinArray(String) - Method in interface org.xmlcml.cml.BondArray
 
getNonBuiltinArray(String) - Method in class org.xmlcml.cml.BondArrayImpl
 
getNonBuiltinArray(String) - Method in interface org.xmlcml.cml.HasBuiltinArrayNames
 
getNonBuiltinVal(String) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
 
getNonBuiltinVal(String) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
getNonBuiltinVal(String) - Method in interface org.xmlcml.cml.HasBuiltinNames
 
getNonHydrogenCount() - Method in interface org.xmlcml.cml.Atom
 
getNonHydrogenCount() - Method in class org.xmlcml.cml.AtomImpl
 
getNonRingAtomSet() - Method in interface org.xmlcml.tools.SpanningTree
get atoms not in rings
getNonRingAtomSet() - Method in class org.xmlcml.tools.SpanningTreeImpl
get atoms not in rings
getObject(double, double) - Method in class jumbo.euclid.Real2RangeHashtable
return the Object indexed by the box in which the point lies.
getObject(int, int) - Method in class jumbo.euclid.Int2RangeHashtable
return the Object indexed by the box in which the point lies.
getObject(String) - Method in class jumbo.euclid.HashedVector
return object with key key, else null
getObjectClass() - Method in class jumbo.euclid.ObjectArray
get the Class of the objects, if this is common to all, else null.
getObjectType() - Method in class jumbo.euclid.ObjectArray
get the type of the Objects as INT, etc
getOccupancy() - Method in interface org.xmlcml.cml.Atom
 
getOccupancy() - Method in class org.xmlcml.cml.AtomImpl
 
getOrder() - Method in interface org.xmlcml.cml.Bond
 
getOrder() - Method in class org.xmlcml.cml.BondImpl
 
getOrderedBondVector() - Method in interface org.xmlcml.tools.RingOverlap
get the ordered bonds in the overlap
getOrderedBondVector() - Method in class org.xmlcml.tools.RingOverlapImpl
 
getOtherAtom(Atom) - Method in interface org.xmlcml.cml.Bond
returns other atom in a 2-atom bond else null
getOtherAtom(Atom) - Method in class org.xmlcml.cml.BondImpl
returns other atom in a 2-atom bond else null
getOtherRing(Ring) - Method in interface org.xmlcml.tools.RingOverlap
if exactly two rings, return the other one.
getOtherRing(Ring) - Method in class org.xmlcml.tools.RingOverlapImpl
if exactly two rings, return the other one
getPCDATAChildNode(Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
if this has a single PCDATA child, returns it, else null
getPCDATAContent(Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
if this has a single PCDATA child, returns its string value, else null
getPoint() - Method in class jumbo.euclid.Line3
get point from line (could be any point on line)
getPoint(Int2, int, int) - Method in class jumbo.euclid.Int2Vector
get the index of the first point within a box centered on p (i.e.
getPoint(Real2, double, double) - Method in class jumbo.euclid.Real2Vector
get the index of the first point within a box centered on p (i.e.
getPoint3(int) - Method in class jumbo.euclid.Point3Vector
get a single point by REFERENCE
getPolar() - Method in class jumbo.euclid.Complex
 
getPWDName() - Static method in class jumbo.xml.util.Util
get current directory
getR() - Method in class jumbo.euclid.Complex
get as polar coords
getR() - Method in class jumbo.euclid.Polar
gets radial part
getRadian() - Method in class jumbo.euclid.Angle
get angle in radians
getRange() - Method in class jumbo.euclid.IntRange
get range (MIN_VALUE if invalid)
getRange() - Method in class jumbo.euclid.RealRange
get range (NaN if invalid)
getRange(Choice2) - Method in class jumbo.euclid.Int2Vector
get range of one coordinate
getRange(Choice2) - Method in class jumbo.euclid.Real2Vector
get range of one coordinate
getRange(Choice3) - Method in class jumbo.euclid.Point3Vector
get range of one coordinate
getRange2() - Method in class jumbo.euclid.Int2Vector
get range of both coordinates
getRange2() - Method in class jumbo.euclid.Real2Array
get max and min value of Real2_Array
getRange2() - Method in class jumbo.euclid.Real2Vector
get range of both coordinates
getRange3() - Method in class jumbo.euclid.Point3Vector
get range of all 3 coordinates
getReal() - Method in class jumbo.euclid.Complex
gets real part
getReal2(int) - Method in class jumbo.euclid.Real2Vector
get the i'th Real2
getRealArray() - Method in class jumbo.euclid.ObjectArray
return contents as a RealArray if REAL , else null
getRealValue() - Method in interface org.xmlcml.cml.FloatVal
 
getRealValue() - Method in class org.xmlcml.cml.FloatValImpl
 
getReorderedArray(IntSet) - Method in class jumbo.euclid.IntArray
reorder by index in IntSet; does NOT modify array
getReorderedArray(IntSet) - Method in class jumbo.euclid.ObjectArray
reorder by index in IntSet; does NOT modify array
getReorderedArray(IntSet) - Method in class jumbo.euclid.RealArray
reorder by index in IntSet; does NOT modify array
getRepeatedValues(Vector) - Static method in class jumbo.xml.util.Util
returns a vector of all repeated values in v.
getResidueID() - Method in interface org.xmlcml.cml.Atom
 
getResidueID() - Method in class org.xmlcml.cml.AtomImpl
 
getResidueType() - Method in interface org.xmlcml.cml.Atom
 
getResidueType() - Method in class org.xmlcml.cml.AtomImpl
 
getReverseArray() - Method in class jumbo.euclid.IntArray
return the elements in reverse order as int[]
getReverseArray() - Method in class jumbo.euclid.ObjectArray
return the elements in reverse order as Object[]
getReverseArray() - Method in class jumbo.euclid.RealArray
return the elements in reverse order as double[]
getRingNucleusTable() - Method in interface org.xmlcml.tools.SubstituentList
returns Hashtable of RingNucleus.
getRingNucleusTable() - Method in class org.xmlcml.tools.SubstituentListImpl
returns Hashtable of RingNucleus.
getRingNucleusVector() - Method in interface org.xmlcml.tools.SpanningTree
 
getRingNucleusVector() - Method in class org.xmlcml.tools.SpanningTreeImpl
get all cyclic bonds after spanning tree is created.
getRingOverlaps() - Method in interface org.xmlcml.tools.RingNucleus
find which rings have bonds in common
getRingOverlaps() - Method in class org.xmlcml.tools.RingNucleusImpl
find which rings have bonds in common
getRingOverlapVector() - Method in interface org.xmlcml.tools.Ring
 
getRingOverlapVector() - Method in class org.xmlcml.tools.RingImpl
 
getRingVector() - Method in class org.xmlcml.tools.SpanningTreeImpl
get rings
getRotationMatrix() - Method in class jumbo.euclid.Transform2
get Unitary matrix (i.e.
getRotationMatrix() - Method in class jumbo.euclid.Transform3
get Unitary matrix (i.e.
getRows() - Method in interface org.xmlcml.cml.FloatMatrix
 
getRows() - Method in class org.xmlcml.cml.FloatMatrixImpl
 
getRows() - Method in class jumbo.euclid.IntMatrix
get number of rows
getRows() - Method in class jumbo.euclid.RealMatrix
get number of rows
getScalarTripleProduct(Vector3, Vector3) - Method in class jumbo.euclid.Vector3
 
getSequence() - Method in interface org.xmlcml.cml.Molecule
extracts the FIRST Sequence if any present
getSequence() - Method in class org.xmlcml.cml.MoleculeImpl
extracts the FIRST Sequence if any present
getSequenceVector() - Method in interface org.xmlcml.cml.Molecule
extracts ALL the Sequences as a Vector
getSequenceVector() - Method in class org.xmlcml.cml.MoleculeImpl
extracts ALL the Sequences as a Vector
getSize() - Method in interface org.xmlcml.cml.FloatArray
 
getSize() - Method in class org.xmlcml.cml.FloatArrayImpl
 
getSize() - Method in interface org.xmlcml.cml.HasSize
 
getSize() - Method in interface org.xmlcml.cml.IntegerArray
 
getSize() - Method in class org.xmlcml.cml.IntegerArrayImpl
 
getSize() - Method in interface org.xmlcml.cml.StringArray
 
getSize() - Method in class org.xmlcml.cml.StringArrayImpl
 
getSSSR() - Method in interface org.xmlcml.tools.RingNucleus
"Smallest set of smallest rings".
getSSSR() - Method in class org.xmlcml.tools.RingNucleusImpl
"Smallest set of smallest rings".
getSTElement(Atom) - Method in class org.xmlcml.tools.SpanningTreeImpl
 
getStereo() - Method in interface org.xmlcml.cml.Bond
 
getStereo() - Method in class org.xmlcml.cml.BondImpl
 
getString(int) - Method in interface org.xmlcml.cml.StringArray
 
getString(int) - Method in class org.xmlcml.cml.StringArrayImpl
 
getStringSet() - Method in class jumbo.euclid.HashedVector
return set of all keys (often the names of objects)
getStringVal(int) - Method in interface org.xmlcml.cml.Bond
 
getStringVal(int) - Method in class org.xmlcml.cml.BondImpl
 
getStringValue() - Method in interface org.xmlcml.cml.AbstractStringVal
defaults to ""
getStringValue() - Method in class org.xmlcml.cml.AbstractStringValImpl
get the String content.
getStringValues() - Method in class jumbo.euclid.IntArray
returns values as strings
getStringValues() - Method in class jumbo.euclid.ObjectArray
returns values as strings
getStringValues() - Method in class jumbo.euclid.RealArray
returns values as strings
getStringVector() - Method in interface org.xmlcml.cml.FloatArray
 
getStringVector() - Method in class org.xmlcml.cml.FloatArrayImpl
 
getStringVector() - Method in interface org.xmlcml.cml.HasSize
 
getStringVector() - Method in interface org.xmlcml.cml.IntegerArray
 
getStringVector() - Method in class org.xmlcml.cml.IntegerArrayImpl
 
getStringVector() - Method in interface org.xmlcml.cml.StringArray
 
getStringVector() - Method in class org.xmlcml.cml.StringArrayImpl
 
getSubArray(int, int) - Method in class jumbo.euclid.IntArray
RHS: get a subIntArray from element start to end
getSubArray(int, int) - Method in class jumbo.euclid.ObjectArray
RHS: get a subObjectArray from element start to end
getSubArray(int, int) - Method in class jumbo.euclid.RealArray
RHS: get a subRealArray from element start to end
getSubClassedElement(String, CMLDocument) - Static method in class org.xmlcml.cml.CMLBaseImpl
create a PMRElement (usually a CMLBase) and processDOM() it.
getSubstituents(Molecule) - Method in interface org.xmlcml.tools.RingNucleus
get substituent atoms (recursively)
getSubstituents(Molecule) - Method in class org.xmlcml.tools.RingNucleusImpl
get substituent atoms (recursively)
getSuffix(String) - Static method in class jumbo.xml.util.Util
gets suffix from filename
getSymbol() - Method in class org.xmlcml.molutil.ChemicalElement
 
getSymbol(int) - Static method in class org.xmlcml.molutil.ChemicalElement
 
getTheta() - Method in class jumbo.euclid.Complex
 
getTheta() - Method in class jumbo.euclid.Polar
gets angular part
getTitle() - Method in class org.xmlcml.cml.CMLBaseImpl
 
getTitle() - Method in interface org.xmlcml.cml.HasTitle
 
getTorsion(Point3, Point3, Point3, Point3) - Static method in class jumbo.euclid.Point3
torsion angle
getTorsionVector() - Method in interface org.xmlcml.cml.Molecule
extracts ALL the Torsions as a Vector
getTorsionVector() - Method in class org.xmlcml.cml.MoleculeImpl
extracts ALL the Torsions as a Vector
getTransformationType() - Method in class jumbo.euclid.Transform2
get transformation type
getTransformationType() - Method in class jumbo.euclid.Transform3
get transformation type
getTranslation() - Method in class jumbo.euclid.Transform2
get translation component only
getTranslation() - Method in class jumbo.euclid.Transform3
get translation component only
getTranspose() - Method in class jumbo.euclid.IntMatrix
transpose matrix - creates new Matrix
getTranspose() - Method in class jumbo.euclid.RealMatrix
transpose matrix - creates new Matrix
getUnits() - Method in interface org.xmlcml.cml.FloatMatrix
 
getUnits() - Method in class org.xmlcml.cml.FloatMatrixImpl
 
getUnits() - Method in interface org.xmlcml.cml.HasUnits
 
getUnits() - Method in interface org.xmlcml.cml.NumericVal
 
getUnits() - Method in class org.xmlcml.cml.NumericValImpl
 
getUnitVector() - Method in class jumbo.euclid.Real2
get unit vector
getUnitVector() - Method in class jumbo.euclid.Vector3
 
getValidity() - Method in class org.xmlcml.cml.AbstractAtomImpl
 
getValidity() - Method in class org.xmlcml.cml.AbstractBondImpl
 
getValidity() - Method in class org.xmlcml.cml.AngleImpl
 
getValidity() - Method in class org.xmlcml.cml.CMLBaseImpl
 
getValidity() - Method in class org.xmlcml.cml.CrystalImpl
 
getValidity() - Method in class org.xmlcml.cml.FloatArrayImpl
 
getValidity() - Method in class org.xmlcml.cml.FloatValImpl
 
getValidity() - Method in class org.xmlcml.cml.IntegerArrayImpl
 
getValidity() - Method in class org.xmlcml.cml.IntegerValImpl
 
getValidity() - Method in class org.xmlcml.cml.TorsionImpl
 
getValidity() - Method in interface uk.co.demon.ursus.dom.PMRElement
Determines whether node is valid (class specific).
getValidity() - Method in class uk.co.demon.ursus.dom.PMRElementImpl
allows subclasses to decide whether the node is valid (default true)
getValue() - Method in class jumbo.xml.util.Choice2
 
getValue() - Method in class jumbo.xml.util.Choice3
 
getValue(Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
returns value of first child if this is Text else ""
getVDWRadius() - Method in class org.xmlcml.molutil.ChemicalElement
 
getVector() - Method in class jumbo.euclid.Line3
get vector from line
getVector() - Method in class jumbo.euclid.Plane3
get vector from plane
getWarnings() - Method in interface org.xmlcml.cml.CMLValidity
 
getWarnings() - Method in class org.xmlcml.cml.CMLValidityImpl
 
getX() - Method in class jumbo.euclid.Int2
get X value
getX() - Method in class jumbo.euclid.Polar
get X, Y and XY coords
getX() - Method in class jumbo.euclid.Real2
get X value
getXorY(Choice2) - Method in class jumbo.euclid.Int2Vector
get a single coordinate array - e.g.
getXorY(Choice2) - Method in class jumbo.euclid.Real2Vector
get a single coordinate array - e.g.
getXRange() - Method in class jumbo.euclid.Int2Range
get xrange
getXRange() - Method in class jumbo.euclid.Real2Range
get xrange
getXRange() - Method in class jumbo.euclid.Real3Range
get xrange
getXY() - Method in class jumbo.euclid.Int2Vector
get the coordinate coordinate array as ints x,y,x,y, ...
getXY() - Method in class jumbo.euclid.Polar
 
getXY() - Method in class jumbo.euclid.Real2Vector
get the coordinate coordinate array as doubles x,y,x,y, ...
getXY2() - Method in interface org.xmlcml.cml.Atom
 
getXY2() - Method in class org.xmlcml.cml.AtomImpl
 
getXYZ() - Method in class jumbo.euclid.Point3Vector
get the coordinate coordinate array as doubles x,y,z,x,y,z, ...
getXYZ(Choice3) - Method in class jumbo.euclid.Point3Vector
get a single coordinate array - e.g.
getXYZ3() - Method in interface org.xmlcml.cml.Atom
 
getXYZ3() - Method in class org.xmlcml.cml.AtomImpl
 
getXYZFract() - Method in interface org.xmlcml.cml.Atom
 
getXYZFract() - Method in class org.xmlcml.cml.AtomImpl
 
getY() - Method in class jumbo.euclid.Int2
get Y value
getY() - Method in class jumbo.euclid.Polar
 
getY() - Method in class jumbo.euclid.Real2
get Y value
getYRange() - Method in class jumbo.euclid.Int2Range
get yrange
getYRange() - Method in class jumbo.euclid.Real2Range
get yrange
getYRange() - Method in class jumbo.euclid.Real3Range
get yrange
getZRange() - Method in class jumbo.euclid.Real3Range
get zrange
greaterThan(Angle) - Method in class jumbo.euclid.Angle
is one angle greater than another (after normalisation)
greaterThan(double) - Method in class jumbo.euclid.Angle
is one angle greater than another (after normalisation)
greaterThanOrEquals(Angle) - Method in class jumbo.euclid.Angle
is one angle greater than or equal to another (after normalisation)
greaterThanOrEquals(double) - Method in class jumbo.euclid.Angle
is one angle greater than or equal to another (after normalisation)

H

HasAtomRefs - interface org.xmlcml.cml.HasAtomRefs.
some Objects (e.g.
HasBuiltinArrayNames - interface org.xmlcml.cml.HasBuiltinArrayNames.
 
HasBuiltinNames - interface org.xmlcml.cml.HasBuiltinNames.
 
HasConvention - interface org.xmlcml.cml.HasConvention.
 
HasCount - interface org.xmlcml.cml.HasCount.
 
HasDictRef - interface org.xmlcml.cml.HasDictRef.
 
HasExecute - interface org.xmlcml.cml.HasExecute.
Some elements can have child elements <execute> which can be executed.
HASH - Static variable in class jumbo.xml.util.Util
 
HashedVector - class jumbo.euclid.HashedVector.
A Vector whose elements are hashed via an internal Hashtable (StringSet)
HashedVector() - Constructor for class jumbo.euclid.HashedVector
 
HashedVector(int) - Constructor for class jumbo.euclid.HashedVector
HashedVector will have case-sensitive keying unless ignoreCase is StringSet.IGNORE_CASE
hashKey() - Method in interface org.xmlcml.cml.Bond
 
hashKey() - Method in class org.xmlcml.cml.BondImpl
 
HasId - interface org.xmlcml.cml.HasId.
identifies and supports those elements which can have id attributes
HasSize - interface org.xmlcml.cml.HasSize.
 
HasTitle - interface org.xmlcml.cml.HasTitle.
 
HasUnits - interface org.xmlcml.cml.HasUnits.
 
HATCH - Static variable in interface org.xmlcml.cml.AbstractBond
hatch bond
help() - Static method in class org.xmlcml.cml.CMLBaseImpl
 
href - Variable in class org.xmlcml.cml.LinkImpl
 
hybridization - Variable in class org.xmlcml.cml.AtomImpl
 
HYDROGEN_COUNT - Static variable in interface org.xmlcml.cml.ConventionCriteria
 
HYDROGEN_COUNT_FLOAT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
HYDROGEN_COUNT_INT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
hydrogenCount - Variable in class org.xmlcml.cml.AtomImpl
 

I

id - Variable in class org.xmlcml.cml.CMLBaseImpl
 
id - Variable in class org.xmlcml.cml.Coordinate3
 
id - Variable in class org.xmlcml.tools.RingImpl
each ring has a unique ID
ID - Static variable in interface org.xmlcml.cml.HasId
"id" attribute name
IDLIST - Static variable in interface uk.co.demon.ursus.dom.PMRNode
output ids
ignorableWhitespace(char[], int, int) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive notification of ignorable whitespace in element content.
IGNORE_CASE - Static variable in class jumbo.euclid.StringSet
 
IGNORECASE - Static variable in class jumbo.xml.util.Util
 
IllCondMatrixException - exception jumbo.euclid.IllCondMatrixException.
thrown by inversion, eigenvalue routines, etc ; superclass for SingMatrixException, NonPositiveDefiniteException, etc.
IllCondMatrixException() - Constructor for class jumbo.euclid.IllCondMatrixException
 
IllCondMatrixException(String) - Constructor for class jumbo.euclid.IllCondMatrixException
 
implementationConstraint(int) - Method in class org.xmlcml.cml.Convention
 
implementationConstraint(int) - Method in interface org.xmlcml.cml.ConventionCriteria
 
includes(double) - Method in class jumbo.euclid.RealRange
is a double within a RealRange? If inValid, return false
includes(int) - Method in class jumbo.euclid.IntRange
is a int within a IntRange? If inValid, return false
includes(Int2) - Method in class jumbo.euclid.Int2Range
is an Int2 within a Int2Range?
includes(Int2Range) - Method in class jumbo.euclid.Int2Range
is one Int2Range completely within another?
includes(IntRange) - Method in class jumbo.euclid.IntRange
does one range include another?
includes(Point3) - Method in class jumbo.euclid.Real3Range
is a Point3 within a Real3Range?
includes(Real2) - Method in class jumbo.euclid.Real2Range
is an Real2 within a Real2Range?
includes(Real2Range) - Method in class jumbo.euclid.Real2Range
is one Real2Range completely within another?
includes(RealRange) - Method in class jumbo.euclid.RealRange
does one range include another?
INCREASE - Static variable in interface org.xmlcml.cml.AbstractBond
 
indexOf(String) - Method in class jumbo.euclid.HashedVector
serial number of object with key, else -1
indexOf(String) - Method in class jumbo.euclid.StringSet
index of a given String (default is case-sensitive); -1 if not found
indexOf(String, String[], int) - Static method in class jumbo.xml.util.Util
get the index of a String in an array
indexOfBalancedBracket(char, String) - Static method in class jumbo.xml.util.Util
return index of balanced bracket; -1 for none.
indexOfLargestElement() - Method in class jumbo.euclid.IntArray
index of largest element; returns -1 if zero element array
indexOfLargestElement() - Method in class jumbo.euclid.IntMatrix
get index of largest element
indexOfLargestElement() - Method in class jumbo.euclid.RealArray
index of largest element; returns -1 if zero element array
indexOfLargestElement() - Method in class jumbo.euclid.RealMatrix
get index of largest element
indexOfLargestElementInColumn(int) - Method in class jumbo.euclid.IntMatrix
get index of largest element in column
indexOfLargestElementInColumn(int) - Method in class jumbo.euclid.RealMatrix
get index of largest element in column
indexOfLargestElementInRow(int) - Method in class jumbo.euclid.IntMatrix
get index of largest element in row (or -1 if default matrix)
indexOfLargestElementInRow(int) - Method in class jumbo.euclid.RealMatrix
get index of largest element in row (or -1 if default matrix)
indexOfSmallestElement() - Method in class jumbo.euclid.IntArray
index of smallest element
indexOfSmallestElement() - Method in class jumbo.euclid.IntMatrix
get index of smallest element
indexOfSmallestElement() - Method in class jumbo.euclid.RealArray
index of smallest element
indexOfSmallestElement() - Method in class jumbo.euclid.RealMatrix
get index of smallest element
indexOfSmallestElementInColumn(int) - Method in class jumbo.euclid.IntMatrix
get index of smallest elem in column
indexOfSmallestElementInColumn(int) - Method in class jumbo.euclid.RealMatrix
get index of smallest elem in column
indexOfSmallestElementInRow(int) - Method in class jumbo.euclid.IntMatrix
get index of smallest element in row
indexOfSmallestElementInRow(int) - Method in class jumbo.euclid.RealMatrix
get index of smallest element in row
indexSortAscending() - Method in class jumbo.euclid.IntArray
 
indexSortAscending() - Method in class jumbo.euclid.ObjectArray
 
indexSortAscending() - Method in class jumbo.euclid.RealArray
 
indexSortAscending() - Method in class jumbo.euclid.StringSet
 
indexSortDescending() - Method in class jumbo.euclid.IntArray
sort array into descending order via indexes; array NOT MODIFIED
indexSortDescending() - Method in class jumbo.euclid.ObjectArray
sort array into descending order via indexes; array NOT MODIFIED
indexSortDescending() - Method in class jumbo.euclid.RealArray
sort array into descending order via indexes; array NOT MODIFIED
indexSortDescending() - Method in class jumbo.euclid.StringSet
sort elem into descending order via indexes; elem NOT MODIFIED
inertialAxes(RealArray, RealSquareMatrix, IllCondMatrixException) - Method in class jumbo.euclid.Point3Vector
get Inertial axes; do not throw exception for pathological cases, but return it.
inertialTensor() - Method in class jumbo.euclid.Point3Vector
get inertial tensor (second moments)
init() - Method in class org.xmlcml.cml.FloatValImpl
 
init() - Method in class org.xmlcml.cml.IntegerValImpl
 
init() - Method in class org.xmlcml.cml.StringValImpl
 
initArray(int, double[], double) - Static method in class jumbo.euclid.Real
set an array to given value
initArray(int, int[], int) - Static method in class jumbo.euclid.Int
set an array to given value
initialise() - Method in class uk.co.demon.ursus.dom.PMRElementImpl
 
innerProduct() - Method in class jumbo.euclid.IntArray
inner product - same as dotProduct
innerProduct() - Method in class jumbo.euclid.RealArray
inner product - same as dotProduct
input(BufferedReader) - Method in class org.xmlcml.noncml.JMEImpl
 
input(BufferedReader) - Method in class org.xmlcml.noncml.MDLMolImpl
 
input(BufferedReader) - Method in interface org.xmlcml.noncml.NonCMLDocument
input from a Reader.
input(BufferedReader) - Method in class org.xmlcml.noncml.SDFImpl
 
input(BufferedReader) - Method in class org.xmlcml.noncml.SMILESImpl
 
input(BufferedReader) - Method in class org.xmlcml.noncml.XYZImpl
 
input(String) - Method in interface org.xmlcml.noncml.SMILES
input from the Smiles String
input(String) - Method in class org.xmlcml.noncml.SMILESImpl
input from the Smiles String
inputCML - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
the CML object created from the input legacy
inputCMLMolecule - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
the molecule created from the input legacy
inRange(IntRange) - Method in class jumbo.euclid.IntArray
return index of elements within a given range
inRange(RealRange) - Method in class jumbo.euclid.RealArray
return index of elements within a given range
insertArray(int, IntArray) - Method in class jumbo.euclid.IntArray
insert a IntArray at position elem and expand
insertArray(int, ObjectArray) - Method in class jumbo.euclid.ObjectArray
insert a ObjectArray at position elem and expand
insertArray(int, RealArray) - Method in class jumbo.euclid.RealArray
insert a RealArray at position elem and expand
insertColumnData(int, IntArray) - Method in class jumbo.euclid.IntMatrix
add data as column or column block into matrix and expand
insertColumnData(int, IntMatrix) - Method in class jumbo.euclid.IntMatrix
add data as column or column block into matrix and expand
insertColumnData(int, RealArray) - Method in class jumbo.euclid.RealMatrix
add data as column or column block into matrix and expand
insertColumnData(int, RealMatrix) - Method in class jumbo.euclid.RealMatrix
add data as column or column block into matrix and expand
insertColumns(int, int) - Method in class jumbo.euclid.IntMatrix
insert a hole into the matric and expand
insertColumns(int, int) - Method in class jumbo.euclid.RealMatrix
insert a hole into the matric and expand
insertElementAt(int, double) - Method in class jumbo.euclid.RealArray
insert element and expand; if outside range, take no action
insertElementAt(int, int) - Method in class jumbo.euclid.IntArray
insert element and expand; if outside range, take no action
insertElementAt(int, Object) - Method in class jumbo.euclid.ObjectArray
insert element and expand; if outside range, take no action
insertRowData(int, IntArray) - Method in class jumbo.euclid.IntMatrix
insert row of data into matrix and expand
insertRowData(int, IntMatrix) - Method in class jumbo.euclid.IntMatrix
insert 2 or more adjacent rows of data into matrix and expand
insertRowData(int, RealArray) - Method in class jumbo.euclid.RealMatrix
insert row of data into matrix and expand
insertRowData(int, RealMatrix) - Method in class jumbo.euclid.RealMatrix
insert 2 or more adjacent rows of data into matrix and expand
insertRows(int, int) - Method in class jumbo.euclid.IntMatrix
make space for new rows in matrix and expand
insertRows(int, int) - Method in class jumbo.euclid.RealMatrix
make space for new rows in matrix and expand
Int - class jumbo.euclid.Int.
Int supports various utilities for integers.
INT - Static variable in class jumbo.euclid.ObjectArray
 
Int() - Constructor for class jumbo.euclid.Int
 
Int2 - class jumbo.euclid.Int2.
Int2 - a pair of integers - no other assumptions
Int2() - Constructor for class jumbo.euclid.Int2
 
Int2(Int2) - Constructor for class jumbo.euclid.Int2
copy constructor
Int2(int, int) - Constructor for class jumbo.euclid.Int2
 
Int2Range - class jumbo.euclid.Int2Range.
Int2Range - 2-D int limits
Int2Range() - Constructor for class jumbo.euclid.Int2Range
 
Int2Range(Int2Range) - Constructor for class jumbo.euclid.Int2Range
copy constructor
Int2Range(IntRange, IntRange) - Constructor for class jumbo.euclid.Int2Range
initialise with min and max values;
Int2RangeHashtable - class jumbo.euclid.Int2RangeHashtable.
Hashtable indexed by boxes, which return an object when a box contains a point (i.e.
Int2RangeHashtable() - Constructor for class jumbo.euclid.Int2RangeHashtable
 
Int2Vector - class jumbo.euclid.Int2Vector.
Int2Vector - a (Java) Vector of Int2s.
Int2Vector() - Constructor for class jumbo.euclid.Int2Vector
 
Int2Vector(int) - Constructor for class jumbo.euclid.Int2Vector
create a Vector with given number of points
Int2Vector(int[]) - Constructor for class jumbo.euclid.Int2Vector
Formed by feeding in an existing array to a 2xn matrix.
Int2Vector(Int2Vector) - Constructor for class jumbo.euclid.Int2Vector
copy constructor from Int2Vector COPIES pv
Int2Vector(IntArray) - Constructor for class jumbo.euclid.Int2Vector
constructor from IntArray - by REFERENCE
Int2Vector(int, int[], int[]) - Constructor for class jumbo.euclid.Int2Vector
from two parallel arrays of x, y - by REFERENCE
intArray - Variable in class org.xmlcml.cml.IntegerArrayImpl
 
IntArray - class jumbo.euclid.IntArray.
IntArray - array of ints
IntArray() - Constructor for class jumbo.euclid.IntArray
default is an array of zero points
IntArray(int) - Constructor for class jumbo.euclid.IntArray
creates n-element array initialised to 0
IntArray(int[]) - Constructor for class jumbo.euclid.IntArray
from an existing int[] (which knows its length)
IntArray(IntArray) - Constructor for class jumbo.euclid.IntArray
copy constructor
IntArray(IntArray, IntArray) - Constructor for class jumbo.euclid.IntArray
use another IntArray to subscript this one; i.e.
IntArray(IntArray, int, int) - Constructor for class jumbo.euclid.IntArray
subarray of another array - inclusive; if low > high or other silly indices, creates default array
IntArray(int, int) - Constructor for class jumbo.euclid.IntArray
set all elements of the array to a given value
IntArray(int, int[]) - Constructor for class jumbo.euclid.IntArray
Formed by feeding in an existing array; requires the size.
IntArray(int, int, int) - Constructor for class jumbo.euclid.IntArray
This gives a nelem-element array initialised to elem1+(i-1)*delta
IntArray(int, String, int) - Constructor for class jumbo.euclid.IntArray
Create a given 'shape' of array for data filtering.
IntArray(String) - Constructor for class jumbo.euclid.IntArray
from a String with space-separated strings representing Ints
IntArray(String[]) - Constructor for class jumbo.euclid.IntArray
from an array of Strings (which must represent Ints)
INTEGER - Static variable in interface org.xmlcml.cml.CMLBase
 
INTEGER_TYPE - Static variable in interface org.xmlcml.cml.CMLBase
 
IntegerArray - interface org.xmlcml.cml.IntegerArray.
 
INTEGERARRAY - Static variable in interface org.xmlcml.cml.CMLBase
 
IntegerArrayImpl - class org.xmlcml.cml.IntegerArrayImpl.
 
IntegerArrayImpl() - Constructor for class org.xmlcml.cml.IntegerArrayImpl
 
IntegerArrayImpl(Document) - Constructor for class org.xmlcml.cml.IntegerArrayImpl
new IntegerArray in document context
IntegerArrayImpl(Element) - Constructor for class org.xmlcml.cml.IntegerArrayImpl
 
IntegerVal - interface org.xmlcml.cml.IntegerVal.
holds an integer with max and minimum values
IntegerValImpl - class org.xmlcml.cml.IntegerValImpl.
holds an integer with max and minimum values
IntegerValImpl() - Constructor for class org.xmlcml.cml.IntegerValImpl
 
IntegerValImpl(Document) - Constructor for class org.xmlcml.cml.IntegerValImpl
new IntegerVal in document context
IntegerValImpl(Document, int, String, String, String, String, String, Units, int, int) - Constructor for class org.xmlcml.cml.IntegerValImpl
 
IntegerValImpl(Element) - Constructor for class org.xmlcml.cml.IntegerValImpl
 
IntegerValImpl(String, Document) - Constructor for class org.xmlcml.cml.IntegerValImpl
new object in document context
intersectionWith(Int2Range) - Method in class jumbo.euclid.Int2Range
intersect two ranges and take the range common to both; return invalid range if no overlap or either is null/invalid
intersectionWith(IntRange) - Method in class jumbo.euclid.IntRange
intersect two ranges and take the range common to both; return invalid range if no overlap
intersectionWith(IntSet) - Method in class jumbo.euclid.IntSet
intersect two sets (i.e.
intersectionWith(Real2Range) - Method in class jumbo.euclid.Real2Range
intersect two ranges and take the range common to both; return invalid range if no overlap or either is null/invalid
intersectionWith(RealRange) - Method in class jumbo.euclid.RealRange
intersect two ranges and take the range common to both; return invalid range if no overlap
IntMatrix - class jumbo.euclid.IntMatrix.
IntMatrix - rectangular integer matrix class
IntMatrix() - Constructor for class jumbo.euclid.IntMatrix
Default matrix, with cols = rows = 0
IntMatrix(int[][]) - Constructor for class jumbo.euclid.IntMatrix
COPY from an existing matrix - check that it is rectangular
IntMatrix(int, int) - Constructor for class jumbo.euclid.IntMatrix
A rows*cols matrix set to 0 (rows or cols < 0 defaults to 0)
IntMatrix(int, int, int) - Constructor for class jumbo.euclid.IntMatrix
initalises all elements in the array with a given int[]
IntMatrix(int, int, int[]) - Constructor for class jumbo.euclid.IntMatrix
Formed by feeding in an existing 1-D array to a rowsXcols matrix.
IntMatrix(IntMatrix) - Constructor for class jumbo.euclid.IntMatrix
copy constructor - COPIES the other matrix
IntMatrix(IntMatrix, int, int, int, int) - Constructor for class jumbo.euclid.IntMatrix
submatrix of another matrix; fails if lowrow > hirow, lowrow < 0, etc.
IntRange - class jumbo.euclid.IntRange.
IntRange - maximum and minimum values
IntRange() - Constructor for class jumbo.euclid.IntRange
creates invalid range from MAX_VALUE to MIN_VALUE
IntRange(int, int) - Constructor for class jumbo.euclid.IntRange
initialise with min and max values; if minv > maxv create inValid IntRange
IntRange(IntRange) - Constructor for class jumbo.euclid.IntRange
copy constructor
IntRangeVector - class jumbo.euclid.IntRangeVector.
a Vector of IntRanges - will be developed so that overlapping ranges can be merged or deleted.
IntRangeVector() - Constructor for class jumbo.euclid.IntRangeVector
 
IntSet - class jumbo.euclid.IntSet.
public class IntSet Stores a unique set of ints (i.e.
IntSet() - Constructor for class jumbo.euclid.IntSet
 
IntSet(int) - Constructor for class jumbo.euclid.IntSet
creates an IntSet with the integers 0...nelem-1
IntSet(int[]) - Constructor for class jumbo.euclid.IntSet
make from an int[] - all values must be distinct;
IntSet(int, int) - Constructor for class jumbo.euclid.IntSet
creates an IntSet with the integers start...end (if start <= end)
IntSet(IntSet) - Constructor for class jumbo.euclid.IntSet
copy constructor
IntSet(IntSet, IntSet) - Constructor for class jumbo.euclid.IntSet
use another IntSet to subscript this one; i.e.
IntSquareMatrix - class jumbo.euclid.IntSquareMatrix.
IntSquareMatrix - square matrix class
IntSquareMatrix() - Constructor for class jumbo.euclid.IntSquareMatrix
This gives a default matrix, with cols = rows = 0.
IntSquareMatrix(int) - Constructor for class jumbo.euclid.IntSquareMatrix
This gives a null matrix
IntSquareMatrix(int[][]) - Constructor for class jumbo.euclid.IntSquareMatrix
form from a Java 2-D array (it holds row and column count)
IntSquareMatrix(int, int) - Constructor for class jumbo.euclid.IntSquareMatrix
initalises all elements in the array with a given int[]
IntSquareMatrix(int, int[]) - Constructor for class jumbo.euclid.IntSquareMatrix
Formed by feeding in an existing array to a colsXcols matrix.
IntSquareMatrix(IntMatrix) - Constructor for class jumbo.euclid.IntSquareMatrix
assign a IntMatrix - i.e.
IntSquareMatrix(IntMatrix, int, int, int) - Constructor for class jumbo.euclid.IntSquareMatrix
submatrix of another matrix
IntSquareMatrix(IntSquareMatrix) - Constructor for class jumbo.euclid.IntSquareMatrix
 
intValue - Variable in class org.xmlcml.cml.IntegerValImpl
 
inverseMap() - Method in class jumbo.euclid.IntSet
Inverse mapping - see introduction.
invert(Hashtable) - Static method in class jumbo.xml.util.Util
invert a Hashtable by interchanging keys and values.
isAllowedFormat(String) - Static method in class jumbo.xml.util.Util
 
isAntiparallelTo(Line3) - Method in class jumbo.euclid.Line3
are two lines antiparallel
isAntiparallelTo(Plane3) - Method in class jumbo.euclid.Plane3
are two planes antiparallel
isClear() - Method in class jumbo.euclid.IntArray
is the array filled with zeros?
isClear() - Method in class jumbo.euclid.RealArray
is the array filled with zeros?
isEmptyAttribute(String) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
UTILITIES
isEqual(double, double) - Static method in class jumbo.euclid.Real
are two numbers equal within EPSILON
isEqual(double, double, double) - Static method in class jumbo.euclid.Real
are two numbers equal within epsilon
isEqual(int, double[], double[]) - Static method in class jumbo.euclid.Real
are all members of an array equal within EPSILON?
isHomogeneous() - Method in class jumbo.euclid.ObjectArray
 
isIdenticalTo(Vector3) - Method in class jumbo.euclid.Vector3
are two vectors identical?
isImproperRotation() - Method in class jumbo.euclid.RealSquareMatrix
is matrix an improper rotation?
isLowerTriangular() - Method in class jumbo.euclid.IntSquareMatrix
is matrix lower triangular (including diagonal)?
isLowerTriangular() - Method in class jumbo.euclid.RealSquareMatrix
is matrix lower triangular (including diagonal)?
isOrigin() - Method in class jumbo.euclid.Point3
is a point at Origin?
isOrthogonal() - Method in class jumbo.euclid.RealMatrix
is matrix Orthogonal (row-wise)? i.e.
isOrthogonal() - Method in class jumbo.euclid.RealSquareMatrix
is matrix orthogonal? (rowwise calculation)
isOrthonormal() - Method in class jumbo.euclid.RealSquareMatrix
is matrix unitary (orthonormal)? (synonym for isUnitary())
isotope - Variable in class org.xmlcml.cml.AtomImpl
 
ISOTOPE_FLOAT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
ISOTOPE_INT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
isParallelTo(Line3) - Method in class jumbo.euclid.Line3
are two lines parallel (not antiparallel)
isParallelTo(Plane3) - Method in class jumbo.euclid.Plane3
are two planes parallel (not antiparallel)
isRegisteredApplet(Applet) - Static method in class jumbo.xml.util.Util
retrive that an object is an applet rather than an application.
isRightMouseClick(MouseEvent) - Static method in class jumbo.xml.util.Util
a crude way of identifying a right mouse click (because I left the Java book behind)
isSquare() - Method in class jumbo.euclid.IntMatrix
is the matrix square?
isSquare() - Method in class jumbo.euclid.RealMatrix
is the matrix square?
isSymmetric() - Method in class jumbo.euclid.IntSquareMatrix
is matrix symmetric?
isSymmetric() - Method in class jumbo.euclid.RealSquareMatrix
is matrix symmetric?
isUnit() - Method in class jumbo.euclid.IntSquareMatrix
is it a unit matrix?
isUnit() - Method in class jumbo.euclid.RealSquareMatrix
is it a unit matrix?
isUnitary() - Method in class jumbo.euclid.RealSquareMatrix
 
isUpperTriangular() - Method in class jumbo.euclid.IntSquareMatrix
is matrix UpperTriangular?
isUpperTriangular() - Method in class jumbo.euclid.RealSquareMatrix
is matrix UpperTriangular?
isValid() - Method in interface org.xmlcml.cml.CMLBase
convenience to avoid analysing Validity
isValid() - Method in class org.xmlcml.cml.CMLBaseImpl
 
isValid() - Method in class org.xmlcml.cml.CMLValidityImpl
 
isValid() - Method in interface uk.co.demon.ursus.dom.Validity
Determines whether node is valid (class specific).
isValid() - Method in class uk.co.demon.ursus.dom.ValidityImpl
Determines whether node is valid (class specific).
isValid() - Method in class jumbo.euclid.Int2Range
a Int2Range is valid if both its constituent ranges are
isValid() - Method in class jumbo.euclid.IntRange
a Range is only valid if its maxval is not less than its minval; this tests for uninitialised ranges
isValid() - Method in class jumbo.euclid.Real2Range
a Real2Range is valid if both its constituent ranges are
isValid() - Method in class jumbo.euclid.RealRange
a Range is only valid if its maxval is not less than its minval; this tests for uninitialised ranges
isZero() - Method in class jumbo.euclid.Vector3
is a vector null?
isZero(double) - Static method in class jumbo.euclid.Real
is a number zero within EPSILON
isZero(double, double) - Static method in class jumbo.euclid.Real
is a number zero within epsilon
iterator() - Method in interface org.xmlcml.tools.ToolHashSet
create an Iterator

J

JME - interface org.xmlcml.noncml.JME.
class for JME files (Peter Ertl's applet);
JME - Static variable in interface org.xmlcml.noncml.NonCMLDocument
 
jmeBondOrder(String) - Static method in class org.xmlcml.noncml.JMEImpl
translates "CML" codes into jme numbers
jmeBondStereo(String) - Static method in class org.xmlcml.noncml.JMEImpl
translates JUMBO-MOL codes into jme numbers
JMEImpl - class org.xmlcml.noncml.JMEImpl.
class to read and write JME files (Peter Ertl's applet)
JMEImpl(BufferedReader, String) - Constructor for class org.xmlcml.noncml.JMEImpl
form a JME object from a local file
JMEImpl(Molecule) - Constructor for class org.xmlcml.noncml.JMEImpl
form a JME object from a CML file

K

KEKULE - Static variable in interface org.xmlcml.cml.ConventionCriteria
 
keys() - Method in interface jumbo.xml.util.XHashtable
from Hashtable

L

LANGLE - Static variable in class jumbo.xml.util.Util
 
largestElement() - Method in class jumbo.euclid.IntArray
value of largest element
largestElement() - Method in class jumbo.euclid.IntMatrix
get largest element
largestElement() - Method in class jumbo.euclid.RealArray
value of largest element
largestElement() - Method in class jumbo.euclid.RealMatrix
get largest element
largestElementInColumn(int) - Method in class jumbo.euclid.IntMatrix
get largest element in a column
largestElementInColumn(int) - Method in class jumbo.euclid.RealMatrix
get largest element in a column
largestElementInRow(int) - Method in class jumbo.euclid.IntMatrix
get largest element in a row
largestElementInRow(int) - Method in class jumbo.euclid.RealMatrix
get largest element in a row
LARK - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 
LBRAK - Static variable in class jumbo.xml.util.Util
 
LCURLY - Static variable in class jumbo.xml.util.Util
 
leftTrim(String) - Static method in class jumbo.xml.util.Util
remove leading blanks
length - Variable in class org.xmlcml.cml.BondImpl
 
LENGTH - Static variable in interface org.xmlcml.cml.AbstractBond
 
lessThan(Angle) - Method in class jumbo.euclid.Angle
is one angle less than another (after normalisation)
lessThan(double) - Method in class jumbo.euclid.Angle
is one angle less than another (after normalisation)
lessThanOrEquals(Angle) - Method in class jumbo.euclid.Angle
is one angle less than or equal to another (after normalisation)
lessThanOrEquals(double) - Method in class jumbo.euclid.Angle
is one angle less than or equal to another (after normalisation)
ligandVector - Variable in class org.xmlcml.cml.AtomImpl
 
line - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
and uses a line as the container
Line3 - class jumbo.euclid.Line3.
Line3 - 3-dimensional line class
Line3() - Constructor for class jumbo.euclid.Line3
 
Line3(Line3) - Constructor for class jumbo.euclid.Line3
copy constructor
Line3(Point3, Point3) - Constructor for class jumbo.euclid.Line3
make a line from two Point3s
Line3(Point3, Vector3) - Constructor for class jumbo.euclid.Line3
formed from line components
Line3(Vector3, Point3) - Constructor for class jumbo.euclid.Line3
other way round!
Link - interface org.xmlcml.cml.Link.
 
LINK - Static variable in interface org.xmlcml.cml.CMLBase
 
LinkImpl - class org.xmlcml.cml.LinkImpl.
 
LinkImpl() - Constructor for class org.xmlcml.cml.LinkImpl
 
LinkImpl(Document) - Constructor for class org.xmlcml.cml.LinkImpl
new Link in context
LinkImpl(Element) - Constructor for class org.xmlcml.cml.LinkImpl
 
linkVector - Variable in class org.xmlcml.noncml.SMILESImpl
 
LINKVECTORSIZE - Static variable in interface org.xmlcml.noncml.SMILES
maximum number of concurrent links (SMILES limit is 9);
List - interface org.xmlcml.cml.List.
 
LIST - Static variable in interface org.xmlcml.cml.CMLBase
 
ListImpl - class org.xmlcml.cml.ListImpl.
 
ListImpl() - Constructor for class org.xmlcml.cml.ListImpl
 
ListImpl(Document) - Constructor for class org.xmlcml.cml.ListImpl
new List in context
ListImpl(Element) - Constructor for class org.xmlcml.cml.ListImpl
 
LOCAL - Static variable in interface uk.co.demon.ursus.dom.PMRElement
local name
log(String) - Static method in class jumbo.xml.util.Util
 
longerThan(Vector3) - Method in class jumbo.euclid.Vector3
vector length > vector length?
lowerTriangle() - Method in class jumbo.euclid.IntSquareMatrix
copy lower triangle into linear array; order: 0,0; 1,0; 1,1; 2,0 ..
lowerTriangle() - Method in class jumbo.euclid.RealSquareMatrix
copy lower triangle into linear array; order: 0,0; 1,0; 1,1; 2,0 ..
LSQUARE - Static variable in class jumbo.xml.util.Util
 

M

main(String[]) - Static method in class org.xmlcml.cml.CMLBaseImpl
 
main(String[]) - Static method in class org.xmlcml.cml.CMLDocumentImpl
 
main(String[]) - Static method in class org.xmlcml.cml.CMLDOMSAXBuilderImpl
Main entry point for an application.
main(String[]) - Static method in class org.xmlcml.noncml.JMEImpl
 
main(String[]) - Static method in class org.xmlcml.noncml.MDLMolImpl
 
main(String[]) - Static method in class org.xmlcml.noncml.SDFImpl
 
main(String[]) - Static method in class org.xmlcml.noncml.SMILESImpl
 
main(String[]) - Static method in class org.xmlcml.noncml.XYZImpl
 
main(String[]) - Static method in class uk.co.demon.ursus.dom.PMRDocumentImpl
 
main(String[]) - Static method in class uk.co.demon.ursus.dom.SAXAdapter
Main entry point for an application.
main(String[]) - Static method in class uk.co.demon.ursus.dom.SAXDOMBuilder
Main entry point for an application.
main(String[]) - Static method in class jumbo.xml.util.Util
 
main(String[]) - Static method in class jumbo.euclid.Angle
 
main(String[]) - Static method in class jumbo.euclid.IntArray
 
main(String[]) - Static method in class jumbo.euclid.IntMatrix
tests IntMatrix routines = new IntMatrix
main(String[]) - Static method in class jumbo.euclid.IntRange
tests IntRange routines
main(String[]) - Static method in class jumbo.euclid.Line3
tests Line3 routines
main(String[]) - Static method in class jumbo.euclid.ObjectArray
 
main(String[]) - Static method in class jumbo.euclid.Plane3
tests Plane3 routines
main(String[]) - Static method in class jumbo.euclid.Point3
tests Point3 routines = new Point3
main(String[]) - Static method in class jumbo.euclid.RealArray
 
main(String[]) - Static method in class jumbo.euclid.RealMatrix
tests RealMatrix routines = new RealMatrix
main(String[]) - Static method in class jumbo.euclid.RealRange
tests RealRange routines
main(String[]) - Static method in class jumbo.euclid.RealSquareMatrix
tests RealSquareMatrix routines
main(String[]) - Static method in class jumbo.euclid.SortableString
 
main(String[]) - Static method in class jumbo.euclid.StringSet
 
main(String[]) - Static method in class jumbo.euclid.Transform2
tests Transform2 routines
main(String[]) - Static method in class jumbo.euclid.Transform3
tests Transform3 routines
main(String[]) - Static method in class jumbo.euclid.Vector3
tests Vector3 routines = new Vector3
main(String[]) - Static method in class jumbo.xml.util.XHashtableImpl
 
main(String[]) - Static method in class org.xmlcml.test.SAXAtomCounter
 
main(String[]) - Static method in class jumbo.xml.util.CyclicVector
 
main(String[]) - Static method in class org.xmlcml.tools.RingImpl
 
main(String[]) - Static method in class org.xmlcml.tools.SpanningTreeImpl
 
main(String[]) - Static method in class org.xmlcml.tools.ToolHashSetImpl
 
makeAbsoluteURL(Applet, String) - Static method in class jumbo.xml.util.Util
If a URL is relative, make it absolute against either the current directory (application) or codebase (applet)
makeAbsoluteURL(String) - Static method in class jumbo.xml.util.Util
If a URL is relative, make it absolute against the current directory.
makeDirectory(String) - Static method in class jumbo.xml.util.Util
truncate filename suffix to make a directory name (without file.separator)
makePoint(double, double) - Method in class jumbo.euclid.Real2
make a new point at (dist, theta) from this
makeString() - Method in class jumbo.euclid.Int2Vector
we are not allowed a toString() here, as Vector is a final class
makeString() - Method in class jumbo.euclid.IntRangeVector
 
makeString() - Method in class jumbo.euclid.Real2Vector
we are not allowed a toString() here, as Vector is a final class
makeString() - Method in class jumbo.euclid.RealRangeVector
 
MatrixShapeException - exception jumbo.euclid.MatrixShapeException.
There may be several matrix shape errors such as non-rectangular, non-square and possibly non-triangular, non-lowerTriangular, etc.
MatrixShapeException() - Constructor for class jumbo.euclid.MatrixShapeException
 
MatrixShapeException(String) - Constructor for class jumbo.euclid.MatrixShapeException
 
MAX - Static variable in interface org.xmlcml.cml.NumericVal
 
MAXELEM - Static variable in class org.xmlcml.molutil.ChemicalElement
maximum number of elements
maximum - Variable in class org.xmlcml.cml.FloatValImpl
 
maximum - Variable in class org.xmlcml.cml.IntegerValImpl
 
maxval - Variable in class jumbo.euclid.IntRange
maximum of range
maxval - Variable in class jumbo.euclid.RealRange
maximum of range
MAY - Static variable in interface org.xmlcml.cml.ConventionCriteria
 
MDLMol - interface org.xmlcml.noncml.MDLMol.
class to read (? and write?) mdl-molfiles as described in chemical MIME.
MDLMOL - Static variable in interface org.xmlcml.noncml.NonCMLDocument
 
MDLMolImpl - class org.xmlcml.noncml.MDLMolImpl.
class to read (? and write?) mdl-molfiles as described in chemical MIME.
MDLMolImpl() - Constructor for class org.xmlcml.noncml.MDLMolImpl
 
MDLMolImpl(BufferedReader, String) - Constructor for class org.xmlcml.noncml.MDLMolImpl
form a MDLMol object from a local file
MDLMolImpl(Molecule) - Constructor for class org.xmlcml.noncml.MDLMolImpl
form a MDLMol object from a CML file
mergeSpiro(Atom, RingNucleus) - Method in interface org.xmlcml.tools.RingNucleus
 
mergeSpiro(Atom, RingNucleus) - Method in class org.xmlcml.tools.RingNucleusImpl
 
message(String) - Static method in class jumbo.xml.util.Util
message - nothing fancy at present
MIN - Static variable in interface org.xmlcml.cml.NumericVal
 
minimum - Variable in class org.xmlcml.cml.FloatValImpl
 
minimum - Variable in class org.xmlcml.cml.IntegerValImpl
 
MINUS - Static variable in class jumbo.xml.util.Util
 
minval - Variable in class jumbo.euclid.IntRange
minimum of range
minval - Variable in class jumbo.euclid.RealRange
minimum of range
molBondOrder(String) - Static method in class org.xmlcml.noncml.MDLMolImpl
translates "CML"-MOL codes into MDL numbers
molBondStereo(String) - Static method in class org.xmlcml.noncml.MDLMolImpl
translates JUMBO-MOL codes into MDL numbers
molecule - Variable in class org.xmlcml.cml.AtomImpl
Atom know which molecule it belongs to.
molecule - Variable in class org.xmlcml.cml.BondImpl
 
molecule - Variable in class org.xmlcml.tools.ChainSetImpl
 
Molecule - interface org.xmlcml.cml.Molecule.
Molecule is the basic container for Atoms, Bonds, Electrons Angles, Torsion, Sequences, Features, Crystal and other objects.
MOLECULE - Static variable in interface org.xmlcml.cml.CMLBase
 
MoleculeImpl - class org.xmlcml.cml.MoleculeImpl.
Molecule is the basic container for Atoms, Bonds, Electrons Angles, Torsion, Sequences, Features, Crystal and other objects.
MoleculeImpl() - Constructor for class org.xmlcml.cml.MoleculeImpl
 
MoleculeImpl(Document) - Constructor for class org.xmlcml.cml.MoleculeImpl
new Molecule in context
MoleculeImpl(Element) - Constructor for class org.xmlcml.cml.MoleculeImpl
replace existing tree nodes by a Molecule
moleculeVector - Variable in class org.xmlcml.cml.MoleculeImpl
 
moveToCentroid() - Method in class jumbo.euclid.Point3Vector
centre molecule on origin - translate to centroid MODIFIES PV
MSXML - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 
multiply(Complex) - Method in class jumbo.euclid.Complex
multiply a complex by a complex
multiply(IntArray) - Method in class jumbo.euclid.IntMatrix
matrix multiplication of a COLUMN vector
multiply(IntMatrix) - Method in class jumbo.euclid.IntMatrix
matrix multiplication - multiplies conformable matrices to give NEW matrix result = 'this' * m; (order matters)
multiply(IntSquareMatrix) - Method in class jumbo.euclid.IntSquareMatrix
matrix multiplication - multiplies conformable matrices; result is this*m
multiply(RealArray) - Method in class jumbo.euclid.RealMatrix
matrix multiplication of a COLUMN vector
multiply(RealMatrix) - Method in class jumbo.euclid.RealMatrix
matrix multiplication - multiplies conformable matrices to give NEW matrix result = 'this' * m; (order matters)
multiply(RealSquareMatrix) - Method in class jumbo.euclid.RealSquareMatrix
matrix multiplication - multiplies conformable matrices; result is this*m
multiplyBy(double) - Method in class jumbo.euclid.Angle
multiply an angle by a scalar
multiplyBy(double) - Method in class jumbo.euclid.Point3
scale point
multiplyBy(double) - Method in class jumbo.euclid.Polar
multiply a polar by a scalar
multiplyBy(double) - Method in class jumbo.euclid.Real2
multiply a point by a scalar
multiplyBy(double) - Method in class jumbo.euclid.Real2Vector
multiply all coordinates be a given scalar (i.e.
multiplyBy(double) - Method in class jumbo.euclid.RealArray
array multiplication by a scalar; does NOT modify 'this'
multiplyBy(double) - Method in class jumbo.euclid.RealMatrix
matrix multiplication by a scalar - MODIFIES matrix
multiplyBy(double) - Method in class jumbo.euclid.Vector3
scalar multiplication v = v*f
multiplyBy(int) - Method in class jumbo.euclid.Int2
multiply a point by a scalar
multiplyBy(int) - Method in class jumbo.euclid.Int2Vector
multiply all coordinates be a given scalar (i.e.
multiplyBy(int) - Method in class jumbo.euclid.IntArray
array multiplication by a scalar; does NOT modify 'this'
multiplyBy(int) - Method in class jumbo.euclid.IntMatrix
matrix multiplication by a scalar - MODIFIES matrix
multiplyBy(Polar) - Method in class jumbo.euclid.Polar
multiply a polar by a polar
MUST - Static variable in interface org.xmlcml.cml.ConventionCriteria
 

N

name - Variable in class org.xmlcml.cml.Units
 
natoms - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
 
nbonds - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
 
negative() - Method in class jumbo.euclid.Complex
unary minus MODIFIES object
negative() - Method in class jumbo.euclid.Int2
multiply both components by -1; MODIFIES 'this'
negative() - Method in class jumbo.euclid.IntArray
change the sign of all elements; MODIFIES this
negative() - Method in class jumbo.euclid.IntMatrix
unary minus - negate all elements of matrix; MODIFIES matrix
negative() - Method in class jumbo.euclid.Plane3
reverse direction of plane
negative() - Method in class jumbo.euclid.Real2
multiply both components by -1; MODIFIES 'this'
negative() - Method in class jumbo.euclid.RealArray
change the sign of all elements; MODIFIES this
negative() - Method in class jumbo.euclid.RealMatrix
unary minus - negate all elements of matrix; MODIFIES matrix
negative() - Method in class jumbo.euclid.Vector3
 
NESTED - Static variable in interface uk.co.demon.ursus.dom.PMRNode
nested JComponents
NESTEDATTS - Static variable in interface uk.co.demon.ursus.dom.PMRNode
nested JComponents with Attributes
NEWLINE - Static variable in class jumbo.xml.util.Util
 
NON_HYDROGEN_COUNT_FLOAT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
NON_HYDROGEN_COUNT_INT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
nonBuiltinTable - Variable in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
nonBuiltinTable - Variable in class org.xmlcml.cml.AtomArrayImpl
 
nonBuiltinTable - Variable in class org.xmlcml.cml.BondArrayImpl
 
NonCMLDocument - interface org.xmlcml.noncml.NonCMLDocument.
an interface for input/output of non-CML information (e.g.
NonCMLDocumentImpl - class org.xmlcml.noncml.NonCMLDocumentImpl.
base class for all nonCML molecules
NonCMLDocumentImpl() - Constructor for class org.xmlcml.noncml.NonCMLDocumentImpl
 
nonHydrogenCount - Variable in class org.xmlcml.cml.AtomImpl
 
NonRectMatrixException - exception jumbo.euclid.NonRectMatrixException.
Non-rectangular matrix, when rectangular required
NonRectMatrixException() - Constructor for class jumbo.euclid.NonRectMatrixException
 
NonRectMatrixException(String) - Constructor for class jumbo.euclid.NonRectMatrixException
 
NonSquareException - exception jumbo.euclid.NonSquareException.
Non-square matrix, when square required
NonSquareException() - Constructor for class jumbo.euclid.NonSquareException
 
NonSquareException(String) - Constructor for class jumbo.euclid.NonSquareException
 
NONUNIQUE - Static variable in interface org.xmlcml.cml.AbstractBuiltinContainer
 
NonValidatingDOMParser - class uk.co.demon.ursus.dom.NonValidatingDOMParser.
Wraps the Xerces DOM parser.
NonValidatingDOMParser() - Constructor for class uk.co.demon.ursus.dom.NonValidatingDOMParser
Default constructor.
NONWHITEPUNC - Static variable in class jumbo.xml.util.Util
 
normalise() - Method in class jumbo.euclid.Vector3
Normalise vector
normalise(double) - Static method in class jumbo.euclid.Angle
normalise angle (in radians) to range 0 -> 2*PI
normaliseByColumns() - Method in class jumbo.euclid.RealMatrix
normalise matrix columns to length of 1.0
normaliseByRows() - Method in class jumbo.euclid.RealMatrix
normalise matrix rows to length of 1.0
normaliseWhitespace(String) - Static method in class jumbo.xml.util.Util
normalise whitespace in a String (all whitespace is transformed to single spaces and the string is NOT trimmed
NOSTEREO - Static variable in interface org.xmlcml.cml.AbstractBond
nostereo bond
not(AtomSet) - Method in interface org.xmlcml.tools.AtomSet
combines this with AtomSet to find elements NOT in AtomSet, else null.
not(AtomSet) - Method in class org.xmlcml.tools.AtomSetImpl
combines this with AtomSet to find elements NOT in AtomSet, else null.
not(BondSet) - Method in interface org.xmlcml.tools.BondSet
combines this with BondSet to find elements NOT in BondSet, else null.
not(BondSet) - Method in class org.xmlcml.tools.BondSetImpl
combines this with BondSet to find elements NOT in BondSet, else null.
not(Hashtable, Hashtable) - Static method in class jumbo.xml.util.Util
create Hashtable with elements in to h1 but not h2.
not(ToolHashSet) - Method in interface org.xmlcml.tools.ToolHashSet
ToolHashSet containing elements in this but not h
not(ToolHashSet) - Method in class org.xmlcml.tools.ToolHashSetImpl
 
not(Vector, Vector) - Static method in class jumbo.xml.util.Util
create Vector with elements in v1 but not v2.
not(XHashtable) - Method in interface jumbo.xml.util.XHashtable
combines this with xHashtable to find elements NOT in xHashtable, else null.
not(XHashtable) - Method in class jumbo.xml.util.XHashtableImpl
combines this with xHashtable to find elements NOT in xHashtable, else null.
notationDecl(String, String, String) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive notification of a notation declaration.
notIn(HashedVector) - Method in class jumbo.euclid.HashedVector
get elements NOT in second Set (crude and slow)
notIn(IntSet) - Method in class jumbo.euclid.IntSet
elements only in first set
nParserTypes - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 
NPDMatrixException - exception jumbo.euclid.NPDMatrixException.
thrown by eigenvalue routines, etc
NPDMatrixException() - Constructor for class jumbo.euclid.NPDMatrixException
 
NPDMatrixException(String) - Constructor for class jumbo.euclid.NPDMatrixException
 
NumericVal - interface org.xmlcml.cml.NumericVal.
supports a number (either Float or Integer).
NumericValImpl - class org.xmlcml.cml.NumericValImpl.
supports a number (either Float or Integer).
NumericValImpl() - Constructor for class org.xmlcml.cml.NumericValImpl
 
NumericValImpl(Element) - Constructor for class org.xmlcml.cml.NumericValImpl
 
NumericValImpl(String, Document) - Constructor for class org.xmlcml.cml.NumericValImpl
new object in document context
NumericValImpl(String, Document, String, String, String, String, String, String, Units) - Constructor for class org.xmlcml.cml.NumericValImpl
 
NYI(String) - Static method in class jumbo.euclid.Status
for placeholders during development

O

OBJECT - Static variable in class jumbo.euclid.ObjectArray
 
ObjectArray - class jumbo.euclid.ObjectArray.
ObjectArray - array of Objects.
ObjectArray() - Constructor for class jumbo.euclid.ObjectArray
default is an array of zero points
ObjectArray(int) - Constructor for class jumbo.euclid.ObjectArray
creates n-element array initialised to null
ObjectArray(IntArray) - Constructor for class jumbo.euclid.ObjectArray
convert an IntArray to a ObjectArray
ObjectArray(int, Object) - Constructor for class jumbo.euclid.ObjectArray
set all elements of the array to a given Object
ObjectArray(ObjectArray) - Constructor for class jumbo.euclid.ObjectArray
copy constructor
ObjectArray(ObjectArray, int, int) - Constructor for class jumbo.euclid.ObjectArray
subarray of another array - inclusive; if low > high or other silly indices, creates default array
ObjectArray(RealArray) - Constructor for class jumbo.euclid.ObjectArray
convert an RealArray to a ObjectArray
occupancy - Variable in class org.xmlcml.cml.AtomImpl
 
OCCUPANCY - Static variable in interface org.xmlcml.cml.AbstractAtom
 
one - Static variable in class jumbo.xml.util.Choice2
 
one - Static variable in class jumbo.xml.util.Choice3
 
or(AtomSet) - Method in interface org.xmlcml.tools.AtomSet
combines this with AtomSet to find all elements.
or(AtomSet) - Method in class org.xmlcml.tools.AtomSetImpl
combines this with AtomSet to find all elements.
or(BondSet) - Method in interface org.xmlcml.tools.BondSet
combines this with BondSet to find all elements.
or(BondSet) - Method in class org.xmlcml.tools.BondSetImpl
combines this with BondSet to find all elements.
or(Hashtable, Hashtable) - Static method in class jumbo.xml.util.Util
create Hashtable with elements in to h1 but not h2.
or(ToolHashSet) - Method in interface org.xmlcml.tools.ToolHashSet
ToolHashSet containing elements in either this and h
or(ToolHashSet) - Method in class org.xmlcml.tools.ToolHashSetImpl
 
or(Vector, Vector) - Static method in class jumbo.xml.util.Util
create Vector with elements in v1 but not v2.
or(XHashtable) - Method in interface jumbo.xml.util.XHashtable
combines this with xHashtable to find all elements.
or(XHashtable) - Method in class jumbo.xml.util.XHashtableImpl
combines this with xHashtable to find all elements.
order - Variable in class org.xmlcml.cml.BondImpl
 
ORDER - Static variable in interface org.xmlcml.cml.AbstractBond
 
orderedBondVector - Variable in class org.xmlcml.tools.RingOverlapImpl
ordered bonds - traversal starts at one bridgehead and ends at the other
orIn(HashedVector) - Method in class jumbo.euclid.HashedVector
get elements in either set (crude and slow)
orTables(Hashtable, Hashtable) - Static method in class jumbo.xml.util.Util
OR 2 Hashtables - inefficient except for small tables.
orthogonalise() - Method in class jumbo.euclid.RealSquareMatrix
orthogonalise matrix (only works for 3x3 at present); MODIFIES matrix
orthonormalise() - Method in class jumbo.euclid.RealSquareMatrix
orthonormalise matrix (only works for 3x3 at present)
outerProduct(IntArray) - Static method in class jumbo.euclid.IntSquareMatrix
special types of matrix (Outerproduct, Diagonal, etc)
outerProduct(RealArray) - Static method in class jumbo.euclid.RealSquareMatrix
special types of matrix (Outerproduct, Diagonal, etc)
outOfRange(IntRange) - Method in class jumbo.euclid.IntArray
return index of elements outside a given range
outOfRange(RealRange) - Method in class jumbo.euclid.RealArray
return index of elements outside a given range
output(Element) - Method in class org.xmlcml.cml.MoleculeImpl
 
output(Writer) - Method in class org.xmlcml.noncml.JMEImpl
outputs Molecule as a JME
output(Writer) - Method in class org.xmlcml.noncml.MDLMolImpl
outputs Molecule as an MDLMofile if possible.
output(Writer) - Method in interface org.xmlcml.noncml.NonCMLDocument
output to a Writer.
output(Writer) - Method in class org.xmlcml.noncml.SDFImpl
outputs CML as an SDF if possible.
output(Writer) - Method in class org.xmlcml.noncml.SMILESImpl
outputs Molecule as a SMILES
output(Writer) - Method in class org.xmlcml.noncml.XYZImpl
outputs Molecule as an YZ
outputChildContent(Element, Writer, int, int) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
subclassed by specialist classes
outputCML - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
a CML object to be output as legacy
outputCMLMolecule - Variable in class org.xmlcml.noncml.NonCMLDocumentImpl
a CML Molecule to be output as legacy
outputEndElement(Element, Writer, int) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
for building the tree.
outputEndTag(Element, Writer, int, int) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
subclassed by specialist classes
outputEventStream(Node, Writer, int, int) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
gets the event stream (as XML or text).
outputFloat(int, int, double) - Static method in class jumbo.xml.util.Util
format e.g.
outputHTML(Element, Writer) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
output node as HTML - normally subclassed
outputHTML(Node, Writer) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
output node as HTML - normally subclassed
outputInteger(int, int) - Static method in class jumbo.xml.util.Util
this is a mess
outputStartElement(Element, Writer, Element, int) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
for building the tree.
outputStartTag(Element, Writer, int, int) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
subclassed by specialist classes
OVERRUN - Static variable in interface org.xmlcml.cml.AbstractBond
 

P

PACKAGE_NAME - Static variable in interface org.xmlcml.cml.CMLBase
 
PACKAGE_NAME - Static variable in interface org.xmlcml.cml.CMLDocument
the package name
PACKAGENAME - Static variable in interface uk.co.demon.ursus.dom.PMRDocument
 
PACKAGENAME - Static variable in interface uk.co.demon.ursus.dom.PMRNode
 
parse(InputSource) - Method in interface uk.co.demon.ursus.dom.DOMParserWrapper
 
parse(InputSource) - Method in class uk.co.demon.ursus.dom.NonValidatingDOMParser
Parses the specified URI and returns the document.
parse(String) - Method in interface org.xmlcml.cml.CMLDOMSAXBuilder
 
parse(String) - Method in class uk.co.demon.ursus.dom.SAXAdapter
create a new SAXTree.
parse(String) - Method in interface uk.co.demon.ursus.dom.DOMParserWrapper
Parses the specified URI and returns the document.
parse(String) - Method in class uk.co.demon.ursus.dom.NonValidatingDOMParser
Parses the specified URI and returns the document.
parse(StringReader) - Method in class uk.co.demon.ursus.dom.SAXAdapter
parse.
parse(String, StringReader, String) - Method in class uk.co.demon.ursus.dom.SAXAdapter
parse.
parser - Variable in class uk.co.demon.ursus.dom.SAXAdapter
 
parserTypeStrings - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 
parseWhitespaceQuotedFields(String) - Static method in class jumbo.xml.util.Util
parse whitespace-separated tokens interspersed with quoted strings, e.g.
this is "a quoted string" and 'another token' as well
parses to:
this/is/a quoted string/and/another token/as well
PERCENT - Static variable in class jumbo.xml.util.Util
 
PERIOD - Static variable in class jumbo.xml.util.Util
 
PIPE - Static variable in class jumbo.xml.util.Util
 
Plane3 - class jumbo.euclid.Plane3.
Plane3 - 3-dimensional plane class
Plane3() - Constructor for class jumbo.euclid.Plane3
 
Plane3(double, double, double, double) - Constructor for class jumbo.euclid.Plane3
formed from plane components; vector is normalised
Plane3(Line3, Point3) - Constructor for class jumbo.euclid.Plane3
make a plane from a line and a point not on the line
Plane3(Plane3) - Constructor for class jumbo.euclid.Plane3
copy constructor:
Plane3(Point3, Point3, Point3) - Constructor for class jumbo.euclid.Plane3
make a plane from three points
Plane3(Vector3, double) - Constructor for class jumbo.euclid.Plane3
formed from plane components
PLUS - Static variable in class jumbo.xml.util.Util
 
plus(Angle) - Method in class jumbo.euclid.Angle
add two angles
plus(Int2) - Method in class jumbo.euclid.Int2
add two points - vector sum;
plus(Int2) - Method in class jumbo.euclid.Int2Vector
add a Int2 to all elements of 'this'; MODIFIES 'this'
plus(Int2Range) - Method in class jumbo.euclid.Int2Range
merge two ranges and take the maximum extents
plus(IntArray) - Method in class jumbo.euclid.IntArray
array addition - adds conformable arrays
plus(IntMatrix) - Method in class jumbo.euclid.IntMatrix
matrix addition - adds conformable matrices giving NEW matrix
plus(IntRange) - Method in class jumbo.euclid.IntRange
combine two ranges if both valid; takes greatest limits of both, else returns InValid
plus(IntSquareMatrix) - Method in class jumbo.euclid.IntSquareMatrix
matrix addition - adds conformable matrices
plus(Point3) - Method in class jumbo.euclid.Point3
New point from point+point - used for finding centrois, etc.
plus(Point3Vector) - Method in class jumbo.euclid.Point3Vector
form the point+point sum for two vectors of points
plus(Polar) - Method in class jumbo.euclid.Polar
add two polars
plus(Real2) - Method in class jumbo.euclid.Real2
add two points - vector sum;
plus(Real2) - Method in class jumbo.euclid.Real2Vector
add a Real2 to all elements of 'this'; MODIFIES 'this'
plus(Real2Range) - Method in class jumbo.euclid.Real2Range
merge two ranges and take the maximum extents
plus(Real3Range) - Method in class jumbo.euclid.Real3Range
 
plus(RealArray) - Method in class jumbo.euclid.RealArray
array addition - adds conformable arrays
plus(RealMatrix) - Method in class jumbo.euclid.RealMatrix
matrix addition - adds conformable matrices giving NEW matrix
plus(RealRange) - Method in class jumbo.euclid.RealRange
combine two ranges if both valid; takes greatest limits of both, else returns InValid
plus(RealSquareMatrix) - Method in class jumbo.euclid.RealSquareMatrix
matrix addition - adds conformable matrices
plus(Vector3) - Method in class jumbo.euclid.Point3
New point from point+vector
plus(Vector3) - Method in class jumbo.euclid.Point3Vector
translate by a vector - do NOT modify this
plus(Vector3) - Method in class jumbo.euclid.Vector3
 
plusXY2(Real2) - Method in interface org.xmlcml.cml.Atom
increase XY2 coordinate; if atom.xy2 is null, sets coordinate to r
plusXY2(Real2) - Method in class org.xmlcml.cml.AtomImpl
increase XY2 coordinate; if atom.xy2 is null, sets coordinate to r
plusXYZ3(Point3) - Method in interface org.xmlcml.cml.Atom
increase XYZ3 coordinate; if atom.xyz3 is null, sets coordinate to r
plusXYZ3(Point3) - Method in class org.xmlcml.cml.AtomImpl
increase XYZ3 coordinate; if atom.xyz3 is null, sets coordinate to r
plusXYZFract(Point3) - Method in interface org.xmlcml.cml.Atom
increase XYZFract coordinate; if atom.xyzFract is null, sets coordinate to p
plusXYZFract(Point3) - Method in class org.xmlcml.cml.AtomImpl
increase XYZFract coordinate; if atom.xyzFract is null, sets coordinate to p
PMRDelegate - class uk.co.demon.ursus.dom.PMRDelegate.
re-usable routines to support PMR* interfaces
PMRDelegate() - Constructor for class uk.co.demon.ursus.dom.PMRDelegate
 
PMRDocument - interface uk.co.demon.ursus.dom.PMRDocument.
DOM-based re-write of JUMBO functionality.
PMRDocumentImpl - class uk.co.demon.ursus.dom.PMRDocumentImpl.
DOM-based re-write of JUMBO functionality.
PMRDocumentImpl() - Constructor for class uk.co.demon.ursus.dom.PMRDocumentImpl
 
PMRDocumentImpl(InputSource) - Constructor for class uk.co.demon.ursus.dom.PMRDocumentImpl
create from source with default parser and builder
PMRDocumentImpl(PMRElement) - Constructor for class uk.co.demon.ursus.dom.PMRDocumentImpl
create from rootNode (which is removed from its current tree)
PMRDocumentImpl(String) - Constructor for class uk.co.demon.ursus.dom.PMRDocumentImpl
create from urlString with default parser and builder
PMRDocumentImpl(URL) - Constructor for class uk.co.demon.ursus.dom.PMRDocumentImpl
create from url with default parser and builder
PMRElement - interface uk.co.demon.ursus.dom.PMRElement.
 
PMRElementImpl - class uk.co.demon.ursus.dom.PMRElementImpl.
 
PMRElementImpl() - Constructor for class uk.co.demon.ursus.dom.PMRElementImpl
should not make an isolated PMRElement
PMRElementImpl(Element) - Constructor for class uk.co.demon.ursus.dom.PMRElementImpl
make a subclassed Element, in context, destroying the original node
PMRElementImpl(Element, Document) - Constructor for class uk.co.demon.ursus.dom.PMRElementImpl
makes a new Element from an existing Element in new document context Adds attributes but not children
PMRElementImpl(String, Document) - Constructor for class uk.co.demon.ursus.dom.PMRElementImpl
have to make an element in conjunction with a document
PMRElementImpl(String, Element) - Constructor for class uk.co.demon.ursus.dom.PMRElementImpl
makes a new Element from an existing Element (ElementNode).
PMRNode - interface uk.co.demon.ursus.dom.PMRNode.
 
Point3 - class jumbo.euclid.Point3.
Point3 - 3-dimensional point class
Point3() - Constructor for class jumbo.euclid.Point3
 
Point3(double[]) - Constructor for class jumbo.euclid.Point3
constructor from a double[] (or a RealArray)
Point3(double, double, double) - Constructor for class jumbo.euclid.Point3
formed from point components
Point3(Point3) - Constructor for class jumbo.euclid.Point3
copy constructor
Point3(Vector3) - Constructor for class jumbo.euclid.Point3
make a point from a vector
Point3Vector - class jumbo.euclid.Point3Vector.
Point3Vector - a (Java) Vector of Point3s.
Point3Vector() - Constructor for class jumbo.euclid.Point3Vector
 
Point3Vector(double[]) - Constructor for class jumbo.euclid.Point3Vector
Formed by feeding in an existing array to a 3xn matrix.
Point3Vector(int) - Constructor for class jumbo.euclid.Point3Vector
create a Vector with given number of points
Point3Vector(int, double[], double[], double[]) - Constructor for class jumbo.euclid.Point3Vector
from three parallel arrays of x, y and z - by REFERENCE
Point3Vector(Point3Vector) - Constructor for class jumbo.euclid.Point3Vector
copy constructor from Point3Vector COPIES pv
Point3Vector(RealArray) - Constructor for class jumbo.euclid.Point3Vector
constructor from RealArray - by REFERENCE
Polar - class jumbo.euclid.Polar.
Polar - Polar coordinates (r, theta)
Polar() - Constructor for class jumbo.euclid.Polar
 
Polar(Complex) - Constructor for class jumbo.euclid.Polar
 
Polar(double, Angle) - Constructor for class jumbo.euclid.Polar
 
Polar(Polar) - Constructor for class jumbo.euclid.Polar
 
POUND - Static variable in class jumbo.xml.util.Util
 
preorderEnumeration(Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
iterate through whole tree.
preorderEnumeration(Node) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
iterate through whole tree.
PRETTY - Static variable in interface uk.co.demon.ursus.dom.PMRNode
the event stream pretty printed
printArray(double[]) - Static method in class jumbo.euclid.Real
print a double[]
printArray(int[]) - Static method in class jumbo.euclid.Int
print a int[]
printChar() - Static method in class jumbo.xml.util.Util
 
process() - Method in class org.xmlcml.cml.StringValImpl
 
processAtomRefs(Molecule) - Method in interface org.xmlcml.cml.Bond
 
processAtomRefs(Molecule) - Method in class org.xmlcml.cml.BondImpl
give each atom an ID.
processDescendants() - Method in interface uk.co.demon.ursus.dom.PMRElement
process descendants of an element using processDOM().
processDescendants() - Method in class uk.co.demon.ursus.dom.PMRElementImpl
process an element.
processDOM() - Method in class org.xmlcml.cml.AbstractStringValImpl
 
processDOM() - Method in class org.xmlcml.cml.AtomArrayImpl
 
processDOM() - Method in class org.xmlcml.cml.AtomImpl
 
processDOM() - Method in class org.xmlcml.cml.BondArrayImpl
 
processDOM() - Method in class org.xmlcml.cml.BondImpl
 
processDOM() - Method in interface org.xmlcml.cml.CMLBase
 
processDOM() - Method in class org.xmlcml.cml.CMLBaseImpl
subclassed if necessary
processDOM() - Method in class org.xmlcml.cml.FloatArrayImpl
 
processDOM() - Method in class org.xmlcml.cml.FloatValImpl
 
processDOM() - Method in class org.xmlcml.cml.IntegerArrayImpl
 
processDOM() - Method in class org.xmlcml.cml.IntegerValImpl
 
processDOM() - Method in class org.xmlcml.cml.MoleculeImpl
 
processDOM() - Method in class org.xmlcml.cml.StringArrayImpl
 
processDOM() - Method in interface uk.co.demon.ursus.dom.PMRElement
carries out class-specific processing for subclasses of PMRElement.
processDOM() - Method in class uk.co.demon.ursus.dom.PMRElementImpl
process an element.
processFlag - Variable in class uk.co.demon.ursus.dom.PMRElementImpl
 
processImmediately() - Method in class org.xmlcml.cml.AtomArrayImpl
do not process on creation
processImmediately() - Method in class org.xmlcml.cml.BondArrayImpl
do not process on creation
processingInstruction(String, String) - Method in class org.xmlcml.cml.CMLDOMSAXBuilderImpl
 
processingInstruction(String, String) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive notification of a processing instruction.
processingInstruction(String, String) - Method in class uk.co.demon.ursus.dom.SAXDOMBuilder
 
processString() - Method in interface org.xmlcml.cml.AbstractStringVal
 
processString() - Method in class org.xmlcml.cml.AbstractStringValImpl
 
productVector - Variable in class org.xmlcml.cml.ReactionImpl
 
projectOnto(Vector3) - Method in class jumbo.euclid.Vector3
projection of this onto v3
PUNC - Static variable in class jumbo.xml.util.Util
 
putDegrees(double) - Method in class jumbo.euclid.Angle
input angle in degrees

Q

QUALIFIED - Static variable in interface uk.co.demon.ursus.dom.PMRElement
prefix COLON local name
QUERY - Static variable in class jumbo.xml.util.Util
 
QUOT - Static variable in class jumbo.xml.util.Util
 
quoteConcatenate(String[]) - Static method in class jumbo.xml.util.Util
concatenate strings into quote-separated string

R

RADIANS - Static variable in class org.xmlcml.cml.AngleUnits
 
RADIANS - Static variable in class jumbo.euclid.Angle
set Radians or degrees for output
range() - Method in class jumbo.euclid.IntArray
range of array (default IntRange for zero array)
range() - Method in class jumbo.euclid.RealArray
range of array (default RealRange for zero array)
RANGLE - Static variable in class jumbo.xml.util.Util
 
RBRAK - Static variable in class jumbo.xml.util.Util
 
RCURLY - Static variable in class jumbo.xml.util.Util
 
reactantVector - Variable in class org.xmlcml.cml.ReactionImpl
 
Reaction - interface org.xmlcml.cml.Reaction.
 
REACTION - Static variable in interface org.xmlcml.cml.CMLBase
 
ReactionImpl - class org.xmlcml.cml.ReactionImpl.
 
ReactionImpl() - Constructor for class org.xmlcml.cml.ReactionImpl
 
ReactionImpl(Document) - Constructor for class org.xmlcml.cml.ReactionImpl
new Reaction in context
ReactionImpl(Element) - Constructor for class org.xmlcml.cml.ReactionImpl
 
readByteArray(DataInputStream) - Static method in class jumbo.xml.util.Util
reads a byte array from DataInputStream, *including* line feeds
readByteArray(String) - Static method in class jumbo.xml.util.Util
reads a byte array from file, *including* line feeds
reader - Variable in class uk.co.demon.ursus.dom.SAXAdapter
 
readZip(String) - Static method in class jumbo.xml.util.Util
read a Zipfile
Real - class jumbo.euclid.Real.
Real supports various utilities for real numbers.
REAL - Static variable in class jumbo.euclid.ObjectArray
 
Real() - Constructor for class jumbo.euclid.Real
 
Real2 - class jumbo.euclid.Real2.
Real2 - a pair of FPt numbers - no other assumptions
Real2() - Constructor for class jumbo.euclid.Real2
 
Real2(double, double) - Constructor for class jumbo.euclid.Real2
 
Real2(Real2) - Constructor for class jumbo.euclid.Real2
copy constructor
Real2Array - class jumbo.euclid.Real2Array.
Real2Array is NOT a Vector of Real2s, but a container for a 2-D array with a variety of ways of managing the data including RealArrays for the x and y arrays, and also an array of Real2s The latter is only stored if required, and then is cached.
Real2Array() - Constructor for class jumbo.euclid.Real2Array
default constructor gives an array of 0 points
Real2Array(RealArray, RealArray) - Constructor for class jumbo.euclid.Real2Array
make an Real2_Array from 2 RealVec's; takes a copy
Real2Range - class jumbo.euclid.Real2Range.
Real2Range - 2-D double limits
Real2Range() - Constructor for class jumbo.euclid.Real2Range
 
Real2Range(Real2Range) - Constructor for class jumbo.euclid.Real2Range
copy constructor
Real2Range(RealRange, RealRange) - Constructor for class jumbo.euclid.Real2Range
initialise with min and max values;
Real2RangeHashtable - class jumbo.euclid.Real2RangeHashtable.
Hashtable indexed by boxes, which return an object when a box contains a point (i.e.
Real2RangeHashtable() - Constructor for class jumbo.euclid.Real2RangeHashtable
 
Real2Vector - class jumbo.euclid.Real2Vector.
Real2Vector - a (Java) Vector of Real2s.
Real2Vector() - Constructor for class jumbo.euclid.Real2Vector
 
Real2Vector(double[]) - Constructor for class jumbo.euclid.Real2Vector
Formed by feeding in an existing array to a 2xn matrix.
Real2Vector(int) - Constructor for class jumbo.euclid.Real2Vector
create a Vector with given number of points
Real2Vector(int, double[], double[]) - Constructor for class jumbo.euclid.Real2Vector
from two parallel arrays of x, y - by REFERENCE
Real2Vector(Real2Vector) - Constructor for class jumbo.euclid.Real2Vector
copy constructor from Real2Vector COPIES pv
Real2Vector(RealArray) - Constructor for class jumbo.euclid.Real2Vector
constructor from RealArray - by REFERENCE
Real3Range - class jumbo.euclid.Real3Range.
Real3Range - 3-D double limits
Real3Range() - Constructor for class jumbo.euclid.Real3Range
default is three default RealRanges
Real3Range(Real3Range) - Constructor for class jumbo.euclid.Real3Range
copy constructor
Real3Range(RealRange, RealRange, RealRange) - Constructor for class jumbo.euclid.Real3Range
initialise with min and max values; takes COPIES
realArray - Variable in class org.xmlcml.cml.FloatArrayImpl
 
RealArray - class jumbo.euclid.RealArray.
RealArray - array of doubles
RealArray() - Constructor for class jumbo.euclid.RealArray
default is an array of zero points
RealArray(double[]) - Constructor for class jumbo.euclid.RealArray
from an existing double[] (which knows its length)
RealArray(int) - Constructor for class jumbo.euclid.RealArray
creates n-element array initialised to 0.0
RealArray(IntArray) - Constructor for class jumbo.euclid.RealArray
convert an IntArray to a RealArray
RealArray(int, double) - Constructor for class jumbo.euclid.RealArray
set all elements of the array to a given value
RealArray(int, double[]) - Constructor for class jumbo.euclid.RealArray
Formed by feeding in an existing array; requires the size.
RealArray(int, double, double) - Constructor for class jumbo.euclid.RealArray
This gives a nelem-element array initialised to elem1+(i-1)*delta
RealArray(int, String, double) - Constructor for class jumbo.euclid.RealArray
Create a given 'shape' of array for data filtering.
RealArray(RealArray) - Constructor for class jumbo.euclid.RealArray
copy constructor
RealArray(RealArray, int, int) - Constructor for class jumbo.euclid.RealArray
subarray of another array - inclusive; if low > high or other silly indices, creates default array
RealArray(String) - Constructor for class jumbo.euclid.RealArray
from a String with space-separated strings representing Reals
RealArray(String[]) - Constructor for class jumbo.euclid.RealArray
from an array of Strings (which must represent Reals)
RealMatrix - class jumbo.euclid.RealMatrix.
RealMatrix - rectangular real number matrix class
RealMatrix() - Constructor for class jumbo.euclid.RealMatrix
Default matrix, with cols = rows = 0
RealMatrix(double[][]) - Constructor for class jumbo.euclid.RealMatrix
COPY from an existing matrix - check that it is rectangular
RealMatrix(int, int) - Constructor for class jumbo.euclid.RealMatrix
A rows*cols matrix set to 0.0 (rows or cols < 0 defaults to 0)
RealMatrix(int, int, double) - Constructor for class jumbo.euclid.RealMatrix
initalises all elements in the array with a given double[]
RealMatrix(int, int, double[]) - Constructor for class jumbo.euclid.RealMatrix
Formed by feeding in an existing 1-D array to a rowsXcols matrix.
RealMatrix(IntMatrix) - Constructor for class jumbo.euclid.RealMatrix
from a IntMatrix
RealMatrix(RealMatrix) - Constructor for class jumbo.euclid.RealMatrix
copy constructor - COPIES the other matrix
RealMatrix(RealMatrix, int, int, int, int) - Constructor for class jumbo.euclid.RealMatrix
submatrix of another matrix; fails if lowrow > hirow, lowrow < 0, etc.
RealRange - class jumbo.euclid.RealRange.
RealRange - maximum and minimum values
RealRange() - Constructor for class jumbo.euclid.RealRange
creates invalid range from POSITIVE_INFINITY to NEGATIVE_INFINITY
RealRange(double, double) - Constructor for class jumbo.euclid.RealRange
initialise with min and max values; if minv > maxv create inValid RealRange
RealRange(IntRange) - Constructor for class jumbo.euclid.RealRange
from an IntRange
RealRange(RealRange) - Constructor for class jumbo.euclid.RealRange
copy constructor
RealRangeVector - class jumbo.euclid.RealRangeVector.
a Vector of RealRanges - will be developed so that overlapping ranges can be merged or deleted.
RealRangeVector() - Constructor for class jumbo.euclid.RealRangeVector
 
RealSquareMatrix - class jumbo.euclid.RealSquareMatrix.
RealSquareMatrix - square matrix class
RealSquareMatrix() - Constructor for class jumbo.euclid.RealSquareMatrix
This gives a default matrix, with cols = rows = 0.
RealSquareMatrix(double[][]) - Constructor for class jumbo.euclid.RealSquareMatrix
form from a Java 2-D array (it holds row and column count)
RealSquareMatrix(int) - Constructor for class jumbo.euclid.RealSquareMatrix
This gives a null matrix
RealSquareMatrix(int, double) - Constructor for class jumbo.euclid.RealSquareMatrix
initalises all elements in the array with a given double[]
RealSquareMatrix(int, double[]) - Constructor for class jumbo.euclid.RealSquareMatrix
Formed by feeding in an existing array to a colsXcols matrix.
RealSquareMatrix(RealMatrix) - Constructor for class jumbo.euclid.RealSquareMatrix
assign a RealMatrix - i.e.
RealSquareMatrix(RealMatrix, int, int, int) - Constructor for class jumbo.euclid.RealSquareMatrix
submatrix of another matrix
RealSquareMatrix(RealSquareMatrix) - Constructor for class jumbo.euclid.RealSquareMatrix
 
realValue - Variable in class org.xmlcml.cml.FloatValImpl
 
registerApplet(Applet) - Static method in class jumbo.xml.util.Util
record that an object is an applet rather than an application.
regularPolygon(int, double) - Static method in class jumbo.euclid.Real2Vector
make a regular polygon, zero point at (0, rad); points go clockwise
remove(Object) - Method in interface org.xmlcml.tools.ToolHashSet
remove element (cf HashSet)
removeAll(Collection) - Method in interface org.xmlcml.tools.ToolHashSet
remove just those elements in Collection (cf HashSet)
removeChildNodes(Element) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
remove all child nodes
removeHTML(String) - Static method in class jumbo.xml.util.Util
remove balanced (well-formed) markup from a string.
removeNode(Node) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
remove a node from its parent.
reorderColumnsBy(IntSet) - Method in class jumbo.euclid.IntMatrix
reorder the columns of a matrix.
reorderColumnsBy(IntSet) - Method in class jumbo.euclid.RealMatrix
reorder the columns of a matrix.
reorderRowsBy(IntSet) - Method in class jumbo.euclid.IntMatrix
reorder the rows of a matrix.
reorderRowsBy(IntSet) - Method in class jumbo.euclid.RealMatrix
reorder the rows of a matrix.
replace(Element, Element) - Method in class uk.co.demon.ursus.dom.PMRDelegate
transfer children from fromElement to toElement; replace toElement by fromElement and copy attributes and children
replaceColumnData(int, double[]) - Method in class jumbo.euclid.RealMatrix
and from double[]
replaceColumnData(int, int[]) - Method in class jumbo.euclid.IntMatrix
and from int[]
replaceColumnData(int, IntArray) - Method in class jumbo.euclid.IntMatrix
replace data in a single column - return false if impossible
replaceColumnData(int, IntMatrix) - Method in class jumbo.euclid.IntMatrix
replace data in a block of columns
replaceColumnData(int, RealArray) - Method in class jumbo.euclid.RealMatrix
replace data in a single column - return false if impossible
replaceColumnData(int, RealMatrix) - Method in class jumbo.euclid.RealMatrix
replace data in a block of columns
replaceRowData(int, double[]) - Method in class jumbo.euclid.RealMatrix
and using a double[]
replaceRowData(int, int[]) - Method in class jumbo.euclid.IntMatrix
and using a int[]
replaceRowData(int, IntArray) - Method in class jumbo.euclid.IntMatrix
overwrite existing row of data
replaceRowData(int, IntMatrix) - Method in class jumbo.euclid.IntMatrix
overwrite existing block of rows; if too big, copying is truncated
replaceRowData(int, RealArray) - Method in class jumbo.euclid.RealMatrix
overwrite existing row of data
replaceRowData(int, RealMatrix) - Method in class jumbo.euclid.RealMatrix
overwrite existing block of rows; if too big, copying is truncated
replaceSubMatrixData(int, int, IntMatrix) - Method in class jumbo.euclid.IntMatrix
replaces the data starting at (low_row, low_col) and extending by the dimensions for the matrix m
replaceSubMatrixData(int, int, RealMatrix) - Method in class jumbo.euclid.RealMatrix
replaces the data starting at (low_row, low_col) and extending by the dimensions for the matrix m
RESIDUE_ID - Static variable in interface org.xmlcml.cml.AbstractAtom
 
RESIDUE_TYPE - Static variable in interface org.xmlcml.cml.AbstractAtom
 
residueID - Variable in class org.xmlcml.cml.AtomImpl
 
residueType - Variable in class org.xmlcml.cml.AtomImpl
 
resolveEntity(String, String) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Resolve an external entity.
retainAll(Collection) - Method in interface org.xmlcml.tools.ToolHashSet
retain just those elements in Collection (cf HashSet)
RETURN - Static variable in class jumbo.xml.util.Util
 
reverse() - Method in class jumbo.euclid.IntArray
MODIFIES array to be in reverse order
reverse() - Method in class jumbo.euclid.ObjectArray
MODIFIES ObjectArray to be in reverse order
reverse() - Method in class jumbo.euclid.RealArray
MODIFIES array to be in reverse order
reverse() - Method in class jumbo.euclid.StringSet
MODIFIES StringSet to be in reverse order
rightTrim(String) - Static method in class jumbo.xml.util.Util
remove trailing blanks
Ring - interface org.xmlcml.tools.Ring.
 
RingImpl - class org.xmlcml.tools.RingImpl.
 
RingImpl() - Constructor for class org.xmlcml.tools.RingImpl
 
RingImpl(Molecule) - Constructor for class org.xmlcml.tools.RingImpl
 
RingNucleus - interface org.xmlcml.tools.RingNucleus.
a nucleus of rings (e.g.
RingNucleusImpl - class org.xmlcml.tools.RingNucleusImpl.
a nucleus of rings (e.g.
RingNucleusImpl() - Constructor for class org.xmlcml.tools.RingNucleusImpl
 
RingNucleusImpl(SpanningTree) - Constructor for class org.xmlcml.tools.RingNucleusImpl
 
RingOverlap - interface org.xmlcml.tools.RingOverlap.
holds information about overlap between two rings (fused or bridged).
RingOverlapImpl - class org.xmlcml.tools.RingOverlapImpl.
holds information about overlap between two rings (fused or bridged).
RingOverlapImpl() - Constructor for class org.xmlcml.tools.RingOverlapImpl
 
RingOverlapImpl(Ring, Ring) - Constructor for class org.xmlcml.tools.RingOverlapImpl
create from two rings.
ringOverlapVector - Variable in class org.xmlcml.tools.RingImpl
what rings does this overlap with (FUSED or BRIDGED)? Vector stores RingOverlaps
ringOverlapVector - Variable in class org.xmlcml.tools.RingNucleusImpl
what RingOverlaps are there between these rings?
rings - Variable in class org.xmlcml.tools.RingOverlapImpl
rings involved
ringVector - Variable in class org.xmlcml.tools.RingNucleusImpl
what Rings are there in this nucleus?
rms() - Method in class jumbo.euclid.RealArray
root mean square sqrt(sigma(x(i)**2)/n)
rms(Point3Vector) - Method in class jumbo.euclid.Point3Vector
rms between two molecules - per atom
rnTable - Variable in class org.xmlcml.tools.SubstituentListImpl
 
ROMAN_NUMERALS - Static variable in class jumbo.xml.util.Util
a list of the first few Roman numerals (e.g.
ROT_ORIG - Static variable in class jumbo.euclid.Transform2
 
ROT_ORIG - Static variable in class jumbo.euclid.Transform3
 
ROT_TRANS - Static variable in class jumbo.euclid.Transform2
 
ROT_TRANS - Static variable in class jumbo.euclid.Transform3
 
ROT_TRANS_AXIAL_SCALE - Static variable in class jumbo.euclid.Transform2
 
ROT_TRANS_AXIAL_SCALE - Static variable in class jumbo.euclid.Transform3
 
ROT_TRANS_SCALE - Static variable in class jumbo.euclid.Transform2
 
ROT_TRANS_SCALE - Static variable in class jumbo.euclid.Transform3
 
ROT_TRANS_SCALE_PERSP - Static variable in class jumbo.euclid.Transform2
 
ROT_TRANS_SCALE_PERSP - Static variable in class jumbo.euclid.Transform3
 
rotateAboutCentroid(Angle) - Method in class jumbo.euclid.Real2Vector
rotate about centroid by given angle; MODIFIES 'this'
roughAlign(Point3Vector) - Method in class jumbo.euclid.Point3Vector
fit two coordinates of same length and alignment - rough private method fit this to ref (i.e.
rows - Variable in class jumbo.euclid.IntMatrix
number of rows
rows - Variable in class jumbo.euclid.RealMatrix
number of rows
RSQUARE - Static variable in class jumbo.xml.util.Util
 
run() - Method in interface org.xmlcml.cml.Execute
run the test
run() - Method in class org.xmlcml.cml.ExecuteImpl
execute is run in context.
run(Execute) - Method in interface org.xmlcml.cml.HasExecute
execute an <execute> child
run(Execute) - Method in interface org.xmlcml.cml.Molecule
run an <execute> child
run(Execute) - Method in class org.xmlcml.cml.MoleculeImpl
run an <execute> child
runExecute() - Method in class org.xmlcml.cml.CMLDOMSAXBuilderImpl
finds and runs any elements

S

SAXAdapter - class uk.co.demon.ursus.dom.SAXAdapter.
David Megginson's SAX demo, adapted gently to form a generic SAX implementation - SAXAdapter implies all methods have minimal implementations.
SAXAdapter() - Constructor for class uk.co.demon.ursus.dom.SAXAdapter
Uses default parser if none supplied later
SAXAdapter(Parser) - Constructor for class uk.co.demon.ursus.dom.SAXAdapter
Uses given parser
SAXAdapter(String) - Constructor for class uk.co.demon.ursus.dom.SAXAdapter
Uses given parser name
SAXAtomCounter - class org.xmlcml.test.SAXAtomCounter.
 
SAXAtomCounter(String) - Constructor for class org.xmlcml.test.SAXAtomCounter
read a URL and parse it.
SAXDOMBuilder - class uk.co.demon.ursus.dom.SAXDOMBuilder.
Builds a DOM from SAX events
SAXDOMBuilder() - Constructor for class uk.co.demon.ursus.dom.SAXDOMBuilder
create with default parser
SAXDOMBuilder(Parser) - Constructor for class uk.co.demon.ursus.dom.SAXDOMBuilder
 
SAXDOMBuilder(String) - Constructor for class uk.co.demon.ursus.dom.SAXDOMBuilder
create a new SAXDOMBuilder with given parserName
SDF - interface org.xmlcml.noncml.SDF.
class to read and write MDL SDFiles
SDF - Static variable in interface org.xmlcml.noncml.NonCMLDocument
 
SDFImpl - class org.xmlcml.noncml.SDFImpl.
class to read and write SDFiles
SDFImpl(BufferedReader, String) - Constructor for class org.xmlcml.noncml.SDFImpl
form a SDF object from a local file
SDFImpl(CML) - Constructor for class org.xmlcml.noncml.SDFImpl
form a SDF object from a CML file
SEMICOLON - Static variable in class jumbo.xml.util.Util
 
Sequence - interface org.xmlcml.cml.Sequence.
 
SEQUENCE - Static variable in interface org.xmlcml.cml.CMLBase
 
SequenceImpl - class org.xmlcml.cml.SequenceImpl.
 
SequenceImpl() - Constructor for class org.xmlcml.cml.SequenceImpl
 
SequenceImpl(Document) - Constructor for class org.xmlcml.cml.SequenceImpl
new Sequence in context
SequenceImpl(Element) - Constructor for class org.xmlcml.cml.SequenceImpl
 
sequenceVector - Variable in class org.xmlcml.cml.MoleculeImpl
 
setAllElements(double) - Method in class jumbo.euclid.RealArray
initialise array to given double[]
setAllElements(double) - Method in class jumbo.euclid.RealMatrix
initialise matrix to given double
setAllElements(int) - Method in class jumbo.euclid.IntArray
initialise array to given int[]
setAllElements(int) - Method in class jumbo.euclid.IntMatrix
initialise matrix to given int
setAngleUnits(AngleUnits) - Method in interface org.xmlcml.cml.AbstractAngle
 
setAngleUnits(AngleUnits) - Method in class org.xmlcml.cml.AbstractAngleImpl
 
setAtom(Atom) - Method in interface org.xmlcml.tools.STElement
 
setAtom(Atom) - Method in class org.xmlcml.tools.STElementImpl
 
setAtomParity(double) - Method in interface org.xmlcml.cml.Atom
 
setAtomParity(double) - Method in class org.xmlcml.cml.AtomImpl
 
setBondLength(double) - Method in interface org.xmlcml.cml.Bond
 
setBondLength(double) - Method in class org.xmlcml.cml.BondImpl
 
setBuiltin(String) - Method in interface org.xmlcml.cml.AbstractStringVal
 
setBuiltin(String) - Method in class org.xmlcml.cml.AbstractStringValImpl
 
setBuiltinArray(int, StringArray) - Method in interface org.xmlcml.cml.AtomArray
 
setBuiltinArray(int, StringArray) - Method in class org.xmlcml.cml.AtomArrayImpl
 
setBuiltinArray(int, StringArray) - Method in interface org.xmlcml.cml.BondArray
 
setBuiltinArray(int, StringArray) - Method in class org.xmlcml.cml.BondArrayImpl
 
setBuiltinArray(int, StringArray) - Method in interface org.xmlcml.cml.HasBuiltinArrayNames
 
setBuiltinVal(int, StringVal) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
 
setBuiltinVal(int, StringVal) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
setBuiltinVal(int, StringVal) - Method in interface org.xmlcml.cml.HasBuiltinNames
 
setColumns(int) - Method in interface org.xmlcml.cml.FloatMatrix
 
setColumns(int) - Method in class org.xmlcml.cml.FloatMatrixImpl
 
setConventionName(String) - Method in class org.xmlcml.cml.CMLBaseImpl
 
setConventionName(String) - Method in interface org.xmlcml.cml.HasConvention
 
setCoordinate2(Atom, Coordinate2) - Method in interface org.xmlcml.tools.AtomSet
set coordinates for atom
setCoordinate2(Atom, Coordinate2) - Method in class org.xmlcml.tools.AtomSetImpl
set coordinates for atom
setCount(double) - Method in interface org.xmlcml.cml.AbstractAtom
 
setCount(double) - Method in class org.xmlcml.cml.AbstractAtomImpl
 
setCount(double) - Method in class org.xmlcml.cml.ElectronImpl
 
setCount(double) - Method in interface org.xmlcml.cml.Formula
 
setCount(double) - Method in class org.xmlcml.cml.FormulaImpl
 
setCount(double) - Method in interface org.xmlcml.cml.HasCount
 
setCount(double) - Method in interface org.xmlcml.cml.Molecule
 
setCount(double) - Method in class org.xmlcml.cml.MoleculeImpl
 
setCovalentRadius(double) - Method in class org.xmlcml.molutil.ChemicalElement
 
setCrystal(Crystal) - Method in interface org.xmlcml.cml.Molecule
replaces Crystal information; if null, deletes any existing Crystal
setCrystal(Crystal) - Method in class org.xmlcml.cml.MoleculeImpl
replaces Crystal information; if null, deletes any existing Crystal
setData(double[][]) - Method in interface org.xmlcml.cml.FloatMatrix
data in format [rows][cols].
setData(double[][]) - Method in class org.xmlcml.cml.FloatMatrixImpl
data in format [rows][cols].
setDataType(int) - Method in class org.xmlcml.cml.AbstractStringValImpl
 
setDelimiter(String) - Method in interface org.xmlcml.cml.FloatArray
 
setDelimiter(String) - Method in class org.xmlcml.cml.FloatArrayImpl
 
setDelimiter(String) - Method in interface org.xmlcml.cml.HasSize
 
setDelimiter(String) - Method in interface org.xmlcml.cml.IntegerArray
 
setDelimiter(String) - Method in class org.xmlcml.cml.IntegerArrayImpl
 
setDelimiter(String) - Method in interface org.xmlcml.cml.StringArray
 
setDelimiter(String) - Method in class org.xmlcml.cml.StringArrayImpl
 
setDictRef(String) - Method in class org.xmlcml.cml.CMLBaseImpl
 
setDictRef(String) - Method in interface org.xmlcml.cml.HasDictRef
 
setDocumentLocator(Locator) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive a Locator object for document events.
setElementAt(double, int) - Method in interface org.xmlcml.cml.FloatArray
 
setElementAt(double, int) - Method in class org.xmlcml.cml.FloatArrayImpl
 
setElementAt(Int2, int) - Method in class jumbo.euclid.Int2Vector
 
setElementAt(int, double) - Method in class jumbo.euclid.RealArray
set a given element into the array; must be less than current max index
setElementAt(int, double) - Method in class jumbo.euclid.Vector3
subscript operator: counts from ZERO
setElementAt(int, int) - Method in interface org.xmlcml.cml.IntegerArray
 
setElementAt(int, int) - Method in class org.xmlcml.cml.IntegerArrayImpl
 
setElementAt(int, int) - Method in class jumbo.euclid.IntArray
set a given element into the array; must be less than current max index
setElementAt(int, int, double) - Method in class jumbo.euclid.RealMatrix
inserts a given element to the matrix - MODIFIES matrix
setElementAt(int, int, int) - Method in class jumbo.euclid.IntMatrix
inserts a given element to the matrix - MODIFIES matrix
setElementAt(int, Object) - Method in class jumbo.euclid.ObjectArray
set a given element into the array; must be less than current max index
setElementAt(Real2, int) - Method in class jumbo.euclid.Real2Vector
 
setElementAt(String, int) - Method in interface org.xmlcml.cml.StringArray
 
setElementAt(String, int) - Method in class org.xmlcml.cml.StringArrayImpl
 
setElementAt(Vector3, int) - Method in class jumbo.euclid.Point3Vector
sets a given coordinate (i) to v.
setElements(int, double[]) - Method in class jumbo.euclid.RealArray
copy a smaller array into the array statrting at start
setElements(int, int[]) - Method in class jumbo.euclid.IntArray
copy a smaller array into the array statrting at start
setElements(int, Object[]) - Method in class jumbo.euclid.ObjectArray
copy a smaller array into the array statrting at start
setElementType(String) - Method in interface org.xmlcml.cml.Atom
 
setElementType(String) - Method in class org.xmlcml.cml.AtomImpl
 
setEpsilon(double) - Static method in class jumbo.euclid.Real
set current version of epsilon
setFormalCharge(int) - Method in interface org.xmlcml.cml.Atom
 
setFormalCharge(int) - Method in class org.xmlcml.cml.AtomImpl
 
setHRef(String) - Method in interface org.xmlcml.cml.Link
 
setHRef(String) - Method in class org.xmlcml.cml.LinkImpl
 
setHybridization(int) - Method in interface org.xmlcml.cml.Atom
 
setHybridization(int) - Method in class org.xmlcml.cml.AtomImpl
 
setHydrogenCount(int) - Method in interface org.xmlcml.cml.Atom
 
setHydrogenCount(int) - Method in class org.xmlcml.cml.AtomImpl
 
setId(String) - Method in class org.xmlcml.cml.CMLBaseImpl
 
setId(String) - Method in interface org.xmlcml.cml.HasId
 
setIntValue(int) - Method in interface org.xmlcml.cml.IntegerVal
 
setIntValue(int) - Method in class org.xmlcml.cml.IntegerValImpl
 
setIsotope(double) - Method in interface org.xmlcml.cml.Atom
 
setIsotope(double) - Method in class org.xmlcml.cml.AtomImpl
 
setMax(int) - Method in class jumbo.euclid.IntSet
 
setMaximum(double) - Method in interface org.xmlcml.cml.FloatVal
set maximum value; must be greater than minimum
setMaximum(double) - Method in class org.xmlcml.cml.FloatValImpl
set maximum value; must be greater than minimum
setMaximum(int) - Method in interface org.xmlcml.cml.IntegerVal
set maximum value; must be greater than minimum
setMaximum(int) - Method in class org.xmlcml.cml.IntegerValImpl
set maximum value; must be greater than minimum
setMaxIndex(int) - Method in class jumbo.euclid.IntArray
reset the maximum index (for when poking elements) (no other effect)
setMaxIndex(int) - Method in class jumbo.euclid.ObjectArray
reset the maximum index (for when poking elements) (no other effect)
setMaxIndex(int) - Method in class jumbo.euclid.RealArray
reset the maximum index (for when poking elements) (no other effect)
setMin(int) - Method in class jumbo.euclid.IntSet
 
setMinimum(double) - Method in interface org.xmlcml.cml.FloatVal
set minimum value; must be less than maximum
setMinimum(double) - Method in class org.xmlcml.cml.FloatValImpl
set minimum value; must be less than maximum
setMinimum(int) - Method in interface org.xmlcml.cml.IntegerVal
set minimum value; must be less than maximum
setMinimum(int) - Method in class org.xmlcml.cml.IntegerValImpl
set minimum value; must be less than maximum
setMolecule(Molecule) - Method in class org.xmlcml.cml.AtomImpl
 
setMolecule(Molecule) - Method in class org.xmlcml.cml.BondImpl
every Bond should be associated with one molecule
setNonBuiltinArray(String, StringArray) - Method in interface org.xmlcml.cml.AtomArray
 
setNonBuiltinArray(String, StringArray) - Method in class org.xmlcml.cml.AtomArrayImpl
 
setNonBuiltinArray(String, StringArray) - Method in interface org.xmlcml.cml.BondArray
 
setNonBuiltinArray(String, StringArray) - Method in class org.xmlcml.cml.BondArrayImpl
 
setNonBuiltinArray(String, StringArray) - Method in interface org.xmlcml.cml.HasBuiltinArrayNames
 
setNonBuiltinVal(String, StringVal) - Method in interface org.xmlcml.cml.AbstractBuiltinContainer
 
setNonBuiltinVal(String, StringVal) - Method in class org.xmlcml.cml.AbstractBuiltinContainerImpl
 
setNonBuiltinVal(String, StringVal) - Method in interface org.xmlcml.cml.HasBuiltinNames
 
setNonHydrogenCount(int) - Method in interface org.xmlcml.cml.Atom
 
setNonHydrogenCount(int) - Method in class org.xmlcml.cml.AtomImpl
 
setOccupancy(double) - Method in interface org.xmlcml.cml.Atom
 
setOccupancy(double) - Method in class org.xmlcml.cml.AtomImpl
 
setOrder(String) - Method in interface org.xmlcml.cml.Bond
 
setOrder(String) - Method in class org.xmlcml.cml.BondImpl
 
setOutputCML(CML) - Method in class org.xmlcml.noncml.SDFImpl
 
setOutputCMLMolecule(Molecule) - Method in class org.xmlcml.noncml.JMEImpl
 
setOutputCMLMolecule(Molecule) - Method in class org.xmlcml.noncml.MDLMolImpl
 
setOutputCMLMolecule(Molecule) - Method in interface org.xmlcml.noncml.NonCMLDocument
to output a CML-Molecule in legacy form the molecule must be added to the NonCMLDocument and then the output() method called
setOutputCMLMolecule(Molecule) - Method in class org.xmlcml.noncml.SDFImpl
 
setOutputCMLMolecule(Molecule) - Method in class org.xmlcml.noncml.SMILESImpl
 
setOutputCMLMolecule(Molecule) - Method in class org.xmlcml.noncml.XYZImpl
 
setParser(Parser) - Method in class uk.co.demon.ursus.dom.SAXAdapter
installs a parser
setParser(String) - Method in class uk.co.demon.ursus.dom.SAXAdapter
creates a parser from the parserClassName and installs
setPCDATAContent(Element, String) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
Sets a string to be the content of an existing single PCDATANode.
setProcessFlag(boolean) - Method in interface uk.co.demon.ursus.dom.PMRElement
set flag indicating element is to be processed.
setProcessFlag(boolean) - Method in class uk.co.demon.ursus.dom.PMRElementImpl
set flag indicating element is to be processed.
setRange(AngleRange) - Method in class jumbo.euclid.Angle
set type of range
setRealValue(double) - Method in interface org.xmlcml.cml.FloatVal
 
setRealValue(double) - Method in class org.xmlcml.cml.FloatValImpl
 
setRef(HasAtomRefs) - Method in class org.xmlcml.cml.AtomImpl
add a reference to this Atom
setResidueID(String) - Method in interface org.xmlcml.cml.Atom
 
setResidueID(String) - Method in class org.xmlcml.cml.AtomImpl
 
setResidueType(String) - Method in interface org.xmlcml.cml.Atom
 
setResidueType(String) - Method in class org.xmlcml.cml.AtomImpl
 
setRows(int) - Method in interface org.xmlcml.cml.FloatMatrix
 
setRows(int) - Method in class org.xmlcml.cml.FloatMatrixImpl
 
setStereo(String) - Method in interface org.xmlcml.cml.Bond
 
setStereo(String) - Method in class org.xmlcml.cml.BondImpl
 
setStringVal(int, StringVal) - Method in interface org.xmlcml.cml.Bond
 
setStringVal(int, StringVal) - Method in class org.xmlcml.cml.BondImpl
 
setStringValue(String) - Method in interface org.xmlcml.cml.AbstractStringVal
 
setStringValue(String) - Method in class org.xmlcml.cml.AbstractStringValImpl
 
setSystemProperty(String, String) - Static method in class jumbo.xml.util.Util
add a property to the System ones.
setTagName(String) - Method in interface uk.co.demon.ursus.dom.PMRElement
A non-DOM extension
setTagName(String) - Method in class uk.co.demon.ursus.dom.AbstractElementImpl
NON-DOM method
setTitle(String) - Method in class org.xmlcml.cml.CMLBaseImpl
 
setTitle(String) - Method in interface org.xmlcml.cml.HasTitle
 
setTransformationType(int) - Method in class jumbo.euclid.Transform2
set transformation type
setTransformationType(int) - Method in class jumbo.euclid.Transform3
set transformation type
setUnits(Units) - Method in interface org.xmlcml.cml.FloatMatrix
 
setUnits(Units) - Method in class org.xmlcml.cml.FloatMatrixImpl
 
setUnits(Units) - Method in interface org.xmlcml.cml.HasUnits
 
setUnits(Units) - Method in interface org.xmlcml.cml.NumericVal
 
setUnits(Units) - Method in class org.xmlcml.cml.NumericValImpl
 
setVDWRadius(double) - Method in class org.xmlcml.molutil.ChemicalElement
 
setX(double) - Method in class jumbo.euclid.Real2
 
setX(int) - Method in class jumbo.euclid.Int2
 
setXY2(double, double) - Method in interface org.xmlcml.cml.Atom
 
setXY2(double, double) - Method in class org.xmlcml.cml.AtomImpl
 
setXY2(Real2) - Method in interface org.xmlcml.cml.Atom
 
setXY2(Real2) - Method in class org.xmlcml.cml.AtomImpl
 
setXYZ3(double, double, double) - Method in interface org.xmlcml.cml.Atom
 
setXYZ3(double, double, double) - Method in class org.xmlcml.cml.AtomImpl
 
setXYZ3(Point3) - Method in interface org.xmlcml.cml.Atom
 
setXYZ3(Point3) - Method in class org.xmlcml.cml.AtomImpl
 
setXYZFract(double, double, double) - Method in interface org.xmlcml.cml.Atom
 
setXYZFract(double, double, double) - Method in class org.xmlcml.cml.AtomImpl
 
setXYZFract(Point3) - Method in interface org.xmlcml.cml.Atom
 
setXYZFract(Point3) - Method in class org.xmlcml.cml.AtomImpl
 
setY(double) - Method in class jumbo.euclid.Real2
 
setY(int) - Method in class jumbo.euclid.Int2
 
shallowCopy(Angle) - Method in class jumbo.euclid.Angle
shallowCopy
shallowCopy(IntArray) - Method in class jumbo.euclid.IntArray
shallowCopy
shallowCopy(IntMatrix) - Method in class jumbo.euclid.IntMatrix
shallowCopy
shallowCopy(IntSquareMatrix) - Method in class jumbo.euclid.IntSquareMatrix
shallowCopy an existing object
shallowCopy(ObjectArray) - Method in class jumbo.euclid.ObjectArray
shallowCopy
shallowCopy(RealArray) - Method in class jumbo.euclid.RealArray
shallowCopy
shallowCopy(RealMatrix) - Method in class jumbo.euclid.RealMatrix
shallowCopy
shallowCopy(RealSquareMatrix) - Method in class jumbo.euclid.RealSquareMatrix
shallowCopy an existing object
shallowCopy(Vector3) - Method in class jumbo.euclid.Vector3
shallowCopy
showBuiltinNames() - Static method in class org.xmlcml.cml.AbstractAtomImpl
 
showBuiltinNames() - Static method in class org.xmlcml.cml.AbstractBondImpl
 
showBuiltinNames() - Static method in class org.xmlcml.cml.CrystalImpl
 
showElementNames() - Static method in class org.xmlcml.cml.CMLBaseImpl
 
SHRIEK - Static variable in class jumbo.xml.util.Util
 
SIGNED - Static variable in class jumbo.euclid.Angle
-PI to PI
SIMPLE_ELEMENTS - Static variable in interface org.xmlcml.noncml.SMILES
simple elements which need not be in [...].
sin() - Method in class jumbo.euclid.Angle
 
sin(String) - Static method in class jumbo.xml.util.Util
 
SINGLE - Static variable in interface org.xmlcml.cml.AbstractBond
single bond
SingMatrixException - exception jumbo.euclid.SingMatrixException.
thrown by inversion, eigenvalue routines, etc
SingMatrixException() - Constructor for class jumbo.euclid.SingMatrixException
 
SingMatrixException(String) - Constructor for class jumbo.euclid.SingMatrixException
 
size() - Method in interface org.xmlcml.cml.AtomArray
 
size() - Method in class org.xmlcml.cml.AtomArrayImpl
 
size() - Method in interface org.xmlcml.cml.BondArray
 
size() - Method in class org.xmlcml.cml.BondArrayImpl
 
size() - Method in class jumbo.euclid.IntArray
get actual number of elements
size() - Method in class jumbo.euclid.IntSet
 
size() - Method in class jumbo.euclid.ObjectArray
get actual number of elements
size() - Method in class jumbo.euclid.Real2Array
 
size() - Method in class jumbo.euclid.RealArray
get actual number of elements
size() - Method in class jumbo.euclid.StringSet
 
size() - Method in interface jumbo.xml.util.XHashtable
from Hashtable
size() - Method in interface org.xmlcml.tools.ToolHashSet
size of Set
skipWhite(BufferedReader) - Static method in class jumbo.xml.util.Util
skip white lines and end with first non-white line.
SLASH - Static variable in class jumbo.xml.util.Util
 
smallestElement() - Method in class jumbo.euclid.IntArray
value of smallest element
smallestElement() - Method in class jumbo.euclid.IntMatrix
get smallest element
smallestElement() - Method in class jumbo.euclid.RealArray
value of smallest element
smallestElement() - Method in class jumbo.euclid.RealMatrix
get smallest element
smallestElementInColumn(int) - Method in class jumbo.euclid.IntMatrix
get smallest element in a column
smallestElementInColumn(int) - Method in class jumbo.euclid.RealMatrix
get smallest element in a column
smallestElementInRow(int) - Method in class jumbo.euclid.IntMatrix
get smallest element in a row
smallestElementInRow(int) - Method in class jumbo.euclid.RealMatrix
get smallest element in a row
SMILES - interface org.xmlcml.noncml.SMILES.
read/write SMILES
SMILES - Static variable in interface org.xmlcml.noncml.NonCMLDocument
 
SMILESATOMS - Static variable in interface org.xmlcml.cml.AbstractAtom
these are the only allowed atoms in SMILES that can be outside [...]
SMILESBondOrder(String) - Static method in class org.xmlcml.noncml.SMILESImpl
translates "CML" codes into SMILES symbols
SMILESImpl - class org.xmlcml.noncml.SMILESImpl.
class to read and write SMILES files
SMILESImpl() - Constructor for class org.xmlcml.noncml.SMILESImpl
 
SMILESImpl(BufferedReader, String) - Constructor for class org.xmlcml.noncml.SMILESImpl
form a SMILES object from a local file
SMILESImpl(Molecule) - Constructor for class org.xmlcml.noncml.SMILESImpl
form a SMILES object from a CML file
smilesString - Variable in class org.xmlcml.noncml.SMILESImpl
 
sort() - Method in class jumbo.euclid.IntRangeVector
arrange the elements in order of ascending minimum Range value
sort() - Method in class jumbo.euclid.RealRangeVector
arrange the elements in order of ascending minimum Range value
sort(Object[]) - Static method in class jumbo.xml.util.Util
sort an object array - very inefficient
sort(Vector) - Static method in class jumbo.euclid.SortableString
sorts a vector of strings; not very efficient
Sortable - interface jumbo.euclid.Sortable.
interface for allowing Objects to be sorted
SortableObject - class jumbo.euclid.SortableObject.
an Object which is sortable (i.e.
SortableObject() - Constructor for class jumbo.euclid.SortableObject
 
SortableString - class jumbo.euclid.SortableString.
a String which can be sorted using ObjectArray.
SortableString(String) - Constructor for class jumbo.euclid.SortableString
 
sortAscending() - Method in class jumbo.euclid.Int2
sorts x and y so that x <= y
sortAscending() - Method in class jumbo.euclid.IntArray
MODIFIES array to be in ascending order
sortAscending() - Method in class jumbo.euclid.IntSet
sort the IntSet; MODIFIES 'this'
sortAscending() - Method in class jumbo.euclid.ObjectArray
MODIFIES ObjectArray to be in ascending order
sortAscending() - Method in class jumbo.euclid.Real2
sorts x and y so that x <= y
sortAscending() - Method in class jumbo.euclid.RealArray
MODIFIES array to be in ascending order
sortAscending() - Method in class jumbo.euclid.StringSet
MODIFIES StringSet to be in ascending order
sortAscending(Choice2) - Method in class jumbo.euclid.Int2Vector
sort ARRAY on X or Y coordinate; returns new array
sortAscending(Choice2) - Method in class jumbo.euclid.Real2Vector
sort ARRAY on X or Y coordinate; returns new array
sortDescending() - Method in class jumbo.euclid.Int2
sorts x and y so that x >= y
sortDescending() - Method in class jumbo.euclid.IntArray
MODIFIES array to be in ascending order
sortDescending() - Method in class jumbo.euclid.ObjectArray
MODIFIES ObjectArray to be in descending order
sortDescending() - Method in class jumbo.euclid.Real2
sorts x and y so that x >= y
sortDescending() - Method in class jumbo.euclid.RealArray
MODIFIES array to be in ascending order
sortDescending() - Method in class jumbo.euclid.StringSet
MODIFIES StringSet to be in descending order
sortDescending(Choice2) - Method in class jumbo.euclid.Int2Vector
sort ARRAY on X or Y coordinate; returns new array
sortDescending(Choice2) - Method in class jumbo.euclid.Real2Vector
sort ARRAY on X or Y coordinate; returns new array
sortVector(Vector) - Static method in class jumbo.xml.util.Util
sort a Vector - VERY crude and inefficient
sortXYAscending() - Method in class jumbo.euclid.Int2Vector
sort X and Y within each point; MODIFIES array
sortXYAscending() - Method in class jumbo.euclid.Real2Vector
sort X and Y within each point; MODIFIES array
sortXYDescending() - Method in class jumbo.euclid.Int2Vector
sort X and Y within each point; MODIFIES array
sortXYDescending() - Method in class jumbo.euclid.Real2Vector
sort X and Y within each point; MODIFIES array
SP - Static variable in interface org.xmlcml.cml.AbstractAtom
 
SP2 - Static variable in interface org.xmlcml.cml.AbstractAtom
 
SP3 - Static variable in interface org.xmlcml.cml.AbstractAtom
 
SPACE - Static variable in class jumbo.xml.util.Util
 
SPACEGROUP - Static variable in interface org.xmlcml.cml.Crystal
 
spaces(int) - Static method in class jumbo.xml.util.Util
make a String of a given number of spaces
spanningTree - Variable in class org.xmlcml.tools.RingNucleusImpl
 
SpanningTree - interface org.xmlcml.tools.SpanningTree.
simple Spanning tree, independent of Molecule (contains pointer into that).
SpanningTreeImpl - class org.xmlcml.tools.SpanningTreeImpl.
 
SpanningTreeImpl() - Constructor for class org.xmlcml.tools.SpanningTreeImpl
 
SpanningTreeImpl(Molecule) - Constructor for class org.xmlcml.tools.SpanningTreeImpl
new spanning tree, starting at first atom and including all its descendants
SpanningTreeImpl(Molecule, Atom) - Constructor for class org.xmlcml.tools.SpanningTreeImpl
new spanning tree, starting at start and including all its descendants
SpanningTreeImpl(Molecule, Atom, Atom) - Constructor for class org.xmlcml.tools.SpanningTreeImpl
new spanning tree, starting at rootAtom.
split(String) - Static method in class jumbo.xml.util.Util
splits a whitespace-separated set of tokens into a String[]
splitBuiltinArrayContainer(CMLBase) - Static method in class org.xmlcml.cml.ArrayDelegate
acts on atomArray, etc which contain StringArray.
SPLITFILES - Static variable in interface uk.co.demon.ursus.dom.PMRNode
split into files after the 2nd level
splitSDF(BufferedReader, String) - Static method in class org.xmlcml.noncml.SDFImpl
 
spTypeStrings - Static variable in interface org.xmlcml.cml.AbstractAtom
 
sqrt(Complex) - Static method in class jumbo.euclid.Complex
complex square root
stack - Variable in class uk.co.demon.ursus.dom.SAXDOMBuilder
 
STAR - Static variable in class jumbo.xml.util.Util
 
start - Variable in class uk.co.demon.ursus.dom.SAXDOMBuilder
 
startDocument() - Method in class org.xmlcml.cml.CMLDOMSAXBuilderImpl
 
startDocument() - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive notification of the beginning of the document.
startDocument() - Method in class uk.co.demon.ursus.dom.SAXDOMBuilder
 
startDocument() - Method in class org.xmlcml.test.SAXAtomCounter
called when the document starts
startElement(String, AttributeList) - Method in class org.xmlcml.cml.CMLDOMSAXBuilderImpl
 
startElement(String, AttributeList) - Method in class org.xmlcml.cml.DefaultCMLDOMSAXBuilder
 
startElement(String, AttributeList) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive notification of the start of an element.
startElement(String, AttributeList) - Method in class uk.co.demon.ursus.dom.SAXDOMBuilder
 
startElement(String, AttributeList) - Method in class org.xmlcml.test.SAXAtomCounter
called when a start tag is found.
Status - class jumbo.euclid.Status.
the superclass for (almost) all jumbo.euclid classes.
Status() - Constructor for class jumbo.euclid.Status
 
STElement - interface org.xmlcml.tools.STElement.
Node for Spanning tree, holds pointer to Atom
STElementImpl - class org.xmlcml.tools.STElementImpl.
Node for Spanning tree, holds pointer to Atom
STElementImpl(Document) - Constructor for class org.xmlcml.tools.STElementImpl
 
STElementImpl(Document, Atom) - Constructor for class org.xmlcml.tools.STElementImpl
 
stereo - Variable in class org.xmlcml.cml.BondImpl
 
STEREO - Static variable in interface org.xmlcml.cml.AbstractBond
 
STRING - Static variable in interface org.xmlcml.cml.CMLBase
 
STRING_TYPE - Static variable in interface org.xmlcml.cml.CMLBase
 
StringArray - interface org.xmlcml.cml.StringArray.
 
STRINGARRAY - Static variable in interface org.xmlcml.cml.CMLBase
 
StringArrayImpl - class org.xmlcml.cml.StringArrayImpl.
 
StringArrayImpl() - Constructor for class org.xmlcml.cml.StringArrayImpl
 
StringArrayImpl(Document) - Constructor for class org.xmlcml.cml.StringArrayImpl
new StringArray in context
StringArrayImpl(Element) - Constructor for class org.xmlcml.cml.StringArrayImpl
 
StringSet - class jumbo.euclid.StringSet.
Stores a unique set of Strings.
StringSet() - Constructor for class jumbo.euclid.StringSet
default contsructor is case-sensitive
StringSet(int) - Constructor for class jumbo.euclid.StringSet
set case insensitivity if 'ignore' arg is 'StringSet.IGNORE_CASE'
StringSet(String[]) - Constructor for class jumbo.euclid.StringSet
create a StringSet from the Strings (duplicates are ignored); case-sensitive
StringSetException - exception jumbo.euclid.StringSetException.
StringSet error
StringSetException() - Constructor for class jumbo.euclid.StringSetException
 
StringSetException(String) - Constructor for class jumbo.euclid.StringSetException
 
StringVal - interface org.xmlcml.cml.StringVal.
 
StringValImpl - class org.xmlcml.cml.StringValImpl.
 
StringValImpl() - Constructor for class org.xmlcml.cml.StringValImpl
 
StringValImpl(Document) - Constructor for class org.xmlcml.cml.StringValImpl
new StringVal in document context
StringValImpl(Element) - Constructor for class org.xmlcml.cml.StringValImpl
 
StringValImpl(String, Document) - Constructor for class org.xmlcml.cml.StringValImpl
new subclassed object in document context
StringValImpl(String, Document, String, String, String, String, String, String) - Constructor for class org.xmlcml.cml.StringValImpl
 
stringValue - Variable in class org.xmlcml.cml.AbstractStringValImpl
 
stringVector - Variable in class org.xmlcml.cml.FloatArrayImpl
 
stringVector - Variable in class org.xmlcml.cml.IntegerArrayImpl
 
stringVector - Variable in class org.xmlcml.cml.StringArrayImpl
 
stripISOControls(String) - Static method in class jumbo.xml.util.Util
remove all control (non-printing) characters
stripNewlines(byte[]) - Static method in class jumbo.xml.util.Util
strip linefeeds from a byte array
STYLE - Static variable in interface uk.co.demon.ursus.dom.PMRNode
style
subArray(IntSet) - Method in class jumbo.euclid.Int2Vector
create a NEW subset of the points; points are COPIED
subArray(IntSet) - Method in class jumbo.euclid.Point3Vector
create a NEW subset of the points; points are COPIED
subArray(IntSet) - Method in class jumbo.euclid.Real2Vector
create a NEW subset of the points; points are COPIED
subSet(Int2Range) - Method in class jumbo.euclid.Int2Vector
create a subset of the points within a box
subSet(Real2Range) - Method in class jumbo.euclid.Real2Vector
create a subset of the points within a box
SubstituentList - interface org.xmlcml.tools.SubstituentList.
a list of substituents (Chains, RingNucleus)- usually on an Atom in a Ring(Nucleus)
SubstituentListImpl - class org.xmlcml.tools.SubstituentListImpl.
a list of substituents (Chains, RingNucleus)- usually on an Atom in a Ring(Nucleus)
SubstituentListImpl() - Constructor for class org.xmlcml.tools.SubstituentListImpl
 
substituteDOSbyAscii(String) - Static method in class jumbo.xml.util.Util
substitute certain DOS-compatible diacriticals by the Unicode value.
substituteEquals(String) - Static method in class jumbo.xml.util.Util
substitute hex representation of character, e.g.
substituteString(String, String, String, int) - Static method in class jumbo.xml.util.Util
make substitutions in a string.
substituteStrings(String, String[], String[]) - Static method in class jumbo.xml.util.Util
make substitutions in a string.
substring(String, String, String) - Static method in class jumbo.xml.util.Util
supports XSL substring
subtract() - Method in class jumbo.euclid.Line3
form coincident antiparallel line
subtract() - Method in class jumbo.euclid.Plane3
form coincident antiparallel plane
subtract() - Method in class jumbo.euclid.Polar
unary minus
subtract(Angle) - Method in class jumbo.euclid.Angle
subtract two angles
subtract(Int2) - Method in class jumbo.euclid.Int2
subtract two points - vector difference;
subtract(Int2) - Method in class jumbo.euclid.Int2Vector
translate negatively; MODIFIES 'this'
subtract(IntArray) - Method in class jumbo.euclid.IntArray
array subtraction - subtracts conformable arrays
subtract(IntMatrix) - Method in class jumbo.euclid.IntMatrix
matrix subtraction - subtracts conformable matrices giving NEW matrix
subtract(IntSquareMatrix) - Method in class jumbo.euclid.IntSquareMatrix
matrix subtraction - subtracts conformable matrices
subtract(Point3) - Method in class jumbo.euclid.Point3
vector between two points
subtract(Point3Vector) - Method in class jumbo.euclid.Point3Vector
form the point+point difference for two vectors of points
subtract(Polar) - Method in class jumbo.euclid.Polar
subtract two polars
subtract(Real2) - Method in class jumbo.euclid.Real2
subtract two points - vector difference;
subtract(Real2) - Method in class jumbo.euclid.Real2Vector
translate negatively; MODIFIES 'this'
subtract(RealArray) - Method in class jumbo.euclid.RealArray
array subtraction - subtracts conformable arrays
subtract(RealMatrix) - Method in class jumbo.euclid.RealMatrix
matrix subtraction - subtracts conformable matrices giving NEW matrix
subtract(RealSquareMatrix) - Method in class jumbo.euclid.RealSquareMatrix
matrix subtraction - subtracts conformable matrices
subtract(Vector3) - Method in class jumbo.euclid.Point3
New point from point-vector
subtract(Vector3) - Method in class jumbo.euclid.Point3Vector
translate negatively
subtract(Vector3) - Method in class jumbo.euclid.Vector3
 
sumAllElements() - Method in class jumbo.euclid.IntArray
sum all elements
sumAllElements() - Method in class jumbo.euclid.RealArray
sum all elements
swap() - Method in class jumbo.euclid.Int2
swaps the x and y values
swap() - Method in class jumbo.euclid.Real2
swaps the x and y values
swapXY() - Method in class jumbo.euclid.Int2Vector
swap all X and Y coordinates; MODIFIES array
swapXY() - Method in class jumbo.euclid.Real2Vector
swap all X and Y coordinates; MODIFIES array

T

TAB - Static variable in class jumbo.xml.util.Util
 
TAGGED - Static variable in interface uk.co.demon.ursus.dom.PMRNode
the event stream with tags (at present identical to XML)
tan() - Method in class jumbo.euclid.Angle
 
test() - Static method in class jumbo.euclid.IntArray
 
test() - Static method in class jumbo.euclid.IntSet
 
test() - Static method in class jumbo.euclid.RealArray
 
test(CMLBase) - Method in class org.xmlcml.cml.CMLDOMSAXBuilderImpl
called from embedded commands in CML file
test1(String) - Static method in class org.xmlcml.cml.CMLDocumentImpl
 
test1(String[]) - Static method in class org.xmlcml.cml.CMLBaseImpl
 
testBuild() - Method in class uk.co.demon.ursus.dom.PMRDocumentImpl
 
testEdit(Node) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
create a deep or shallow copy of an element, including correct classes; tag and owner document set to those from element.
testRead(String) - Method in class uk.co.demon.ursus.dom.PMRDocumentImpl
 
TILDE - Static variable in class jumbo.xml.util.Util
 
title - Variable in class org.xmlcml.cml.CMLBaseImpl
 
title - Variable in class org.xmlcml.cml.Coordinate3
 
TITLE - Static variable in interface org.xmlcml.cml.HasTitle
"title" attribute name
toCamelCase(String) - Static method in class jumbo.xml.util.Util
 
ToolHashSet - interface org.xmlcml.tools.ToolHashSet.
has to provide the functionality of HashSet
ToolHashSetImpl - class org.xmlcml.tools.ToolHashSetImpl.
 
ToolHashSetImpl() - Constructor for class org.xmlcml.tools.ToolHashSetImpl
 
Torsion - interface org.xmlcml.cml.Torsion.
 
TORSION - Static variable in interface org.xmlcml.cml.CMLBase
 
torsion(int, int, int, int) - Method in class jumbo.euclid.Point3Vector
get torsion angle between 4 points
torsion(IntSet) - Method in class jumbo.euclid.Point3Vector
get torsion angle between 4 points
TorsionImpl - class org.xmlcml.cml.TorsionImpl.
 
TorsionImpl() - Constructor for class org.xmlcml.cml.TorsionImpl
 
TorsionImpl(Document) - Constructor for class org.xmlcml.cml.TorsionImpl
new Torsion in document context
TorsionImpl(Element) - Constructor for class org.xmlcml.cml.TorsionImpl
 
torsionVector - Variable in class org.xmlcml.cml.MoleculeImpl
 
toSMILES() - Method in interface org.xmlcml.tools.SpanningTree
 
toSMILES() - Method in class org.xmlcml.tools.SpanningTreeImpl
 
toString() - Method in class org.xmlcml.cml.AtomImpl
 
toString() - Method in class org.xmlcml.cml.BondImpl
 
toString() - Method in class org.xmlcml.molutil.ChemicalElement
 
toString() - Method in class jumbo.euclid.Angle
 
toString() - Method in class jumbo.euclid.Complex
 
toString() - Method in class jumbo.euclid.Int2
 
toString() - Method in class jumbo.euclid.Int2Range
 
toString() - Method in class jumbo.euclid.IntArray
concatenates values with spaces
toString() - Method in class jumbo.euclid.IntMatrix
output matrix - very crude...
toString() - Method in class jumbo.euclid.IntRange
output
toString() - Method in class jumbo.euclid.IntSet
 
toString() - Method in class jumbo.euclid.Line3
 
toString() - Method in class jumbo.euclid.ObjectArray
concatenates values with spaces
toString() - Method in class jumbo.euclid.Plane3
 
toString() - Method in class jumbo.euclid.Point3
 
toString() - Method in class jumbo.euclid.Polar
 
toString() - Method in class jumbo.euclid.Real2
 
toString() - Method in class jumbo.euclid.Real2Range
 
toString() - Method in class jumbo.euclid.Real3Range
 
toString() - Method in class jumbo.euclid.RealArray
concatenates values with spaces
toString() - Method in class jumbo.euclid.RealMatrix
output matrix - very crude...
toString() - Method in class jumbo.euclid.RealRange
output
toString() - Method in class jumbo.euclid.SortableString
 
toString() - Method in class jumbo.euclid.StringSet
outputs the components as a list separated by "\n" - bad luck if they already contain this!
toString() - Method in class jumbo.euclid.Transform2
 
toString() - Method in class jumbo.euclid.Vector3
 
toString() - Method in class org.xmlcml.tools.AtomSetImpl
 
toString() - Method in class org.xmlcml.tools.BondSetImpl
 
toString() - Method in class org.xmlcml.tools.ChainSetImpl
create a String
toString() - Method in class org.xmlcml.tools.RingImpl
a String representation (mainly for diagnostics)
toString() - Method in interface org.xmlcml.tools.RingNucleus
 
toString() - Method in class org.xmlcml.tools.RingNucleusImpl
 
toString() - Method in class org.xmlcml.tools.RingOverlapImpl
 
toString() - Method in class org.xmlcml.tools.SpanningTreeImpl
 
trace() - Method in class jumbo.euclid.IntSquareMatrix
trace
trace() - Method in class jumbo.euclid.RealSquareMatrix
trace
transfer(Document, Document) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
transfers complete fromDocument, changing ownership and subsclassing
transform(Transform2) - Method in interface org.xmlcml.cml.Atom
transform XY2 coordinate; if atom.xy2 is null, no op
transform(Transform2) - Method in class org.xmlcml.cml.AtomImpl
transforms 2D coordinates of atom
transform(Transform2) - Method in interface org.xmlcml.tools.AtomSet
transform coordinates of all atoms in the set (rather inefficient) Works on original molecule - probably obsolete
transform(Transform2) - Method in class org.xmlcml.tools.AtomSetImpl
transform coordinates of all atoms in the set (rather inefficient)
transform(Transform3) - Method in class jumbo.euclid.Line3
transform a line
transform(Transform3) - Method in class jumbo.euclid.Point3
transform a point; does NOT modify 'this'
transform(Transform3) - Method in class jumbo.euclid.Point3Vector
transform all coordinates MODIFIES Vector
transform(Transform3) - Method in class jumbo.euclid.Vector3
transform a vector
transform(Transform3, IntSet) - Method in class jumbo.euclid.Point3Vector
transform subset of coordinates - MODIFIES Vector
Transform2 - class jumbo.euclid.Transform2.
Transform2 - 2-D transformation matrix class
Transform2() - Constructor for class jumbo.euclid.Transform2
default is a unit matrix
Transform2(Angle) - Constructor for class jumbo.euclid.Transform2
rotation about z- axis
Transform2(double[]) - Constructor for class jumbo.euclid.Transform2
Formed by feeding in an existing array to a cols*cols matrix.
Transform2(int) - Constructor for class jumbo.euclid.Transform2
This gives a default unit matrix of type t (default ROT_ORIG).
Transform2(Real2, Real2) - Constructor for class jumbo.euclid.Transform2
from 2 vector components - NOT checked for validity
Transform2(RealSquareMatrix) - Constructor for class jumbo.euclid.Transform2
from a 2x2 or 3x3 matrix
Transform2(RealSquareMatrix, Vector2) - Constructor for class jumbo.euclid.Transform2
from a 2x2 rotation matrix and a translation vector
Transform2(Transform2) - Constructor for class jumbo.euclid.Transform2
copy constructors - assumed to be an OK matrix
Transform2(Transform2, Real2) - Constructor for class jumbo.euclid.Transform2
from rotation about a point, given a matrix NOT CHECKED
Transform2(Vector2) - Constructor for class jumbo.euclid.Transform2
identity matrix with translation component
Transform2(Vector2, Vector2) - Constructor for class jumbo.euclid.Transform2
rotation of one vector onto another
Transform3 - class jumbo.euclid.Transform3.
Transform3 - 3-D transformation matrix class
Transform3() - Constructor for class jumbo.euclid.Transform3
default is a unit matrix
Transform3(Angle, Angle, Angle) - Constructor for class jumbo.euclid.Transform3
from rotation about the three orthogonal axes (X then Y then Z)
Transform3(Choice3, Angle) - Constructor for class jumbo.euclid.Transform3
from rotation about an axis (use (Choice3.X), etc.
Transform3(double[]) - Constructor for class jumbo.euclid.Transform3
Formed by feeding in an existing array to a cols*cols matrix.
Transform3(int) - Constructor for class jumbo.euclid.Transform3
This gives a default unit matrix of type t (default ROT_ORIG).
Transform3(Line3, Angle) - Constructor for class jumbo.euclid.Transform3
Rotation about a line
Transform3(RealSquareMatrix) - Constructor for class jumbo.euclid.Transform3
from a 3x3 or 4x4 matrix
Transform3(RealSquareMatrix, Vector3) - Constructor for class jumbo.euclid.Transform3
from a 3x3 rotation matrix and a translation vector
Transform3(Transform3) - Constructor for class jumbo.euclid.Transform3
copy constructors - assumed to be an OK matrix
Transform3(Transform3, Point3) - Constructor for class jumbo.euclid.Transform3
from rotation about a point, given a matrix
Transform3(Vector3) - Constructor for class jumbo.euclid.Transform3
identity matrix with translation component
Transform3(Vector3, Angle) - Constructor for class jumbo.euclid.Transform3
from rotation about a vector
Transform3(Vector3, Vector3) - Constructor for class jumbo.euclid.Transform3
rotation of one vector onto another
Transform3(Vector3, Vector3, Vector3) - Constructor for class jumbo.euclid.Transform3
from 3 vector components - NOT checked
transformBy(Transform2) - Method in class jumbo.euclid.Real2
transforms the point by a rot-trans matrix; MODIFIES 'this'
transformBy(Transform2) - Method in class jumbo.euclid.Real2Vector
transforms 'this' by rotation-translation matrix; MODIFIES 'this'
translateBy(Int2) - Method in class jumbo.euclid.Int2Vector
translate by a vector, synonym for 'plus'; MODIFIES 'this'
translateBy(Real2) - Method in class jumbo.euclid.Real2Vector
translate by a vector, synonym for 'plus'; MODIFIES 'this'
translateBy(Real2) - Method in interface org.xmlcml.tools.AtomSet
translate coordinates of all atoms in the setWorks on original molecule - probably obsolete
translateBy(Real2) - Method in class org.xmlcml.tools.AtomSetImpl
translate coordinates of all atoms in the set
transpose() - Method in class jumbo.euclid.IntSquareMatrix
transpose - MODIFIES matrix
transpose() - Method in class jumbo.euclid.RealSquareMatrix
transpose - MODIFIES matrix
TRFORM3_ANY - Static variable in class jumbo.euclid.Transform2
 
TRFORM3_ANY - Static variable in class jumbo.euclid.Transform3
 
TRFORM3_NULL - Static variable in class jumbo.euclid.Transform2
 
TRFORM3_NULL - Static variable in class jumbo.euclid.Transform3
 
TRIPLE - Static variable in interface org.xmlcml.cml.AbstractBond
triple bond
truncate(String, int) - Static method in class jumbo.xml.util.Util
return the first n characters of a string and add ellipses if truncated
two - Static variable in class jumbo.xml.util.Choice3
 
type - Variable in class org.xmlcml.tools.RingOverlapImpl
type of overlap (FUSED/BRIDGED)
typeString - Static variable in interface org.xmlcml.tools.RingOverlap
 
typeString - Static variable in class org.xmlcml.tools.RingOverlapImpl
 

U

UNDER - Static variable in class jumbo.xml.util.Util
 
UnequalArraysException - exception jumbo.euclid.UnequalArraysException.
Arrays are required to be equal lengths for some operations
UnequalArraysException() - Constructor for class jumbo.euclid.UnequalArraysException
 
UnequalArraysException(String) - Constructor for class jumbo.euclid.UnequalArraysException
 
UnequalMatricesException - exception jumbo.euclid.UnequalMatricesException.
Unconformable matrices (i.e.
UnequalMatricesException() - Constructor for class jumbo.euclid.UnequalMatricesException
 
UnequalMatricesException(String) - Constructor for class jumbo.euclid.UnequalMatricesException
 
UnimplementedException - exception jumbo.euclid.UnimplementedException.
Routine not yet implemented
UnimplementedException() - Constructor for class jumbo.euclid.UnimplementedException
 
UnimplementedException(String) - Constructor for class jumbo.euclid.UnimplementedException
 
UninitialisedException - exception jumbo.euclid.UninitialisedException.
a Object has not been initialised
UninitialisedException() - Constructor for class jumbo.euclid.UninitialisedException
a Object has not been initialised
UninitialisedException(String) - Constructor for class jumbo.euclid.UninitialisedException
 
UNIQUE - Static variable in interface org.xmlcml.cml.AbstractBuiltinContainer
 
units - Variable in class org.xmlcml.cml.Coordinate3
 
units - Variable in class org.xmlcml.cml.NumericValImpl
 
Units - class org.xmlcml.cml.Units.
supports scientific units.
UNITS - Static variable in interface org.xmlcml.cml.HasUnits
"units" attribute
UNITS - Static variable in interface org.xmlcml.cml.NumericVal
 
Units(String) - Constructor for class org.xmlcml.cml.Units
 
unitVector() - Method in class jumbo.euclid.RealArray
get unit vector
UNIVERSAL - Static variable in interface uk.co.demon.ursus.dom.PMRElement
concatenation of URN and local name
UNK - Static variable in interface org.xmlcml.cml.CMLBase
 
UNK_ELEM - Static variable in interface org.xmlcml.cml.CMLBase
 
UNKNOWN - Static variable in interface org.xmlcml.cml.CMLBase
 
UNKNOWN - Static variable in class jumbo.xml.util.Util
general code for unset or unknown variables
UNKNOWN - Static variable in interface org.xmlcml.tools.RingOverlap
state is unknown
UNKNOWN - Static variable in class org.xmlcml.tools.RingOverlapImpl
state is unknown
UNLIMITED - Static variable in class jumbo.euclid.Angle
Any value
unparsedEntityDecl(String, String, String, String) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive notification of an unparsed entity declaration.
UNSIGNED - Static variable in class jumbo.euclid.Angle
0 to 2*PI
UNTAGGED - Static variable in interface uk.co.demon.ursus.dom.PMRNode
the event stream with tag removed
updateDOM() - Method in class org.xmlcml.cml.AbstractAtomImpl
 
updateDOM() - Method in class org.xmlcml.cml.AngleImpl
 
updateDOM() - Method in class org.xmlcml.cml.AtomArrayImpl
 
updateDOM() - Method in class org.xmlcml.cml.AtomImpl
 
updateDOM() - Method in class org.xmlcml.cml.BondArrayImpl
 
updateDOM() - Method in class org.xmlcml.cml.BondImpl
 
updateDOM() - Method in interface org.xmlcml.cml.CMLBase
 
updateDOM() - Method in class org.xmlcml.cml.CMLBaseImpl
 
updateDOM() - Method in class org.xmlcml.cml.CMLImpl
 
updateDOM() - Method in class org.xmlcml.cml.CrystalImpl
 
updateDOM() - Method in class org.xmlcml.cml.ElectronImpl
 
updateDOM() - Method in class org.xmlcml.cml.ExecuteImpl
 
updateDOM() - Method in class org.xmlcml.cml.FeatureImpl
 
updateDOM() - Method in class org.xmlcml.cml.FloatMatrixImpl
 
updateDOM() - Method in class org.xmlcml.cml.FormulaImpl
 
updateDOM() - Method in class org.xmlcml.cml.LinkImpl
 
updateDOM() - Method in class org.xmlcml.cml.ListImpl
 
updateDOM() - Method in class org.xmlcml.cml.MoleculeImpl
when the DOM is built from legacy the tree may be delayed.
updateDOM() - Method in class org.xmlcml.cml.NumericValImpl
 
updateDOM() - Method in class org.xmlcml.cml.ReactionImpl
 
updateDOM() - Method in class org.xmlcml.cml.SequenceImpl
 
updateDOM() - Method in class org.xmlcml.cml.StringValImpl
 
updateDOM() - Method in class org.xmlcml.cml.TorsionImpl
 
updateDOMHasConvention() - Method in class org.xmlcml.cml.CMLBaseImpl
 
updateDOMHasConvention() - Method in interface org.xmlcml.cml.HasConvention
 
updateDOMHasConvention(HasConvention) - Static method in class org.xmlcml.cml.CMLBaseImpl
 
updateDOMHasCount() - Method in class org.xmlcml.cml.AbstractAtomImpl
 
updateDOMHasCount() - Method in class org.xmlcml.cml.ElectronImpl
 
updateDOMHasCount() - Method in class org.xmlcml.cml.FormulaImpl
 
updateDOMHasCount() - Method in interface org.xmlcml.cml.HasCount
 
updateDOMHasCount() - Method in class org.xmlcml.cml.MoleculeImpl
 
updateDOMHasCount(HasCount) - Static method in class org.xmlcml.cml.CMLBaseImpl
 
updateDOMHasDictRef() - Method in class org.xmlcml.cml.CMLBaseImpl
 
updateDOMHasDictRef() - Method in interface org.xmlcml.cml.HasDictRef
 
updateDOMHasDictRef(HasDictRef) - Static method in class org.xmlcml.cml.CMLBaseImpl
 
updateDOMHasId() - Method in class org.xmlcml.cml.CMLBaseImpl
 
updateDOMHasId() - Method in interface org.xmlcml.cml.HasId
 
updateDOMHasId(HasId) - Static method in class org.xmlcml.cml.CMLBaseImpl
 
updateDOMHasTitle() - Method in class org.xmlcml.cml.CMLBaseImpl
 
updateDOMHasTitle() - Method in interface org.xmlcml.cml.HasTitle
 
updateDOMHasTitle(HasTitle) - Static method in class org.xmlcml.cml.CMLBaseImpl
 
updateDOMHasUnits() - Method in class org.xmlcml.cml.FloatMatrixImpl
 
updateDOMHasUnits() - Method in interface org.xmlcml.cml.HasUnits
 
updateDOMHasUnits() - Method in class org.xmlcml.cml.NumericValImpl
 
updateDOMHasUnits(HasUnits) - Static method in class org.xmlcml.cml.CMLBaseImpl
 
urlString - Variable in class uk.co.demon.ursus.dom.SAXAdapter
 
Util - class jumbo.xml.util.Util.
A number of miscellaneous tools.
Util() - Constructor for class jumbo.xml.util.Util
 

V

valences - Static variable in interface org.xmlcml.cml.AbstractAtom
 
validity - Variable in class org.xmlcml.cml.CMLBaseImpl
 
Validity - interface uk.co.demon.ursus.dom.Validity.
A class-specific tool to allow validity information to be attached to a node
ValidityImpl - class uk.co.demon.ursus.dom.ValidityImpl.
A class-specific tool to allow validity information to be attached to a node
ValidityImpl() - Constructor for class uk.co.demon.ursus.dom.ValidityImpl
 
value() - Method in class jumbo.euclid.AngleType
 
vect - Variable in class jumbo.euclid.Plane3
vector of plane (normalised)
Vector2 - class jumbo.euclid.Vector2.
a 2-D vector.
Vector2(double, double) - Constructor for class jumbo.euclid.Vector2
 
Vector2(Real2) - Constructor for class jumbo.euclid.Vector2
 
Vector3 - class jumbo.euclid.Vector3.
Vector3 - 3-dimensional vector
Vector3() - Constructor for class jumbo.euclid.Vector3
null constructor
Vector3(Choice3) - Constructor for class jumbo.euclid.Vector3
axial unit vector constructor: unit vectors along X, Y, Z axes
Vector3(double[]) - Constructor for class jumbo.euclid.Vector3
formed from vector components
Vector3(double, double, double) - Constructor for class jumbo.euclid.Vector3
formed from vector components
Vector3(Point3) - Constructor for class jumbo.euclid.Vector3
make a vector from a point
Vector3(RealArray) - Constructor for class jumbo.euclid.Vector3
copy constructor from RealArray:
Vector3(Vector3) - Constructor for class jumbo.euclid.Vector3
copy constructor:
vneigl(int, double[], double[], double[], IllCondMatrixException) - Static method in class jumbo.euclid.Diagonalise
diagonalisation routine

W

warning(SAXParseException) - Method in class uk.co.demon.ursus.dom.SAXAdapter
Receive notification of a parser warning.
warning(SAXParseException) - Method in class uk.co.demon.ursus.dom.NonValidatingDOMParser
Warning.
warning(String) - Static method in class jumbo.xml.util.Util
Warning message - nothing fancy at present
warningVector - Variable in class org.xmlcml.cml.CMLValidityImpl
 
WEDGE - Static variable in interface org.xmlcml.cml.AbstractBond
wedge bond
WHITESPACE - Static variable in interface uk.co.demon.ursus.dom.PMRNode
the event stream with whitespace highlighted by comments
WHITESPACE - Static variable in class jumbo.xml.util.Util
 
write(Writer, Document, int, int) - Static method in class uk.co.demon.ursus.dom.PMRDelegate
 
writeAtoms(Writer) - Method in class org.xmlcml.noncml.JMEImpl
 
writeAtoms(Writer) - Method in class org.xmlcml.noncml.MDLMolImpl
 
writeAtoms(Writer) - Method in class org.xmlcml.noncml.SMILESImpl
 
writeAtoms(Writer) - Method in class org.xmlcml.noncml.XYZImpl
 
writeBonds(Writer) - Method in class org.xmlcml.noncml.JMEImpl
 
writeBonds(Writer) - Method in class org.xmlcml.noncml.MDLMolImpl
 
writeBonds(Writer) - Method in class org.xmlcml.noncml.SMILESImpl
 
writeData(Writer) - Method in class org.xmlcml.noncml.SDFImpl
 
writeFooter(Writer) - Method in class org.xmlcml.noncml.JMEImpl
 
writeFooter(Writer) - Method in class org.xmlcml.noncml.MDLMolImpl
 
writeFooter(Writer) - Method in class org.xmlcml.noncml.SMILESImpl
 
writeHeader(Writer) - Method in class org.xmlcml.noncml.JMEImpl
 
writeHeader(Writer) - Method in class org.xmlcml.noncml.MDLMolImpl
 
writeHeader(Writer) - Method in class org.xmlcml.noncml.XYZImpl
 

X

x - Variable in class jumbo.euclid.Real2
the first floating point value
X - Static variable in class jumbo.xml.util.Choice2
 
X - Static variable in class jumbo.xml.util.Choice3
 
X_COMMENTC - Static variable in class jumbo.xml.util.Util
 
X_COMMENTO - Static variable in class jumbo.xml.util.Util
 
X_DOCTYPEE - Static variable in class jumbo.xml.util.Util
 
X_DOCTYPEO - Static variable in class jumbo.xml.util.Util
 
X_ELEMDEFC - Static variable in class jumbo.xml.util.Util
 
X_ELEMDEFO - Static variable in class jumbo.xml.util.Util
 
X_EMPTAGC - Static variable in class jumbo.xml.util.Util
 
X_EMPTAGO - Static variable in class jumbo.xml.util.Util
 
X_ENTDEFC - Static variable in class jumbo.xml.util.Util
 
X_ENTDEFO - Static variable in class jumbo.xml.util.Util
 
X_ETAGC - Static variable in class jumbo.xml.util.Util
 
X_ETAGO - Static variable in class jumbo.xml.util.Util
 
X_GENENTC - Static variable in class jumbo.xml.util.Util
 
X_GENENTO - Static variable in class jumbo.xml.util.Util
 
X_PARAMENTC - Static variable in class jumbo.xml.util.Util
 
X_PARAMENTDEFC - Static variable in class jumbo.xml.util.Util
 
X_PARAMENTDEFO - Static variable in class jumbo.xml.util.Util
 
X_PARAMENTO - Static variable in class jumbo.xml.util.Util
 
X_STAGC - Static variable in class jumbo.xml.util.Util
 
X_STAGO - Static variable in class jumbo.xml.util.Util
 
X_STARTDEF - Static variable in class jumbo.xml.util.Util
 
X2 - Static variable in interface org.xmlcml.cml.AbstractAtom
 
X3 - Static variable in interface org.xmlcml.cml.AbstractAtom
 
XERCESNV - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 
XERCESSAX - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 
XFRACT - Static variable in interface org.xmlcml.cml.AbstractAtom
 
XHashtable - interface jumbo.xml.util.XHashtable.
extensions to java.util.Hashtable such as boolean operations
XHashtableImpl - class jumbo.xml.util.XHashtableImpl.
extensions to java.util.Hashtable such as boolean operations
XHashtableImpl() - Constructor for class jumbo.xml.util.XHashtableImpl
 
XML4J - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 
XMLCONTENT - Static variable in interface uk.co.demon.ursus.dom.PMRNode
the CONTENT as raw XML stream
xor(AtomSet) - Method in interface org.xmlcml.tools.AtomSet
combines this with AtomSet to find elements NOT in common, else null.
xor(AtomSet) - Method in class org.xmlcml.tools.AtomSetImpl
combines this with AtomSet to find elements NOT in common, else null.
xor(BondSet) - Method in interface org.xmlcml.tools.BondSet
combines this with BondSet to find elements NOT in common, else null.
xor(BondSet) - Method in class org.xmlcml.tools.BondSetImpl
combines this with BondSet to find elements NOT in common, else null.
xor(Ring) - Method in interface org.xmlcml.tools.Ring
create a new ring as the XOR of this and ring (i.e.
xor(Ring) - Method in class org.xmlcml.tools.RingImpl
create a new ring as the XOR of this and ring (i.e.
xor(ToolHashSet) - Method in interface org.xmlcml.tools.ToolHashSet
ToolHashSet containing elements in this or h but not both
xor(ToolHashSet) - Method in class org.xmlcml.tools.ToolHashSetImpl
 
xor(XHashtable) - Method in interface jumbo.xml.util.XHashtable
combines this with xHashtable to find elements NOT in common, else null.
xor(XHashtable) - Method in class jumbo.xml.util.XHashtableImpl
combines this with xHashtable to find elements NOT in common, else null.
xorIn(HashedVector) - Method in class jumbo.euclid.HashedVector
get elements in not more than one set (crude and slow)
xorTables(Hashtable, Hashtable) - Static method in class jumbo.xml.util.Util
XOR 2 Hashtables - inefficient except for small tables.
XP - Static variable in class uk.co.demon.ursus.dom.SAXAdapter
 
xy2 - Variable in class org.xmlcml.cml.AtomImpl
 
XYZ - interface org.xmlcml.noncml.XYZ.
class for JMOL XYZ files
XYZ - Static variable in interface org.xmlcml.noncml.NonCMLDocument
 
xyz3 - Variable in class org.xmlcml.cml.AtomImpl
 
xyzFract - Variable in class org.xmlcml.cml.AtomImpl
 
XYZImpl - class org.xmlcml.noncml.XYZImpl.
class to read and write xyz files (Peter Ertl's applet)
XYZImpl(BufferedReader, String) - Constructor for class org.xmlcml.noncml.XYZImpl
form an XYZ object from a local file
XYZImpl(Molecule) - Constructor for class org.xmlcml.noncml.XYZImpl
form a XYZ object from a CML file

Y

y - Variable in class jumbo.euclid.Real2
the second floating point value
Y - Static variable in class jumbo.xml.util.Choice2
 
Y - Static variable in class jumbo.xml.util.Choice3
 
Y2 - Static variable in interface org.xmlcml.cml.AbstractAtom
 
Y3 - Static variable in interface org.xmlcml.cml.AbstractAtom
 
YFRACT - Static variable in interface org.xmlcml.cml.AbstractAtom
 

Z

Z - Static variable in class jumbo.xml.util.Choice3
 
Z_FLOAT - Static variable in interface org.xmlcml.cml.Crystal
 
Z_INT - Static variable in interface org.xmlcml.cml.Crystal
 
Z3 - Static variable in interface org.xmlcml.cml.AbstractAtom
 
zero - Static variable in class jumbo.xml.util.Choice2
 
zero - Static variable in class jumbo.xml.util.Choice3
 
ZERO - Static variable in interface org.xmlcml.cml.AbstractBond
zero bond (disjoint == "." in SMILES)
zeroArray(int, double[]) - Static method in class jumbo.euclid.Real
set an array to zero
zeroArray(int, int[]) - Static method in class jumbo.euclid.Int
set an array to zero
ZeroVectorException - exception jumbo.euclid.ZeroVectorException.
Vector has zero length (e.g.
ZeroVectorException() - Constructor for class jumbo.euclid.ZeroVectorException
 
ZeroVectorException(String) - Constructor for class jumbo.euclid.ZeroVectorException
 
ZFRACT - Static variable in interface org.xmlcml.cml.AbstractAtom
 

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