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A
- ADDRESS_BITS_PER_UNIT - Static variable in class joelib.util.BitSet14
- ArrayHelper - class joelib.util.ArrayHelper.
- Array helper methods for writing and loading arrays.
- ArrayHelper() - Constructor for class joelib.util.ArrayHelper
- Constructor for the JOERandom object
- acceptedProperties() - Method in interface joelib.util.PropertyAcceptor
- and(BitSet14) - Method in class joelib.util.BitSet14
- Performs a logical AND of this target bit set with the argument bit set.
- and(JOEBitVec) - Method in class joelib.util.JOEBitVec
- Description of the Method
- and(JOEBitVec, JOEBitVec) - Static method in class joelib.util.JOEBitVec
- Description of the Method
- andCount(BitSet14) - Method in class joelib.util.JOEBitVec
- Returns the number of bits which are set in this BitSet14 AND the BitSet14 b.
- andNot(BitSet14) - Method in class joelib.util.BitSet14
- Clears all of the bits in this
BitSet14whose corresponding bit is set in the specifiedBitSet14. - andSet(JOEBitVec) - Method in class joelib.util.JOEBitVec
- Description of the Method
- arrayHelper - Static variable in class joelib.util.ArrayHelper
B
- BABEL_VERSION - Static variable in class joelib.util.JOEHelper
- Description of the Field
- BINARY_COMPARISON - Static variable in class joelib.util.ComparisonHelper
- BITS_PER_UNIT - Static variable in class joelib.util.BitSet14
- BIT_INDEX_MASK - Static variable in class joelib.util.BitSet14
- BUFF_SIZE - Static variable in class joelib.util.JOEHelper
- Description of the Field
- BitSet14 - class joelib.util.BitSet14.
- This class implements a vector of bits that grows as needed.
- BitSet14() - Constructor for class joelib.util.BitSet14
- Creates a new bit set.
- BitSet14(int) - Constructor for class joelib.util.BitSet14
- Creates a bit set whose initial size is large enough to explicitly
represent bits with indices in the range
0throughnbits-1. - bit(int) - Static method in class joelib.util.BitSet14
- Given a bit index, return a unit that masks that bit in its unit.
- bitCount(long) - Static method in class joelib.util.BitSet14
- Returns the number of bits set in val.
- bitIsOn(int) - Method in class joelib.util.JOEBitVec
- Description of the Method
- bitIsSet(int) - Method in class joelib.util.JOEBitVec
- Description of the Method
- bitLen(int) - Static method in class joelib.util.BitSet14
- bitLen(val) is the number of bits in val.
- bits - Variable in class joelib.util.BitSet14
- The bits in this BitSet14.
- bitsLeftOf(int) - Static method in class joelib.util.BitSet14
- Returns a long that has all the bits that are more significant than or equal to the specified index set to 1.
- bitsRightOf(int) - Static method in class joelib.util.BitSet14
- Returns a long that has all bits that are less significant than the specified index set to 1.
- booleanArrayFromSimpleString(String) - Method in class joelib.util.ArrayHelper
- booleanArrayFromSimpleString(String, String) - Static method in class joelib.util.ArrayHelper
- Loads boolean array from String .
- booleanArrayFromString(String) - Method in class joelib.util.ArrayHelper
- Loads boolean array from String .
- booleanArrayFromString(String, String, int) - Static method in class joelib.util.ArrayHelper
- Loads boolean array from String .
- booleanArrayFromString(String) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- booleanArrayFromString(Reader) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- booleanArrayFromString(String, int) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- booleanArrayFromString(Reader, int) - Static method in class joelib.util.LineArrayHelper
- Gets boolean arrays from a Reader.
- booleanArrayFromString(StringTokenizer, int) - Static method in class joelib.util.LineArrayHelper
- Gets boolean arrays from a Reader.
- booleanArrayFromTrueFalseString(String) - Method in class joelib.util.ArrayHelper
- booleanArrayFromTrueFalseString(String, String) - Static method in class joelib.util.ArrayHelper
- Loads boolean array from String .
- buildOERTreeVector(JOEAtom, JOERTree, JOERTree[], JOEBitVec) - Static method in class joelib.util.JHM
- byteMatrixFromString(String) - Method in class joelib.util.MatrixHelper
- Description of the Method
- byteMatrixFromString(String, String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
C
- CISTRANS_ISOMERISM_UNDEFINED - Static variable in class joelib.util.IsomerismDetection
- CIS_ISOMERISM - Static variable in class joelib.util.IsomerismDetection
- CONTACT_E_MAIL - Static variable in class joelib.util.JOEHelper
- Description of the Field
- ComparisonHelper - class joelib.util.ComparisonHelper.
- Example for converting molecules.
- ComparisonHelper(IOType, String) - Constructor for class joelib.util.ComparisonHelper
- ComparisonHelper(IOType, String, int) - Constructor for class joelib.util.ComparisonHelper
- Constructor for the ComparisonHelper object
- ComparisonHelper(JOEMol) - Constructor for class joelib.util.ComparisonHelper
- Constructor for the ComparisonHelper object
- ComparisonHelper() - Constructor for class joelib.util.ComparisonHelper
- calcRMS(double[], double[], int) - Method in class joelib.util.JHM
- cardinality() - Method in class joelib.util.BitSet14
- Returns the number of bits set to true in this
BitSet14. - cartesianToInternal(Vector, JOEMol) - Method in class joelib.util.JHM
- centerCoords(double[], int) - Method in class joelib.util.JHM
- checkProperties(PropertyAcceptor, Map) - Static method in class joelib.util.JOEPropertyHelper
- Description of the Method
- clear(int) - Method in class joelib.util.BitSet14
- Sets the bit specified by the index to
false. - clear(int, int) - Method in class joelib.util.BitSet14
- Sets the bits from the specified fromIndex(inclusive) to the
specified toIndex(exclusive) to
false. - clear() - Method in class joelib.util.BitSet14
- Sets all of the bits in this BitSet14 to
false. - clone() - Method in class joelib.util.BitSet14
- Cloning this
BitSet14produces a newBitSet14that is equal to it. - compare(JOEMol) - Method in class joelib.util.ComparisonHelper
- Description of the Method
- compare(JOEMol, String, double[]) - Method in class joelib.util.ComparisonHelper
- Description of the Method.
- compare(JOEMol, JOEMol) - Method in class joelib.util.ComparisonHelper
- compareBonds(JOEBond, JOEBond) - Method in class joelib.util.JHM
- Description of the Method
- comparisonType - Variable in class joelib.util.ComparisonHelper
- contains(String) - Method in class joelib.util.MDMatrixCache
- correctBadResonanceForm(JOEMol) - Static method in class joelib.util.JHM
- Description of the Method
- countBits() - Method in class joelib.util.JOEBitVec
- Description of the Method
D
- DEFAULT_SEPARATOR - Static variable in class joelib.util.ArrayHelper
- Description of the Field
- DEFAULT_SEPARATOR - Static variable in class joelib.util.MatrixHelper
- Description of the Field
- DEG_TO_RAD - Static variable in class joelib.util.JHM
- Description of the Field
- DIST_METRIC_COMPARISON - Static variable in class joelib.util.ComparisonHelper
- defaultProperty - Variable in class joelib.util.JOEProperty
- descBinaryValue - Variable in class joelib.util.ComparisonHelper
- descValues - Variable in class joelib.util.ComparisonHelper
- description - Variable in class joelib.util.JOEProperty
- descriptors - Variable in class joelib.util.ComparisonHelper
- determineFRJ(JOEMol) - Static method in class joelib.util.JHM
- Description of the Method
- distMetricValue - Variable in class joelib.util.ComparisonHelper
- distance(JOEBitVec, int) - Method in class joelib.util.ComparisonHelper
- Description of the Method
- distance(JOEBitVec, JOEBitVec) - Method in class joelib.util.ComparisonHelper
- distance(DistanceMetricValue, int) - Method in class joelib.util.ComparisonHelper
- Description of the Method
- distance(DistanceMetricValue, DistanceMetricValue) - Method in class joelib.util.ComparisonHelper
- distance(double[], int) - Method in class joelib.util.ComparisonHelper
- Description of the Method
- distance(double[], double[]) - Method in class joelib.util.ComparisonHelper
- doubleArrayFromSimpleString(String) - Method in class joelib.util.ArrayHelper
- Loads integer array from String .
- doubleArrayFromSimpleString(String, String) - Static method in class joelib.util.ArrayHelper
- Loads integer array from String .
- doubleArrayFromString(String) - Method in class joelib.util.ArrayHelper
- Loads double array from String .
- doubleArrayFromString(String, String, int) - Static method in class joelib.util.ArrayHelper
- Loads double array from String .
- doubleArrayFromString(String) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- doubleArrayFromString(Reader) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- doubleArrayFromString(String, int) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- doubleArrayFromString(Reader, int) - Static method in class joelib.util.LineArrayHelper
- Gets double arrays from a Reader.
- doubleArrayFromString(StringTokenizer, int) - Static method in class joelib.util.LineArrayHelper
- Gets double arrays from a Reader.
- doubleMatrixFromRectangleString(String) - Method in class joelib.util.MatrixHelper
- Description of the Method
- doubleMatrixFromRectangleString(String, String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- doubleMatrixFromSimpleString(String, int, int) - Method in class joelib.util.MatrixHelper
- doubleMatrixFromSimpleString(String, int, int, String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- doubleMatrixFromString(String) - Static method in class joelib.util.LineMatrixHelper
- Description of the Method
- doubleMatrixFromString(String) - Method in class joelib.util.MatrixHelper
- Description of the Method
- doubleMatrixFromString(String, String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
E
- EQ(String, String) - Static method in class joelib.util.JOEHelper
- Description of the Method
- EQn(String, String, int) - Static method in class joelib.util.JOEHelper
- Description of the Method
- EUKLIDIAN_COMPARISON - Static variable in class joelib.util.ComparisonHelper
- EZ_ISOMERISM_UNDEFINED - Static variable in class joelib.util.IsomerismDetection
- E_ISOMERISM - Static variable in class joelib.util.IsomerismDetection
- empty() - Method in class joelib.util.JOEBitVec
- Description of the Method
- endBit() - Method in class joelib.util.JOEBitVec
- Description of the Method
- ensureCapacity(int) - Method in class joelib.util.BitSet14
- Ensures that the BitSet14 can hold enough units.
- eol - Static variable in class joelib.util.JHM
- equals(Object) - Method in class joelib.util.BitSet14
- Compares this object against the specified object.
- equals(Object) - Method in class joelib.util.JOEProperty
- expandKekule(JOEMol, Vector, AtomIterator, int[], boolean) - Static method in class joelib.util.JHM
F
- findRings(JOEMol, Vector, JOEBitVec, JOEBitVec, int, int) - Static method in class joelib.util.JHM
- firstBit() - Method in class joelib.util.JOEBitVec
- Returns the index of the first bit that is set to true.
- flip(int) - Method in class joelib.util.BitSet14
- Sets the bit at the specified index to to the complement of its current value.
- flip(int, int) - Method in class joelib.util.BitSet14
- Sets each bit from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the complement of its current value.
- fold(int) - Method in class joelib.util.JOEBitVec
- Description of the Method
- fromBoolArray(boolean[]) - Method in class joelib.util.JOEBitVec
- fromIntArray(int[]) - Method in class joelib.util.JOEBitVec
- Description of the Method
- fromString(String) - Method in class joelib.util.JOEBitVec
- Reads this bit vector from a String.
- fromVectorWithIntArray(Vector) - Method in class joelib.util.JOEBitVec
G
- get(int) - Method in class joelib.util.BitSet14
- Returns the value of the bit with the specified index.
- get(int, int) - Method in class joelib.util.BitSet14
- Returns a new BitSet14 composed of bits from this BitSet14 from fromIndex(inclusive) to toIndex(exclusive).
- get(String) - Method in class joelib.util.MDMatrixCache
- getBits(int) - Method in class joelib.util.BitSet14
- Returns the unit of this bitset at index j as if this bitset had an infinite amount of storage.
- getBitset(JOEMol) - Method in class joelib.util.ComparisonHelper
- getCisTransFrom2D3D(JOEBond) - Static method in class joelib.util.IsomerismDetection
- Checks bonds for cis/trans isomerism using 2D/3D informations.
- getCisTransFrom2D3D(JOEBond, boolean) - Static method in class joelib.util.IsomerismDetection
- Checks bonds for cis/trans isomerism using 2D/3D informations.
- getCurrentValence(JOEAtom) - Static method in class joelib.util.JHM
- Gets the currentValence attribute of the JHM class
- getDFFVector(JOEMol, Vector, JOEBitVec) - Static method in class joelib.util.JHM
- getDefaultProperty() - Method in class joelib.util.JOEProperty
- getDescriptors(JOEMol, double[]) - Method in class joelib.util.ComparisonHelper
- getDistMetricValue(JOEMol) - Method in class joelib.util.ComparisonHelper
- getDoubleDesc(JOEMol, String) - Method in class joelib.util.ComparisonHelper
- Gets the doubleDesc attribute of the ComparisonHelper object
- getHTMLInfo(double, double) - Method in interface joelib.util.ToolTipInfo
- Gets the tool tip text.
- getProperty(String, Map) - Static method in class joelib.util.JOEPropertyHelper
- Gets single process property.
- getProperty(PropertyAcceptor, String, Map) - Static method in class joelib.util.JOEPropertyHelper
- Gets single process property or default value if not defined or null .
- getSeparator() - Method in class joelib.util.ArrayHelper
- Gets the separator attribute of the ArrayHelper object
- getSeparator() - Method in class joelib.util.MatrixHelper
- Gets the separator attribute of the MatrixHelper object
- getTargetMols() - Method in class joelib.util.ComparisonHelper
- getTempFileBase() - Static method in class joelib.util.JHM
- getType() - Method in interface joelib.util.ToolTipInfo
- Gets the information type for this tool tip, e.g "infrared data"
H
- hasInterface(Object, String) - Static method in class joelib.util.JOEHelper
- Checks if an class implements an interface.
- hashCode() - Method in class joelib.util.BitSet14
- Returns a hash code value for this bit set.
I
- IsomerismDetection - class joelib.util.IsomerismDetection.
- Helper class to detect E/Z isomerism.
- IsomerismDetection() - Constructor for class joelib.util.IsomerismDetection
- in(InputStream) - Method in class joelib.util.JOEBitVec
- Description of the Method
- instance() - Static method in class joelib.util.ArrayHelper
- Description of the Method
- instance() - Static method in class joelib.util.JHM
- Description of the Method
- instance() - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- instance() - Static method in class joelib.util.LineMatrixHelper
- Description of the Method
- instance - Static variable in class joelib.util.MDMatrixCache
- instance() - Static method in class joelib.util.MDMatrixCache
- instance() - Static method in class joelib.util.MatrixHelper
- Description of the Method
- intArrayFromSimpleString(String) - Method in class joelib.util.ArrayHelper
- Loads integer array from String .
- intArrayFromSimpleString(String, String) - Static method in class joelib.util.ArrayHelper
- Loads integer array from String .
- intArrayFromString(String) - Method in class joelib.util.ArrayHelper
- Loads integer array from String .
- intArrayFromString(String, String, int) - Static method in class joelib.util.ArrayHelper
- Loads integer array from String .
- intArrayFromString(String) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- intArrayFromString(Reader) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- intArrayFromString(String, int) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- intArrayFromString(Reader, int) - Static method in class joelib.util.LineArrayHelper
- Gets int arrays from a Reader.
- intArrayFromString(StringTokenizer, int) - Static method in class joelib.util.LineArrayHelper
- Gets int arrays from a Reader.
- intMatrixFromSimpleString(String, int, int) - Method in class joelib.util.MatrixHelper
- intMatrixFromSimpleString(String, int, int, String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- intMatrixFromString(String) - Static method in class joelib.util.LineMatrixHelper
- Description of the Method
- intMatrixFromString(String) - Method in class joelib.util.MatrixHelper
- Description of the Method
- intMatrixFromString(String, String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- internalToCartesian(Vector, JOEMol) - Method in class joelib.util.JHM
- intersects(BitSet14) - Method in class joelib.util.BitSet14
- Returns true if the specified
BitSet14has any bits set totruethat are also set totruein thisBitSet14. - isCisTransBond(JOEBond) - Static method in class joelib.util.IsomerismDetection
- Checks bonds for cis/trans isomerism using the SMILES flags up/down bond connected to a double bond.
Cases:
E/trans -- bondUP/doubleBond/bondUP
E/trans -- bondDOWN/doubleBond/bondDOWN
Z/cis -- bondUP/doubleBond/bondDOWN
Z/cis -- bondDOWN/doubleBond/bondUP
This method does not check multiple definitions. - isCisTransBond(JOEBond, boolean) - Static method in class joelib.util.IsomerismDetection
- Checks bonds for cis/trans isomerism using the SMILES flags up/down bond connected to a double bond.
Cases:
E/trans -- bondUP/doubleBond/bondUP
E/trans -- bondDOWN/doubleBond/bondDOWN
Z/cis -- bondUP/doubleBond/bondDOWN
Z/cis -- bondDOWN/doubleBond/bondUP
This method does not check multiple definitions. - isEmpty() - Method in class joelib.util.BitSet14
- Returns true if this
BitSet14contains no bits that are set totrue. - isOptional() - Method in class joelib.util.JOEProperty
- isUnsatType(String) - Static method in class joelib.util.JOEHelper
- Gets the unsatType attribute of the JOEHelper class
J
- JHM - class joelib.util.JHM.
- JOELib hepler methods.
- JHM() - Constructor for class joelib.util.JHM
- Constructor for the JHM object
- JOEBitVec - class joelib.util.JOEBitVec.
- BitSet14 extensions.
- JOEBitVec() - Constructor for class joelib.util.JOEBitVec
- java.util.Vector of int[1]
- JOEBitVec(int) - Constructor for class joelib.util.JOEBitVec
- Constructor for the JOEBitVec object
- JOEBitVec(JOEBitVec) - Constructor for class joelib.util.JOEBitVec
- Constructor for the JOEBitVec object
- JOEHelper - class joelib.util.JOEHelper.
- JOELib helper methods.
- JOEHelper() - Constructor for class joelib.util.JOEHelper
- JOEProperty - class joelib.util.JOEProperty.
- JOELib property representation.
- JOEProperty(String, String, String, boolean) - Constructor for class joelib.util.JOEProperty
- Constructor for a JOELib property without default value.
- JOEProperty(String, String, String, boolean, Object) - Constructor for class joelib.util.JOEProperty
- Constructor for a JOELib property.
- JOEPropertyException - exception joelib.util.JOEPropertyException.
- JOELib property exception.
- JOEPropertyException() - Constructor for class joelib.util.JOEPropertyException
- Constructor for the DescriptorException object
- JOEPropertyException(String) - Constructor for class joelib.util.JOEPropertyException
- Constructor for the DescriptorException object
- JOEPropertyHelper - class joelib.util.JOEPropertyHelper.
- Some helper methods for calling classes which accept properties (PropertyAcceptor).
- JOEPropertyHelper() - Constructor for class joelib.util.JOEPropertyHelper
- Don't let anyone instantiate this class
- JOERandom - class joelib.util.JOERandom.
- Random generator.
- JOERandom() - Constructor for class joelib.util.JOERandom
- Constructor for the JOERandom object
- JOERandom(int) - Constructor for class joelib.util.JOERandom
- Constructor for the JOERandom object
- jhm - Static variable in class joelib.util.JHM
- joelib.util - package joelib.util
- Provides classes for processing, converting molecular chemical data and calculate chemical properties (descriptors).
K
- kekulePropagate(JOEAtom, Vector, Vector, int) - Static method in class joelib.util.JHM
L
- LineArrayHelper - class joelib.util.LineArrayHelper.
- Helper methods for writing and loading line arrays.
- LineArrayHelper() - Constructor for class joelib.util.LineArrayHelper
- Constructor for the JOERandom object
- LineMatrixHelper - class joelib.util.LineMatrixHelper.
- Helper methods for writing and loading line matrices.
- LineMatrixHelper() - Constructor for class joelib.util.LineMatrixHelper
- Constructor for the JOERandom object
- length() - Method in class joelib.util.BitSet14
- Returns the "logical size" of this
BitSet14: the index of the highest set bit in theBitSet14plus one. - lineArrayHelper - Static variable in class joelib.util.LineArrayHelper
- lineMatrixHelper - Static variable in class joelib.util.LineMatrixHelper
- logger - Static variable in class joelib.util.ArrayHelper
- logger - Static variable in class joelib.util.ComparisonHelper
- logger - Static variable in class joelib.util.IsomerismDetection
- logger - Static variable in class joelib.util.JHM
- logger - Static variable in class joelib.util.JOEBitVec
- Obtain a suitable logger.
- logger - Static variable in class joelib.util.JOEPropertyHelper
- Obtain a suitable logger.
- logger - Static variable in class joelib.util.LineArrayHelper
- logger - Static variable in class joelib.util.LineMatrixHelper
- logger - Static variable in class joelib.util.MDMatrixCache
- logger - Static variable in class joelib.util.MatrixHelper
M
- MDMatrixCache - class joelib.util.MDMatrixCache.
- Regression helper.
- MDMatrixCache() - Constructor for class joelib.util.MDMatrixCache
- MatrixHelper - class joelib.util.MatrixHelper.
- Helper methods for wrinting and loading matrices.
- MatrixHelper() - Constructor for class joelib.util.MatrixHelper
- Constructor for the JOERandom object
- matrixHelper - Static variable in class joelib.util.MatrixHelper
- mdMatrix - Variable in class joelib.util.MDMatrixCache
- minimumPairRMS(JOEMol, double[], double[], boolean[]) - Static method in class joelib.util.JHM
- Description of the Method
- moleculeToFile(String, JOEMol, IOType, boolean) - Static method in class joelib.util.JHM
N
- NOT_DEFINED - Static variable in class joelib.util.ComparisonHelper
- negate() - Method in class joelib.util.JOEBitVec
- Description of the Method
- nextBit(int) - Method in class joelib.util.JOEBitVec
- Returns the index of the first bit that is set to true that occurs on or after the specified starting index.
- nextClearBit(int) - Method in class joelib.util.BitSet14
- Returns the index of the first bit that is set to
falsethat occurs on or after the specified starting index. - nextFloat() - Method in class joelib.util.JOERandom
- Description of the Method
- nextInt() - Method in class joelib.util.JOERandom
- Description of the Method
- nextSetBit(int) - Method in class joelib.util.BitSet14
- Returns the index of the first bit that is set to
truethat occurs on or after the specified starting index.
O
- OELipoGrid - Static variable in class joelib.util.JOEHelper
- Description of the Field
- OEPolarGrid - Static variable in class joelib.util.JOEHelper
- Description of the Field
- OE_RTREE_CUTOFF - Static variable in class joelib.util.JHM
- optional - Variable in class joelib.util.JOEProperty
- true if this parameter is optional, false otherwise.
- or(BitSet14) - Method in class joelib.util.BitSet14
- Performs a logical OR of this bit set with the bit set argument.
- or(JOEBitVec) - Method in class joelib.util.JOEBitVec
- Description of the Method
- or(JOEBitVec, JOEBitVec) - Static method in class joelib.util.JOEBitVec
- Description of the Method
- orSet(JOEBitVec) - Method in class joelib.util.JOEBitVec
- Description of the Method
- out(OutputStream) - Method in class joelib.util.JOEBitVec
- Description of the Method
P
- PT_ACCEPTOR - Static variable in class joelib.util.JOEHelper
- Description of the Field
- PT_ANION - Static variable in class joelib.util.JOEHelper
- Description of the Field
- PT_CATION - Static variable in class joelib.util.JOEHelper
- Description of the Field
- PT_DONOR - Static variable in class joelib.util.JOEHelper
- Description of the Field
- PT_HYDROPHOBIC - Static variable in class joelib.util.JOEHelper
- Description of the Field
- PT_METAL - Static variable in class joelib.util.JOEHelper
- Description of the Field
- PT_OTHER - Static variable in class joelib.util.JOEHelper
- Description of the Field
- PT_POLAR - Static variable in class joelib.util.JOEHelper
- Description of the Field
- PropertyAcceptor - interface joelib.util.PropertyAcceptor.
- Descriptor base class.
- propName - Variable in class joelib.util.JOEProperty
- put(String, Object) - Method in class joelib.util.MDMatrixCache
R
- RAD_TO_DEG - Static variable in class joelib.util.JHM
- Description of the Field
- readObject(ObjectInputStream) - Method in class joelib.util.BitSet14
- This override of readObject makes sure unitsInUse is set properly when deserializing a bitset
- recalculateUnitsInUse() - Method in class joelib.util.BitSet14
- Set the field unitsInUse with the logical size in units of the bit set.
- representation - Variable in class joelib.util.JOEProperty
- resetVisit(JOEMol, Vector, int) - Static method in class joelib.util.JHM
- rotateCoords(double[], double[][], int) - Method in class joelib.util.JHM
S
- SQUARE(double) - Static method in class joelib.util.JOEHelper
- Description of the Method
- seed - Variable in class joelib.util.JOERandom
- separator - Variable in class joelib.util.ArrayHelper
- separator - Variable in class joelib.util.MatrixHelper
- serialVersionUID - Static variable in class joelib.util.BitSet14
- set(int) - Method in class joelib.util.BitSet14
- Sets the bit at the specified index to
true. - set(int, boolean) - Method in class joelib.util.BitSet14
- Sets the bit at the specified index to the specified value.
- set(int, int) - Method in class joelib.util.BitSet14
- Sets the bits from the specified fromIndex(inclusive) to the
specified toIndex(exclusive) to
true. - set(int, int, boolean) - Method in class joelib.util.BitSet14
- Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the specified value.
- set(JOEBitVec) - Method in class joelib.util.JOEBitVec
- Description of the Method
- setBitOff(int) - Method in class joelib.util.JOEBitVec
- Clears the bits from the specified fromIndex(inclusive) to the specified toIndex(inclusive) to false.
- setBitOn(int) - Method in class joelib.util.JOEBitVec
- Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(inclusive) to false.
- setCisTransBond(JOEBond, int) - Static method in class joelib.util.IsomerismDetection
- Sets up/down informations for cis/trans isomerism of a double bond.
Cases:
E/trans -- bondUP/doubleBond/bondUP
Z/cis -- bondDOWN/doubleBond/bondUP
The method gets two heavy atoms with the highest atomic number and sets the corresponding up/down bond flags for cis/trans isomeres. - setComparisonDescriptor(String) - Method in class joelib.util.ComparisonHelper
- Sets the comparisonDescriptor attribute of the ComparisonHelper object
- setComparisonDescriptors(String[]) - Method in class joelib.util.ComparisonHelper
- Sets the comparisonDescriptors attribute of the ComparisonHelper object
- setDefaultProperty(Object) - Method in class joelib.util.JOEProperty
- setIntVectorToValue(Vector, int) - Static method in class joelib.util.JHM
- setProperty(String, Map, Object) - Static method in class joelib.util.JOEPropertyHelper
- Sets the property attribute of the JOEPropertyHelper class
- setRangeOff(int, int) - Method in class joelib.util.JOEBitVec
- Clears the bits from the specified fromIndex(inclusive) to the specified toIndex(inclusive) to false.
- setRangeOn(int, int) - Method in class joelib.util.JOEBitVec
- Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(inclusive) to false.
- setRotorToAngle(double[], JOEAtom[], double, Vector) - Static method in class joelib.util.JHM
- This methodName will rotate the coordinates of 'atoms' such that tor == ang - atoms in 'tor' should be ordered such that the 3rd atom is the pivot around which atoms rotate ang is in degrees.
- setSeparator(String) - Method in class joelib.util.ArrayHelper
- Sets the separator attribute of the ArrayHelper object
- setSeparator(String) - Method in class joelib.util.MatrixHelper
- Sets the separator attribute of the MatrixHelper object
- signedVolume(XYZVector, XYZVector, XYZVector, XYZVector) - Static method in class joelib.util.JHM
- Calculate the signed volume for an atom.
- size() - Method in class joelib.util.BitSet14
- Returns the number of bits of space actually in use by this
BitSet14to represent bit values. - sub(JOEBitVec) - Method in class joelib.util.JOEBitVec
- Description of the Method
- sub(JOEBitVec, JOEBitVec) - Static method in class joelib.util.JOEBitVec
- Description of the Method
- subSet(JOEBitVec) - Method in class joelib.util.JOEBitVec
- Description of the Method
T
- TRANS_ISOMERISM - Static variable in class joelib.util.IsomerismDetection
- ToolTipInfo - interface joelib.util.ToolTipInfo.
- Tool tip information for chart visualisations.
- tanimoto(BitSet14) - Method in class joelib.util.JOEBitVec
- Returns the tanimoto similarity coefficient between this BitSet14 with the BitSet14 b.
- targetFile - Variable in class joelib.util.ComparisonHelper
- targetMols - Variable in class joelib.util.ComparisonHelper
- timeSeed() - Method in class joelib.util.JOERandom
- Description of the Method
- tmpValues - Variable in class joelib.util.ComparisonHelper
- toBoolArr(int) - Method in class joelib.util.JOEBitVec
- toBoolArray() - Method in class joelib.util.JOEBitVec
- toIntArray() - Method in class joelib.util.JOEBitVec
- toRectangleString(StringBuffer, double[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toRectangleString(StringBuffer, double[][], String, DecimalFormatter) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toRectangleString(StringBuffer, int[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toRectangleString(StringBuffer, int[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toRectangleString(StringBuffer, double[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toRectangleString(StringBuffer, double[][], DecimalFormatter) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toRectangleString(StringBuffer, byte[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toRectangleString(StringBuffer, byte[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toSimpleString(StringBuffer, int[]) - Method in class joelib.util.ArrayHelper
- Write integer array to String .
- toSimpleString(StringBuffer, double[]) - Method in class joelib.util.ArrayHelper
- Write integer array to String .
- toSimpleString(StringBuffer, double[], DecimalFormatter) - Method in class joelib.util.ArrayHelper
- Write integer array to String .
- toSimpleString(StringBuffer, boolean[]) - Method in class joelib.util.ArrayHelper
- Write boolean array to String .
- toSimpleString(StringBuffer, int[], String) - Static method in class joelib.util.ArrayHelper
- Write integer array to String .
- toSimpleString(StringBuffer, double[], String) - Static method in class joelib.util.ArrayHelper
- Write integer array to String .
- toSimpleString(StringBuffer, double[], String, DecimalFormatter) - Static method in class joelib.util.ArrayHelper
- Write integer array to String .
- toSimpleString(StringBuffer, boolean[], String) - Static method in class joelib.util.ArrayHelper
- Write boolean array to String .
- toSimpleString(StringBuffer, double[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toSimpleString(StringBuffer, double[][], DecimalFormatter) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toSimpleString(StringBuffer, double[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toSimpleString(StringBuffer, double[][], String, DecimalFormatter) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toSimpleString(StringBuffer, int[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toSimpleString(StringBuffer, int[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toSimpleString(StringBuffer, boolean[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toSimpleString(StringBuffer, boolean[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toString(StringBuffer, int[]) - Method in class joelib.util.ArrayHelper
- Write integer array to String .
- toString(StringBuffer, int[], String, boolean) - Static method in class joelib.util.ArrayHelper
- Write integer array to String .
- toString(StringBuffer, double[]) - Method in class joelib.util.ArrayHelper
- Description of the Method
- toString(StringBuffer, double[], DecimalFormatter) - Method in class joelib.util.ArrayHelper
- Description of the Method
- toString(StringBuffer, double[], String, boolean) - Static method in class joelib.util.ArrayHelper
- Description of the Method
- toString(StringBuffer, double[], String, boolean, DecimalFormatter) - Static method in class joelib.util.ArrayHelper
- Description of the Method
- toString(StringBuffer, boolean[]) - Method in class joelib.util.ArrayHelper
- Description of the Method
- toString(StringBuffer, boolean[], String, boolean) - Static method in class joelib.util.ArrayHelper
- Description of the Method
- toString() - Method in class joelib.util.BitSet14
- Returns a string representation of this bit set.
- toString() - Method in class joelib.util.JOEBitVec
- Writes this bit vector to a String.
- toString(StringBuffer, int[]) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- toString(StringBuffer, int[], boolean) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- toString(StringBuffer, double[]) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- toString(StringBuffer, double[], DecimalFormatter) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- toString(StringBuffer, double[], boolean) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- toString(StringBuffer, double[], boolean, DecimalFormatter) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- toString(StringBuffer, boolean[]) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- toString(StringBuffer, boolean[], boolean) - Static method in class joelib.util.LineArrayHelper
- Description of the Method
- toString(StringBuffer, int[][]) - Static method in class joelib.util.LineMatrixHelper
- Description of the Method
- toString(StringBuffer, double[][]) - Static method in class joelib.util.LineMatrixHelper
- Description of the Method
- toString(StringBuffer, double[][], DecimalFormatter) - Static method in class joelib.util.LineMatrixHelper
- Description of the Method
- toString(StringBuffer, byte[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toString(StringBuffer, byte[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toString(StringBuffer, int[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toString(StringBuffer, int[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toString(StringBuffer, double[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toString(StringBuffer, double[][], DecimalFormatter) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toString(StringBuffer, double[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toString(StringBuffer, double[][], String, DecimalFormatter) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toTranspRectString(StringBuffer, int[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toTranspRectString(StringBuffer, int[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toTranspRectString(StringBuffer, double[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toTranspRectString(StringBuffer, double[][], DecimalFormatter) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toTranspRectString(StringBuffer, byte[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toTranspRectString(StringBuffer, byte[][]) - Method in class joelib.util.MatrixHelper
- Description of the Method
- toTranspRectString(StringBuffer, double[][], String) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toTranspRectString(StringBuffer, double[][], String, DecimalFormatter) - Static method in class joelib.util.MatrixHelper
- Description of the Method
- toTrueFalseString(StringBuffer, boolean[], String) - Static method in class joelib.util.ArrayHelper
- Write boolean array to String .
- toVectorWithIntArray(Vector) - Method in class joelib.util.JOEBitVec
- tokenize(Vector, String) - Static method in class joelib.util.JHM
- tokenize(Vector, String, String) - Static method in class joelib.util.JHM
- tokenize(Vector, String, String, int) - Static method in class joelib.util.JHM
- trailingZeroCnt(long) - Static method in class joelib.util.BitSet14
- trailingZeroTable - Static variable in class joelib.util.BitSet14
U
- unitIndex(int) - Static method in class joelib.util.BitSet14
- Given a bit index return unit index containing it.
- unitsInUse - Variable in class joelib.util.BitSet14
- The number of units in the logical size of this BitSet14.
V
- valenceSum(JOEAtom) - Static method in class joelib.util.JHM
- Description of the Method
W
- WORD_MASK - Static variable in class joelib.util.BitSet14
- wheel - Variable in class joelib.util.JOERandom
- writeTitles(OutputStream, JOEMol) - Method in class joelib.util.JHM
- Description of the Method
X
- xor(BitSet14) - Method in class joelib.util.BitSet14
- Performs a logical XOR of this bit set with the bit set argument.
- xor(JOEBitVec) - Method in class joelib.util.JOEBitVec
- Description of the Method
- xor(JOEBitVec, JOEBitVec) - Static method in class joelib.util.JOEBitVec
- Description of the Method
- xorSet(JOEBitVec) - Method in class joelib.util.JOEBitVec
- Description of the Method
Z
- Z_ISOMERISM - Static variable in class joelib.util.IsomerismDetection
A B C D E F G H I J K L M N O P R S T U V W X Z
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