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A
- ACCEPTED_PROPERTIES - Static variable in class joelib.process.types.CreateFileName
- ACCEPTED_PROPERTIES - Static variable in class joelib.process.types.MoleculeFileCreation
- ACCEPTED_PROPERTIES - Static variable in class joelib.process.types.MoleculeFileDeletion
- acceptedProperties() - Method in class joelib.process.types.CreateFileName
- Description of the Method
- acceptedProperties() - Method in class joelib.process.types.MoleculeFileCreation
- acceptedProperties() - Method in class joelib.process.types.MoleculeFileDeletion
B
- bins - Variable in class joelib.process.types.DescBinning
C
- CreateFileName - class joelib.process.types.CreateFileName.
- Calling processor classes if the filter rule fits.
- CreateFileName() - Constructor for class joelib.process.types.CreateFileName
- Constructor for the DescSelectionWriter object
- checkDescriptorNames(JOEMol) - Method in class joelib.process.types.DescSelectionWriter
- Description of the Method
- clear() - Method in class joelib.process.types.CreateFileName
- Description of the Method
- clear() - Method in class joelib.process.types.DescBinning
- Description of the Method
- clear() - Method in class joelib.process.types.DescSelectionWriter
- Description of the Method
- clear() - Method in class joelib.process.types.DescStatistic
- Description of the Method
- clear() - Method in class joelib.process.types.DescVarianceNorm
- Description of the Method
- clear() - Method in class joelib.process.types.DistanceCalculation
- Description of the Method
- clear() - Method in class joelib.process.types.MoleculeFileCreation
- clear() - Method in class joelib.process.types.MoleculeFileDeletion
- commentString - Variable in class joelib.process.types.DescSelectionWriter
- comparison - Variable in class joelib.process.types.DistanceCalculation
D
- DEFAULT_DESC_OTYPE - Static variable in class joelib.process.types.DescSelectionWriter
- Description of the Field
- DESCRIPTORS - Static variable in class joelib.process.types.DescSelectionWriter
- Description of the Field
- DescBinning - class joelib.process.types.DescBinning.
- Calling processor classes if the filter rule fits.
- DescBinning() - Constructor for class joelib.process.types.DescBinning
- Constructor for the DescSelectionWriter object
- DescSelectionWriter - class joelib.process.types.DescSelectionWriter.
- Calling processor classes if the filter rule fits.
- DescSelectionWriter() - Constructor for class joelib.process.types.DescSelectionWriter
- Constructor for the DescSelectionWriter object
- DescStatistic - class joelib.process.types.DescStatistic.
- Calling processor classes if the filter rule fits.
- DescStatistic() - Constructor for class joelib.process.types.DescStatistic
- Constructor for the DescSelectionWriter object
- DescVarianceNorm - class joelib.process.types.DescVarianceNorm.
- Scales the values in one descriptor so that they have similar magnitudes.
- DescVarianceNorm() - Constructor for class joelib.process.types.DescVarianceNorm
- Constructor for the DescSelectionWriter object
- DistanceCalculation - class joelib.process.types.DistanceCalculation.
- Calling processor classes if the filter rule fits.
- DistanceCalculation() - Constructor for class joelib.process.types.DistanceCalculation
- Constructor for the DescSelectionWriter object
- delimiterString - Variable in class joelib.process.types.DescSelectionWriter
- desc2ignore - Variable in class joelib.process.types.DescBinning
- desc2ignore - Variable in class joelib.process.types.DescStatistic
- desc2ignore - Variable in class joelib.process.types.DescVarianceNorm
- descNamesChecked - Variable in class joelib.process.types.DescSelectionWriter
- descOutputType - Variable in class joelib.process.types.DescSelectionWriter
- descriptorNames - Variable in class joelib.process.types.DescSelectionWriter
- descriptors2ignore() - Method in class joelib.process.types.DescVarianceNorm
- distanceValues - Variable in class joelib.process.types.DistanceCalculation
E
- existsBinningFileFor(String) - Static method in class joelib.process.types.DescBinning
- Description of the Method
- existsStatisticFileFor(String) - Static method in class joelib.process.types.DescStatistic
- Description of the Method
F
- FILE_EXT - Static variable in class joelib.process.types.DescBinning
- FILE_EXT - Static variable in class joelib.process.types.DescStatistic
- firstLineWritten - Variable in class joelib.process.types.DescSelectionWriter
- fromFile(String) - Method in class joelib.process.types.DescBinning
- Description of the Method
- fromFile(String) - Method in class joelib.process.types.DescStatistic
- Description of the Method
- fromFileFor(String) - Method in class joelib.process.types.DescBinning
- fromFileFor(String) - Method in class joelib.process.types.DescStatistic
G
- getComment() - Method in class joelib.process.types.DescSelectionWriter
- Gets the comment attribute of the DescSelectionWriter object
- getDelimiter() - Method in class joelib.process.types.DescSelectionWriter
- Gets the delimiter attribute of the DescSelectionWriter object
- getDescBinning(IOType, String) - Static method in class joelib.process.types.DescBinning
- Gets the descBinning attribute of the DescBinning class
- getDescBinning(JOEMolVector) - Static method in class joelib.process.types.DescBinning
- Gets the descBinning attribute of the DescBinning class
- getDescBinning(IOType, String, int) - Static method in class joelib.process.types.DescBinning
- getDescStatistic() - Method in class joelib.process.types.DescBinning
- Gets the descStatistic attribute of the DescBinning object
- getDescStatistic(JOEMolVector) - Static method in class joelib.process.types.DescStatistic
- getDescStatistic(IOType, String) - Static method in class joelib.process.types.DescStatistic
- Gets the descStatistic attribute of the DescStatistic class
- getDescriptorBinning(String) - Method in class joelib.process.types.DescBinning
- Gets the descriptorBinning attribute of the DescBinning object
- getDescriptorStatistic(String) - Method in class joelib.process.types.DescStatistic
- Gets the descriptorStatistic attribute of the DescStatistic object
- getDescriptors() - Method in class joelib.process.types.DescBinning
- Gets the descriptors attribute of the DescBinning object
- getDescriptors() - Method in class joelib.process.types.DescStatistic
- Gets the descriptors attribute of the DescStatistic object
- getDistanceValues() - Method in class joelib.process.types.DistanceCalculation
- getProcessInfo() - Method in class joelib.process.types.CreateFileName
- Gets the processInfo attribute of the ProcessPipe object
- getProcessInfo() - Method in class joelib.process.types.MoleculeFileCreation
- Gets the processInfo attribute of the ProcessPipe object
- getProcessInfo() - Method in class joelib.process.types.MoleculeFileDeletion
- Gets the processInfo attribute of the ProcessPipe object
- getTargetMols() - Method in class joelib.process.types.DistanceCalculation
H
- hasDescriptorStatistic(String) - Method in class joelib.process.types.DescStatistic
- Description of the Method
I
- info - Variable in class joelib.process.types.CreateFileName
- info - Variable in class joelib.process.types.MoleculeFileCreation
- info - Variable in class joelib.process.types.MoleculeFileDeletion
- init(DescStatistic) - Method in class joelib.process.types.DescBinning
- Description of the Method
- init(DescStatistic, int) - Method in class joelib.process.types.DescBinning
- Description of the Method
- init(IOType, String) - Method in class joelib.process.types.DescBinning
- Description of the Method
- init(IOType, String, int) - Method in class joelib.process.types.DescBinning
- Description of the Method
- init(OutputStream, IOType) - Method in class joelib.process.types.DescSelectionWriter
- Description of the Method
- init(String, IOType) - Method in class joelib.process.types.DescSelectionWriter
- Description of the Method
- init(String, IOType, Vector, int) - Method in class joelib.process.types.DescSelectionWriter
- Description of the Method
- init(OutputStream, IOType, Vector, int) - Method in class joelib.process.types.DescSelectionWriter
- Description of the Method
- init(DescStatistic) - Method in class joelib.process.types.DescVarianceNorm
- Description of the Method
- init(IOType, String) - Method in class joelib.process.types.DescVarianceNorm
- Description of the Method
- init(ComparisonHelper) - Method in class joelib.process.types.DistanceCalculation
- Description of the Method
- init(IOType, String, String) - Method in class joelib.process.types.DistanceCalculation
- Description of the Method
- init(IOType, String, String[]) - Method in class joelib.process.types.DistanceCalculation
- init(JOEMol, String) - Method in class joelib.process.types.DistanceCalculation
- init(JOEMol, String[]) - Method in class joelib.process.types.DistanceCalculation
- isNative(String) - Method in class joelib.process.types.DescStatistic
- Gets the descriptorStatistic attribute of the DescStatistic object
J
- joelib.process.types - package joelib.process.types
- Provides classes for defining molecular processing modules.
L
- logger - Static variable in class joelib.process.types.CreateFileName
- Obtain a suitable logger.
- logger - Static variable in class joelib.process.types.DescBinning
- Obtain a suitable logger.
- logger - Static variable in class joelib.process.types.DescSelectionWriter
- Obtain a suitable logger.
- logger - Static variable in class joelib.process.types.DescStatistic
- Obtain a suitable logger.
- logger - Static variable in class joelib.process.types.DescVarianceNorm
- Obtain a suitable logger.
- logger - Static variable in class joelib.process.types.DistanceCalculation
- Obtain a suitable logger.
- logger - Static variable in class joelib.process.types.MoleculeFileCreation
- Obtain a suitable logger.
- logger - Static variable in class joelib.process.types.MoleculeFileDeletion
- Obtain a suitable logger.
M
- MOL_AND_DESCRIPTORS - Static variable in class joelib.process.types.DescSelectionWriter
- Description of the Field
- MoleculeFileCreation - class joelib.process.types.MoleculeFileCreation.
- Calling processor classes if the filter rule fits.
- MoleculeFileCreation() - Constructor for class joelib.process.types.MoleculeFileCreation
- Constructor for the DescSelectionWriter object
- MoleculeFileDeletion - class joelib.process.types.MoleculeFileDeletion.
- Calling processor classes if the filter rule fits.
- MoleculeFileDeletion() - Constructor for class joelib.process.types.MoleculeFileDeletion
- Constructor for the DescSelectionWriter object
- molCounter - Variable in class joelib.process.types.DescSelectionWriter
N
- neededProperties() - Method in class joelib.process.types.DescBinning
- Description of the Method
- neededProperties() - Method in class joelib.process.types.DescSelectionWriter
- Description of the Method
- neededProperties() - Method in class joelib.process.types.DescStatistic
- Description of the Method
- neededProperties() - Method in class joelib.process.types.DescVarianceNorm
- Description of the Method
- neededProperties() - Method in class joelib.process.types.DistanceCalculation
- Description of the Method
- notNative - Variable in class joelib.process.types.DescStatistic
- numberOfBins - Variable in class joelib.process.types.DescBinning
- numberOfDescriptors() - Method in class joelib.process.types.DescBinning
- Description of the Method
O
- outStream - Variable in class joelib.process.types.DescSelectionWriter
- outType - Variable in class joelib.process.types.DescSelectionWriter
- outWriter - Variable in class joelib.process.types.DescSelectionWriter
P
- process(JOEMol, Map) - Method in class joelib.process.types.CreateFileName
- Description of the Method
- process(JOEMol, Map) - Method in class joelib.process.types.DescBinning
- Description of the Method
- process(JOEMol, Map) - Method in class joelib.process.types.DescSelectionWriter
- Description of the Method
- process(JOEMol, Map) - Method in class joelib.process.types.DescStatistic
- Description of the Method
- process(JOEMol, Map) - Method in class joelib.process.types.DescVarianceNorm
- Description of the Method
- process(JOEMol, Map) - Method in class joelib.process.types.DistanceCalculation
- Description of the Method
- process(JOEMol, Map) - Method in class joelib.process.types.MoleculeFileCreation
- Description of the Method
- process(JOEMol, Map) - Method in class joelib.process.types.MoleculeFileDeletion
- Description of the Method
- putArrayStatistic(String, ArrayStatistic) - Method in class joelib.process.types.DescStatistic
- Description of the Method
S
- setComment(String) - Method in class joelib.process.types.DescSelectionWriter
- Sets the comment attribute of the DescSelectionWriter object
- setDelimiter(String) - Method in class joelib.process.types.DescSelectionWriter
- Sets the delimiter attribute of the DescSelectionWriter object
- setProcessInfo(ProcessInfo) - Method in class joelib.process.types.CreateFileName
- Sets the processInfo attribute of the ProcessPipe object
- setProcessInfo(ProcessInfo) - Method in class joelib.process.types.MoleculeFileCreation
- Sets the processInfo attribute of the ProcessPipe object
- setProcessInfo(ProcessInfo) - Method in class joelib.process.types.MoleculeFileDeletion
- Sets the processInfo attribute of the ProcessPipe object
- setSkipStream(OutputStream, IOType) - Method in class joelib.process.types.DescSelectionWriter
- Sets the skipStream attribute of the DescSelectionWriter object
- showDescriptorStatistic(String) - Method in class joelib.process.types.DescStatistic
- Description of the Method
- skipCounter - Variable in class joelib.process.types.DescSelectionWriter
- skipStream - Variable in class joelib.process.types.DescSelectionWriter
- skipType - Variable in class joelib.process.types.DescSelectionWriter
- skipWriter - Variable in class joelib.process.types.DescSelectionWriter
- statistic - Variable in class joelib.process.types.DescBinning
- statistic - Variable in class joelib.process.types.DescStatistic
- statistic - Variable in class joelib.process.types.DescVarianceNorm
T
- toString() - Method in class joelib.process.types.DescBinning
- Description of the Method
- toString() - Method in class joelib.process.types.DescStatistic
- Description of the Method
- toString() - Method in class joelib.process.types.DescVarianceNorm
- Description of the Method
W
- writeBinningFileFor(String) - Method in class joelib.process.types.DescBinning
- writeFirstLine() - Method in class joelib.process.types.DescSelectionWriter
- Description of the Method
- writeStatisticFileFor(String) - Method in class joelib.process.types.DescStatistic
A B C D E F G H I J L M N O P S T W
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