MDParameters (Marvin API documentation (c) 1998-2020 ChemAxon Ltd.)

java.lang.Object
- chemaxon.descriptors.MDParameters

Direct Known Subclasses:

BCUTParameters, CDParameters, CFParameters, ECFPParameters, PFParameters, RFParameters, SDParameters, ShapeParameters
```
@PublicAPI
public class MDParameters
extends java.lang.Object
```
MolecularDescriptor parameter settings. This class serves as the base class for the parameter classes of specific MolecularDescriptor derivatives.
Descriptor objects of the same type share one common MDParameter object that stores all parameters.
Besides storing parameters and other internal data that are better kept in this class than in individual MolecularDescriptor objects for the sake of memory efficiency.
The naming convention - similarly to the derivates of the MolecularDescriptor class - is as follows: derived class name begins with the name of the corresponding MolecularDescriptor class and postfixed by Parameters. For instance that parameters class of the descriptor class MDXyZ is XyZParameters.
Parameters are read from configuration files. MDParameters provides an extensive functionality to process XML configuration files, however, further parameter classes extending MDParameters do not necessarily have to use XML for storing parameters.
MDParameters plays an important role in providing so called Screening Configurations for the dissimilarity calculations. Such configurations contain so called parameterized metrics that are based on dissimilarity metrics implemented in classes that extend the MolecularDescriptor class. It is important to make clear distinction between the above two cathegories: dissimilarity metrics are the basis of the parametrized metrics. MDParameters stores metrics parameters and provides services for retrieving and storing parametrized metrics, access them by either name or index.
Another important functionality of this class is to allow the creation of new parametrized metrics and write them into the XML document.

Since:

JChem 2.2

Author:

Miklos Vargyas

Field Summary

Fields
Modifier and Type	Field and Description
`protected java.util.ArrayList`	`asymmetryFactors` asymmetry ratio of parametrized asymmetric metrics
`protected int`	`cellSize` size - number of bits - of one descriptor cell
`protected java.util.ArrayList`	`cellwiseWeights` is cell weights for parametrized metrics
`protected java.lang.String`	`configFilePath` location of the configuration file
`protected int`	`currentMetricIndex` index of the parametrized metric currently in use
`protected byte[]`	`data` buffer for external data format generation, used in `MolecularDescriptor.toData()`
`protected java.text.NumberFormat`	`decForm` to format floating point output
`static float`	`DEFAULT_ASYMMETRY_FACTOR`
`static int`	`DEFAULT_OUTPUT_PRECISION`
`static float`	`DEFAULT_SCALE_FACTOR` constants, default parameter values
`static float`	`DEFAULT_WEIGHT`
`protected float`	`defaultWeight` value for all missing weight parameters
`protected org.dom4j.Document`	`document` contains the XML document
`protected MDGenerator`	`generator` generates `MolecularDescriptors`
`protected int`	`internalSize` required memory size of one descriptor instance
`protected int`	`length` the length of the descriptor: the number of cells
`protected MolecularDescriptor`	`md` this object is needed to access default dissimilarity functions
`protected java.util.ArrayList`	`metricIndexes` convert parameterized indexes to MolecularDescriptor metric indexes
`protected java.util.ArrayList`	`normalized` flags indicating if the metric is normalized or not
`protected int`	`outputPrecision` number of fraction digits in floating point output format
`protected java.util.List`	`parametrizedMetricNodes`
`protected java.util.ArrayList`	`parametrizedMetrics` symbolic names (mnemonics) of parametrized metrics
`protected org.dom4j.Element`	`parametrizedMetricsNode`
`protected java.util.ArrayList`	`scaleFactors` scale factor of scalable parametrized metrics
`protected org.dom4j.Node`	`screeningConfigurationNode`
`protected org.dom4j.Element`	`similarityNode` node holding the similarity calculations related parameters
`protected Standardizer`	`standardizer` transform molecules into standard form before descriptor generation
`protected org.dom4j.Node`	`standardizerConfigurationNode` node defining the Standardizer configuration
`protected java.util.ArrayList`	`thresholds` dissimilarity thresholds values
`protected java.util.ArrayList<java.lang.Float>`	`tverskyA` alpha values for tversky dissimilarity
`protected java.util.ArrayList<java.lang.Float>`	`tverskyB` beta values for tversky dissimilarity
`protected java.util.ArrayList`	`weights` weights for parametrized metrics

Constructor Summary

Constructors
Modifier Constructor and Description

protected MDParameters()
Creates and initializes an empty object.

Constructors
Modifier	Constructor and Description
`protected`	`MDParameters()` Creates and initializes an empty object.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addParameters(java.io.File parameterFile)` Sets parameters from an XML config file keeping all previous settings.
`void`	`addParameters(java.lang.String parameterString)` Sets parameters from an XML string representation keeping all previous settings.
`int`	`addParametrizedMetric(java.lang.String name, java.lang.String metric, java.lang.String activeFamily)` Expands the set of parametrized metrics with a new item.
`protected org.dom4j.Element`	`addParametrizedMetricNode(java.lang.String name, java.lang.String activeFamily, java.lang.String metric)` Adds a `ParametrizedMetric` node to the DOM tree.
`protected void`	`addParametrizedMetricsNode()` Adds the `ParametrizedMetrics` node to the DOM tree.
`protected int`	`appendParametrizedMetric(java.lang.String name, java.lang.String metric)` Extends internal data with a new parametrized metric.
`protected void`	`checkDocumentVersion(java.lang.String docType, java.lang.String version)` Checks if the document is the right version
`void`	`fromFile(java.io.File parameterFile)` Sets parameters from an XML file.
`void`	`fromString(java.lang.String parameterString)` Sets parameters from a string representation.
`float`	`getAsymmetryFactor()` Gets the asymmetry factor used in the current parametrized asymmetric metrics.
`int`	`getCellSize()` Gets the number of bits of an atomic cell in the descriptor.
`int`	`getCurrentMetricIndex()`
`byte[]`	`getData()` Gets the byte array which is used for conversions between internal and external data formats.
`java.text.DecimalFormat`	`getDecForm()` Gets the formatter object that is capable of formatting fractions with given precision.
`java.lang.String`	`getDefaultDocumentFrame()` Gets the default XML configuration string.
`static java.lang.String`	`getDefaultStandardizerConfiguration()` Gets the default configuration of the standardizer.
`static java.lang.String`	`getDescriptorTypeName(java.lang.String xmlConfig)` Takes the descriptor type name from the root element of the XML configuration.
`int`	`getInternalMetricIndex()` Gets the MolecularDescriptor specific metric index of the current parametrized metric.
`int`	`getInternalSize()` Gets the required memory size to store the descriptor according to the specified parameters.
`int`	`getLength()` Returns the number of cells forming the descriptor.
`int`	`getMetricIndex(java.lang.String name)` Gets the index of the given parametrized metric.
`java.lang.String`	`getMetricName()` Gets the user defined symbolic name of the current parametrized metric.
`java.lang.String`	`getMetricName(int metricIndex)` Gets the user defined symbolic name of the specified parametrized metric.
`int`	`getNumberOfMetrics()` Gets the total number of parametrized metrics available in the present configuration.
`int`	`getNumberOfWeights()` Gets the number of weights the current parametrized metric takes.
`protected int`	`getNumberOfWeights(int parametrizedMetricIndex)` Gets the number of weight factors used by the specified metric.
`float`	`getScaleFactor()` Gets the scale factor used in the current parametrized scalable metrics.
`MolecularDescriptor`	`getScalingHypothesis()` Gets the scaling hypothesis used in scaled metrics.
`java.lang.String`	`getScreeningConfigurationString(java.lang.String nodeName, java.lang.String attrib, java.lang.String value)` Returns parts of the parameter values in string.
`float`	`getThreshold()` Gets the threshold value being set for the current parametrized version.
`float`	`getThreshold(int metricIndex)` Gets a metric dependent threshold value.
`float`	`getTverskyAlpha()` Gets Tversky alpha value for the given parametrized metric.
`float`	`getTverskyBeta()` Gets Tversky beta value for the given parametrized metric.
`float[]`	`getWeights()` Gets all weights for the given parametrized metric.
`protected boolean`	`importNodes(org.dom4j.Document doc, boolean merge)` Imports nodes from the specified `Document` into the current (main) `Document`.
`protected void`	`initParameters()` Initializes object after configuration parameters are loaded.
`boolean`	`isAsymmetric()` Returns whether current parametrized metric is asymmetric or not.
`boolean`	`isCellwiseWeights()` Gets boolean telling whether cell weights are to be generated for current parametrized metric.
`boolean`	`isNormalized()` Returns whether current parametrized metric is normalized or not.
`boolean`	`isScaled()` Returns whether current parametrized metric is scaled or not.
`boolean`	`isStandardizationMandatory()` Checks is Standardization of molecules is mandatory for the corresponding `MolecularDescriptor` before descriptor generation.
`boolean`	`isWeighted()` Returns whether current parametrized metric is weighted or not.
`protected void`	`processDocument(boolean all)` Searches the DOM tree for relevant nodes and sets internal variables to some these nodes for the sake of easier information processing.
`protected void`	`readFromXmlFile(java.io.File file, boolean merge, boolean all)` Reads configuration from XML file.
`protected void`	`readFromXmlString(java.lang.String xml, boolean merge, boolean all)` Reads configuration from XML string.
`protected void`	`readMetricParameters()` Processes all `ParametrizedMetric` nodes in the DOM tree.
`protected void`	`readMetricWeights(org.dom4j.Element parametrizedMetric, int metricIndex)`
`protected void`	`readValues(boolean all)` Picks attribute values from the document tree that are relevant to the actual `MDParameters` sub-class.
`void`	`setAsymmetryFactor(float af)` Sets the value of the asymmetry factor of the current parametrized metric.
`void`	`setCellSize(int cellSize)` Sets the size (number of bits) of the bins (cells).
`void`	`setCellwiseWeights(boolean c)` Sets boolean telling whether cell weights are to be generated for current parametrized metric.
`void`	`setCreateStatistics(boolean createStatistics)` Toggles the create statistics flag of the `MDGenerator` object.
`void`	`setCurrentParametrizedMetric(int metricIndex)` Selects the specified parametrized metric to be the current.
`void`	`setLength(int length)` Sets the length (number of cells) of the descriptor.
`void`	`setNormalized(boolean yes)` Toggles the normalized flag of the current parametrized metric.
`void`	`setOutputPrecision(int precision)` Specifies the output precision for floating point values.
`void`	`setParameters(java.io.File parametersFile)` Sets parameters from an XML file representation overwriting all previous settings with the new ones.
`void`	`setParameters(java.lang.String parametersString)` Sets parameters from an XML string representation overwriting all previous parameters settings with the new ones.
`void`	`setScaleFactor(float scaleFactor)` Sets scaleFactor used with the current parametrized metrics.
`void`	`setScalingHypothesis(MolecularDescriptor scalingHypothesis)` Sets (stores) the specified scaling hypothesis.
`void`	`setThreshold(float th)` Sets the value of the threshold of the current parametrized metric.
`void`	`setWeights(float[] w)` Sets the cell-wise weight factors for the current parametrized metric.
`Molecule`	`standardize(Molecule m)` Standardizes the `Molecule` and returns the standardized form.
`java.lang.String`	`toString()` Returns the parameter values in string.
`protected java.lang.String`	`toString(org.dom4j.Node node)` Returns parts of the parameter values in string.
`protected void`	`writeMetricParameter(java.util.ArrayList pl, java.lang.String attr, int mi, boolean useDecForm)` Writes a given parameter of the specified metric into the corresponding tree node.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - DEFAULT_SCALE_FACTOR
```
public static final float DEFAULT_SCALE_FACTOR
```
    constants, default parameter values
    
    See Also:
    
    Constant Field Values
  - DEFAULT_ASYMMETRY_FACTOR
```
public static final float DEFAULT_ASYMMETRY_FACTOR
```
    See Also:
    
    Constant Field Values
  - DEFAULT_WEIGHT
```
public static final float DEFAULT_WEIGHT
```
    See Also:
    
    Constant Field Values
  - DEFAULT_OUTPUT_PRECISION
```
public static final int DEFAULT_OUTPUT_PRECISION
```
    See Also:
    
    Constant Field Values
  - cellSize
```
protected int cellSize
```
    size - number of bits - of one descriptor cell
  - length
```
protected int length
```
    the length of the descriptor: the number of cells
  - internalSize
```
protected int internalSize
```
    required memory size of one descriptor instance
  - data
```
protected byte[] data
```
    buffer for external data format generation, used in MolecularDescriptor.toData()
  - configFilePath
```
protected java.lang.String configFilePath
```
    location of the configuration file
  - document
```
protected org.dom4j.Document document
```
    contains the XML document
  - standardizerConfigurationNode
```
protected org.dom4j.Node standardizerConfigurationNode
```
    node defining the Standardizer configuration
  - similarityNode
```
protected org.dom4j.Element similarityNode
```
    node holding the similarity calculations related parameters
  - screeningConfigurationNode
```
protected org.dom4j.Node screeningConfigurationNode
```
  - parametrizedMetricsNode
```
protected org.dom4j.Element parametrizedMetricsNode
```
  - parametrizedMetricNodes
```
protected java.util.List parametrizedMetricNodes
```
  - parametrizedMetrics
```
protected java.util.ArrayList parametrizedMetrics
```
    symbolic names (mnemonics) of parametrized metrics
  - metricIndexes
```
protected java.util.ArrayList metricIndexes
```
    convert parameterized indexes to MolecularDescriptor metric indexes
  - scaleFactors
```
protected java.util.ArrayList scaleFactors
```
    scale factor of scalable parametrized metrics
  - tverskyA
```
protected java.util.ArrayList<java.lang.Float> tverskyA
```
    alpha values for tversky dissimilarity
  - tverskyB
```
protected java.util.ArrayList<java.lang.Float> tverskyB
```
    beta values for tversky dissimilarity
  - asymmetryFactors
```
protected java.util.ArrayList asymmetryFactors
```
    asymmetry ratio of parametrized asymmetric metrics
  - thresholds
```
protected java.util.ArrayList thresholds
```
    dissimilarity thresholds values
  - normalized
```
protected java.util.ArrayList normalized
```
    flags indicating if the metric is normalized or not
  - defaultWeight
```
protected float defaultWeight
```
    value for all missing weight parameters
  - weights
```
protected java.util.ArrayList weights
```
    weights for parametrized metrics
  - cellwiseWeights
```
protected java.util.ArrayList cellwiseWeights
```
    is cell weights for parametrized metrics
  - outputPrecision
```
protected int outputPrecision
```
    number of fraction digits in floating point output format
  - currentMetricIndex
```
protected int currentMetricIndex
```
    index of the parametrized metric currently in use
  - md
```
protected MolecularDescriptor md
```
    this object is needed to access default dissimilarity functions
  - decForm
```
protected java.text.NumberFormat decForm
```
    to format floating point output
  - generator
```
protected MDGenerator generator
```
    generates MolecularDescriptors
  - standardizer
```
protected Standardizer standardizer
```
    transform molecules into standard form before descriptor generation
- Constructor Detail
  - MDParameters
```
protected MDParameters()
```
    Creates and initializes an empty object. This class is not allowed to be instantiated directly. Only its derived classes can call the superclass constructors.
- Method Detail
  - initParameters
```
protected void initParameters()
```
    Initializes object after configuration parameters are loaded.
  - fromString
```
public void fromString(java.lang.String parameterString)
                throws MDParametersException
```
    Sets parameters from a string representation. This method assumes that parameters are described in XML format.
    
    Parameters:
    
    parameterString - configuration parameters in string
    
    Throws:
    
    MDParametersException - when the parameter string is not well-formed
  - fromFile
```
public void fromFile(java.io.File parameterFile)
              throws MDParametersException
```
    Sets parameters from an XML file. Stores filepath in configFilePath.
    
    Parameters:
    
    parameterFile - initialized parameter file
    
    Throws:
    
    MDParametersException - failed to process parameter file
  - addParameters
```
public void addParameters(java.lang.String parameterString)
                   throws MDParametersException
```
    Sets parameters from an XML string representation keeping all previous settings.
    
    Parameters:
    
    parameterString - parameters in string
    
    Throws:
    
    MDParametersException - when the parameter string is not well-formed
  - addParameters
```
public void addParameters(java.io.File parameterFile)
                   throws MDParametersException
```
    Sets parameters from an XML config file keeping all previous settings.
    
    Parameters:
    
    parameterFile - parameter file
    
    Throws:
    
    MDParametersException - when the parameter string is not well-formed
  - setParameters
```
public void setParameters(java.lang.String parametersString)
                   throws MDParametersException
```
    Sets parameters from an XML string representation overwriting all previous parameters settings with the new ones.
    
    Parameters:
    
    parametersString - parameters in string
    
    Throws:
    
    MDParametersException - when the parameter string is not well-formed
  - setParameters
```
public void setParameters(java.io.File parametersFile)
                   throws MDParametersException
```
    Sets parameters from an XML file representation overwriting all previous settings with the new ones. Stores filepath in configFilePath.
    
    Parameters:
    
    parametersFile - parameters File
    
    Throws:
    
    MDParametersException - when the parameter string is not well-formed
  - toString
```
public java.lang.String toString()
```
    Returns the parameter values in string. This implementation uses XML for the external format of parameters, however derived classes may use different formats.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    parameter string
    
    Throws:
    
    MDParametersException - when creating the parameter string fails
  - getScreeningConfigurationString
```
public java.lang.String getScreeningConfigurationString(java.lang.String nodeName,
                                                        java.lang.String attrib,
                                                        java.lang.String value)
                                                 throws MDParametersException
```
    Returns parts of the parameter values in string. Selects a sub-tree of the DOM tree specified by the tagname of one of its nodes, and writes the subtree into an XML string.
    
    Parameters:
    
    nodeName - name of the node to be printed
    
    attrib - attribute name
    
    value - value of the attribute
    
    Returns:
    
    parameter string
    
    Throws:
    
    MDParametersException - when creating the parameter string fails
  - toString
```
protected java.lang.String toString(org.dom4j.Node node)
                             throws MDParametersException
```
    Returns parts of the parameter values in string. Selects a sub-tree of the DOM tree specified by a node, and writes the subtree into an XML string.
    
    Parameters:
    
    node - rootnode of the subtree to be printed
    
    Returns:
    
    parameter string
    
    Throws:
    
    MDParametersException - when creating the parameter string fails
  - setCellSize
```
public void setCellSize(int cellSize)
```
    Sets the size (number of bits) of the bins (cells). This has to be at least 1, but should not exceed 32.
    
    Parameters:
    
    cellSize - the width of one (and each) cell (bin) in bits
  - setLength
```
public void setLength(int length)
               throws MDParametersException
```
    Sets the length (number of cells) of the descriptor.
    
    Parameters:
    
    length - the required length (cell count)
    
    Throws:
    
    MDParametersException - if argument is not positive
  - setScalingHypothesis
```
public void setScalingHypothesis(MolecularDescriptor scalingHypothesis)
```
    Sets (stores) the specified scaling hypothesis. It is used by various scaled metrics. It cannot be passed to these metrics directly as an argument, because of the uniform method header of metric functions (which has to be preserved).
    
    Parameters:
    
    scalingHypothesis - the consensus hypothesis used for scaling
  - setScaleFactor
```
public void setScaleFactor(float scaleFactor)
```
    Sets scaleFactor used with the current parametrized metrics.
    
    Parameters:
    
    scaleFactor - the new value of the scaleFactor
  - setAsymmetryFactor
```
public void setAsymmetryFactor(float af)
```
    Sets the value of the asymmetry factor of the current parametrized metric.
    
    Parameters:
    
    af - asymmetry factor
  - setThreshold
```
public void setThreshold(float th)
```
    Sets the value of the threshold of the current parametrized metric.
    
    Parameters:
    
    th - dissimilarity threshold value
  - setWeights
```
public void setWeights(float[] w)
```
    Sets the cell-wise weight factors for the current parametrized metric.
    
    Parameters:
    
    w - weights
  - setCellwiseWeights
```
public void setCellwiseWeights(boolean c)
```
    Sets boolean telling whether cell weights are to be generated for current parametrized metric.
    
    Parameters:
    
    c - true if cell weights
  - setNormalized
```
public void setNormalized(boolean yes)
```
    Toggles the normalized flag of the current parametrized metric.
    
    Parameters:
    
    yes - true, if the metric is normalized
  - setOutputPrecision
```
public void setOutputPrecision(int precision)
```
    Specifies the output precision for floating point values. This method can be used in conjunction with getDecForm().
    
    Parameters:
    
    precision - number of digits after the decimal point
  - setCurrentParametrizedMetric
```
public void setCurrentParametrizedMetric(int metricIndex)
```
    Selects the specified parametrized metric to be the current.
    
    Parameters:
    
    metricIndex - index of the selected parametrized metric
  - setCreateStatistics
```
public void setCreateStatistics(boolean createStatistics)
```
    Toggles the create statistics flag of the MDGenerator object.
    
    Parameters:
    
    createStatistics - new value for the create statistics flag
  - addParametrizedMetric
```
public int addParametrizedMetric(java.lang.String name,
                                 java.lang.String metric,
                                 java.lang.String activeFamily)
                          throws MDParametersException
```
    Expands the set of parametrized metrics with a new item. The first parameter is optional, if not specified the symbolic name is formed from the second and the third parameters (both of these are mandatory).
    
    Parameters:
    
    name - symbolic name of the parametrized metric
    
    metric - name of the metric (like Tanimoto, Euclidean etc)
    
    activeFamily - name of the active compounds family
    
    Throws:
    
    MDParametersException
  - getCellSize
```
public int getCellSize()
```
    Gets the number of bits of an atomic cell in the descriptor.
    
    Returns:
    
    the number of bits in one single descriptor cell
  - getLength
```
public int getLength()
```
    Returns the number of cells forming the descriptor.
  - getInternalSize
```
public int getInternalSize()
```
    Gets the required memory size to store the descriptor according to the specified parameters.
    
    Returns:
    
    size of a suitable array that can store one descriptor
  - getData
```
public byte[] getData()
```
    Gets the byte array which is used for conversions between internal and external data formats. Internal is the memory representation, while external is used for storing descriptors in files.
    
    Returns:
    
    an array large enough to hold the descriptor in external format
  - getCurrentMetricIndex
```
public int getCurrentMetricIndex()
```
  - getNumberOfMetrics
```
public int getNumberOfMetrics()
```
    Gets the total number of parametrized metrics available in the present configuration.
    
    Returns:
    
    number of metrics
  - getNumberOfWeights
```
public int getNumberOfWeights()
```
    Gets the number of weights the current parametrized metric takes.
    
    Returns:
    
    number of weight factors corresponding to the current metric
  - getNumberOfWeights
```
protected int getNumberOfWeights(int parametrizedMetricIndex)
                          throws java.lang.IllegalArgumentException
```
    Gets the number of weight factors used by the specified metric. This method can be applied to the dissimilarity metrics provided by the MolecularDescriptor class or its derived classes, but not to parametrized metric.
    
    Parameters:
    
    parametrizedMetricIndex - parametrized metric index
    
    Returns:
    
    number of weights the metric uses
    
    Throws:
    
    java.lang.IllegalArgumentException - if the given parameter is not a valid metric index
  - getThreshold
```
public float getThreshold(int metricIndex)
```
    Gets a metric dependent threshold value. Ideally, this value should be based on statistics, though the actual value is not too critical, since these are only used in user interfaces to simplify the use of applications for beginners. Note: this parametrized version of getThreshold() is kept for compatibility reasons.
    
    Parameters:
    
    metricIndex - index of a parametrized metric
    
    Returns:
    
    threshold corresponding to the given metric index
  - getThreshold
```
public float getThreshold()
```
    Gets the threshold value being set for the current parametrized version.
    
    Returns:
    
    dissimilarity threshold corresponding to the curent metric
  - getScalingHypothesis
```
public MolecularDescriptor getScalingHypothesis()
```
    Gets the scaling hypothesis used in scaled metrics.
    
    Returns:
    
    the scaling hypothesis
  - getInternalMetricIndex
```
public int getInternalMetricIndex()
```
    Gets the MolecularDescriptor specific metric index of the current parametrized metric.
    
    Returns:
    
    metric index
  - getMetricName
```
public java.lang.String getMetricName()
```
    Gets the user defined symbolic name of the current parametrized metric.
    
    Returns:
    
    metric name
  - getMetricName
```
public java.lang.String getMetricName(int metricIndex)
```
    Gets the user defined symbolic name of the specified parametrized metric.
    
    Returns:
    
    metric name
  - getMetricIndex
```
public int getMetricIndex(java.lang.String name)
```
    Gets the index of the given parametrized metric.
    
    Parameters:
    
    name - name of the parametrized metric
    
    Returns:
    
    metric index
  - getScaleFactor
```
public float getScaleFactor()
```
    Gets the scale factor used in the current parametrized scalable metrics.
    
    Returns:
    
    the scale factor
  - getAsymmetryFactor
```
public float getAsymmetryFactor()
```
    Gets the asymmetry factor used in the current parametrized asymmetric metrics.
    
    Returns:
    
    the value of the asymmetry factor
  - getWeights
```
public float[] getWeights()
```
    Gets all weights for the given parametrized metric. If the specified metric is not a weighted metric or correspong weights are not set, null is returned.
    
    Returns:
    
    all weights as float values
  - getTverskyAlpha
```
public float getTverskyAlpha()
```
    Gets Tversky alpha value for the given parametrized metric.
    
    Returns:
    
    alpha as float value
  - getTverskyBeta
```
public float getTverskyBeta()
```
    Gets Tversky beta value for the given parametrized metric.
    
    Returns:
    
    beta as float value
  - isCellwiseWeights
```
public boolean isCellwiseWeights()
```
    Gets boolean telling whether cell weights are to be generated for current parametrized metric.
    
    Returns:
    
    true if weights are assigned to each individual descriptor cell
  - getDecForm
```
public java.text.DecimalFormat getDecForm()
```
    Gets the formatter object that is capable of formatting fractions with given precision. Precision can be set by calling setOutputPrecision( int precision ).
    
    Returns:
    
    decimal number formatter object (not localized)
  - isScaled
```
public boolean isScaled()
```
    Returns whether current parametrized metric is scaled or not.
    
    Returns:
    
    true if the metric is scaled
  - isAsymmetric
```
public boolean isAsymmetric()
```
    Returns whether current parametrized metric is asymmetric or not.
    
    Returns:
    
    true if the metric is asymmetric
  - isWeighted
```
public boolean isWeighted()
```
    Returns whether current parametrized metric is weighted or not.
    
    Returns:
    
    true if the metric is weighted
  - isNormalized
```
public boolean isNormalized()
```
    Returns whether current parametrized metric is normalized or not.
    
    Returns:
    
    true if the metric is normalized
  - isStandardizationMandatory
```
public boolean isStandardizationMandatory()
```
    Checks is Standardization of molecules is mandatory for the corresponding MolecularDescriptor before descriptor generation. This method always returns true. Derived classes should override in case when standardization is not obligatory.
    
    Returns:
    
    whether or not standardization of molecules is needed
    
    Since:
    
    JChem 2.2
  - getDefaultStandardizerConfiguration
```
public static java.lang.String getDefaultStandardizerConfiguration()
```
    Gets the default configuration of the standardizer. This method is called if no standardizer configuration is set in the parameters configuration but standardization is mandatory for the corresponding MolecularDescriptor. The default on this top level is aromatization and dehydrogenization, but derived parameter classes may overload this behaviour.
    
    Returns:
    
    standardizer configuration XML string
    
    Since:
    
    JChem 2.2
  - getDefaultDocumentFrame
```
public java.lang.String getDefaultDocumentFrame()
```
    Gets the default XML configuration string. This is needed when an optional XML configuration is not specified. Descriptor files and descriptor tables always store the configuration that corresponds to the descriptors stored, thus sg. has to be storedeven when nothing is specified.
    
    Returns:
    
    default XML configuration string of the actual Parameters class
    
    Since:
    
    JChem 2.2
  - standardize
```
public Molecule standardize(Molecule m)
```
    Standardizes the Molecule and returns the standardized form. The standardization is configured via XML. StandardizerConfiguration is the corresponding XML tag. If no standardizar is set up, null is returned.
    
    Parameters:
    
    m - molecular structure to be standardized
    
    Returns:
    
    standardized form of the input structure, or null if standardization is mandatory for the corresponding descriptor
    
    Since:
    
    JChem 2.2
  - readFromXmlFile
```
protected void readFromXmlFile(java.io.File file,
                               boolean merge,
                               boolean all)
                        throws MDParametersException
```
    Reads configuration from XML file. Builds a DOM tree, picks nodes, elements that store information that can be processed on this level (leaves others for derived classes), and processes this information by converting values in to internal format and stores them in data members of this class. Stores filepath in configFilePath.
    
    Parameters:
    
    file - the XML file to read configuration data from
    
    merge - merge config from file into already existing parameters or overwrite existing parameter values
    
    all - process the complete document or only the ScreeningConfiguration tag
    
    Throws:
    
    MDParametersException - in the case of any failure
  - readFromXmlString
```
protected void readFromXmlString(java.lang.String xml,
                                 boolean merge,
                                 boolean all)
                          throws MDParametersException
```
    Reads configuration from XML string. Builds a DOM tree, picks nodes, elements that store information that can be processed on this level (leaves others for derived classes), and processes this information by converting values in to internal format and stores them in data members of this class.
    
    Parameters:
    
    xml - the XML string to get the configuration data from
    
    merge - merge config from file into already existing parameters or overwrite existing parameter values
    
    all - process the complete document or only the ScreeningConfiguration tag
    
    Throws:
    
    MDParametersException - in the case of any failure
  - checkDocumentVersion
```
protected void checkDocumentVersion(java.lang.String docType,
                                    java.lang.String version)
                             throws MDParametersException
```
    Checks if the document is the right version
    
    Parameters:
    
    docType - the required document type
    
    version - the expected version number
    
    Throws:
    
    MDParametersException
  - processDocument
```
protected void processDocument(boolean all)
                        throws MDParametersException
```
    Searches the DOM tree for relevant nodes and sets internal variables to some these nodes for the sake of easier information processing.
    
    Parameters:
    
    all - process the complete document or only the ScreeningConfiguration tag
    
    Throws:
    
    MDParametersException
  - readValues
```
protected void readValues(boolean all)
                   throws MDParametersException
```
    Picks attribute values from the document tree that are relevant to the actual MDParameters sub-class.
    
    Parameters:
    
    all - process the complete document or only the ScreeningConfiguration tag
    
    Throws:
    
    MDParametersException
  - readMetricParameters
```
protected void readMetricParameters()
                             throws MDParametersException
```
    Processes all ParametrizedMetric nodes in the DOM tree. Reads parameterized metric names and associated parameter setting and stores them in data member for faster and easier access in getter methods.
    
    Throws:
    
    MDParametersException - if one of the nodes is not well-formed
  - readMetricWeights
```
protected void readMetricWeights(org.dom4j.Element parametrizedMetric,
                                 int metricIndex)
                          throws MDParametersException
```
    Throws:
    
    MDParametersException
  - writeMetricParameter
```
protected void writeMetricParameter(java.util.ArrayList pl,
                                    java.lang.String attr,
                                    int mi,
                                    boolean useDecForm)
```
    Writes a given parameter of the specified metric into the corresponding tree node.
    
    Parameters:
    
    pl - list of parameters (for all metric indexes)
    
    attr - name of the attribute which the parameter corresponds to
    
    mi - index of the metric
    
    useDecForm - use precision for writing floating point values
  - appendParametrizedMetric
```
protected int appendParametrizedMetric(java.lang.String name,
                                       java.lang.String metric)
```
    Extends internal data with a new parametrized metric. Neither the DOM tree nor the XML document is modified.
    
    Parameters:
    
    name - name of the parametrized metric
    
    metric - dissimilarity metric name (as defined in its implementor class
  - addParametrizedMetricsNode
```
protected void addParametrizedMetricsNode()
```
    Adds the ParametrizedMetrics node to the DOM tree.
  - addParametrizedMetricNode
```
protected org.dom4j.Element addParametrizedMetricNode(java.lang.String name,
                                                      java.lang.String activeFamily,
                                                      java.lang.String metric)
```
    Adds a ParametrizedMetric node to the DOM tree.
    
    Parameters:
    
    name - name of the parameterized metric, given by the user
    
    activeFamily - name of the active compound family (e.g. ACE)
    
    metric - name of the dissimilarity metric
  - importNodes
```
protected boolean importNodes(org.dom4j.Document doc,
                              boolean merge)
```
    Imports nodes from the specified Document into the current (main) Document. New nodes can either merged into the existing ones without removing them, or new nodes may overwrite exisiting nodes.
    
    Parameters:
    
    doc - import nodes from this document
    
    merge - merge (add new) or overwrite (replace with new) existing nodes
  - getDescriptorTypeName
```
public static java.lang.String getDescriptorTypeName(java.lang.String xmlConfig)
```
    Takes the descriptor type name from the root element of the XML configuration.
    
    Parameters:
    
    xmlConfig - configuration string
    
    Returns:
    
    descriptor type name

Class MDParameters

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_SCALE_FACTOR

DEFAULT_ASYMMETRY_FACTOR

DEFAULT_WEIGHT

DEFAULT_OUTPUT_PRECISION

cellSize

length

internalSize

data

configFilePath

document

standardizerConfigurationNode

similarityNode

screeningConfigurationNode

parametrizedMetricsNode

parametrizedMetricNodes

parametrizedMetrics

metricIndexes

scaleFactors

tverskyA

tverskyB

asymmetryFactors

thresholds

normalized

defaultWeight

weights

cellwiseWeights

outputPrecision

currentMetricIndex

md

decForm

generator

standardizer

Constructor Detail

MDParameters

Method Detail

initParameters

fromString

fromFile

addParameters

addParameters

setParameters

setParameters

toString

getScreeningConfigurationString

toString

setCellSize

setLength

setScalingHypothesis

setScaleFactor

setAsymmetryFactor

setThreshold

setWeights

setCellwiseWeights

setNormalized

setOutputPrecision

setCurrentParametrizedMetric

setCreateStatistics

addParametrizedMetric

getCellSize

getLength

getInternalSize

getData

getCurrentMetricIndex

getNumberOfMetrics

getNumberOfWeights

getNumberOfWeights

getThreshold

getThreshold

getScalingHypothesis

getInternalMetricIndex

getMetricName

getMetricName

getMetricIndex

getScaleFactor