chemaxon.descriptors

Class PFParameters

java.lang.Object

chemaxon.descriptors.MDParameters

chemaxon.descriptors.PFParameters

@PublicAPI
public class PFParameters
extends MDParameters

Manages 2D pharmacophore fingerprint parameters. This class has multiple roles: 1. reads, stores and provides parameters for PharmacophoreFingerprint ; and 2. acts as a shared memory area of all PharmacophoreFingerprint instances. This latter serves pure running-time and storage efficiency needs by removing redundant data from PharmacophoreFingerprint objects and easing the communication (that is passing data) between parts of the program. Example for these include the following data members: compressedData, xyz, asymmetricXYZSum. Most of these members have public access for the sake of ease. (The use of private access members and the introduction of corresponding setter/getter methods would not increase the safety (or any other quality) quality of the code at all (as they would not add any further functionality, than the mere change or retrieval of the value, which can now be done directly).)

Since:

JChem 2.2

Author:

Miklos Vargyas, Zsuzsanna Szabo

Field Summary

Fields

Modifier and Type	Field and Description
float	asymmetricXYZSum Stores last calculatred asymmetric Tanimoto sum.
protected chemaxon.pharmacophore.ColorDecoder	colDec atom set colors
protected byte[][]	compressedData Buffer for compressed data, used in MolecularDescriptor.toData( final int[] ).
static float	DEFAULT_FUZZINESS_FACTOR
static float	DEFAULT_FUZZY_CUTOFF
static int	DEFAULT_FUZZY_LOWER_BOUND
static int	DEFAULT_RESOLUTION default values
static java.lang.String	DEFAULT_XML_CONFIG
protected java.util.ArrayList	fuzzinessFactors fuzziness factors of parametrized metrics
protected float[][]	fuzzyExp fuzzi exponent for the FBPA metric, calculated from the fuzziness factor
protected float[][]	gFuzzyIncrements Fuzzy smoothing values for gaussian smoothing.
protected java.lang.String[]	pptNames Pharmacophore point type names.
protected float[][][]	svFuzzyIncrements Fuzzy smoothing values for smoothing with user defined smoothing vector.
float[]	xyz The calculateXYZ() methods (in PharmacophoreFingerprint sub-classes) calculate three numbers (denoted by x,y and z), but methods in java cannot have output parameters.

Fields inherited from class chemaxon.descriptors.MDParameters

asymmetryFactors, cellSize, cellwiseWeights, configFilePath, currentMetricIndex, data, decForm, DEFAULT_ASYMMETRY_FACTOR, DEFAULT_OUTPUT_PRECISION, DEFAULT_SCALE_FACTOR, DEFAULT_WEIGHT, defaultWeight, document, generator, internalSize, length, md, metricIndexes, normalized, outputPrecision, parametrizedMetricNodes, parametrizedMetrics, parametrizedMetricsNode, scaleFactors, screeningConfigurationNode, similarityNode, standardizer, standardizerConfigurationNode, thresholds, tverskyA, tverskyB, weights

Constructor Summary

Constructors

Constructor and Description
PFParameters() Creates an empty object.
PFParameters(java.io.File configFile) Creates a new object based on a given configuration file.
PFParameters(java.lang.String XMLconfig) Creates a new object based on a given configuration string.

Method Summary

Modifier and Type	Method and Description
protected int	appendParametrizedMetric(java.lang.String name, java.lang.String metric) Extends internal data with a new parametrized metric.
void	fromFile(java.io.File parameterFile) Sets parameters from an XML file.
void	fromString(java.lang.String parameterString) Sets parameters from a string representation.
protected java.lang.String[]	generate(Molecule m, MolecularDescriptor cd) Calls the corresponding MolecularDescriptorGenerator and generates the descriptor for the given molecule.
java.awt.Color[]	getAtomSetColors() Gets the coloring of atoms as defined in the XML configuration file.
int[]	getAtomSetIndexes(Molecule m, PharmacophoreFingerprint pfp) Gets the individual atom colors by pharmcophore point type.
java.lang.String[]	getAtomSetNames() Gets the name of atom sets (pharmacophore point type set), as defined in the configuration file/string.
float[]	getCustomFuzzyIncrements(int fa, int fb) Gets fuzzy increments for the fuzzy smoothing with a user-defined custom distribution (fuzzy smoothing vector).
java.lang.String	getDefaultDocumentFrame() Gets the default XML configuration string.
static java.lang.String	getDefaultStandardizerConfiguration() Gets the default configuration of the standardizer.
float[][]	getFuzzyExponents() Gets the precalculated fuzzy exponent used in the Fuzzy Bipolar Autocorrelogram (FBPA) metric.
float	getFuzzyLowerBound()
float	getFuzzySmoothingFactor() Gets the fuzzy smoothing factor used in the construction of fuzzy fingerprints.
float[][]	getGaussianFuzzyIncrements() Gets fuzzy increments for the fuzzy smoothing with a normal distribution.
boolean	getIgnoreRotatableBonds()
int	getMaxDist() Gets the miximum distance of pharmacophore points that is considered.
int	getMinDist() Gets the minimum distance of pharmacophore points that is considered.
int	getNDists() Gets the number of histograms bars, that is that number of distance values disguished.
int	getNumberOfFeatures() The number of pharmacophore features (aka types, properties) used in the fingerprints.
protected int	getNumberOfWeights(int parametrizedMetricIndex) Gets the number of weight factors used by the specified metric.
PSymbols	getPSymbols() Gets the pharmacophore type symbols used in the current configuration.
int	getResolution() Gets the resolution of histograms.
java.lang.String	getSymbol(int i) Gets the symbol associated with the specified Pharmacophore.
int	getSymbolIndex(java.lang.String symbol) Gets the index associated with the specified Pharmacophore symbol.
protected boolean	importNodes(org.dom4j.Document doc, boolean merge) Imports nodes from the specified Document into the current (main) Document.
protected void	init() Initializes the object.
protected void	initGenerator() Creates and initializes a PFGenerator instance.
protected void	initParameters() Initializes those data members that depend on the XML configuration but are not directly taken from it.
boolean	isFuzzyFingerprint() Gets whether the fuzzy fingerprints are used or not.
boolean	isGaussianSmoothing() Gets if fuzzy smmoothing is based on normal distribution.
boolean	isSymmetricalFuzzy()
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	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	setCurrentParametrizedMetric(int metricIndex) Selects a metric to be used.
void	setFuzzinessFactor(float alpha) Sets the value of the fuzziness factor, used in fuzzy bipolar pharmacophore autocorrelogram (FBPA) based convolution product in non-parametrized (generic) FBPA metric.
void	setFuzzyCutOff(float fco)
void	setFuzzyLowerBound(int flb)
void	setFuzzySmoothingFactor(float fsf) Sets the value of the fuzzy smoothing factor used in the generation of fuzzy fingerprints.
void	setIgnoreRotatableBonds(boolean irb)
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	setPMAPTagName(java.lang.String tagName) Sets the name of the pharmacophore map tag to be considered in the input SDfile.
void	setSymmetricalFuzzy(boolean sf)
void	setUsePMAP(java.lang.String pmapTagName) Pharmacophore map data in imported Molecule-s should be used.
void	setWeights(float[] featureWeights, float[] distanceWeights) Sets the cell-wise weight factors for the current parametrized metric.
java.lang.String	toString() Returns the XML configuration in a string.
int	tripletIndex(int f1, int f2, int d) Calculates the index of a feature pair and distance triplet in the linearised representation of histograms.

Methods inherited from class chemaxon.descriptors.MDParameters

addParameters, addParameters, addParametrizedMetric, addParametrizedMetricNode, addParametrizedMetricsNode, checkDocumentVersion, getAsymmetryFactor, getCellSize, getCurrentMetricIndex, getData, getDecForm, getDescriptorTypeName, getInternalMetricIndex, getInternalSize, getLength, getMetricIndex, getMetricName, getMetricName, getNumberOfMetrics, getNumberOfWeights, getScaleFactor, getScalingHypothesis, getScreeningConfigurationString, getThreshold, getThreshold, getTverskyAlpha, getTverskyBeta, getWeights, isAsymmetric, isCellwiseWeights, isNormalized, isScaled, isStandardizationMandatory, isWeighted, readFromXmlFile, readFromXmlString, setAsymmetryFactor, setCellSize, setCellwiseWeights, setCreateStatistics, setLength, setNormalized, setOutputPrecision, setScaleFactor, setScalingHypothesis, setThreshold, setWeights, standardize, toString, writeMetricParameter

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

DEFAULT_RESOLUTION

public static final int DEFAULT_RESOLUTION

default values

See Also:

Constant Field Values

DEFAULT_FUZZINESS_FACTOR

public static final float DEFAULT_FUZZINESS_FACTOR

See Also:

Constant Field Values

DEFAULT_FUZZY_CUTOFF

public static final float DEFAULT_FUZZY_CUTOFF

See Also:

Constant Field Values

DEFAULT_FUZZY_LOWER_BOUND

public static final int DEFAULT_FUZZY_LOWER_BOUND

See Also:

Constant Field Values

DEFAULT_XML_CONFIG

public static final java.lang.String DEFAULT_XML_CONFIG

See Also:

Constant Field Values

fuzzinessFactors

protected java.util.ArrayList fuzzinessFactors

fuzziness factors of parametrized metrics

fuzzyExp

protected float[][] fuzzyExp

fuzzi exponent for the FBPA metric, calculated from the fuzziness factor

colDec

protected chemaxon.pharmacophore.ColorDecoder colDec

atom set colors

pptNames

protected java.lang.String[] pptNames

Pharmacophore point type names. These are similar to the above coloring scheme, though instead of colors, this array contains the IDs of pharmacophore point types as defined in the XML configuration. Tha names of combined types (e.g. d - (Donor Minus) are obtained by concatenating the corresponding IDs.

gFuzzyIncrements

protected float[][] gFuzzyIncrements

Fuzzy smoothing values for gaussian smoothing. The first index is the number of rotatable bonds while the second is the distance value. For the sake of efficiency, distances from 0 to maxDist() are stored.

svFuzzyIncrements

protected float[][][] svFuzzyIncrements

Fuzzy smoothing values for smoothing with user defined smoothing vector. The first and the second indexes are the pharmacophore point type indexes the third is the distance value.

compressedData

protected byte[][] compressedData

Buffer for compressed data, used in MolecularDescriptor.toData( final int[] ). Element 'i' is either null or is an array of 'i' bytes.

xyz

public float[] xyz

The calculateXYZ() methods (in PharmacophoreFingerprint sub-classes) calculate three numbers (denoted by x,y and z), but methods in java cannot have output parameters. We could (1) pass an array of three elements, but in that case the array was either a data member of PharmacophoreFingerprint, which has to be avoided in order to keep the size of a descriptor as small as possible; or alternatively (2) the array could be allocated in the caller of calculateXYZ() each time, which clearly had time and storage overhead. Keeping a preallocated instance in parameters is efficient though apparently not nice in terms of object oriented principles.

asymmetricXYZSum

public float asymmetricXYZSum

Stores last calculatred asymmetric Tanimoto sum.

Constructor Detail

PFParameters

public PFParameters()

Creates an empty object. Use setConfig( String paramString ) to initialize it properly.

PFParameters

public PFParameters(java.io.File configFile)
             throws MDParametersException

Creates a new object based on a given configuration file.

Parameters:

configFile - XML configuration file

Throws:

MDParametersException - missing or bad XML configuration

PFParameters

public PFParameters(java.lang.String XMLconfig)
             throws MDParametersException

Creates a new object based on a given configuration string.

Parameters:

XMLconfig - XML configuration string

Throws:

MDParametersException - missing or bad XML configuration

Method Detail

fromString

public void fromString(java.lang.String parameterString)
                throws MDParametersException

Sets parameters from a string representation. This method processes an XML format, but derived classes may overload this and define their own format.

Overrides:

fromString in class MDParameters

Parameters:

parameterString - 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. Derived classes may overload this and define their own format (even other than XML).

Overrides:

fromFile in class MDParameters

Parameters:

parameterFile - initialized configuration file

Throws:

MDParametersException - failed to process parameter file

toString

public java.lang.String toString()

Returns the XML configuration in a string.

Overrides:

toString in class MDParameters

Returns:

configuration string in XML format

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.

Overrides:

setParameters in class MDParameters

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.

Overrides:

setParameters in class MDParameters

Parameters:

parametersFile - parameter configuration file

Throws:

MDParametersException - when the parameter string is not well-formed

init

protected void init()

Initializes the object. Only those fundamental data members are set that do not depend on the XML configuration.

initGenerator

protected void initGenerator()
                      throws MDParametersException

Creates and initializes a PFGenerator instance. The generator is stored in the MDParameters in order to spare memory space: the PFParameter object is shared among multiple instances of PharmacophoreFingerprint, thus they refer to the same generator object too via the parameters field.

Throws:

MDParametersException

initParameters

protected void initParameters()

Initializes those data members that depend on the XML configuration but are not directly taken from it.

Overrides:

initParameters in class MDParameters

generate

protected java.lang.String[] generate(Molecule m,
                                      MolecularDescriptor cd)
                               throws MDGeneratorException

Calls the corresponding MolecularDescriptorGenerator and generates the descriptor for the given molecule. Note, that it is the responsibility of subclasses to initialize the generator upfront any call to this function.

Parameters:

m - a molecular structure

cd - the chemical descriptor generated for the given molecule, an output parameter

Returns:

names of Molecule Property-s (SDfile tags) set by the generator

Throws:

MDGeneratorException - when failed to generate descriptor

setCurrentParametrizedMetric

public void setCurrentParametrizedMetric(int metricIndex)

Selects a metric to be used. When a metric is selected all properties and related parameters can be retrieved with the getter methods of this class.

Overrides:

setCurrentParametrizedMetric in class MDParameters

Parameters:

metricIndex - index of a parametrized metric to be used

setFuzzySmoothingFactor

public void setFuzzySmoothingFactor(float fsf)

Sets the value of the fuzzy smoothing factor used in the generation of fuzzy fingerprints. The smoothing process fits a Guassian curve to all values to be put into histogram bins, and this value is the standard deviation of the corresponding normal distribution.

Parameters:

fsf - the fuzzy smoothing factor

setFuzzyCutOff

public void setFuzzyCutOff(float fco)

setFuzzyLowerBound

public void setFuzzyLowerBound(int flb)

setSymmetricalFuzzy

public void setSymmetricalFuzzy(boolean sf)

setIgnoreRotatableBonds

public void setIgnoreRotatableBonds(boolean irb)

setFuzzinessFactor

public void setFuzzinessFactor(float alpha)

Sets the value of the fuzziness factor, used in fuzzy bipolar pharmacophore autocorrelogram (FBPA) based convolution product in non-parametrized (generic) FBPA metric.

Parameters:

alpha - fuzziness factor used in the convolution product

setUsePMAP

public void setUsePMAP(java.lang.String pmapTagName)

Pharmacophore map data in imported Molecule-s should be used. The generator will not generate PMAP data, but will use the exsiting one.

Parameters:

pmapTagName - name of the SDfile tag storing the PMAP data

setPMAPTagName

public void setPMAPTagName(java.lang.String tagName)

Sets the name of the pharmacophore map tag to be considered in the input SDfile.

Parameters:

tagName - name of the SDfile tag that stores pharmacophore map

setWeights

public void setWeights(float[] featureWeights,
                       float[] distanceWeights)

Sets the cell-wise weight factors for the current parametrized metric.

Parameters:

featureWeights - weights for each pharmacophore type

distanceWeights - weights for each point pair distance

getNumberOfFeatures

public int getNumberOfFeatures()

The number of pharmacophore features (aka types, properties) used in the fingerprints.

Returns:

number of pharmacophore features

getPSymbols

public PSymbols getPSymbols()

Gets the pharmacophore type symbols used in the current configuration.

Returns:

pharmacophore symbols

getSymbol

public java.lang.String getSymbol(int i)

Gets the symbol associated with the specified Pharmacophore.

Parameters:

i - index of the pharmacophore property (feature)

Returns:

the symbol string of the feature

getSymbolIndex

public int getSymbolIndex(java.lang.String symbol)
                   throws java.lang.IllegalArgumentException

Gets the index associated with the specified Pharmacophore symbol.

Parameters:

symbol - pharmacophore property (feature) symbol

Returns:

the index of the feature, -1 if not found

Throws:

java.lang.IllegalArgumentException

getMinDist

public int getMinDist()

Gets the minimum distance of pharmacophore points that is considered.

Returns:

value of minimal distance

getMaxDist

public int getMaxDist()

Gets the miximum distance of pharmacophore points that is considered.

Returns:

value of miximal distance

getResolution

public int getResolution()

Gets the resolution of histograms. THe resolution is the width of a histogram bin, that is the distance values considered to be indistinguishable.

Returns:

value of the current resolution

getNDists

public int getNDists()

Gets the number of histograms bars, that is that number of distance values disguished.

Returns:

hte number of ditance values in one histogram

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.

Overrides:

getNumberOfWeights in class MDParameters

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

isFuzzyFingerprint

public boolean isFuzzyFingerprint()

Gets whether the fuzzy fingerprints are used or not.

Returns:

fuzzy flag

isGaussianSmoothing

public boolean isGaussianSmoothing()

Gets if fuzzy smmoothing is based on normal distribution.

Returns:

true if smoothing has gaussian

getFuzzySmoothingFactor

public float getFuzzySmoothingFactor()

Gets the fuzzy smoothing factor used in the construction of fuzzy fingerprints.

Returns:

the fuzzy smoothing factor

isSymmetricalFuzzy

public boolean isSymmetricalFuzzy()

getIgnoreRotatableBonds

public boolean getIgnoreRotatableBonds()

getFuzzyLowerBound

public float getFuzzyLowerBound()

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. The default standardization for PharmacophoreFingerprint includes aromatization and the removal of small disjoint fragments (largest component is kept only).

Returns:

standardizer confiuration XML string

Since:

JChem 2.3

getDefaultDocumentFrame

public java.lang.String getDefaultDocumentFrame()

Gets the default XML configuration string. This is needed when the PharmacophoreFingerprint XML configuration is not specified.

Overrides:

getDefaultDocumentFrame in class MDParameters

Returns:

default XML configuration string of the PFParameters class

Since:

JChem 2.3

getGaussianFuzzyIncrements

public float[][] getGaussianFuzzyIncrements()

Gets fuzzy increments for the fuzzy smoothing with a normal distribution. The first index of the raturned array is the number of rotatable bonds, while the second is the distance of the two pharmacophoric points considered. These values represent a normal distribution with a standard deviation equal to the product of the number of rotatable bonds plus one and the fuzzy smoothing factor. Therefore, the more rotatable bonds are found between the two pharmacophoric point, the larger the deviation of the normal distribution is (the wider and flatter the Gaussian curve is). Note, that the normal distribution is standard (its peek is in zero), and that only the right hand side of the curve is returned (the left is a mirror image).

Returns:

fuzzy increments

getCustomFuzzyIncrements

public float[] getCustomFuzzyIncrements(int fa,
                                        int fb)

Gets fuzzy increments for the fuzzy smoothing with a user-defined custom distribution (fuzzy smoothing vector).

Parameters:

fa - pharmacophore point type of the first component of the pair

fb - pharmacophore point type of the second component of the pair

Returns:

fuzzy increments

getFuzzyExponents

public float[][] getFuzzyExponents()

Gets the precalculated fuzzy exponent used in the Fuzzy Bipolar Autocorrelogram (FBPA) metric.

Returns:

fuzzy exponents

getAtomSetColors

public java.awt.Color[] getAtomSetColors()

Gets the coloring of atoms as defined in the XML configuration file.

Returns:

array of colors of different pharmacophore point types

getAtomSetNames

public java.lang.String[] getAtomSetNames()

Gets the name of atom sets (pharmacophore point type set), as defined in the configuration file/string.

Returns:

names of pharmacophore point types

getAtomSetIndexes

public int[] getAtomSetIndexes(Molecule m,
                               PharmacophoreFingerprint pfp)

Gets the individual atom colors by pharmcophore point type. This method is implemented in this class because it calls the pharmacophore fingerprint generator.

Parameters:

m - a molecule to assign pharmacophore point colors to

Returns:

array of color indexes indexed by atom indexes

processDocument

protected void processDocument(boolean all)
                        throws MDParametersException

Description copied from class: MDParameters

Searches the DOM tree for relevant nodes and sets internal variables to some these nodes for the sake of easier information processing.

Overrides:

processDocument in class MDParameters

Parameters:

all - process the complete document or only the ScreeningConfiguration tag

Throws:

MDParametersException

readValues

protected void readValues(boolean all)
                   throws MDParametersException

Description copied from class: MDParameters

Picks attribute values from the document tree that are relevant to the actual MDParameters sub-class.

Overrides:

readValues in class MDParameters

Parameters:

all - process the complete document or only the ScreeningConfiguration tag

Throws:

MDParametersException

readMetricParameters

protected void readMetricParameters()
                             throws MDParametersException

Description copied from class: MDParameters

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.

Overrides:

readMetricParameters in class MDParameters

Throws:

MDParametersException - if one of the nodes is not well-formed

readMetricWeights

protected void readMetricWeights(org.dom4j.Element parametrizedMetric,
                                 int metricIndex)
                          throws MDParametersException

Overrides:

readMetricWeights in class MDParameters

Throws:

MDParametersException

appendParametrizedMetric

protected int appendParametrizedMetric(java.lang.String name,
                                       java.lang.String metric)

Description copied from class: MDParameters

Extends internal data with a new parametrized metric. Neither the DOM tree nor the XML document is modified.

Overrides:

appendParametrizedMetric in class MDParameters

Parameters:

name - name of the parametrized metric

metric - dissimilarity metric name (as defined in its implementor class

importNodes

protected boolean importNodes(org.dom4j.Document doc,
                              boolean merge)

Description copied from class: MDParameters

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.

Overrides:

importNodes in class MDParameters

Parameters:

doc - import nodes from this document

merge - merge (add new) or overwrite (replace with new) existing nodes

tripletIndex

public int tripletIndex(int f1,
                        int f2,
                        int d)

Calculates the index of a feature pair and distance triplet in the linearised representation of histograms. Features are ordered as described above.

Parameters:

f1 - index of the first feature

f2 - index of the other feature

d - distance value

Returns:

the index of the triplet