Package 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

  • Field Details

    • DEFAULT_RESOLUTION

      public static final int DEFAULT_RESOLUTION
      default values
      See Also:

    • DEFAULT_FUZZINESS_FACTOR

      public static final float DEFAULT_FUZZINESS_FACTOR
      See Also:

    • DEFAULT_FUZZY_CUTOFF

      public static final float DEFAULT_FUZZY_CUTOFF
      See Also:

    • DEFAULT_FUZZY_LOWER_BOUND

      public static final int DEFAULT_FUZZY_LOWER_BOUND
      See Also:

    • DEFAULT_XML_CONFIG

      public static final String DEFAULT_XML_CONFIG
      See Also:

    • fuzzinessFactors

      protected 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 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 Details

    • PFParameters

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

    • PFParameters

      public PFParameters(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(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 Details

    • fromString

      public void fromString(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(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 String toString()
      Returns the XML configuration in a string.
      Overrides:
      toString in class MDParameters
      Returns:
      configuration string in XML format

    • setParameters

      public void setParameters(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(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 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(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(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 chemaxon.pharmacophore.PSymbols getPSymbols()
      Gets the pharmacophore type symbols used in the current configuration.
      Returns:
      pharmacophore symbols

    • getSymbol

      public 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(String symbol) throws 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:
      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 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:
      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 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 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 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 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(String name, 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