Class PMapper

java.lang.Object
chemaxon.pharmacophore.PMapper
All Implemented Interfaces:
chemaxon.license.Licensable

@PublicApi public class PMapper extends Object implements chemaxon.license.Licensable
Class for searching for pharmacophore properties in a molecule.

An example for running PharmacophoreMapper:


 String pmConfigFileName; // path to the pharmacophore XML config file
 String stConfigFileName; // path to the molecule standardization config file
 ...
 Standardizer st = new Standardizer(new File(stConfigFileName));
 PMapper pm = new PMapper(new File(pmConfigFileName), st);
 PSymbols symbols = pm.getSymbols();
 ...
 while ( ...  there are more molecules ... ) {
     // getting the next molecule from file or database
     Molecule target = ... ;
     // get the feature ID -> atom index BitSet HashMap
     PMap pmap = pm.createFeatureMap(target);
     // get the feature symbol string
     String result = pmap.toString(symbols);
     System.out.println(result);
 }
 
Since:
JChem 2.0
  • Field Details

    • DEFAULT_TAG_NAME

      public static final String DEFAULT_TAG_NAME
      Default SDFile tag to store the Pharmacophore Map.
      See Also:
  • Constructor Details

    • PMapper

      public PMapper(File config) throws IOException, chemaxon.nfunk.jep.ParseException
      Constructor. Sets the pharmacophore configuration.
      Parameters:
      config - is the XML config file
      Throws:
      IOException - on IO error in molecule input
      chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error
    • PMapper

      public PMapper(File config, Standardizer standardizer) throws IOException, chemaxon.nfunk.jep.ParseException
      Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.
      Parameters:
      config - is the XML config file
      standardizer - is the Standardizer object (may be null)
      Throws:
      IOException - on IO error in molecule input
      chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error
      IllegalArgumentException - on standardizer configuration error
    • PMapper

      public PMapper(String config) throws IOException, chemaxon.nfunk.jep.ParseException
      Constructor. Sets the pharmacophore configuration.
      Parameters:
      config - is the XML config string
      Throws:
      IOException - on IO error in molecule input
      chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error
      IllegalArgumentException - on standardizer configuration error
    • PMapper

      public PMapper(String config, Standardizer standardizer) throws IOException, chemaxon.nfunk.jep.ParseException
      Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.
      Parameters:
      config - is the XML config string
      standardizer - is the Standardizer object (may be null)
      Throws:
      IOException - on IO error in molecule input
      chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error
      IllegalArgumentException - on standardizer configuration error
    • PMapper

      public PMapper(org.dom4j.Element config, String dir) throws IOException, chemaxon.nfunk.jep.ParseException
      Constructor. Sets the pharmacophore configuration.
      Parameters:
      config - is the XML config root node
      dir - is the root directory
      Throws:
      IOException - on IO error in molecule input
      chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error
    • PMapper

      public PMapper(org.dom4j.Element config) throws IOException, chemaxon.nfunk.jep.ParseException
      Constructor. Sets the pharmacophore configuration.
      Parameters:
      config - is the XML config root node
      Throws:
      IOException - on IO error in molecule input
      chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error
    • PMapper

      public PMapper(org.dom4j.Element config, Standardizer standardizer, String dir) throws IOException, chemaxon.nfunk.jep.ParseException
      Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.
      Parameters:
      config - is the XML config root node
      standardizer - is the Standardizer object (may be null)
      dir - is the root directory
      Throws:
      IOException - on IO error in molecule input
      chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error
    • PMapper

      public PMapper(org.dom4j.Element config, Standardizer standardizer) throws IOException, chemaxon.nfunk.jep.ParseException
      Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.
      Parameters:
      config - is the XML config root node
      standardizer - is the Standardizer object (may be null)
      Throws:
      IOException - on IO error in molecule input
      chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error
    • PMapper

      public PMapper(org.dom4j.Element config, org.dom4j.Element stconfig, String dir) throws IOException, chemaxon.nfunk.jep.ParseException
      Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.
      Parameters:
      config - is the XML config root node
      stconfig - is the standardizer config root node
      dir - is the root directory
      Throws:
      IOException - on IO error in molecule input
      chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error
      IllegalArgumentException - if the standardizer object creation fails
    • PMapper

      public PMapper(org.dom4j.Element config, org.dom4j.Element stconfig) throws IOException, chemaxon.nfunk.jep.ParseException
      Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.
      Parameters:
      config - is the XML config root node
      stconfig - is the standardizer config root node
      Throws:
      IOException - on IO error in molecule input
      chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error
      IllegalArgumentException - if the standardizer object creation fails
  • Method Details

    • setVerbose

      public void setVerbose(boolean verbose)
      Sets verbose output.
      Parameters:
      verbose - is true if verbose output
    • getMolConstant

      public Molecule getMolConstant(String id)
      Returns the molecule constant corresponding to the given ID.
      Parameters:
      id - is the molecule ID
      Returns:
      the molecule constant with the given ID or null if no such molecule
    • getSymbols

      public PSymbols getSymbols()
      Returns the symbol storing object.
      Returns:
      the symbol storing object
    • getID

      public String getID(String symbol)
      Returns the ID corresponding to the given symbol.
      Parameters:
      symbol - is the feature symbol
      Returns:
      the ID corresponding to the given symbol
    • createFeatureMap

      public PMap createFeatureMap(Molecule target) throws SearchException, chemaxon.nfunk.jep.ParseException, LicenseException
      Creates the feature ID -> atom index BitSet HashMap for the given target molecule. The i-th bit in the BitSet is 1 if the i-th atom has the feature, 0 otherwise.
      Parameters:
      target - is the target molecule
      Returns:
      the feature ID -> atom index BitSet HashMap
      Throws:
      SearchException - if the standardization fails
      chemaxon.nfunk.jep.ParseException - if the feature expression cannot be evaluated
      LicenseException - if no license found
    • setLicenseEnvironment

      public void setLicenseEnvironment(String env)
      Specified by:
      setLicenseEnvironment in interface chemaxon.license.Licensable
    • isLicensed

      public boolean isLicensed()
      Specified by:
      isLicensed in interface chemaxon.license.Licensable
    • main

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JAN_01_2025) public static void main(String[] args) throws Exception
      Deprecated, for removal: This API element is subject to removal in a future version.
      This main method will be removed, CLI interfaces should not be used directly from Java code.
      The command line version entry point. Parameter parsing, initialization then start.
      Parameters:
      args - the command line parameters
      Throws:
      Exception