Package chemaxon.pharmacophore
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 Summary
Fields Modifier and Type Field Description static String
DEFAULT_TAG_NAME
Default SDFile tag to store the Pharmacophore Map.
-
Constructor Summary
Constructors Constructor Description PMapper(File config)
Constructor.PMapper(File config, Standardizer standardizer)
Constructor.PMapper(String config)
Constructor.PMapper(String config, Standardizer standardizer)
Constructor.PMapper(org.dom4j.Element config)
Constructor.PMapper(org.dom4j.Element config, Standardizer standardizer)
Constructor.PMapper(org.dom4j.Element config, Standardizer standardizer, String dir)
Constructor.PMapper(org.dom4j.Element config, String dir)
Constructor.PMapper(org.dom4j.Element config, org.dom4j.Element stconfig)
Constructor.PMapper(org.dom4j.Element config, org.dom4j.Element stconfig, String dir)
Constructor.
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description PMap
createFeatureMap(Molecule target)
Creates the feature ID -> atom index BitSet HashMap for the given target molecule.String
getID(String symbol)
Returns the ID corresponding to the given symbol.Molecule
getMolConstant(String id)
Returns the molecule constant corresponding to the given ID.PSymbols
getSymbols()
Returns the symbol storing object.boolean
isLicensed()
static void
main(String[] args)
The command line version entry point.void
setLicenseEnvironment(String env)
void
setVerbose(boolean verbose)
Sets verbose output.
-
-
-
Field Detail
-
DEFAULT_TAG_NAME
public static final String DEFAULT_TAG_NAME
Default SDFile tag to store the Pharmacophore Map.- See Also:
- Constant Field Values
-
-
Constructor Detail
-
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 inputchemaxon.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 filestandardizer
- is the Standardizer object (may be null)- Throws:
IOException
- on IO error in molecule inputchemaxon.nfunk.jep.ParseException
- on DOM parse error or configuration errorIllegalArgumentException
- 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 inputchemaxon.nfunk.jep.ParseException
- on DOM parse error or configuration errorIllegalArgumentException
- 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 stringstandardizer
- is the Standardizer object (may be null)- Throws:
IOException
- on IO error in molecule inputchemaxon.nfunk.jep.ParseException
- on DOM parse error or configuration errorIllegalArgumentException
- 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 nodedir
- is the root directory- Throws:
IOException
- on IO error in molecule inputchemaxon.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 inputchemaxon.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 nodestandardizer
- is the Standardizer object (may be null)dir
- is the root directory- Throws:
IOException
- on IO error in molecule inputchemaxon.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 nodestandardizer
- is the Standardizer object (may be null)- Throws:
IOException
- on IO error in molecule inputchemaxon.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 nodestconfig
- is the standardizer config root nodedir
- is the root directory- Throws:
IOException
- on IO error in molecule inputchemaxon.nfunk.jep.ParseException
- on DOM parse error or configuration errorIllegalArgumentException
- 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 nodestconfig
- is the standardizer config root node- Throws:
IOException
- on IO error in molecule inputchemaxon.nfunk.jep.ParseException
- on DOM parse error or configuration errorIllegalArgumentException
- if the standardizer object creation fails
-
-
Method Detail
-
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, chemaxon.license.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 failschemaxon.nfunk.jep.ParseException
- if the feature expression cannot be evaluatedchemaxon.license.LicenseException
- if no license found
-
setLicenseEnvironment
public void setLicenseEnvironment(String env)
- Specified by:
setLicenseEnvironment
in interfacechemaxon.license.Licensable
-
isLicensed
public boolean isLicensed()
- Specified by:
isLicensed
in interfacechemaxon.license.Licensable
-
-