jklustor-all-api-0.0.7-20140619012755 (ChemAxon)


com.chemaxon.descriptors.fingerprints.pf2d
Interface PfGenerator

All Superinterfaces:
DescriptorGenerator<FloatVectorDescriptor>, Serializable

public interface PfGenerator
extends DescriptorGenerator<FloatVectorDescriptor>

Generates 2D pharmacophore fingerprints.

Author:
Laszlo Antal

Method Summary
 PharmacophoreFP generateDescriptor(chemaxon.struc.Molecule m)
          Calculates the associated descriptor for the given Molecule.
 PfComparator getDefaultComparator()
          Gets the default comparator object.
 PfComparator getFloatVectorComparator(FloatVectorMetrics metrics)
          Creates a new comparator instance according to the given metric.
 FloatVectorDescriptor readFromDB(byte[] desc)
          Read fingerprint from database.
 
Methods inherited from interface com.chemaxon.descriptors.common.DescriptorGenerator
fromByteArray, fromString, getBareDescriptor, getGuardObject, getParameters, toByteArray, toString
 

Method Detail

generateDescriptor

PharmacophoreFP generateDescriptor(chemaxon.struc.Molecule m)
Description copied from interface: DescriptorGenerator
Calculates the associated descriptor for the given Molecule.

Note that different descriptors/application scenatios might need different structure standardization. Currently structure standardization is generally not in the scope of the responsibilities of DescriptorGenerator to the possible maximal extent.

Since the returned descriptor might contain additional data (refrence to input Molecule, etc) if it is stored for later compariosn it is recommended to use the bare-only representation returned by DescriptorGenerator.getBareDescriptor(com.chemaxon.descriptors.common.Descriptor).

Specified by:
generateDescriptor in interface DescriptorGenerator<FloatVectorDescriptor>
Parameters:
m - Input molecule
Returns:
The calculated descriptor. If the implementation discriminates between rich and bare types then the rich type is returned, otherwise the bare type. Note that the bare type is always available using DescriptorGenerator.getBareDescriptor(com.chemaxon.descriptors.common.Descriptor) on either the rich or the bare representation.

readFromDB

FloatVectorDescriptor readFromDB(byte[] desc)
Read fingerprint from database.

Parameters:
desc - byte array representation
Returns:
descriptor

getDefaultComparator

PfComparator getDefaultComparator()
Description copied from interface: DescriptorGenerator
Gets the default comparator object.

Specified by:
getDefaultComparator in interface DescriptorGenerator<FloatVectorDescriptor>
Returns:
default comparator

getFloatVectorComparator

PfComparator getFloatVectorComparator(FloatVectorMetrics metrics)
Creates a new comparator instance according to the given metric.

Parameters:
metrics - float vector metric
Returns:
a comparator object

jklustor-all-api-0.0.7-20140619012755 (ChemAxon)