Package chemaxon.alignment

Class AlignmentBase

java.lang.Object
chemaxon.alignment.AlignmentBase
All Implemented Interfaces:
Licensable
Direct Known Subclasses:
Alignment, AlignOnPairedAtoms, MinMaxDistance
@PublicApi public sealed class AlignmentBase extends Object implements Licensable permits Alignment, AlignOnPairedAtoms, MinMaxDistance
Base class for the alignment algorithms. It contains the common data structures and methods. It is not intended to be used directly by the users.

  • Method Details

    • setProperty

      public void setProperty(AlignmentProperties props)
      Sets the properties for the alignment. The properties are used to configure the alignment algorithm. The properties are set to the factory and the factory is used to create the alignment molecules.
      Parameters:
      props - the properties to set

    • getMaxGradLimit

      public double getMaxGradLimit()
      Returns the maximum gradient component limit used for the optimization.
      Returns:
      the maximum gradient component limit

    • getNodeType

      public AlignmentProperties.NodeType getNodeType()
      Returns the node type used for the alignment.
      Returns:
      the node type

    • getNodeColor

      public NodeColor getNodeColor()
      Returns the node color used for the alignment.
      Returns:
      the node color

    • setFlexibleRingSize

      public void setFlexibleRingSize(int s)
      Sets the maximum gradient component limit used for the optimization.
      Parameters:
      s - the maximum gradient component limit

    • setFlexibleRingRotatableBondCount

      public void setFlexibleRingRotatableBondCount(int b)
      Sets the maximum gradient component limit used for the optimization.
      Parameters:
      b - the maximum gradient component limit

    • getMolecules

      public Collection<AlignmentMolecule> getMolecules()
      Returns the collection of alignment molecules.
      Returns:
      the collection of alignment molecules

    • isLicensed

      public boolean isLicensed()
      Description copied from interface: Licensable
      Checks if the required license is available for using this class or product.
      Specified by:
      isLicensed in interface Licensable
      Returns:
      true if this software component is correctly licensed

    • setLicenseEnvironment

      public void setLicenseEnvironment(String env)
      Description copied from interface: Licensable
      Sets the current license environment identifier. For internal use only!
      Specified by:
      setLicenseEnvironment in interface Licensable
      Parameters:
      env - license environment. It is string identifier of a certain integration environment.

    • getStepLimit

      public int getStepLimit()

    • setStepLimit

      public void setStepLimit(int stepLimit)

    • getTimeLimit

      public int getTimeLimit()

    • setNodeType

      public void setNodeType(AlignmentProperties.NodeType t)

    • setTimeLimit

      public void setTimeLimit(int timeLimit)
      Sets the maximum time used for the alignment. If reached returns the partly aligned structures.
      Parameters:
      timeLimit - time limit in millisecond. if -1 then disabled.

    • setProgressMonitor

      public void setProgressMonitor(ProgressMonitor progressMonitor)
      Sets the progress monitor for the alignment. The progress monitor is used to report the progress of the alignment.
      Parameters:
      progressMonitor - the progress monitor to set

    • setProximity

      public void setProximity(AlignmentProperties.ProximityPotentialType pot)
      Sets the proximity potential type used for the alignment.
      Parameters:
      pot - the proximity potential type to set