Class RatomChecker

All Implemented Interfaces:
StructureChecker, chemaxon.license.Licensable, PropertyChangeListener, Cloneable, EventListener

@PublicApi public class RatomChecker extends AbstractStructureChecker
A descendant of AbstractStructureChecker detecting R-atoms.
Since:
Marvin 5.7
  • Field Details

    • PROPERTY_KEY_SEARCH_ALL

      public static final String PROPERTY_KEY_SEARCH_ALL
      This constant String represents the name of the property which is responsible for searching all ratoms in the molecule
      Since:
      5.7
      See Also:
    • PROPERTY_KEY_SEARCH_DISCONNECTED

      public static final String PROPERTY_KEY_SEARCH_DISCONNECTED
      This constant String represents the name of the property which is responsible for searching disconnected ratoms in the molecule
      Since:
      5.7
      See Also:
    • PROPERTY_KEY_SEARCH_GENERIC

      public static final String PROPERTY_KEY_SEARCH_GENERIC
      This constant String represents the name of the property which is responsible for searching generic ratoms in the molecule
      Since:
      5.7
      See Also:
    • PROPERTY_KEY_SEARCH_LINKER

      public static final String PROPERTY_KEY_SEARCH_LINKER
      This private constant String represents the name of the property which is responsible for searching linker ratoms in the molecule
      Since:
      5.7
      See Also:
    • PROPERTY_KEY_SEARCH_NESTED

      public static final String PROPERTY_KEY_SEARCH_NESTED
      This private constant String represents the name of the property which is responsible for searching nested ratoms in the molecule
      Since:
      5.7
      See Also:
  • Constructor Details

    • RatomChecker

      public RatomChecker()
      Creates a new anyChecker instance detecting all R-atoms.
    • RatomChecker

      public RatomChecker(Map<String,String> params)
      Creates a new anyChecker instance reading checking options from the params argument.
      Parameters:
      params - a Map instance which contains String pairs. Key is the name of the parameter.
  • Method Details

    • check1

      protected StructureCheckerResult check1(Molecule molecule)
      Description copied from class: AbstractStructureChecker
      This method contains the current checking mechanism.
      Specified by:
      check1 in class AbstractStructureChecker
      Parameters:
      molecule - the Molecule instance to be checked for problems
      Returns:
      a StructureCheckerResult which represents the problem or null if no problem found
    • isSearchAll

      public boolean isSearchAll()
      Gets the option determining if the checker detects all R-atoms or not.
      Returns:
      true if all R-atoms are detected
    • isSearchDisconnected

      public boolean isSearchDisconnected()
      Gets the option determining if the checker detects R-atoms not connected to any other atoms or not.
      Returns:
      true if the nested R-atoms are detected
    • isSearchGeneric

      public boolean isSearchGeneric()
      Gets the option determining if the checker detects R-atoms without identifier numbers or not.
      Returns:
      true if the generic R-atoms are detected
    • isSearchLinker

      public boolean isSearchLinker()
      Gets the option determining if the checker detects R-atoms with more than one connection or not.
      Returns:
      true if the linker R-atoms are detected
    • isSearchNested

      public boolean isSearchNested()
      Gets the option determining if the checker detects R-atoms within R-groups or not.
      Returns:
      true if the nested R-atoms are detected
    • setSearchAll

      public void setSearchAll(boolean value)
      Sets the option determining if the checker detects all R-atoms or not.
      Parameters:
      value - if true, all R-atoms are detected
    • setSearchDisconnected

      public void setSearchDisconnected(boolean value)
      Sets the option determining if the checker detects R-atoms not connected to any other atoms or not.
      Parameters:
      value - if true, disconnected R-atoms are detected
    • setSearchGeneric

      public void setSearchGeneric(boolean value)
      Sets the option determining if the checker detects R-atoms without identifier numbers or not.
      Parameters:
      value - if true, generic R-atoms are detected
    • setSearchLinker

      public void setSearchLinker(boolean value)
      Sets the option determining if the checker detects R-atoms with more than one connection or not.
      Parameters:
      value - if true, linker R-atoms are detected
    • setSearchNested

      public void setSearchNested(boolean value)
      Sets the option determining if the checker detects R-atoms within R-groups or not.
      Parameters:
      value - if true, nested R-atoms are detected