RgroupReferenceErrorChecker (Marvin API documentation (c) 1998-2014 ChemAxon Ltd.)

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`PROPERTY_KEY_SEARCH_CIRCULAR_REFERENCE` Deprecated. This private constant `String` represents the name of the property which is responsible for searching self references in the molecule
`static String`	`PROPERTY_KEY_SEARCH_MISSING_RATOM` Deprecated.
`static String`	`PROPERTY_KEY_SEARCH_MISSING_RGROUP` Deprecated. This private constant `String` represents the name of the property which is responsible for searching missing rgroups in the molecule
`static String`	`PROPERTY_KEY_SEARCH_SELF_REFERENCE` Deprecated.
`static String`	`PROPERTY_KEY_SEARCH_UNUSED_RGROUP` Deprecated. This private constant `String` represents the name of the property which is responsible for searching unused rgroups in the molecule

Fields inherited from class chemaxon.checkers.AbstractStructureChecker
errorType, propertyChangeSupport

Fields inherited from interface chemaxon.checkers.StructureChecker
PROPERTY_KEY_VALID

Constructor Summary

Constructors
Constructor and Description
`RgroupReferenceErrorChecker()` Deprecated. Creates a new RgroupReferenceErrorChecker instance checking all R-group errors by default.
`RgroupReferenceErrorChecker(Map<String,String> params)` Deprecated. Creates a new RgroupRefereceErrorChecker instance reading checking options from the params argument.

Method Summary

Methods
Modifier and Type	Method and Description
`protected StructureCheckerResult`	`check1(Molecule molecule)` Deprecated. This method contains the current checking mechanism.
`protected void`	`convertResult(Molecule originalMolecule, Molecule expandedMolecule, StructureCheckerResult result, Map<MolAtom,MolAtom> atomMap, Map<MolBond,MolBond> bondMap)` Deprecated. This implementation does nothing.
`protected Molecule`	`expandMolecule(Molecule molecule, Map<MolAtom,MolAtom> atomMap, Map<MolBond,MolBond> bondMap)` Deprecated. This implementation does nothing.
`boolean`	`isSearchCircularReference()` Deprecated. Sets the option determining if the checker detects nested R-atoms referencing to their own R-groups directly or in circularly or not.
`boolean`	`isSearchMissingRatom()` Deprecated.
`boolean`	`isSearchMissingRgroup()` Deprecated. Gets the option determining if the checker detects missing R-groups or not.
`boolean`	`isSearchSelfReference()` Deprecated.
`boolean`	`isSearchUnusedRgroup()` Deprecated. Gets the option determining if the checker detects unused R-groups or not.
`void`	`setSearchCircularReference(boolean value)` Deprecated. Sets the option determining if the checker detects nested R-atoms referencing to their own R-groups directly or in circularly or not.
`void`	`setSearchMissingRatom(boolean value)` Deprecated.
`void`	`setSearchMissingRgroup(boolean value)` Deprecated. Sets the option determining if the checker detects missing R-groups or not.
`void`	`setSearchSelfReference(boolean value)` Deprecated.
`void`	`setSearchUnusedRgroup(boolean value)` Deprecated. Sets the option determining if the checker detects missing R-atoms or not.

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - PROPERTY_KEY_SEARCH_MISSING_RATOM
```
@Deprecated
public static final String PROPERTY_KEY_SEARCH_MISSING_RATOM
```
    Deprecated.
    
    This private constant String represents the name of the property which is responsible for searching missing ratoms in the molecule Use PROPERTY_KEY_SEARCH_UNUSED_RGROUP instead
    
    Since:
    
    5.7
    
    See Also:
    Constant Field Values
  - PROPERTY_KEY_SEARCH_UNUSED_RGROUP
```
public static final String PROPERTY_KEY_SEARCH_UNUSED_RGROUP
```
    Deprecated.
    
    This private constant String represents the name of the property which is responsible for searching unused rgroups in the molecule
    
    Since:
    
    5.10
    
    See Also:
    Constant Field Values
  - PROPERTY_KEY_SEARCH_MISSING_RGROUP
```
public static final String PROPERTY_KEY_SEARCH_MISSING_RGROUP
```
    Deprecated.
    
    This private constant String represents the name of the property which is responsible for searching missing rgroups in the molecule
    
    Since:
    
    5.7
    
    See Also:
    Constant Field Values
  - PROPERTY_KEY_SEARCH_SELF_REFERENCE
```
@Deprecated
public static final String PROPERTY_KEY_SEARCH_SELF_REFERENCE
```
    Deprecated.
    
    This private constant String represents the name of the property which is responsible for searching self references in the molecule Use PROPERTY_KEY_SEARCH_CIRCULAR_REFERENCE instead
    
    Since:
    
    5.7
    
    See Also:
    Constant Field Values
  - PROPERTY_KEY_SEARCH_CIRCULAR_REFERENCE
```
public static final String PROPERTY_KEY_SEARCH_CIRCULAR_REFERENCE
```
    Deprecated.
    
    This private constant String represents the name of the property which is responsible for searching self references in the molecule
    
    Since:
    
    5.10
    
    See Also:
    Constant Field Values
- Constructor Detail
  - RgroupReferenceErrorChecker
```
public RgroupReferenceErrorChecker()
```
    Deprecated.
    
    Creates a new RgroupReferenceErrorChecker instance checking all R-group errors by default.
  - RgroupReferenceErrorChecker
```
public RgroupReferenceErrorChecker(Map<String,String> params)
```
    Deprecated.
    
    Creates a new RgroupRefereceErrorChecker 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 Detail
  - check1
```
protected StructureCheckerResult check1(Molecule molecule)
```
    Deprecated.
    
    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
  - isSearchMissingRatom
```
@Deprecated
public boolean isSearchMissingRatom()
```
    Deprecated.
    
    Gets the option determining if the checker detects missing R-atoms or not. Use isSearchUnusedRgroup instead
    
    Returns:
    true if the missing R-atoms are detected
  - isSearchUnusedRgroup
```
public boolean isSearchUnusedRgroup()
```
    Deprecated.
    
    Gets the option determining if the checker detects unused R-groups or not.
    
    Returns:
    true if the missing R-atoms are detected
  - isSearchMissingRgroup
```
public boolean isSearchMissingRgroup()
```
    Deprecated.
    
    Gets the option determining if the checker detects missing R-groups or not.
    
    Returns:
    true if the missing R-groups are detected
  - isSearchSelfReference
```
@Deprecated
public boolean isSearchSelfReference()
```
    Deprecated.
    
    Sets the option determining if the checker detects nested R-atoms referencing to their own R-groups directly or in circularly or not. Use isSearchCircularReference instead
    
    Returns:
    true if the self-referencing R-groups are detected
  - isSearchCircularReference
```
public boolean isSearchCircularReference()
```
    Deprecated.
    
    Sets the option determining if the checker detects nested R-atoms referencing to their own R-groups directly or in circularly or not.
    
    Returns:
    true if the self-referencing R-groups are detected
  - setSearchMissingRatom
```
@Deprecated
public void setSearchMissingRatom(boolean value)
```
    Deprecated.
    
    Sets the option determining if the checker detects missing R-atoms or not. Use setSearchUnusedRgroup method instead.
    
    Parameters:
    value - if true, missing R-atoms are detected
  - setSearchUnusedRgroup
```
public void setSearchUnusedRgroup(boolean value)
```
    Deprecated.
    
    Sets the option determining if the checker detects missing R-atoms or not.
    
    Parameters:
    value - if true, missing R-atoms are detected
  - setSearchMissingRgroup
```
public void setSearchMissingRgroup(boolean value)
```
    Deprecated.
    
    Sets the option determining if the checker detects missing R-groups or not.
    
    Parameters:
    value - if true, missing R-groups are detected
  - setSearchSelfReference
```
@Deprecated
public void setSearchSelfReference(boolean value)
```
    Deprecated.
    
    Sets the option determining if the checker detects nested R-atoms referencing to their own R-groups directly or in circularly or not. Use setSearchCircularReference instead
    
    Parameters:
    value - if true, self-referencing R-atoms are detected
  - setSearchCircularReference
```
public void setSearchCircularReference(boolean value)
```
    Deprecated.
    
    Sets the option determining if the checker detects nested R-atoms referencing to their own R-groups directly or in circularly or not.
    
    Parameters:
    value - if true, self-referencing R-atoms are detected
  - convertResult
```
protected void convertResult(Molecule originalMolecule,
                 Molecule expandedMolecule,
                 StructureCheckerResult result,
                 Map<MolAtom,MolAtom> atomMap,
                 Map<MolBond,MolBond> bondMap)
```
    Deprecated.
    
    This implementation does nothing.
    
    Overrides:
    
    convertResult in class AbstractStructureChecker
    
    Parameters:
    originalMolecule - the original molecule
    expandedMolecule - the cloned then expanded molecule
    result - the structure checker result on cloned molecule
    atomMap - the mapping of cloned molecule and original molecule atoms
    bondMap - the mapping of cloned molecule and original molecule bonds
  - expandMolecule
```
protected Molecule expandMolecule(Molecule molecule,
                      Map<MolAtom,MolAtom> atomMap,
                      Map<MolBond,MolBond> bondMap)
```
    Deprecated.
    
    This implementation does nothing.
    
    Overrides:
    
    expandMolecule in class AbstractStructureChecker
    
    Parameters:
    molecule - the molecule to check
    
    Returns:
    the molecule

Class RgroupReferenceErrorChecker

Field Summary

Fields inherited from class chemaxon.checkers.AbstractStructureChecker

Fields inherited from interface chemaxon.checkers.StructureChecker

Constructor Summary

Method Summary

Methods inherited from class chemaxon.checkers.AbstractStructureChecker

Methods inherited from class java.lang.Object

Field Detail

PROPERTY_KEY_SEARCH_MISSING_RATOM

PROPERTY_KEY_SEARCH_UNUSED_RGROUP

PROPERTY_KEY_SEARCH_MISSING_RGROUP

PROPERTY_KEY_SEARCH_SELF_REFERENCE

PROPERTY_KEY_SEARCH_CIRCULAR_REFERENCE

Constructor Detail

RgroupReferenceErrorChecker

RgroupReferenceErrorChecker

Method Detail

check1

isSearchMissingRatom

isSearchUnusedRgroup

isSearchMissingRgroup

isSearchSelfReference

isSearchCircularReference

setSearchMissingRatom

setSearchUnusedRgroup

setSearchMissingRgroup

setSearchSelfReference

setSearchCircularReference

convertResult

expandMolecule