AbbreviatedGroupChecker (Marvin API documentation (c) 1998-2020 ChemAxon Ltd.)

java.lang.Object
- chemaxon.checkers.AbstractStructureChecker
- - chemaxon.checkers.AbbreviatedGroupChecker

All Implemented Interfaces:

StructureChecker, chemaxon.license.Licensable, java.beans.PropertyChangeListener, java.lang.Cloneable, java.util.EventListener
```
@PublicAPI
public class AbbreviatedGroupChecker
extends AbstractStructureChecker
```
A descendant of AbstractStructureChecker detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.

Since:

Marvin 5.3

Version:

5.7

Author:

Attila Szabo

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`PROPERTY_KEY_CONTRACTED` This public constant `String` represents the name of the configuration file property which is responsible for searching contracted abbreviated groups
`static java.lang.String`	`PROPERTY_KEY_EXCLUDED` This public constant `String` represents the name of the property which is responsible for the list of excluded groups
`static java.lang.String`	`PROPERTY_KEY_EXPANDED` This public constant `String` represents the name of the configuration file property which is responsible for searching expanded abbreviated groups
`static java.lang.String`	`PROPERTY_KEY_SEARCH_CONTRACTED` This public constant `String` represents the name of the property which is responsible for searching contracted abbreviated groups
`static java.lang.String`	`PROPERTY_KEY_SEARCH_EXCLUDED` This public constant `String` represents the name of the property which is responsible for the list of excluded groups
`static java.lang.String`	`PROPERTY_KEY_SEARCH_EXPANDED` This public constant `String` represents the name of the property which is responsible for searching expanded abbreviated groups

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
`AbbreviatedGroupChecker()` Default constructor.
`AbbreviatedGroupChecker(java.util.Map<java.lang.String,java.lang.String> params)` Parameterized constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected StructureCheckerResult`	`check1(Molecule molecule)` This method contains the current checking mechanism.
`protected void`	`convertResult(Molecule originalMolecule, Molecule expandedMolecule, StructureCheckerResult result, java.util.Map<MolAtom,MolAtom> atomMap, java.util.Map<MolBond,MolBond> bondMap)` This implementation does nothing.
`boolean`	`equals(java.lang.Object obj)`
`protected Molecule`	`expandMolecule(Molecule molecule, java.util.Map<MolAtom,MolAtom> atomMap, java.util.Map<MolBond,MolBond> bondMap)` This implementation does nothing.
`chemaxon.checkers.util.AtomLabels`	`getExcluded()` Gets the excluded abbreviations
`int`	`hashCode()`
`boolean`	`isSearchContracted()` Returns if the checker is searching for contracted SGroups or not
`boolean`	`isSearchExpanded()` Returns if the checker is searching for expanded SGroups or not
`boolean`	`isValid()` Excluded object is initialized.
`void`	`setExcluded(chemaxon.checkers.util.AtomLabels excluded)` Sets the abbreviations to be excluded
`void`	`setSearchContracted(boolean searchContracted)` Sets the checker should search for contracted abbreviated groups or not
`void`	`setSearchExpanded(boolean searchExpanded)` Sets the checker should search for expanded abbreviated groups or not

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

- Field Detail
  - PROPERTY_KEY_EXPANDED
```
public static final java.lang.String PROPERTY_KEY_EXPANDED
```
    This public constant String represents the name of the configuration file property which is responsible for searching expanded abbreviated groups
    
    Since:
    
    5.4
    
    See Also:
    
    Constant Field Values
  - PROPERTY_KEY_CONTRACTED
```
public static final java.lang.String PROPERTY_KEY_CONTRACTED
```
    This public constant String represents the name of the configuration file property which is responsible for searching contracted abbreviated groups
    
    Since:
    
    5.4
    
    See Also:
    
    Constant Field Values
  - PROPERTY_KEY_SEARCH_CONTRACTED
```
public static final java.lang.String PROPERTY_KEY_SEARCH_CONTRACTED
```
    This public constant String represents the name of the property which is responsible for searching contracted abbreviated groups
    
    Since:
    
    5.7
    
    See Also:
    
    Constant Field Values
  - PROPERTY_KEY_SEARCH_EXPANDED
```
public static final java.lang.String PROPERTY_KEY_SEARCH_EXPANDED
```
    This public constant String represents the name of the property which is responsible for searching expanded abbreviated groups
    
    Since:
    
    5.7
    
    See Also:
    
    Constant Field Values
  - PROPERTY_KEY_EXCLUDED
```
public static final java.lang.String PROPERTY_KEY_EXCLUDED
```
    This public constant String represents the name of the property which is responsible for the list of excluded groups
    
    Since:
    
    5.12
    
    See Also:
    
    Constant Field Values
  - PROPERTY_KEY_SEARCH_EXCLUDED
```
public static final java.lang.String PROPERTY_KEY_SEARCH_EXCLUDED
```
    This public constant String represents the name of the property which is responsible for the list of excluded groups
    
    Since:
    
    5.12
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - AbbreviatedGroupChecker
```
public AbbreviatedGroupChecker()
```
    Default constructor. Search for both expanded and contracted abbreviated groups.
  - AbbreviatedGroupChecker
```
public AbbreviatedGroupChecker(java.util.Map<java.lang.String,java.lang.String> params)
```
    Parameterized constructor. If "expanded" parameter given, and its value is "true" expanded abbreviated groups will be detected during the checking mechanism. Otherwise no expanded group will be found. If "contracted" parameter given, and its value is "true" contracted abbreviated groups will be detected during the checking mechanism. Otherwise no contracted group will be found.
    
    Parameters:
    
    params - a Map instance which contains String pairs. Key is the name of the parameter.
- Method Detail
  - isSearchContracted
```
public boolean isSearchContracted()
```
    Returns if the checker is searching for contracted SGroups or not
    
    Returns:
    
    if the checker is searching for contracted SGroups or not
  - isSearchExpanded
```
public boolean isSearchExpanded()
```
    Returns if the checker is searching for expanded SGroups or not
    
    Returns:
    
    if the checker is searching for expanded SGroups or not
  - expandMolecule
```
protected Molecule expandMolecule(Molecule molecule,
                                  java.util.Map<MolAtom,MolAtom> atomMap,
                                  java.util.Map<MolBond,MolBond> bondMap)
```
    This implementation does nothing.
    
    Overrides:
    
    expandMolecule in class AbstractStructureChecker
    
    Parameters:
    
    molecule - the molecule to check
    
    Returns:
    
    the molecule
  - convertResult
```
protected void convertResult(Molecule originalMolecule,
                             Molecule expandedMolecule,
                             StructureCheckerResult result,
                             java.util.Map<MolAtom,MolAtom> atomMap,
                             java.util.Map<MolBond,MolBond> bondMap)
```
    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
  - 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
  - equals
```
public boolean equals(java.lang.Object obj)
```
    Overrides:
    
    equals in class AbstractStructureChecker
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class AbstractStructureChecker
  - setSearchExpanded
```
public void setSearchExpanded(boolean searchExpanded)
```
    Sets the checker should search for expanded abbreviated groups or not
    
    Parameters:
    
    searchExpanded - is a boolean property. If true expanded abbreviated groups will be checked during the checking mechanism.
    
    Since:
    
    5.4
  - setSearchContracted
```
public void setSearchContracted(boolean searchContracted)
```
    Sets the checker should search for contracted abbreviated groups or not
    
    Parameters:
    
    searchContracted - is a boolean property. If true contracted abbreviated groups will be checked during the checking mechanism.
    
    Since:
    
    5.4
  - setExcluded
```
public void setExcluded(chemaxon.checkers.util.AtomLabels excluded)
```
    Sets the abbreviations to be excluded
    
    Parameters:
    
    excluded - the abbreviations to be excluded
  - isValid
```
public boolean isValid()
```
    Excluded object is initialized. If it is null, the parse was not successful.
    
    Specified by:
    
    isValid in interface StructureChecker
    
    Overrides:
    
    isValid in class AbstractStructureChecker
    
    Returns:
    
    true if the checker's configuration is valid, false otherwise
  - getExcluded
```
public chemaxon.checkers.util.AtomLabels getExcluded()
```
    Gets the excluded abbreviations
    
    Returns:
    
    the excluded abbreviations

Class AbbreviatedGroupChecker

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_EXPANDED

PROPERTY_KEY_CONTRACTED

PROPERTY_KEY_SEARCH_CONTRACTED

PROPERTY_KEY_SEARCH_EXPANDED

PROPERTY_KEY_EXCLUDED

PROPERTY_KEY_SEARCH_EXCLUDED

Constructor Detail

AbbreviatedGroupChecker

AbbreviatedGroupChecker

Method Detail

isSearchContracted

isSearchExpanded

expandMolecule

convertResult

check1

equals

hashCode

setSearchExpanded

setSearchContracted

setExcluded

isValid

getExcluded