chemaxon.standardizer.advancedactions

Class GroupDefinition

java.lang.Object

chemaxon.standardizer.advancedactions.GroupDefinition

All Implemented Interfaces:

java.lang.Cloneable, java.lang.Comparable<GroupDefinition>

@PublicAPI
public class GroupDefinition
extends java.lang.Object
implements java.lang.Cloneable, java.lang.Comparable<GroupDefinition>

Pattern of a group. Consists of an abbreviation as a text and a definition as a molecule.

Since:

5.7

Version:

5.11

Author:

Imre Barna

Constructor Summary

Constructors

Constructor and Description
GroupDefinition() Creates an empty group pattern.
GroupDefinition(java.lang.String abbreviation, Molecule original) Creates a new group pattern.

Method Summary

Modifier and Type	Method and Description
GroupDefinition	clone()
int	compareTo(GroupDefinition o)
boolean	equals(java.lang.Object obj)
java.lang.String	getAbbreviation() Gets the abbreviation of the group.
int	getAttachCount(java.lang.Integer index) Gets the attachment point count for the atom specified by the index
java.util.Collection<java.lang.Integer>	getAttachmentPointOrders(int atomIndex) Returns the attachment point orders of the atom specified by atomIndex.
java.util.List<java.lang.Integer>	getConnectionAtoms() Gets the indexes of atoms connection to any atoms
Molecule	getGroup() Gets the definition of the group.
static java.util.List<GroupDefinition>	getGroupsOf(java.lang.String text, java.util.List<GroupDefinition> groupDefinition) Gets the group from a list of group definitions, based on the abbreviation.
Molecule	getOriginal() Gets the original molecule of the group.
int	hashCode()
boolean	isAminoAcid() Gets whether the group represents an amino-acid
void	setAbbreviation(java.lang.String abbreviation) Sets the abbreviation of the group.
void	setAminoAcid(boolean aminoAcid) Sets whether the group represents an amino-acid
void	setOriginal(Molecule original) Sets the original molecule of the group.
java.lang.String	toString()

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

GroupDefinition

public GroupDefinition()

Creates an empty group pattern.

GroupDefinition

public GroupDefinition(java.lang.String abbreviation,
                       Molecule original)

Creates a new group pattern.

Parameters:

abbreviation - The abbreviation of the group.

original - the original molecule of the group definition

Method Detail

getAbbreviation

public java.lang.String getAbbreviation()

Gets the abbreviation of the group.

Returns:

The abbreviation of the group.

setAbbreviation

public void setAbbreviation(java.lang.String abbreviation)

Sets the abbreviation of the group.

Parameters:

abbreviation - The abbreviation of the group.

getGroup

public Molecule getGroup()

Gets the definition of the group.

Returns:

The definition of the group.

getOriginal

public Molecule getOriginal()

Gets the original molecule of the group.

Returns:

The original molecule of the group.

setOriginal

public void setOriginal(Molecule original)

Sets the original molecule of the group.

Parameters:

original - The original molecule of the group.

getGroupsOf

public static java.util.List<GroupDefinition> getGroupsOf(java.lang.String text,
                                                          java.util.List<GroupDefinition> groupDefinition)

Gets the group from a list of group definitions, based on the abbreviation.

Parameters:

text - The abbreviation of the group.

groupDefinition - The list of group definitions

Returns:

The group molecule. (null if not found)

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

getConnectionAtoms

public java.util.List<java.lang.Integer> getConnectionAtoms()

Gets the indexes of atoms connection to any atoms

Returns:

the indexes of atoms connection to any atoms

getAttachCount

public int getAttachCount(java.lang.Integer index)

Gets the attachment point count for the atom specified by the index

Parameters:

index -

Returns:

the attachment point count for the atom specified by the index

getAttachmentPointOrders

public java.util.Collection<java.lang.Integer> getAttachmentPointOrders(int atomIndex)

Returns the attachment point orders of the atom specified by atomIndex.

clone

public GroupDefinition clone()
                      throws java.lang.CloneNotSupportedException

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

compareTo

public int compareTo(GroupDefinition o)

Specified by:

compareTo in interface java.lang.Comparable<GroupDefinition>

setAminoAcid

public void setAminoAcid(boolean aminoAcid)

Sets whether the group represents an amino-acid

Parameters:

aminoAcid - whether the group represents an amino-acid

isAminoAcid

public boolean isAminoAcid()

Gets whether the group represents an amino-acid

Returns:

whether the group represents an amino-acid