Package chemaxon.standardizer

Class Changes

java.lang.Object

chemaxon.standardizer.Changes

@PublicAPI
public class Changes
extends Object

The change set of the standardization procedure.

Contains a clone of the original molecule, the result molecule and a map of atoms and atom-indexes for each atom of the input molecule. All modifications (added removed and modified) made by the standardization process atoms should be stored here.

The mapping of the indexes can be gathered using the methods newToOld() and oldToNew()

Getting the mapping based on a list of sequential changes on a molecule can be gathered using the methods newToOld(List, Molecule) and newToOld(List, Molecule)

To merge more than one Changes object is possible using append(Changes) method.

Since:

5.11

Constructor Summary

Constructors

Constructor	Description
Changes(Molecule original)	Initializes the changes object.
Changes(Molecule molecule, StandardizerAction action)	Initializes the changes object.
Changes(Molecule original, Molecule result)	Initializes the changes object.

Method Summary

Modifier and Type	Method	Description
void	addAllAtoms(Collection<MolAtom> atoms)	Adds atoms to the "added atom" list.
void	addAllAtoms(Collection<MolAtom> atoms, boolean cleanRelevant)	Adds atoms to the "added atom" list.
void	addAtom(MolAtom atom)	Adds an atom to the "added atom" list.
void	addAtom(MolAtom atom, boolean cleanRelevant)	Adds an atom to the "added atom" list.
void	append(Changes changes)	Appends a set of changes to the already existing changes.
StandardizerAction	getAction()	Gets the base StandardizerAction of the changes
List<MolAtom>	getAddedAtoms()	Gets the list of atoms added during the standardization procedure
List<MolAtom>	getCleanRelevantAtoms()	Gets the list of atoms changed during the standardization procedure, and needs to be cleaned
List<MolAtom>	getModifiedAtoms()	Gets the list of modified atoms during the standardization procedure
Molecule	getOriginal()	Gets the original molecule of the standardization process.
List<MolAtom>	getRemovedAtoms()	Gets the list of atoms removed during the standardization procedure
Molecule	getResult()	Gets the result molecule of the standardization process
boolean	isModified()	Gets whether any modifications were applied on the molecule.
void	modifyAllAtoms(Collection<MolAtom> atoms)	Adds atoms to the "modified atom" list.
void	modifyAllAtoms(Collection<MolAtom> atoms, boolean cleanRelevant)	Adds atoms to the "modified atom" list.
void	modifyAtom(MolAtom atom)	Adds an atom to the "modified atom" list.
void	modifyAtom(MolAtom atom, boolean cleanRelevant)	Adds an atom to the "modified atom" list.
int[]	newToOld()	Returns the new -> old atom index mapping. newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.
static int[]	newToOld(List<Changes> changeList, Molecule target)	Calculates the new -> old atom index mapping based on a list of changes. newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.
int[]	oldToNew()	Returns the old -> new atom index mapping. oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.
static int[]	oldToNew(List<Changes> changeList, Molecule target)	Calculates the old -> new atom index mapping based on a list of changes. oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.
void	removeAllAtoms(Collection<MolAtom> atoms)	Adds atoms to the "removed atom" list
void	removeAllAtoms(Collection<MolAtom> atoms, boolean cleanRelevant)	Adds atoms to the "removed atom" list
void	removeAtom(MolAtom atom)	Adds an atom to the "removed atom" list.
void	removeAtom(MolAtom atom, boolean cleanRelevant)	Adds an atom to the "removed atom" list.
void	setAction(StandardizerAction action)	Sets the base StandardizerAction of the changes
void	setModified(boolean modified)	Sets whether any modifications were applied on the molecule.
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Changes

public Changes(Molecule original)

Initializes the changes object. Default index mapping is based on the original molecule. A clone of the original molecule is created and stored to represent the molecule in the state before standardization process.

Parameters:

original - the original molecule

Changes

public Changes(Molecule original,
               Molecule result)

Initializes the changes object. Default index mapping is based on the original molecule. The clone of the original molecule is stored to represent the molecule in the state before standardization process.

Parameters:

original - the original molecule

result - the result molecule to be standardized. should be different of the original molecule

Changes

public Changes(Molecule molecule,
               StandardizerAction action)

Initializes the changes object. Default index mapping is based on the original molecule. A clone of the original molecule is created and stored to represent the molecule in the state before standardization process.

Parameters:

molecule - the original molecule

action - the action generating the changes

Method Detail

getOriginal

public Molecule getOriginal()

Gets the original molecule of the standardization process. (It is a clone of the original molecule in the state before the standardization)

Returns:

the clone of the original molecule in the state before the standardization process

getResult

public Molecule getResult()

Gets the result molecule of the standardization process

Returns:

the result molecule of the standardization process

getAddedAtoms

public List<MolAtom> getAddedAtoms()

Gets the list of atoms added during the standardization procedure

Returns:

the list of atoms added during the standardization procedure. This list should be not modified, as it affects the changes object!

getRemovedAtoms

public List<MolAtom> getRemovedAtoms()

Gets the list of atoms removed during the standardization procedure

Returns:

the list of atoms removed during the standardization procedure. This list should be not modified, as it affects the changes object!

getModifiedAtoms

public List<MolAtom> getModifiedAtoms()

Gets the list of modified atoms during the standardization procedure

Returns:

the list of modified atoms during the standardization procedure. This list should be not modified, as it affects the changes object!

getCleanRelevantAtoms

public List<MolAtom> getCleanRelevantAtoms()

Gets the list of atoms changed during the standardization procedure, and needs to be cleaned

Returns:

the list of atoms changed during the standardization procedure. This list should be not modified, as it affects the changes object!

addAtom

public void addAtom(MolAtom atom)

Adds an atom to the "added atom" list.

Parameters:

atom - an atom to be added to the "added atom" list.

addAtom

public void addAtom(MolAtom atom,
                    boolean cleanRelevant)

Adds an atom to the "added atom" list.

Parameters:

atom - an atom to be added to the "added atom" list.

cleanRelevant - whether the atom is relevant for cleaning the output molecule

removeAtom

public void removeAtom(MolAtom atom)

Adds an atom to the "removed atom" list.

Parameters:

atom - an atom to be added to the "removed atom" list.

removeAtom

public void removeAtom(MolAtom atom,
                       boolean cleanRelevant)

Adds an atom to the "removed atom" list.

Parameters:

atom - an atom to be added to the "removed atom" list.

cleanRelevant - whether the atom is relevant for cleaning the output molecule

modifyAtom

public void modifyAtom(MolAtom atom)

Adds an atom to the "modified atom" list.

Parameters:

atom - an atom to be added to the "modified atom" list.

modifyAtom

public void modifyAtom(MolAtom atom,
                       boolean cleanRelevant)

Adds an atom to the "modified atom" list.

Parameters:

atom - an atom to be added to the "modified atom" list.

cleanRelevant - whether the atom is relevant for cleaning the output molecule

addAllAtoms

public void addAllAtoms(Collection<MolAtom> atoms)

Adds atoms to the "added atom" list.

Parameters:

atoms - atoms to be added to the "added atom" list.

addAllAtoms

public void addAllAtoms(Collection<MolAtom> atoms,
                        boolean cleanRelevant)

Adds atoms to the "added atom" list.

Parameters:

atoms - atoms to be added to the "added atom" list.

cleanRelevant - whether the atoms are relevant for cleaning the output molecule

removeAllAtoms

public void removeAllAtoms(Collection<MolAtom> atoms)

Adds atoms to the "removed atom" list

Parameters:

atoms - atoms to be added to the "removed atom" list

removeAllAtoms

public void removeAllAtoms(Collection<MolAtom> atoms,
                           boolean cleanRelevant)

Adds atoms to the "removed atom" list

Parameters:

atoms - atoms to be added to the "removed atom" list

cleanRelevant - whether the atoms are relevant for cleaning the output molecule

modifyAllAtoms

public void modifyAllAtoms(Collection<MolAtom> atoms)

Adds atoms to the "modified atom" list.

Parameters:

atoms - atoms to be added to the "modified atom" list.

modifyAllAtoms

public void modifyAllAtoms(Collection<MolAtom> atoms,
                           boolean cleanRelevant)

Adds atoms to the "modified atom" list.

Parameters:

atoms - atoms to be added to the "modified atom" list.

cleanRelevant - whether the atoms are relevant for cleaning the output molecule

setModified

public void setModified(boolean modified)

Sets whether any modifications were applied on the molecule.

Parameters:

modified - whether any modifications were applied on the molecule.

isModified

public boolean isModified()

Gets whether any modifications were applied on the molecule.

Returns:

whether any modifications were applied on the molecule.

oldToNew

public int[] oldToNew()

Returns the old -> new atom index mapping.
oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.

Returns:

the old -> new atom index mapping

newToOld

public int[] newToOld()

Returns the new -> old atom index mapping.
newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.

Returns:

the new -> old atom index mapping

oldToNew

public static int[] oldToNew(List<Changes> changeList,
                             Molecule target)

Calculates the old -> new atom index mapping based on a list of changes.
oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.

Parameters:

changeList - the target list of changes

target - the target molecule (needed in case of no changes)

Returns:

the old -> new atom index mapping based on a list of changes

newToOld

public static int[] newToOld(List<Changes> changeList,
                             Molecule target)

Calculates the new -> old atom index mapping based on a list of changes.
newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.

Parameters:

changeList - the target list of changes

target - the target molecule (needed in case of no changes)

Returns:

the new -> old atom index mapping based on a list of changes

toString

public String toString()

Overrides:

toString in class Object

append

public void append(Changes changes)

Appends a set of changes to the already existing changes. Added / Removed / Modified molecules contained by the parameter are added to this object.

Parameters:

changes - the set of changes to be appended

getAction

public StandardizerAction getAction()

Gets the base StandardizerAction of the changes

Returns:

the base StandardizerAction of the changes

setAction

public void setAction(StandardizerAction action)

Sets the base StandardizerAction of the changes

Parameters:

action - the base StandardizerAction of the changes