com.chemaxon.virtuallib.sc.model.sdf

Class Attachment

java.lang.Object

com.chemaxon.virtuallib.sc.model.sdf.Attachment

All Implemented Interfaces:

Serializable

public class Attachment
extends Object
implements Serializable

Represents an attachment point. This class can describe attachment points for scaffolds as well fragments.

An attachment atom is a MolAtom in a Molecule which denotes rgroup attachment. In case of scaffold definitions it is denoted as Rn, having special atom type: MolAtom.getAtno() is MolAtom.RGROUP and n is returned by MolAtom.getRgroup(). Fragment definitions represent such pseudo atom with atom having alias string Zx returned by MolAtom.getAliasstr().

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
Attachment(int attachmentAtomIndex, int attachedAtomIndex, int attachmentIndex, int bondOrder)

Method Summary

Modifier and Type	Method and Description
static Attachment	addZAttachment(Molecule mol, int attachedAtomIndex, int attachmentIndex, int bondOrder)
void	ensureValidRepresentation(Molecule mol, String prefix) Ensure that structure mapping is consistent.
static Attachment	forFragmentZ(Molecule mol, int attachmentAtomIndex) Create attachment description for a fragment Z atom.
static Attachment	forScaffoldR(Molecule mol, int attachmentAtomIndex) Create attachment description for scaffold's R atom.
int	getAttachedAtomIndex() Attached atom index.
int	getAttachmentAtomIndex() Attachment atom index.
int	getAttachmentIndex() Attachemnt index.
int	getBondOrder() Represented bond order.
static boolean	isRAtom(Molecule mol, int atomindex) Check if a given atom is an R atom.
static boolean	isZAtom(Molecule mol, int atomindex) Check if a given atom has an alias string.
static Attachment	replaceAtomWithR(Molecule mol, int attachmentAtomIndex)
static Attachment	replaceAtomWithR(Molecule mol, int attachmentAtomIndex, int rno) Replace an atom with an Rn atom and return the appropriate attachment descriptor.
String	toString()
Attachment	transform(com.chemaxon.calculations.sc.util.IntListSet atomSelection) Transform attachment for molecule subset selection.

Methods inherited from class java.lang.Object

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

Constructor Detail

Attachment

public Attachment(int attachmentAtomIndex,
                  int attachedAtomIndex,
                  int attachmentIndex,
                  int bondOrder)

Method Detail

isRAtom

public static boolean isRAtom(Molecule mol,
                              int atomindex)

Check if a given atom is an R atom.

Parameters:

mol - Input molecule

atomindex - R atom candidate index

Returns:

true when the given atom is an R atom. No further consistency check is made.

isZAtom

public static boolean isZAtom(Molecule mol,
                              int atomindex)

Check if a given atom has an alias string.

Parameters:

mol - Input molecule

atomindex - Z atom candidate index

Returns:

true when the given atom has alias string

ensureValidRepresentation

public void ensureValidRepresentation(Molecule mol,
                                      String prefix)

Ensure that structure mapping is consistent.

Parameters:

mol - Mapped structure

prefix - Pseudo atom label prefix

Throws:

IllegalArgumentException - in case of bond type, label or connectivity mismatch

forScaffoldR

public static Attachment forScaffoldR(Molecule mol,
                                      int attachmentAtomIndex)

Create attachment description for scaffold's R atom.

Parameters:

mol - Scaffold molecule

attachmentAtomIndex - index of the Rn atom to be represented

Returns:

Attachment definition

Throws:

IllegalArgumentException - in case of consistency error or when the given atom is not an R atom

forFragmentZ

public static Attachment forFragmentZ(Molecule mol,
                                      int attachmentAtomIndex)

Create attachment description for a fragment Z atom.

Parameters:

mol - Fragment molecule

attachmentAtomIndex - index of the Zn atom to be represented

Returns:

Attachment definition

Throws:

IllegalArgumentException - in case of consistency error or when the given atom is not an R atom

addZAttachment

public static Attachment addZAttachment(Molecule mol,
                                        int attachedAtomIndex,
                                        int attachmentIndex,
                                        int bondOrder)

replaceAtomWithR

public static Attachment replaceAtomWithR(Molecule mol,
                                          int attachmentAtomIndex,
                                          int rno)

Replace an atom with an Rn atom and return the appropriate attachment descriptor.

Parameters:

mol - Target molecule to modify

attachmentAtomIndex - Index of attachment atom to replace

rno - R number

Returns:

Attachment descriptor

Throws:

IllegalArgumentException - in case of consistency error

replaceAtomWithR

public static Attachment replaceAtomWithR(Molecule mol,
                                          int attachmentAtomIndex)

getAttachmentIndex

public int getAttachmentIndex()

Attachemnt index.

Returns:

Value n from represented Rn or Zn

getAttachedAtomIndex

public int getAttachedAtomIndex()

Attached atom index.

Returns:

Index of atom to which this attachment is connected

getAttachmentAtomIndex

public int getAttachmentAtomIndex()

Attachment atom index.

Returns:

Index of pseudo atom representing this attachment

getBondOrder

public int getBondOrder()

Represented bond order.

Returns:

Represented bond order

toString

public String toString()

Overrides:

toString in class Object

transform

public Attachment transform(com.chemaxon.calculations.sc.util.IntListSet atomSelection)

Transform attachment for molecule subset selection. Atom indices of the attachment pseudo atom and its attached neighbor is transformed according to the given selection. Attachment index and bond order is retained. The selection is order sensitive, caller must ensure consistent handling.

Parameters:

atomSelection - Selection to be executed. Formally, in the selected molecule, atom with index i is originated from the original molecule's atom with index atomSelection[i] (using array notation)

Returns:

Transformed attachment

Throws:

IllegalArgumentException - when the represented attachment or the attached atom is not part of the selection