com.chemaxon.virtuallib.sc.model.sdf

Class RgFrag

java.lang.Object

com.chemaxon.virtuallib.sc.model.sdf.RgFrag

All Implemented Interfaces:

Serializable

public class RgFrag
extends Object
implements Serializable

An RGroup fragment definition.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	REACTANT_ID_SDFIELD SD field storing Reactant ID.

Constructor Summary

Constructors

Constructor and Description
RgFrag(Molecule mol) Construct for a Molecule.
RgFrag(Molecule mol, String reactantId, Collection<Attachment> zAttachments) Construct for a molecule and attachment descriptor.

Method Summary

Modifier and Type	Method and Description
com.chemaxon.calculations.sc.util.IntListSet	allAtoms()
List<ScaffoldExtension>	constructSingleAtomExtensions(int firstR) Enumerate all possible single atom scaffold extensions.
List<ScaffoldExtension>	constructSingleAtomExtensions(ScaffoldExtension base) Construct further single atom extensions.
com.chemaxon.calculations.sc.util.IntListSet	getAllNeighborAtoms(int atomIndex) Get all neighbor atom indices.
int	getAtomCount() All atom count.
com.chemaxon.calculations.sc.graph.Connectivity	getConnectivity()
Molecule	getMolecule()
String	getReactantId()
int	getRealAtomCount() Chemical atom count.
com.chemaxon.calculations.sc.util.IntListSet	getRealNeighborAtoms(int atomIndex) Get all real atom neighbor indices.
com.chemaxon.calculations.sc.util.IntListSet	realAtoms()
String	toCxSmiles() Return CxSmiles format.
String	toString()
String	toString(boolean multiline) Details into human readable String.
IndexedAttachmentGroup	zAttachments() Z attachments.

Methods inherited from class java.lang.Object

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

Field Detail

REACTANT_ID_SDFIELD

public static final String REACTANT_ID_SDFIELD

SD field storing Reactant ID.

See Also:

Constant Field Values

Constructor Detail

RgFrag

public RgFrag(Molecule mol,
              String reactantId,
              Collection<Attachment> zAttachments)

Construct for a molecule and attachment descriptor.

Parameters:

mol - Molecule representation, including Z attachments

reactantId - Reactant ID of this fragment

zAttachments - Z attachment descriptors

RgFrag

public RgFrag(Molecule mol)

Construct for a Molecule.

Parameters:

mol - Fragment molecule

Method Detail

zAttachments

public IndexedAttachmentGroup zAttachments()

Z attachments.

Returns:

Z attachments

getAllNeighborAtoms

public com.chemaxon.calculations.sc.util.IntListSet getAllNeighborAtoms(int atomIndex)

Get all neighbor atom indices.

Parameters:

atomIndex - An atom, possibly an attachment atom

Returns:

Index of all its neighbors, including attachment atoms

getRealNeighborAtoms

public com.chemaxon.calculations.sc.util.IntListSet getRealNeighborAtoms(int atomIndex)

Get all real atom neighbor indices.

Parameters:

atomIndex - An atom, possibly an attachment atom

Returns:

Index of all its neighboring real atoms

allAtoms

public com.chemaxon.calculations.sc.util.IntListSet allAtoms()

realAtoms

public com.chemaxon.calculations.sc.util.IntListSet realAtoms()

getAtomCount

public int getAtomCount()

All atom count.

Returns:

All atom count including pseudo (Z) atoms.

getRealAtomCount

public int getRealAtomCount()

Chemical atom count.

Returns:

Chemical atom count

constructSingleAtomExtensions

public List<ScaffoldExtension> constructSingleAtomExtensions(ScaffoldExtension base)

Construct further single atom extensions. Terminal extensions are not returned. Internal workflow:

• All possible matches of the extension are enumerated
• The remainder fragment is constructed
• Single atom extensions are calculated for the remainders

Parameters:

base - Basis extension to further grow

Returns:

List of possible extensions

Throws:

IllegalStateException - when basis extension does not match

constructSingleAtomExtensions

public List<ScaffoldExtension> constructSingleAtomExtensions(int firstR)

Enumerate all possible single atom scaffold extensions. Terminal extensions are not returned.

Parameters:

firstR - Index of first R attachment to use

Returns:

List of possible scaffold extensions

toString

public String toString(boolean multiline)

Details into human readable String.

Parameters:

multiline - Write multi line String

Returns:

Human readable String

toCxSmiles

public String toCxSmiles()

Return CxSmiles format.

Returns:

Structure in CxSmiles format

toString

public String toString()

Overrides:

toString in class Object

getReactantId

public String getReactantId()

getMolecule

public Molecule getMolecule()

getConnectivity

public com.chemaxon.calculations.sc.graph.Connectivity getConnectivity()