chemaxon.struc
Class Molecule

java.lang.Object
  chemaxon.struc.CGraph
      chemaxon.struc.MoleculeGraph
          chemaxon.struc.Molecule

All Implemented Interfaces:

java.lang.Cloneable, java.io.Serializable, StereoConstants

Direct Known Subclasses:

RgMolecule, RxnMolecule

public class Molecule

extends MoleculeGraph

Molecule class. A MoleculeGraph that may also contain S-groups.

Version:

3.3, 12/17/2003

Author:

Peter Csizmadia, Andras Volford

See Also:

Serialized Form

Field Summary

Fields inherited from class chemaxon.struc.MoleculeGraph

DIM_MASK, flags, isMultiChiral, orix, oriy, oriz, RMCLEANUP_STEREO

Fields inherited from class chemaxon.struc.CGraph

btab, ctab, edgeCount, edges, fragIds, grinv, grinvCC, INITIAL_CAPACITY, nFrags, nGrinv, nodeCount, nodes, parentGraph, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_NONE, sssr, superGraph

Fields inherited from interface chemaxon.struc.StereoConstants

ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_MASK, CHIRALITY_R, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, TRANS

Constructor Summary

Molecule()
Construct a molecule.

Molecule(Molecule p)
Construct a molecule or fragment.

Molecule(Molecule p, int na, int nb)
Construct a molecule or fragment with the specified number of atoms and bonds.

Molecule(Molecule p, MolAtom a)
Construct a graph consisting of a single vertex (atom).

Molecule(Molecule p, MolBond b)
Construct a graph consisting of a single edge (bond).

Method Summary

protected void	addNode0(CNode node) Adds a node.
protected void	addSgroupsOf(Molecule m) Adds S-groups to this object and its parent.
double	bondlength() Calculate the regular bond length for the unified structure.
void	clear() Clears the molecule.
void	clearCalcResults()
void	clearForImport(java.lang.String format) Initializes molecule for import.
void	clearProperties() Clears RDfile/SDfile properties.
java.lang.Object	clone() Make an identical copy of the molecule.
void	clonecopy(CGraph g) Make another molecule identical to this one.
void	clonelesscopy(CGraph g) Copy to selection.
boolean	contractSgroups() Contracts all S-groups.
Molecule[]	convertToFrags() Converts this molecule to its disconnected fragments.
void	draw(java.awt.Graphics g, java.lang.String opts) Draws the molecule into a graphics context.
void	endReuse(int n) End reusing atoms.
boolean	expandSgroups() Expands all S-groups.
boolean	expandSgroups(int opts) Expands all S-groups.
protected void	fillSelectionMolecule(SelectionMolecule s) Adds all atoms and bonds to the specified molecule.
Sgroup	findContractableSgroup() Finds an expanded residue.
Sgroup	findExpandableSgroup() Finds a contracted residue.
SelectionMolecule[]	findFrags() Determines the disconnected fragments and puts them into an array.
Sgroup	findSgroupContaining(MolAtom a) Finds the S-group that contains the specified node.
Sgroup	findSgroupOf(MolAtom a) Finds the S-group related to the specified node.
java.lang.String	getComment() Gets the comment.
long	getEndPosition() Gets the end position of this molecule in the input file.
protected SelectionMolecule	getGraphUnionAsSelection() Gets a selection molecule containing all the atoms and bonds.
chemaxon.marvin.util.MolImageSize	getImageSize(java.lang.String fmt) Gets size information of an image created with the specified format string.
java.lang.String	getInputFormat() Gets the input file format.
java.lang.String	getName() Gets the molecule name.
java.lang.String	getProperty(java.lang.String key) Gets an RDfile/SDfile property.
int	getPropertyCount() Gets the total number of RDfile/SDfile properties.
java.lang.String	getPropertyKey(int n) Gets an RDfile/SDfile property key.
java.util.Enumeration	getPropertyKeys() Gets the keys for the RDfile/SDfile properties.
java.lang.Object	getPropertyObject(java.lang.String key) Gets an RDfile/SDfile property object.
Sgroup	getSgroup(int i) Gets an S-group.
Sgroup[]	getSgroupArray() Gets the array of S-groups.
int	getSgroupCount() Gets the number of S-groups.
MolAtom[]	getSgroupLigands() Gets the S-group's ligands if the structure represents an S-group.
Molecule	getSimplifiedMolecule() Gets the simplified molecule object.
long	getStartPosition() Gets the starting position of this molecule in the input file.
int	indexOf(Sgroup sg) Gets the array index of an S-group.
boolean	isReaction() Checks if the structure represents a reaction or not.
boolean	isSgroup() Checks if the structure represents an S-group or not.
protected void	makeItSimilar(CGraph g) Copies some properties of this molecule to the other one specified as argument.
void	mergeNodes(CNode that, CNode node) Merges bonds of an atom with another atom, then add the atom to the molecule.
CGraph	newInstance() Creates a new Molecule object.
void	removeAll() Removes all the nodes and edges.
void	removeAllEdges() Removes all edges.
protected void	removeAllSgroups() Removes all S-groups.
protected void	removeEdge(CEdge edge, int cleanupFlags) Removes an edge by reference.
protected void	removeEdge(int i, int cleanupFlags) Removes an edge.
protected void	removeNode(CNode node, int cleanupFlags) Removes a node and its edges.
protected void	removeNode(int i, int cleanupFlags) Remove a node and its edges.
protected void	removeSgroupsOf(Molecule m) Removes S-groups from this object and its parent.
protected void	reparentSgroups(Molecule p) Change parents of all S-groups in this molecule.
static java.lang.String	residueSymbolOf(int id) Gets the name of a residue.
static int	residueTypeOf(java.lang.String name) Gets the residue identifier for a residue name.
MolAtom	reuseAtom(int z, int i) Reuse an atom or create a new one.
void	setComment(java.lang.String s) Sets the comment.
void	setDim(int d) Sets the dimension.
void	setEndPosition(long off) Sets the end position of this molecule in the input file.
void	setInputFormat(java.lang.String format) Sets the input file format.
void	setName(java.lang.String s) Sets the molecule name.
protected void	setNode0(int i, CNode node) Sets the node at the specified index.
void	setProperty(java.lang.String key, java.lang.String value) Sets an RDfile/SDfile property.
void	setPropertyObject(java.lang.String key, java.lang.Object value) Sets an RDfile/SDfile property object.
void	setSgroupParent(MolAtom a, Sgroup sg, boolean set) Sets or unsets an S-group as a parent of an atom.
void	setStartPosition(long off) Sets the starting position of this molecule in the input file.
byte[]	toBinFormat(java.lang.String fmt) Creates a binary representation of the molecule.
java.lang.String	toFormat(java.lang.String fmt) Creates a string representation of the molecule.
java.lang.Object	toObject(java.lang.String fmt) Creates a String, byte[] array or Image representation of the molecule.
boolean	ungroupSgroups() Expand and ungroup all S-groups.

Methods inherited from class chemaxon.struc.MoleculeGraph

adjustMultiChiralFlag, aromatize, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcOutRectCenter, calcWidth, canBeCT, clean, contains, createBHtab, createCHtab, createDehydrogenizedReadOnlyGraph, getAromrings, getAromrings, getAtom, getAtomArray, getAtomCount, getBond, getBondCount, getChirality, getDesiredLength, getDesiredLength, getDim, getDocument, getFormula, getGraphUnion, getGrinv, getGrinv, getImplicitHcount, getLocation, getMass, getNonAromrings, getNonAromrings, getParity, getPoints, getSSSRBondSet, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, hasImplicitH, hydrogenize, implicitizeHydrogens, isAbsStereo, isAtom, isBond, isMultiChiral, isRingBond, moveTo, qpropCheck, setAbsStereo, setChirality, setLocation, setParity, setParity, setSetSeqs, stereoClean, transform, transform, valenceCheck, valenceCheck

Methods inherited from class chemaxon.struc.CGraph

add, add, addEdge0, addEdgeWithoutChangingIt, addNodeWithoutChangingIt, contains, findFrag, findFrags, fuse, fuse0, getBtab, getCtab, getEdge, getEdgeCount, getEdgeVector, getForefather, getFragCount, getFragIds, getGrinv, getGrinvCC, getLock, getNode, getNodeCount, getNodeVector, getParent, getSSSR, indexOf, indexOf, isEmpty, isRealNodeParent, pack, regenEdges, removeEdge, removeEdge, removeNode, removeNode, resetCtab, resetGrinvInParents, setEdge, setNode, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

Molecule

public Molecule(Molecule p,
                int na,
                int nb)

Construct a molecule or fragment with the specified number of atoms and bonds.

Parameters:

p - the molecule that contains the created fragment

na - no reallocation needed until the number of atoms is less than this value

nb - no reallocation needed until the number of bonds is less than this value

Molecule

public Molecule(Molecule p,
                MolAtom a)

Construct a graph consisting of a single vertex (atom).

Parameters:

p - the parent structure

a - the atom

Molecule

public Molecule(Molecule p,
                MolBond b)

Construct a graph consisting of a single edge (bond).

Parameters:

p - the parent structure

b - the bond

Molecule

public Molecule(Molecule p)

Construct a molecule or fragment.

Parameters:

p - the parent structure

Molecule

public Molecule()

Construct a molecule.

Method Detail

setDim

public void setDim(int d)

Sets the dimension.

Overrides:

setDim in class MoleculeGraph

Parameters:

d - 0, 2, or 3

See Also:

MoleculeGraph.flags

clear

public void clear()

Clears the molecule.

Overrides:

clear in class MoleculeGraph

See Also:

MoleculeGraph.clearForImport(java.lang.String), CGraph.nodes

clearForImport

public void clearForImport(java.lang.String format)

Initializes molecule for import.

Overrides:

clearForImport in class MoleculeGraph

Parameters:

format - input file format

Since:

2.7

See Also:

CGraph.edges, MoleculeGraph.orix, MoleculeGraph.oriy, MoleculeGraph.oriz, MoleculeGraph.flags

getStartPosition

public long getStartPosition()

Gets the starting position of this molecule in the input file.

Returns:

the starting position

setStartPosition

public void setStartPosition(long off)

Sets the starting position of this molecule in the input file.

Parameters:

off - the starting position

getEndPosition

public long getEndPosition()

Gets the end position of this molecule in the input file.

Returns:

the end position

setEndPosition

public void setEndPosition(long off)

Sets the end position of this molecule in the input file.

Parameters:

off - the end position

getName

public java.lang.String getName()

Gets the molecule name.

Returns:

the molecule name or an empty string

Since:

2.7

setName

public void setName(java.lang.String s)

Sets the molecule name.

Parameters:

s - the molecule name, empty string or null (null is equivalent to empty string)

Since:

2.7

getComment

public final java.lang.String getComment()

Gets the comment.

Returns:

the comment or empty string

Since:

2.9

setComment

public final void setComment(java.lang.String s)

Sets the comment.

Parameters:

s - the comment, empty string or null (null is equivalent to empty string)

Since:

2.9

getInputFormat

public final java.lang.String getInputFormat()

Gets the input file format. Set by the import module if the molecule is from a file.

Returns:

"mol", "csmol", "sdf", "cssdf", "rdf", "csrdf", "smiles", "sybyl", "pdb" or "xyz"

Since:

2.7

setInputFormat

public void setInputFormat(java.lang.String format)

Sets the input file format.

Parameters:

format - the input format

Since:

2.7

See Also:

getInputFormat()

clearProperties

public void clearProperties()

Clears RDfile/SDfile properties.

getPropertyCount

public int getPropertyCount()

Gets the total number of RDfile/SDfile properties.

Returns:

number of properties

Since:

2.7

getPropertyKeys

public java.util.Enumeration getPropertyKeys()

Gets the keys for the RDfile/SDfile properties.

Returns:

enumeration of keys (names)

Since:

2.7

getPropertyKey

public java.lang.String getPropertyKey(int n)

Gets an RDfile/SDfile property key.

Parameters:

n - property index

Returns:

the property name

Since:

2.7

getProperty

public java.lang.String getProperty(java.lang.String key)

Gets an RDfile/SDfile property.

Parameters:

key - property name

Returns:

the value of the property, or null if the key is not found

getPropertyObject

public java.lang.Object getPropertyObject(java.lang.String key)

Gets an RDfile/SDfile property object.

Parameters:

key - property name

Returns:

the value of the property, or null if the key is not found

Since:

3.1.2

setProperty

public void setProperty(java.lang.String key,
                        java.lang.String value)

Sets an RDfile/SDfile property. Setting null value removes the property.

Parameters:

key - the property name

value - the value or null

setPropertyObject

public void setPropertyObject(java.lang.String key,
                              java.lang.Object value)

Sets an RDfile/SDfile property object. Setting null value removes the property.

Parameters:

key - the property name

value - the value or null

Since:

3.1.2

residueTypeOf

public static int residueTypeOf(java.lang.String name)

Gets the residue identifier for a residue name.

Parameters:

name - residue name

Returns:

the residue type

residueSymbolOf

public static java.lang.String residueSymbolOf(int id)

Gets the name of a residue.

Parameters:

id - the residue identifier

Returns:

the residue symbol

setNode0

protected void setNode0(int i,
                        CNode node)

Sets the node at the specified index. Overridden because Sgroups must be set correctly in RgMolecule.clone() and RxnMolecule.clone().

Overrides:

setNode0 in class CGraph

Parameters:

i - the atom index

node - the atom

removeNode

protected void removeNode(CNode node,
                          int cleanupFlags)

Removes a node and its edges.

Overrides:

removeNode in class MoleculeGraph

Parameters:

node - the node

cleanupFlags - extra clean-up methods

Since:

3.1

See Also:

CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO

removeNode

protected void removeNode(int i,
                          int cleanupFlags)

Remove a node and its edges.

Overrides:

removeNode in class MoleculeGraph

Parameters:

i - the node index

cleanupFlags - extra clean-up methods

Since:

3.1

See Also:

CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO

removeEdge

protected void removeEdge(CEdge edge,
                          int cleanupFlags)

Removes an edge by reference.

Overrides:

removeEdge in class CGraph

Parameters:

edge - the edge

cleanupFlags - extra clean-up methods

Since:

3.1

See Also:

CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO

removeEdge

protected void removeEdge(int i,
                          int cleanupFlags)

Removes an edge.

Overrides:

removeEdge in class CGraph

Parameters:

i - the edge index

cleanupFlags - extra clean-up methods

Since:

3.1

See Also:

CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO

removeAllEdges

public void removeAllEdges()

Removes all edges.

Overrides:

removeAllEdges in class CGraph

removeAll

public void removeAll()

Removes all the nodes and edges.

Overrides:

removeAll in class CGraph

clonecopy

public void clonecopy(CGraph g)

Make another molecule identical to this one.

Overrides:

clonecopy in class MoleculeGraph

Parameters:

g - the target molecule

clonelesscopy

public void clonelesscopy(CGraph g)

Copy to selection. Make another molecule identical to this one, but do not clone atoms, bonds, and the properties.

Overrides:

clonelesscopy in class MoleculeGraph

Parameters:

g - the target molecule object (the selection)

clone

public java.lang.Object clone()

Make an identical copy of the molecule.

Overrides:

clone in class MoleculeGraph

Returns:

the copy

getImageSize

public chemaxon.marvin.util.MolImageSize getImageSize(java.lang.String fmt)

Gets size information of an image created with the specified format string. Examples:

 MolImageSize g1 = mol.getImageSize("image:scale24");
     // (g1.width, g2.width) is the bounding box size for an image created
     // with scaling factor 24
 MolImageSize g2 = mol.getImageSize("image:w100h100");
     // g2.scale is the maximum scaling factor for 100x100 image
 

Parameters:

fmt - format string that contains the image export options

Returns:

an object containing the image size and the scaling factor

Throws:

java.lang.IllegalArgumentException - Invalid format string.

java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).

Since:

2.9.11

See Also:

toBinFormat(java.lang.String), toObject(java.lang.String)

toFormat

public final java.lang.String toFormat(java.lang.String fmt)

Creates a string representation of the molecule. The format descriptor string can also contain export options. Format and options are separated by a colon, multiple options can be separated by commas. See the text formats and their options on the File Formats in Marvin page. Examples:

 s1 = mol.toFormat("mol");
 s2 = mol.toFormat("smiles:a-H"); // aromatize and remove Hydrogens
 

Parameters:

fmt - the format descriptor string

Returns:

string representation of the molecule in the specified format

Throws:

java.lang.IllegalArgumentException - Invalid format string.

java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).

See Also:

toObject(java.lang.String)

toBinFormat

public final byte[] toBinFormat(java.lang.String fmt)

Creates a binary representation of the molecule. Works with all the text formats that are supported by the toFormat method, and also with the binary image formats (jpeg, png, ppm). When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples:

 byte[] d1 = mol.toBinFormat("mol");
 byte[] d2 = mol.toBinFormat("smiles:a-H"); // aromatize and remove H
 byte[] d3 = mol.toBinFormat("ppm:w300,h300,#ffff00");
 byte[] d4 = mol.toBinFormat("png:w300,h300,b32,#00ffff00");
 byte[] d5 = mol.toBinFormat("jpeg:w300,h300,Q95,#ffff00,spacefill");
 

Parameters:

fmt - the format descriptor string

Returns:

a binary representation of the molecule in the specified format

Throws:

java.lang.IllegalArgumentException - Invalid format string.

java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).

Since:

2.7.11

See Also:

toObject(java.lang.String), getImageSize(java.lang.String)

toObject

public java.lang.Object toObject(java.lang.String fmt)

Creates a String, byte[] array or Image representation of the molecule. When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples:

 import java.awt.Image;
 ...
 String s1 = (String)mol.toObject("mol");
 String s2 = (String)mol.toObject("smiles:a-H"); // aromatize, remove H
 Image img = (Image)mol.toObject("image:w300,h300,#ffff00");
 byte[] d3 = (byte[])mol.toObject("ppm:w300,h300,#ffff00");
 byte[] d4 = (byte[])mol.toObject("png:w300,h300,b32,#00ffff00");
 byte[] d5 = (byte[])mol.toObject("jpeg:w300,h300,Q95,#ffff00,spacefill");
 

Parameters:

fmt - the format descriptor string

Returns:

a String, a byte[] array or an Image

Throws:

java.lang.IllegalArgumentException - Invalid format string.

java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).

Since:

2.8.1

See Also:

toFormat(java.lang.String), toBinFormat(java.lang.String), getImageSize(java.lang.String)

draw

public void draw(java.awt.Graphics g,
                 java.lang.String opts)

Draws the molecule into a graphics context.

Parameters:

g - the graphics context

opts - the export options

Throws:

java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).

Since:

3.3

See Also:

toObject(java.lang.String)

reuseAtom

public MolAtom reuseAtom(int z,
                         int i)

Reuse an atom or create a new one. If an atom is reused, all its properties except the corners are initialized.

Parameters:

z - the atomic number

i - the atom index

Returns:

the atom reference

Since:

2.6

endReuse

public void endReuse(int n)

End reusing atoms.

Parameters:

n - number of atoms

Since:

2.6

newInstance

public CGraph newInstance()

Creates a new Molecule object. The dimension and the origin coordinates will be the same as in the original molecule.

Overrides:

newInstance in class MoleculeGraph

Returns:

a Molecule object

makeItSimilar

protected void makeItSimilar(CGraph g)

Copies some properties of this molecule to the other one specified as argument. Copies the input format.

Overrides:

makeItSimilar in class MoleculeGraph

Parameters:

g - the molecule to change

getSimplifiedMolecule

public Molecule getSimplifiedMolecule()

Gets the simplified molecule object. It returns this usually. In case of RgMolecule, it returns the root structure if there are no R-groups present.

Returns:

this

Since:

3.0.1

isReaction

public boolean isReaction()

Checks if the structure represents a reaction or not.

Returns:

false

Since:

3.0

isSgroup

public boolean isSgroup()

Checks if the structure represents an S-group or not.

Returns:

true if the structure is an S-group

Since:

3.0

getSgroupLigands

public MolAtom[] getSgroupLigands()

Gets the S-group's ligands if the structure represents an S-group.

Returns:

the array of ligands if the structure is an S-group with ligands, null otherwise

Since:

3.0

findExpandableSgroup

public final Sgroup findExpandableSgroup()

Finds a contracted residue.

Returns:

the S-group if found, null if all S-groups are expanded

Since:

3.0

findContractableSgroup

public final Sgroup findContractableSgroup()

Finds an expanded residue.

Returns:

the S-group if found, null if all S-groups are contracted

Since:

3.0

getSgroupArray

public final Sgroup[] getSgroupArray()

Gets the array of S-groups.

Returns:

an array containing all the S-groups

Since:

3.0

getSgroupCount

public final int getSgroupCount()

Gets the number of S-groups.

Returns:

the number of S-groups

Since:

3.0

getSgroup

public final Sgroup getSgroup(int i)

Gets an S-group.

Parameters:

i - S-group index

Since:

3.0

indexOf

public final int indexOf(Sgroup sg)

Gets the array index of an S-group.

Parameters:

sg - the S-group

Since:

3.0

findSgroupOf

public final Sgroup findSgroupOf(MolAtom a)

Finds the S-group related to the specified node.

Parameters:

a - the node

Returns:

the S-group or null if not found

Since:

3.0

findSgroupContaining

public final Sgroup findSgroupContaining(MolAtom a)

Finds the S-group that contains the specified node.

Parameters:

a - the node

Returns:

the S-group or null if not found

Since:

3.0

setSgroupParent

public void setSgroupParent(MolAtom a,
                            Sgroup sg,
                            boolean set)

Sets or unsets an S-group as a parent of an atom.

Parameters:

a - the atom

sg - the S-group

set - set (true) or unset (false)

Throws:

java.lang.IllegalArgumentException - molecule does not contain the atom

Since:

3.0

reparentSgroups

protected final void reparentSgroups(Molecule p)

Change parents of all S-groups in this molecule.

Parameters:

p - the new parent

Throws:

java.lang.IllegalArgumentException - molecule does not contain the atom

Since:

3.0

mergeNodes

public void mergeNodes(CNode that,
                       CNode node)

Merges bonds of an atom with another atom, then add the atom to the molecule.

Overrides:

mergeNodes in class CGraph

Parameters:

that - the atom

node - the other atom

addNode0

protected void addNode0(CNode node)

Adds a node.

Overrides:

addNode0 in class CGraph

Parameters:

node - the node reference

contractSgroups

public final boolean contractSgroups()

Contracts all S-groups.

Returns:

true if the operation was successful, false if nothing changed

Since:

3.0

See Also:

Expandable.contract(int), Expandable.DEFAULT_OPTIONS

expandSgroups

public final boolean expandSgroups(int opts)

Expands all S-groups.

Parameters:

opts - expansion options

Returns:

true if the operation was successful, false if nothing changed

Since:

3.3

See Also:

Expandable.expand(int), Expandable.DEFAULT_OPTIONS, Expandable.MDL_EXPAND

expandSgroups

public final boolean expandSgroups()

Expands all S-groups.

Returns:

true if the operation was successful, false if nothing changed

Since:

3.0

See Also:

expandSgroups(int)

ungroupSgroups

public final boolean ungroupSgroups()

Expand and ungroup all S-groups.

Returns:

true if the operation was successful, false if nothing changed

Since:

3.0

addSgroupsOf

protected final void addSgroupsOf(Molecule m)

Adds S-groups to this object and its parent.

removeSgroupsOf

protected final void removeSgroupsOf(Molecule m)

Removes S-groups from this object and its parent.

removeAllSgroups

protected void removeAllSgroups()

Removes all S-groups.

getGraphUnionAsSelection

protected final SelectionMolecule getGraphUnionAsSelection()

Gets a selection molecule containing all the atoms and bonds. Returns the same object until the unified structure is (or might be) changed, then recreates it.

Returns:

a selection molecule object containing the unified structure

Since:

3.0, 11/05/2002

See Also:

SelectionMolecule

bondlength

public double bondlength()

Calculate the regular bond length for the unified structure.

Overrides:

bondlength in class MoleculeGraph

Returns:

the regular bond length

convertToFrags

public final Molecule[] convertToFrags()

Converts this molecule to its disconnected fragments.

Warning: Atoms are removed from the original molecule object to the created fragments, therefore the original molecule becomes inconsistent.

The original node order is preserved in the returned fragments. Fragment order is also determined by the original node order. The first fragment is the one containing node 0, the second fragment is the one containing the smallest indexed node not in the first fragment, etc.

Returns:

array of fragments

Since:

3.1

findFrags

public final SelectionMolecule[] findFrags()

Determines the disconnected fragments and puts them into an array.

The original node order is preserved in the returned fragments. Fragment order is also determined by the original node order. The first fragment is the one containing node 0, the second fragment is the one containing the smallest indexed node not in the first fragment, etc.

Returns:

array of fragments

Since:

3.0

fillSelectionMolecule

protected void fillSelectionMolecule(SelectionMolecule s)

Adds all atoms and bonds to the specified molecule.

Parameters:

s - the selection molecule

Since:

3.0, 11/05/2002

clearCalcResults

public void clearCalcResults()