chemaxon.struc
Class RgMolecule

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

All Implemented Interfaces:

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

public class RgMolecule

extends Molecule

A molecule or reaction containing R-groups.

Since:

2.6

Version:

3.3, 12/25/2003

Author:

Peter Csizmadia

See Also:

Serialized Form

Field Summary

static int	RG_ID_MASK R-group id mask in R-logic.
static int	RG_ID2_MASK Mask of the other R-group's id in R-logic.
static int	RG_ID2_OFF Offset of the other R-group's id in R-logic.
static int	RG_RESTH The RestH flag in R-logic.

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

RgMolecule()
Creates an RgMolecule.

Method Summary

void	add(CEdge edge) Adds a bond to the root structure.
void	add(CNode node) Adds an atom to the root structure.
int	addRgroup(int rgid, Molecule m) Adds an R-group member.
RgMolecule	addRgroupsTo(Molecule m) Creates a read only RgMolecule from a simple molecule object.
void	clearForImport(java.lang.String fmt) Clear the edges vector and the properties.
void	clearProperties() Clears RDfile/SDfile properties in the root structure.
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	contains(java.lang.Object o) Checks if the root structure or an R-group contains the specified node or edge.
static Molecule	createMol(java.lang.String fmt) Create molecule object for the specified input file format.
void	endReuse(int n) End reusing atoms.
protected void	fillSelectionMolecule(SelectionMolecule s) Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
int	findRgroupIndex(int rgroup) Finds R-group R#.
void	fuse(CGraph graph) Add the atoms and bonds of another molecule.
protected void	fuse0(CGraph graph) Add those nodes and edges of a graph that are not already elements.
int[][]	getBtab() Gets the bond table of the root structre.
int[][]	getCtab() Gets the connection table of the root structure.
CEdge	getEdge(int i) Gets an edge of the root structure.
int	getEdgeCount() Gets the number of edges.
java.lang.String	getFormula() Gets the molecular formula in Hill order.
MoleculeGraph	getGraphUnion() Gets a graph containing all the atoms and bonds.
protected int[]	getGrinv() Gets the graph invariants of the root structure.
int	getGrinv(int[] gi) Gets the graph invariants of the root structure.
double	getMass() Calculates the molecular weight of the molecule.
java.lang.String	getName() Gets the name of the root molecule.
CNode	getNode(int i) Gets a node of the root structure.
int	getNodeCount() Gets the number of nodes in the root structure.
java.lang.String	getProperty(java.lang.String key) Gets an RDfile/SDfile property in the root structure.
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 in the root structure.
int	getRgroupCount() Gets the number of R-groups.
int	getRgroupId(int i) Gets the id of an R-group.
Molecule	getRgroupMember(int i, int j) Gets an R-group member.
int	getRgroupMemberCount(int i) Gets the number of R-group members.
int	getRlogic(int i) Gets R-logic flags.
java.lang.String	getRlogicRange(int i) Gets R-logic occurence range.
Molecule	getRoot() Gets the root structure.
Molecule	getSimplifiedMolecule() Gets the simplified molecule object.
void	implicitizeHydrogens(int f) Removes explicit bound Hydrogens from the graph and converts them to implicit.
int	indexOf(CEdge edge) Gets the index of the specified edge.
int	indexOf(CNode node) Gets the index of the specified node.
boolean	isAtom() Determines whether the structure represents only one atom and an arbitrary number of bonds.
boolean	isBond() Determines whether the structure represents only one bond and zero or two atoms.
boolean	isEmpty() Ask if the molecule is empty or not.
boolean	isIncompleteReaction() Check whether the reaction is incomplete or not.
boolean	isReaction() Checks if the structure represents a reaction or not.
protected boolean	isRealNodeParent() R-group molecule objects cannot be real node parents.
void	mergeNodes(CNode that, CNode a) Merges bonds of an atom with another atom, then add the atom to the molecule.
CGraph	newInstance() Creates a new RgMolecule object.
void	regenEdges() Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
void	removeAll() Remove all the atoms and bonds from the root structure, and from all the R-groups.
void	removeAllEdges() Remove all bonds from the root structure, and from all the R-groups.
protected void	removeEdge(CEdge edge, int cleanupFlags) Remove a bond from the root structure, and from all the R-groups.
protected void	removeEdge(int i, int cleanupFlags) Remove a bond from the root structure.
protected void	removeNode(CNode node, int cleanupFlags) Removes an atom and its bonds from the root structure and from all the R-groups.
protected void	removeNode(int i, int cleanupFlags) Removes an atom and its bonds from the root structure.
MolAtom	reuseAtom(int z, int i) Reuse an atom or create a new one.
int	rgroupIdOf(CNode node) Finds the ID of the R-group (the number in R#) that contains the specified atom.
int	rgroupIndexOf(CNode node) Finds the index of the R-group (the number in R#) that contains the specified atom.
void	setAbsStereo(boolean c) Sets the absolute stereoconfiguration flag for the root structure and the R-groups.
void	setDim(int d) Sets the dimension of the root structure and the R-groups.
void	setEdge(int i, CEdge edge) Sets the edge at the specified index.
void	setInputFormat(java.lang.String format) Sets the input file format.
void	setLocation(DPoint3 p) Set the origin of the molecule.
void	setName(java.lang.String s) Sets the name of the root molecule.
void	setNode(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 in the root structure.
void	setPropertyObject(java.lang.String key, java.lang.Object value) Sets an RDfile/SDfile property in the root structure.
void	setRlogic(int i, int f) Sets R-logic flags.
void	setRlogicRange(int index, java.lang.String range) Sets R-logic occurence range.
void	setRoot(Molecule mol) Sets the root structure.
void	setSgroupParent(MolAtom a, Sgroup sg, boolean set) Sets or unsets an S-group as a parent of an atom in the root structure or an R-group.
protected void	transform(CTransform3D t, boolean incg) Apply a transformation matrix to the atomic coordinates.

Methods inherited from class chemaxon.struc.Molecule

addNode0, addSgroupsOf, bondlength, clear, clearCalcResults, contractSgroups, convertToFrags, draw, expandSgroups, expandSgroups, findContractableSgroup, findExpandableSgroup, findFrags, findSgroupContaining, findSgroupOf, getComment, getEndPosition, getGraphUnionAsSelection, getImageSize, getInputFormat, getSgroup, getSgroupArray, getSgroupCount, getSgroupLigands, getStartPosition, indexOf, isSgroup, makeItSimilar, removeAllSgroups, removeSgroupsOf, reparentSgroups, residueSymbolOf, residueTypeOf, setComment, setEndPosition, setNode0, setStartPosition, toBinFormat, toFormat, toObject, ungroupSgroups

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, getGrinv, getImplicitHcount, getLocation, getNonAromrings, getNonAromrings, getParity, getPoints, getSSSRBondSet, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, hasImplicitH, hydrogenize, isAbsStereo, isMultiChiral, isRingBond, moveTo, qpropCheck, setChirality, setParity, setParity, setSetSeqs, stereoClean, transform, valenceCheck, valenceCheck

Methods inherited from class chemaxon.struc.CGraph

addEdge0, addEdgeWithoutChangingIt, addNodeWithoutChangingIt, findFrag, findFrags, getEdgeVector, getForefather, getFragCount, getFragIds, getGrinvCC, getLock, getNodeVector, getParent, getSSSR, pack, removeEdge, removeEdge, removeNode, removeNode, resetCtab, resetGrinvInParents, toString

Methods inherited from class java.lang.Object

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

Field Detail

RG_ID_MASK

public static final int RG_ID_MASK

R-group id mask in R-logic.

See Also:

getRlogic(int), setRlogic(int, int), Constant Field Values

RG_ID2_OFF

public static final int RG_ID2_OFF

Offset of the other R-group's id in R-logic.

See Also:

getRlogic(int), setRlogic(int, int), Constant Field Values

RG_ID2_MASK

public static final int RG_ID2_MASK

Mask of the other R-group's id in R-logic.

See Also:

getRlogic(int), setRlogic(int, int), Constant Field Values

RG_RESTH

public static final int RG_RESTH

The RestH flag in R-logic.

See Also:

getRlogic(int), setRlogic(int, int), Constant Field Values

Constructor Detail

RgMolecule

public RgMolecule()

Creates an RgMolecule.

Method Detail

setRoot

public void setRoot(Molecule mol)

Sets the root structure.

Parameters:

mol - the root structure

getRoot

public Molecule getRoot()

Gets the root structure.

Returns:

the root

getRgroupCount

public int getRgroupCount()

Gets the number of R-groups.

Returns:

number of R-groups

getRgroupId

public int getRgroupId(int i)

Gets the id of an R-group.

Parameters:

i - R-group index

Returns:

number between 1 and 32, or -1 if not found

findRgroupIndex

public int findRgroupIndex(int rgroup)

Finds R-group R#.

Parameters:

rgroup - number between 1 and 32

Returns:

R-group index, or -1 if not found

getRgroupMemberCount

public int getRgroupMemberCount(int i)

Gets the number of R-group members.

Parameters:

i - R-group index

Returns:

number of R-group members

getRgroupMember

public Molecule getRgroupMember(int i,
                                int j)

Gets an R-group member.

Parameters:

i - R-group index

j - member index

Returns:

the R-group member

addRgroup

public int addRgroup(int rgid,
                     Molecule m)

Adds an R-group member.

Parameters:

rgid - number between 1 and 32

m - the R-group

Returns:

the Rgroup index

getRlogic

public int getRlogic(int i)

Gets R-logic flags.

Parameters:

i - R-group index

Returns:

number between 1 and 32, or -1 if not found

setRlogic

public void setRlogic(int i,
                      int f)

Sets R-logic flags.

Parameters:

i - R-group index

f - R-logic flags

getRlogicRange

public java.lang.String getRlogicRange(int i)

Gets R-logic occurence range.

Parameters:

i - R-group index

Returns:

the occurence range

setRlogicRange

public void setRlogicRange(int index,
                           java.lang.String range)
                    throws java.lang.IllegalArgumentException

Sets R-logic occurence range.

Parameters:

index - R-group index

range - range of occurance

Throws:

java.lang.IllegalArgumentException - bad occurence range

clearForImport

public void clearForImport(java.lang.String fmt)

Clear the edges vector and the properties.

Overrides:

clearForImport in class Molecule

Parameters:

fmt - input file format

setName

public void setName(java.lang.String s)

Sets the name of the root molecule.

Overrides:

setName in class Molecule

Parameters:

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

getName

public java.lang.String getName()

Gets the name of the root molecule.

Overrides:

getName in class Molecule

Returns:

the molecule name or an empty string

setInputFormat

public void setInputFormat(java.lang.String format)

Sets the input file format.

Overrides:

setInputFormat in class Molecule

Parameters:

format - the input format

See Also:

Molecule.getInputFormat()

clearProperties

public void clearProperties()

Clears RDfile/SDfile properties in the root structure.

Overrides:

clearProperties in class Molecule

getPropertyCount

public int getPropertyCount()

Gets the total number of RDfile/SDfile properties.

Overrides:

getPropertyCount in class Molecule

Returns:

number of properties

getPropertyKeys

public java.util.Enumeration getPropertyKeys()

Gets the keys for the RDfile/SDfile properties.

Overrides:

getPropertyKeys in class Molecule

Returns:

enumeration of keys (names)

getPropertyKey

public java.lang.String getPropertyKey(int n)

Gets an RDfile/SDfile property key.

Overrides:

getPropertyKey in class Molecule

Parameters:

n - property index

Returns:

the property name

getProperty

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

Gets an RDfile/SDfile property in the root structure.

Overrides:

getProperty in class Molecule

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 in the root structure.

Overrides:

getPropertyObject in class Molecule

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 in the root structure. Setting null value removes the property.

Overrides:

setProperty in class Molecule

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 in the root structure. Setting null value removes the property.

Overrides:

setPropertyObject in class Molecule

Parameters:

key - the property name

value - the value or null

Since:

3.1.2

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.

Overrides:

reuseAtom in class Molecule

Parameters:

z - atomic number

i - atom index

Returns:

the new or old atom

endReuse

public void endReuse(int n)

End reusing atoms.

Overrides:

endReuse in class Molecule

Parameters:

n - number of atoms

Since:

2.6

getCtab

public int[][] getCtab()

Gets the connection table of the root structure. If there is no connection table for the molecule, then create it. ctab[i][j] will be the index of the jth neighbor of the ith atom.

Overrides:

getCtab in class CGraph

Returns:

the ctab array

getBtab

public int[][] getBtab()

Gets the bond table of the root structre. If there is no bond table for the molecule, then create it. btab[i][j] will be the index of the bond between atoms i and j, or -1 if there is no bond.

Overrides:

getBtab in class CGraph

Returns:

the btab array

getGrinv

public int getGrinv(int[] gi)

Gets the graph invariants of the root structure.

Overrides:

getGrinv in class MoleculeGraph

Parameters:

gi - the output array

Returns:

zero

getGrinv

protected int[] getGrinv()

Gets the graph invariants of the root structure.

Overrides:

getGrinv in class CGraph

Returns:

the graph invariants array

rgroupIdOf

public int rgroupIdOf(CNode node)

Finds the ID of the R-group (the number in R#) that contains the specified atom.

Parameters:

node - the atom

Returns:

the R-group ID if found or -1 if not found

rgroupIndexOf

public int rgroupIndexOf(CNode node)

Finds the index of the R-group (the number in R#) that contains the specified atom.

Parameters:

node - the atom

Returns:

the R-group index if found or -1 if not found

setDim

public void setDim(int d)

Sets the dimension of the root structure and the R-groups.

Overrides:

setDim in class Molecule

Parameters:

d - 0, 2 or 3

See Also:

MoleculeGraph.flags

setAbsStereo

public void setAbsStereo(boolean c)

Sets the absolute stereoconfiguration flag for the root structure and the R-groups.

Overrides:

setAbsStereo in class MoleculeGraph

Parameters:

c - the absolute stereoconfiguration flag

See Also:

MoleculeGraph.flags

getNodeCount

public int getNodeCount()

Gets the number of nodes in the root structure.

Overrides:

getNodeCount in class CGraph

Returns:

number of nodes

getNode

public CNode getNode(int i)

Gets a node of the root structure.

Overrides:

getNode in class CGraph

Parameters:

i - node index

Returns:

the node object

setNode

public void setNode(int i,
                    CNode node)

Sets the node at the specified index.

Overrides:

setNode in class CGraph

Parameters:

i - the atom index

node - the atom

add

public void add(CNode node)

Adds an atom to the root structure.

Overrides:

add in class CGraph

Parameters:

node - the atom

getEdgeCount

public int getEdgeCount()

Description copied from class: CGraph

Gets the number of edges.

Overrides:

getEdgeCount in class CGraph

Returns:

number of edges

getEdge

public CEdge getEdge(int i)

Gets an edge of the root structure.

Overrides:

getEdge in class CGraph

Parameters:

i - edge index

Returns:

the edge object

setEdge

public void setEdge(int i,
                    CEdge edge)

Sets the edge at the specified index.

Overrides:

setEdge in class CGraph

Parameters:

i - the bond index

edge - the bond

add

public void add(CEdge edge)

Adds a bond to the root structure.

Overrides:

add in class CGraph

Parameters:

edge - the bond to add

indexOf

public int indexOf(CNode node)

Gets the index of the specified node.

Overrides:

indexOf in class CGraph

Parameters:

node - the node

Returns:

the index, or -1 if not found

indexOf

public int indexOf(CEdge edge)

Gets the index of the specified edge.

Overrides:

indexOf in class CGraph

Parameters:

edge - the edge

Returns:

the index, or -1 if not found

contains

public boolean contains(java.lang.Object o)

Checks if the root structure or an R-group contains the specified node or edge.

Overrides:

contains in class CGraph

Parameters:

o - the node or edge object

Returns:

true if the graph contains the object, false otherwise

isEmpty

public boolean isEmpty()

Ask if the molecule is empty or not.

Overrides:

isEmpty in class CGraph

Returns:

true if the graph does not contain any nodes or edges.

isAtom

public boolean isAtom()

Determines whether the structure represents only one atom and an arbitrary number of bonds.

Overrides:

isAtom in class MoleculeGraph

Returns:

true the root structure represents an atom and there are no R-groups, false otherwise

isBond

public boolean isBond()

Determines whether the structure represents only one bond and zero or two atoms. Determines whether the structure represents only one atom and an arbitrary number of bonds.

Overrides:

isBond in class MoleculeGraph

Returns:

true the root structure represents a bond and there are no R-groups, false otherwise

isReaction

public boolean isReaction()

Checks if the structure represents a reaction or not.

Overrides:

isReaction in class Molecule

Returns:

true if the root structure is a reaction

Since:

3.0

getSimplifiedMolecule

public Molecule getSimplifiedMolecule()

Gets the simplified molecule object.

Overrides:

getSimplifiedMolecule in class Molecule

Returns:

the root structure if there are no R-groups present, this otherwise

Since:

3.0.1

addRgroupsTo

public RgMolecule addRgroupsTo(Molecule m)

Creates a read only RgMolecule from a simple molecule object.

Parameters:

m - the simple molecule object

Returns:

RgMolecule containing R-groups from this object and the specified molecule as root

Since:

3.1

removeNode

protected void removeNode(CNode node,
                          int cleanupFlags)

Removes an atom and its bonds from the root structure and from all the R-groups.

Overrides:

removeNode in class Molecule

Parameters:

node - the atom

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)

Removes an atom and its bonds from the root structure.

Overrides:

removeNode in class Molecule

Parameters:

i - the atom 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)

Remove a bond from the root structure, and from all the R-groups.

Overrides:

removeEdge in class Molecule

Parameters:

edge - the bond

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)

Remove a bond from the root structure.

Overrides:

removeEdge in class Molecule

Parameters:

i - the bond 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()

Remove all bonds from the root structure, and from all the R-groups.

Overrides:

removeAllEdges in class Molecule

removeAll

public void removeAll()

Remove all the atoms and bonds from the root structure, and from all the R-groups.

Overrides:

removeAll in class Molecule

isRealNodeParent

protected boolean isRealNodeParent()

R-group molecule objects cannot be real node parents.

Overrides:

isRealNodeParent in class CGraph

Returns:

false

Since:

3.0

regenEdges

public void regenEdges()

Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.

Overrides:

regenEdges in class CGraph

setLocation

public void setLocation(DPoint3 p)

Set the origin of the molecule. The MolAtom coordinates are relative to this origin.

Overrides:

setLocation in class MoleculeGraph

Parameters:

p - the location

See Also:

MoleculeGraph.orix

fuse

public void fuse(CGraph graph)

Add the atoms and bonds of another molecule.

Overrides:

fuse in class CGraph

Parameters:

graph - the other molecule

fuse0

protected void fuse0(CGraph graph)

Add those nodes and edges of a graph that are not already elements. If the graph is a reaction and the root structure is not a reaction then the root structure will become a reaction determined by the reaction arrow corresponding to the graph. For each connected component of the graph checks if it contains an atom connected to an RGgroup in this RgMolecule; if yes then also adds the component to that RGroup, otherwise adds it to the root structure.

Overrides:

fuse0 in class CGraph

Parameters:

graph - the graph that will be fused into this molecule

mergeNodes

public void mergeNodes(CNode that,
                       CNode a)

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

Overrides:

mergeNodes in class Molecule

Parameters:

that - the atom

a - the other atom

setSgroupParent

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

Sets or unsets an S-group as a parent of an atom in the root structure or an R-group.

Overrides:

setSgroupParent in class Molecule

Parameters:

a - the atom

sg - the S-group

set - set (true) or unset (false)

Throws:

java.lang.IllegalArgumentException - if neither root, nor any R-group contains the atom

Since:

3.0

clonecopy

public void clonecopy(CGraph g)

Make another molecule identical to this one.

Overrides:

clonecopy in class Molecule

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 props.

Overrides:

clonelesscopy in class Molecule

Parameters:

g - the target molecule

clone

public java.lang.Object clone()

Make an identical copy of the molecule.

Overrides:

clone in class Molecule

Returns:

the copy

getFormula

public java.lang.String getFormula()

Gets the molecular formula in Hill order.

Overrides:

getFormula in class MoleculeGraph

Returns:

the formula

getMass

public double getMass()

Calculates the molecular weight of the molecule. Returns 0 if the molecule contains R-group or reaction

Overrides:

getMass in class MoleculeGraph

newInstance

public CGraph newInstance()

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

Overrides:

newInstance in class Molecule

Returns:

an RgMolecule object

isIncompleteReaction

public boolean isIncompleteReaction()

Check whether the reaction is incomplete or not.

Returns:

true if something is missing, false if it seems to be okay

Since:

2.9

transform

protected void transform(CTransform3D t,
                         boolean incg)

Apply a transformation matrix to the atomic coordinates.

Overrides:

transform in class MoleculeGraph

Parameters:

t - the transformation matrix

incg - increase grinvCC or not

createMol

public static Molecule createMol(java.lang.String fmt)

Create molecule object for the specified input file format.

Parameters:

fmt - the file format

Returns:

a Molecule, RgMolecule or RxnMolecule object

getGraphUnion

public MoleculeGraph getGraphUnion()

Gets a graph containing all the atoms and bonds.

Overrides:

getGraphUnion in class MoleculeGraph

Returns:

root.getGraphUnion() if there are no R-groups, getGraphUnionAsSelection() otherwise

Since:

3.0, 11/11/2002

See Also:

Molecule.getGraphUnionAsSelection()

fillSelectionMolecule

protected void fillSelectionMolecule(SelectionMolecule s)

Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.

Overrides:

fillSelectionMolecule in class Molecule

Parameters:

s - the selection molecule

Since:

3.0, 11/05/2002

implicitizeHydrogens

public void implicitizeHydrogens(int f)

Removes explicit bound Hydrogens from the graph and converts them to implicit. Only those explicit H atoms are converted for which MolAtom.isImplicitizableH(int) returns true.

Overrides:

implicitizeHydrogens in class MoleculeGraph

Parameters:

f - flags specifying special H atom types to include

Since:

3.1

See Also:

MolAtom.LONELY_H, MolAtom.ISOTOPE_H, MolAtom.CHARGED_H, MolAtom.RADICAL_H, MolAtom.MAPPED_H