chemaxon.struc
Class RxnMolecule

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

All Implemented Interfaces:

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

public class RxnMolecule

extends Molecule

Reaction.

Since:

2.9

Version:

3.3, 08/14/2003

Author:

Peter Csizmadia

See Also:

Serialized Form

Field Summary

static int	AGENTS "Agent" structure type.
static int	PRODUCTS "Product" structure type.
static int	REACTANTS "Reactant" structure type.
static int	RGROUPED Add R-groups to component structure.
static int	TYPE_MASK Structure type mask.

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

RxnMolecule()
Create a reaction.

Method Summary

void	add(CEdge e) Adds a bond to a reactant, product, agent.
void	add(CNode node) Adds an atom to a reactant, product or agent structure.
void	addStructure(Molecule m, int type) Adds a reactant, product or agent.
void	addStructure(Molecule m, int type, boolean beNew) Adds a reactant, product or agent.
void	clearForImport(java.lang.String format) Clear the edges vector and the 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	contains(java.lang.Object o) Checks if a reactant, agent or product structure contains the specified node or edge.
int[][]	createBHtab() Creates the graph union's bond table extended with implicit hydrogen atoms.
int[][]	createCHtab() Creates the graph union's connection table extended with implicit hydrogen atoms.
static RxnMolecule	createReaction(Molecule mol, DPoint3[] arw) Creates a reaction.
static double	determineArrowDistance(double x, double y, double z, DPoint3[] ar) Project the point (x,y,z) to the line of the reaction arrow 'ar'.
int	determineType(double x, double y, double z) Determines whether a point should be in a reactant, in a product or in an agent.
protected void	fillSelectionMolecule(SelectionMolecule s) Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
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.
Molecule	getAgent(int i) Gets an agent.
int	getAgentCount() Gets the number of agents.
int[][]	getBtab() Gets the bond table for the graph union.
DPoint3	getCenter(int type, int i) Gets the geometrical center of a reaction component.
int[][]	getCtab() Gets the connection table for the graph union.
CEdge	getEdge(int i) Gets an edge.
int	getEdgeCount() Gets the number of edges in the graph union.
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 for the graph union.
int	getGrinv(int[] gi) Gets the graph invariants for the graph union.
double	getMass() Calculates the molecular weight of the molecule.
CNode	getNode(int i) Gets a node.
int	getNodeCount() Returns the number of nodes in the graph union.
Molecule	getProduct(int i) Gets a product.
int	getProductCount() Gets the number of products.
Molecule	getReactant(int i) Gets a reactant.
int	getReactantCount() Gets the number of reactants.
static RxnMolecule	getReaction(CGraph g) Returns the reaction represented by the given molecule if exists, otherwise null.
DPoint3[]	getReactionArrow() Gets a two-element array containing the endpoints of the reaction arrow.
Molecule	getStructure(int flags, int i) Gets a reactant, product or agent.
int	getStructureCount(int type) Gets the number of reactants, products or agents.
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 in the graph union.
int	indexOf(CNode node) Gets the index of the specified node in the graph union.
boolean	isAtom() A reaction molecule cannot represent an atom.
boolean	isBond() A reaction molecule cannot represent a bond.
boolean	isEmpty() Ask if the reaction is empty or not.
boolean	isReaction() Checks if the structure represents a reaction or not.
protected boolean	isRealNodeParent() Reaction molecules cannot be real node parents.
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 RxnMolecule object.
void	rebuildStructures() For each structure (reactant or product) determines whether it should be a reactant or a product depending on its the relative position to the reaction arrow.
void	rebuildStructures(DPoint3[] arw) Sets the reaction arrow.
void	recalcReactionArrow() Recalculates the reaction arrow, forced recalculation.
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() Removes all bonds from the reactants, products and agents.
protected void	removeEdge(CEdge edge, int cleanupFlags) Removes a bond from the reactants, products or agents.
protected void	removeEdge(int iu, int cleanupFlags) Removes an edge from a reactant, agent or product.
protected void	removeNode(CNode node, int cleanupFlags) Removes an atom from the reactants, products or agents.
protected void	removeNode(int iu, int cleanupFlags) Removes an atom from the reactants, products or agents.
void	setAbsStereo(boolean c) Sets the absolute stereoconfiguration flag for all the structures.
void	setDim(int d) Sets the dimension for all the structures.
void	setEdge(int iu, CEdge edge) Sets the edge at the specified index.
void	setLocation(DPoint3 p) Set the origin of the molecule.
void	setNode(int iu, CNode node) Sets the node at the specified index.
void	setReactionArrow() Sets the stored reaction arrow.
void	setReactionArrow(DPoint3[] arw) Sets the reaction arrow.
void	setReactionArrow0() Sets the stored reaction arrow 'arrowPoints' to its calculated value.
void	setSgroupParent(MolAtom a, Sgroup sg, boolean set) Sets or unsets an S-group as a parent of an atom in reactants, products or agents.
protected void	transform(CTransform3D t, boolean incg) Apply a transformation matrix to the atomic coordinates and the reaction arrow.
protected void	transformReactionArrow(CTransform3D t) Apply a transformation matrix to the reaction arrow.

Methods inherited from class chemaxon.struc.Molecule

addNode0, addSgroupsOf, bondlength, clear, clearCalcResults, clearProperties, contractSgroups, convertToFrags, draw, endReuse, expandSgroups, expandSgroups, findContractableSgroup, findExpandableSgroup, findFrags, findSgroupContaining, findSgroupOf, getComment, getEndPosition, getGraphUnionAsSelection, getImageSize, getInputFormat, getName, getProperty, getPropertyCount, getPropertyKey, getPropertyKeys, getPropertyObject, getSgroup, getSgroupArray, getSgroupCount, getSgroupLigands, getSimplifiedMolecule, getStartPosition, indexOf, isSgroup, makeItSimilar, removeAllSgroups, removeSgroupsOf, reparentSgroups, residueSymbolOf, residueTypeOf, reuseAtom, setComment, setEndPosition, setInputFormat, setName, setNode0, setProperty, setPropertyObject, setStartPosition, toBinFormat, toFormat, toObject, ungroupSgroups

Methods inherited from class chemaxon.struc.MoleculeGraph

adjustMultiChiralFlag, aromatize, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcOutRectCenter, calcWidth, canBeCT, clean, contains, 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

REACTANTS

public static final int REACTANTS

"Reactant" structure type.

See Also:

getStructure(int, int), Constant Field Values

PRODUCTS

public static final int PRODUCTS

"Product" structure type.

See Also:

getStructure(int, int), Constant Field Values

AGENTS

public static final int AGENTS

"Agent" structure type.

See Also:

getStructure(int, int), Constant Field Values

RGROUPED

public static final int RGROUPED

Add R-groups to component structure.

Since:

3.1

See Also:

Constant Field Values

TYPE_MASK

public static final int TYPE_MASK

Structure type mask.

Since:

3.1

See Also:

REACTANTS, PRODUCTS, AGENTS, Constant Field Values

Constructor Detail

RxnMolecule

public RxnMolecule()

Create a reaction.

Method Detail

isEmpty

public boolean isEmpty()

Ask if the reaction is empty or not.

Overrides:

isEmpty in class CGraph

Returns:

true if there are no reactants, products or agents

isAtom

public boolean isAtom()

A reaction molecule cannot represent an atom.

Overrides:

isAtom in class MoleculeGraph

Returns:

false

isBond

public boolean isBond()

A reaction molecule cannot represent a bond.

Overrides:

isBond in class MoleculeGraph

Returns:

false

isReaction

public boolean isReaction()

Checks if the structure represents a reaction or not.

Overrides:

isReaction in class Molecule

Returns:

true

Since:

3.0

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. Always returns 0 for reactions

Overrides:

getMass in class MoleculeGraph

getReaction

public static RxnMolecule getReaction(CGraph g)

Returns the reaction represented by the given molecule if exists, otherwise null. The corresponding reaction molecule is either the molecule itself or its root structure.

Parameters:

g - the molecule graph

Returns:

the corresponding reaction molecule

getReactantCount

public int getReactantCount()

Gets the number of reactants.

Returns:

the number of reactants

getProductCount

public int getProductCount()

Gets the number of products.

Returns:

the number of products

getAgentCount

public int getAgentCount()

Gets the number of agents.

Returns:

the number of agents

getStructureCount

public int getStructureCount(int type)

Gets the number of reactants, products or agents.

Parameters:

type - REACTANTS, PRODUCTS or AGENTS

Returns:

the number of reactants, products or agents

getReactant

public Molecule getReactant(int i)

Gets a reactant.

Parameters:

i - reactant index

Returns:

a reactant

getProduct

public Molecule getProduct(int i)

Gets a product.

Parameters:

i - product index

Returns:

a product

getAgent

public Molecule getAgent(int i)

Gets an agent.

Parameters:

i - agent index

Returns:

an agent

getStructure

public Molecule getStructure(int flags,
                             int i)

Gets a reactant, product or agent.

Warning! The RGROUPED flag returns an RgMolecule object having the same atom objects as the original reactant/product/agent. The parent of the atom objects is unchanged (it is the original reactant/product/agent).

Parameters:

flags - REACTANTS, PRODUCTS or AGENTS, can be combined with RGROUPED

i - reactant, product or agent index

Returns:

a reactant, product or agent

getCenter

public DPoint3 getCenter(int type,
                         int i)

Gets the geometrical center of a reaction component.

Parameters:

type - REACTANTS, PRODUCTS or AGENTS

i - reactant, product or agent index

Returns:

the center of mass

setReactionArrow0

public void setReactionArrow0()

Sets the stored reaction arrow 'arrowPoints' to its calculated value.

getReactionArrow

public DPoint3[] getReactionArrow()

Gets a two-element array containing the endpoints of the reaction arrow.

Returns:

the arrow

setReactionArrow

public void setReactionArrow(DPoint3[] arw)

Sets the reaction arrow.

Parameters:

arw - is the new reaction arrow

setReactionArrow

public void setReactionArrow()

Sets the stored reaction arrow. to its calculated value.

recalcReactionArrow

public void recalcReactionArrow()

Recalculates the reaction arrow, forced recalculation.

rebuildStructures

public void rebuildStructures()

For each structure (reactant or product) determines whether it should be a reactant or a product depending on its the relative position to the reaction arrow. Rebuilds the reactant and product vectors accordingly.

rebuildStructures

public void rebuildStructures(DPoint3[] arw)

Sets the reaction arrow. For each structure (reactant or product) determines whether it should be a reactant or a product depending on its the relative position to the reaction arrow. Rebuilds the reactant and product vectors accordingly.

Parameters:

arw - is the new reaction arrow

determineArrowDistance

public static double determineArrowDistance(double x,
                                            double y,
                                            double z,
                                            DPoint3[] ar)

Project the point (x,y,z) to the line of the reaction arrow 'ar'. Return the signed distance of the projected point from the start-point of the arrow divided by the arrow length.

Parameters:

x - is the x coordinate of the point

y - is the y coordinate of the point

z - is the z coordinate of the point

ar - is the reaction arrow

Returns:

the signed distance of the projected point from the start-point of the arrow divided by the arrow length

determineType

public int determineType(double x,
                         double y,
                         double z)

Determines whether a point should be in a reactant, in a product or in an agent.

Parameters:

x - point x coordinate

y - point y coordinate

z - point z coordinate

Returns:

REACTANTS, PRODUCTS or AGENTS

addStructure

public void addStructure(Molecule m,
                         int type)

Adds a reactant, product or agent. If atoms in the specified structure are already part of some other reactants, products or agents then removes them from those structures.

Parameters:

m - the reactant, product or agent

type - REACTANTS, PRODUCTS or AGENTS

addStructure

public void addStructure(Molecule m,
                         int type,
                         boolean beNew)

Adds a reactant, product or agent. If atoms in the specified structure are already part of some other reactants, products or agents then removes them from those structures.

Parameters:

m - the reactant, product or agent

type - REACTANTS, PRODUCTS or AGENTS

beNew - m should be a new structure if true

clearForImport

public void clearForImport(java.lang.String format)

Clear the edges vector and the properties.

Overrides:

clearForImport in class Molecule

Parameters:

format - input file format

setDim

public void setDim(int d)

Sets the dimension for all the structures.

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 all the structures.

Overrides:

setAbsStereo in class MoleculeGraph

Parameters:

c - the absolute stereoconfiguration flag

See Also:

MoleculeGraph.flags

getNodeCount

public int getNodeCount()

Returns the number of nodes in the graph union.

Overrides:

getNodeCount in class CGraph

Returns:

the number of nodes

getNode

public CNode getNode(int i)

Gets a node.

Overrides:

getNode in class CGraph

Parameters:

i - node index

Returns:

the node object

setNode

public void setNode(int iu,
                    CNode node)

Sets the node at the specified index.

Overrides:

setNode in class CGraph

Parameters:

iu - node index in the graph union

node - new node reference

getCtab

public int[][] getCtab()

Gets the connection table for the graph union. 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 for the graph union. 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

createCHtab

public int[][] createCHtab()

Creates the graph union's connection table extended with implicit hydrogen atoms.

Overrides:

createCHtab in class MoleculeGraph

Returns:

the chtab array

Since:

3.0

createBHtab

public int[][] createBHtab()

Creates the graph union's bond table extended with implicit hydrogen atoms.

Overrides:

createBHtab in class MoleculeGraph

Returns:

the chtab array

Since:

3.0

getGrinv

public int getGrinv(int[] gi)

Gets the graph invariants for the graph union.

Overrides:

getGrinv in class MoleculeGraph

Parameters:

gi - output array

Returns:

the number of different graph invariants

Throws:

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

getGrinv

protected int[] getGrinv()

Gets the graph invariants for the graph union.

Overrides:

getGrinv in class CGraph

Returns:

the graph invariants array

contains

public boolean contains(java.lang.Object o)

Checks if a reactant, agent or product structure 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

indexOf

public int indexOf(CNode node)

Gets the index of the specified node in the graph union.

Overrides:

indexOf in class CGraph

Parameters:

node - the node

Returns:

the index, or -1 if not found

Since:

2.7

indexOf

public int indexOf(CEdge edge)

Gets the index of the specified edge in the graph union.

Overrides:

indexOf in class CGraph

Parameters:

edge - the edge

Returns:

the index, or -1 if not found

Since:

2.7

add

public void add(CNode node)

Adds an atom to a reactant, product or agent structure. If a neighbour of the atom is in a reactant, product or agent, then adds the atom to that structure. Otherwise creates a new reactant or product.

Overrides:

add in class CGraph

Parameters:

node - the new node

getEdgeCount

public int getEdgeCount()

Gets the number of edges in the graph union.

Overrides:

getEdgeCount in class CGraph

Returns:

the number of edges

getEdge

public CEdge getEdge(int i)

Gets an edge.

Overrides:

getEdge in class CGraph

Parameters:

i - edge index in the graph union

Returns:

the edge object

setEdge

public void setEdge(int iu,
                    CEdge edge)

Sets the edge at the specified index.

Overrides:

setEdge in class CGraph

Parameters:

iu - edge index in the graph union

edge - new node reference

add

public void add(CEdge e)

Adds a bond to a reactant, product, agent. If an endpoint of the edge is in a reactant, product or agent, then adds the edge to that structure.

Overrides:

add in class CGraph

Parameters:

e - the new edge

removeNode

protected void removeNode(CNode node,
                          int cleanupFlags)

Removes an atom from the reactants, products or agents.

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 iu,
                          int cleanupFlags)

Removes an atom from the reactants, products or agents.

Overrides:

removeNode in class Molecule

Parameters:

iu - atom index in the graph union

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 a bond from the reactants, products or agents.

Overrides:

removeEdge in class Molecule

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 iu,
                          int cleanupFlags)

Removes an edge from a reactant, agent or product.

Overrides:

removeEdge in class Molecule

Parameters:

iu - edge index in the graph union

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 bonds from the reactants, products and agents.

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()

Reaction molecules 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 origin

See Also:

MoleculeGraph.orix

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 Molecule

Parameters:

that - the atom

node - the other atom

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 has an atom connected to a reactant or product, then also adds the graph to that structure. Handles one connected component.

Overrides:

fuse0 in class CGraph

Parameters:

graph - the structure to fuse into this one

setSgroupParent

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

Sets or unsets an S-group as a parent of an atom in reactants, products or agents.

Overrides:

setSgroupParent in class Molecule

Parameters:

a - the atom

sg - the S-group

set - set (true) or unset (false)

Throws:

java.lang.IllegalArgumentException - neither reactants, nor products or agents contain 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 structure

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 structure

clone

public java.lang.Object clone()

Make an identical copy of the molecule.

Overrides:

clone in class Molecule

Returns:

the copy

newInstance

public CGraph newInstance()

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

Overrides:

newInstance in class Molecule

Returns:

the new reaction

transform

protected void transform(CTransform3D t,
                         boolean incg)

Apply a transformation matrix to the atomic coordinates and the reaction arrow.

Overrides:

transform in class MoleculeGraph

Parameters:

t - the transformation matrix

incg - increase grinvCC or not

transformReactionArrow

protected void transformReactionArrow(CTransform3D t)

Apply a transformation matrix to the reaction arrow.

Parameters:

t - the transformation matrix

createReaction

public static RxnMolecule createReaction(Molecule mol,
                                         DPoint3[] arw)

Creates a reaction.

Parameters:

mol - contains the atoms of reactants and products

arw - two-element array containing the endpoints of the reaction arrow

Returns:

the reaction

getGraphUnion

public MoleculeGraph getGraphUnion()

Gets a graph containing all the atoms and bonds.

Overrides:

getGraphUnion in class MoleculeGraph

Returns:

the unified structure

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