chemaxon.struc

Class MolBond

java.lang.Object

chemaxon.struc.MolBond

All Implemented Interfaces:

StereoConstants, Serializable

Direct Known Subclasses:

QueryBond

public class MolBond
extends Object
implements StereoConstants, Serializable

Chemical bond.

Version:

5.3, 09/28/2009

Author:

Peter Csizmadia, Tamas Karpati, Andras Volford, Szilveszter Juhos, Erika Biro

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	ANY Any bond type.
static int	AROMATIC Aromatic bond type.
static int	BOLD "Bold" attribute of the bond.
static double	CCLENGTH Default bond length.
static int	CONJUGATED Conjugation state of the bond.
static int	COORDINATE Coordinate bond flag.
static int	DOUBLE_OR_AROMATIC Double or aromatic query bond type.
static int	DOWN Single bond down flag.
static int	HASHED "Hashed" attribute of the bond.
static int	HYDROGEN Hydrogen bond type.
static int	RC_CHANGE The bond (order) has changed in the reaction.
static int	RC_MAKE_AND_CHANGE The bond is created and changed.
static int	RC_MAKE_OR_BREAK The bond is made or broken in the reaction.
static int	RC_NOT_CENTER The bond is not a reacting center.
static int	RC_NOT_MODIFIED The bond is not modified in the reaction.
static int	RC_REACTING_CENTER The bond is a reacting center.
static int	RC_UNMAPPED Unmapped bond in reacting center.
static int	REACTING_CENTER_MASK Mask for reacting center bits.
static int	SETSEQ_MAX Maximum bond set sequence number.
static int	SETSEQ_OFF Bond set sequence number offset in flags.
static int	SINGLE_OR_AROMATIC Single or aromatic query bond type.
static int	SINGLE_OR_DOUBLE Single or double query bond type.
static int	STEREO_MASK Single and double bond stereo mask.
static int	STEREO1_MASK Single bond stereo mask.
static int	STEREO2_CARE Cis/trans info of this bond is taken care of during the SSS process if this flag is set - used only for query bonds.
static int	TOPOLOGY_CHAIN Bond is in a chain.
static int	TOPOLOGY_MASK Bond topology mask.
static int	TOPOLOGY_RING Bond is in a ring.
static int	TYPE_MASK The lowest bits of the flags that store the bond type.
static int	UP Single bond up flag.
static int	WAVY Single bond wavy flag.

Fields inherited from interface chemaxon.struc.StereoConstants

ANTI, ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_M, CHIRALITY_MASK, CHIRALITY_P, CHIRALITY_r, CHIRALITY_R, CHIRALITY_s, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS

Constructor Summary

Constructors

Modifier	Constructor and Description
	MolBond(MolAtom a1, MolAtom a2) Construct a single bond between two atoms.
	MolBond(MolAtom a1, MolAtom a2, int f) Construct a bond between two atoms.
protected	MolBond(MolBond b) Copy constructor.

Method Summary

Methods

Modifier and Type	Method and Description
int	calcOrderFromLength() Calculate the bond order from the atomic distances.
int	calcOrderFromValence() Calculate bond order from the types and charges of the two atoms.
int	calcStereo2() Computes the stereochemistry of the bond based on the atomic coordinates.
int	calcStereo2(MolAtom atom1, MolAtom atom4) Computes the stereochemistry of the bond based on the atomic coordinates.
static int	calcStereo2(MolAtom atom1, MolAtom atom2, MolAtom atom3, MolAtom atom4) Computes the stereochemistry of the atom sequence (scheme a1-a2=a3-a4) based on the atomic coordinates.
void	clearProperties() Removes all properties from this bond.
Object	clone() Make a copy of this object.
MolBond	cloneBond(MolAtom a1, MolAtom a2) Clones this bond.
boolean	containsPropertyKey(String key) Returns true if this bond has a mapping for the specified property key.
static double	desiredLength(int atno1, int atno2, int type, int dim) Desired length of a bond between two atoms in Angstroms.
MolAtom	getAtom1() Gets the first endpoint.
MolAtom	getAtom2() Gets the second endpoint.
chemaxon.struc.BondType	getBondType() Gets the type of the bond.
MolAtom	getCTAtom1() Gets the first atom for cis/trans stereo calculation.
MolAtom	getCTAtom4() Gets the fourth atom for cis/trans stereo calculation.
double	getDesiredLength() Deprecated. since 5.11, replaced by desiredLength(int, int, int, int).
double	getDesiredLength(boolean shortenHbonds) Deprecated. since 5.11, replaced by desiredLength(int, int, int, int).
int	getFlags() Gets bond type (4 bits), stereo (2+2+1 bits), topology (2 bits), bond set (5 bits) and reacting center (7 bits) information.
double	getLength() Gets the actual length of the bond.
protected Object	getLock() Gets lock object for synchronization.
MolAtom	getOtherAtom(MolAtom atom) Gets the other end of the bond.
MoleculeGraph	getParent() Gets the parent graph.
Object	getProperty(String key) Returns the property value to which the specified property key is mapped at this bond, or null if this bond has no mapping for this property key.
String	getQuerystr() Gets the query properties.
int	getSetSeq() Gets the bond set.
int	getStereo1(MolAtom o) Gets wedge bond type relative to the specified chiral atom.
int	getType() Gets the bond type.
boolean	haveEqualProperties(MolBond b) Tests whether two bonds have the same properties.
boolean	isBold() Decides whether this bond is bold or not.
boolean	isCollinear(MolAtom atom) Returns whether atom is collinear with the bond or not.
boolean	isConjugated() Gets the conjugation state of the bond set by the conjugation modul.
boolean	isCoordinate() Tests whether the bond is coordinate.
boolean	isHashed() Decides whether this bond is hashed or not.
boolean	isPositionVariation() Decides whether this bond is a position variation bond.
boolean	isQuery() Tests whether it is query bond or has query property: any single or double single or aromatic double or aromatic smarts bond ring or chain topology For more information on smarts bond and query bonds, see The JChem Query Guide
boolean	isRemovable() Deprecated. As of Marvin 6.2, no replacement. Not supported feature.
protected boolean	overridesAtMerge(MolBond e) Checks if this bond should override another one when two structures are merged.
int	propertyCount() Returns the number of property (property key - property value) mappings of this bond.
Set<String>	propertyKeySet() Returns a set view of the property keys of this bond.
Set<Map.Entry<String,Object>>	propertySet() Returns a set view of the properties (property key - property value mappings) of this bond.
void	putProperty(String key, Object value) Associates the specified value with the specified key at this bond.
Object	removeProperty(String key) Removes the mapping for this property key from this bond if present.
void	setFlags(int f) Sets bond type (4 bit), stereo (2+2+1 bit), topology (2 bit) bond set (5 bit) and reacting center (7 bits) information.
void	setFlags(int f, int mask) Sets bond type (3 bit), stereo (2+2+1 bit), and topology (2 bit) information.
void	setSetSeq(int g) Sets the bond set.
void	setStereo2Flags(MolAtom a1, MolAtom a4, int stereo2) Sets double bond stereo information.
void	setType(int t) Sets bond type and does valence checking for the endpoints.
boolean	stepWedge() Set the bond from 0 to UP or UP to DOWN.
static boolean	stepWedge(MolBond[] bs) Flip the given bonds to the next state ONLY 1 bond is set to chiral starting from the last bond
void	swap() Change orientation.
String	toString() Overrides Object.toString() to ease debugging.
int	transformCT(MolAtom a1, MolAtom a4, int f) Transform cis/trans stereo information into the `reference frame' of this bond.

Methods inherited from class java.lang.Object

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

Field Detail

CCLENGTH

public static final double CCLENGTH

Default bond length.

See Also:

Constant Field Values

ANY

public static final int ANY

Any bond type.

See Also:

Constant Field Values

TYPE_MASK

public static final int TYPE_MASK

The lowest bits of the flags that store the bond type.

See Also:

Constant Field Values

AROMATIC

public static final int AROMATIC

Aromatic bond type.

See Also:

Constant Field Values

SINGLE_OR_DOUBLE

public static final int SINGLE_OR_DOUBLE

Single or double query bond type.

See Also:

Constant Field Values

SINGLE_OR_AROMATIC

public static final int SINGLE_OR_AROMATIC

Single or aromatic query bond type.

See Also:

Constant Field Values

DOUBLE_OR_AROMATIC

public static final int DOUBLE_OR_AROMATIC

Double or aromatic query bond type.

See Also:

Constant Field Values

CONJUGATED

public static final int CONJUGATED

Conjugation state of the bond.

Since:

Marvin 4.1, 06/13/2006

See Also:

Constant Field Values

COORDINATE

public static final int COORDINATE

Coordinate bond flag.

Since:

Marvin 5.0, 12/04/2007

See Also:

Constant Field Values

HYDROGEN

public static final int HYDROGEN

Hydrogen bond type.

Since:

Marvin 6.2, 15/07/2013

See Also:

Constant Field Values

UP

public static final int UP

Single bond up flag.

See Also:

Constant Field Values

DOWN

public static final int DOWN

Single bond down flag.

See Also:

Constant Field Values

WAVY

public static final int WAVY

Single bond wavy flag. It equals UP | DOWN.

Since:

Marvin 4.1

See Also:

UP, DOWN, Constant Field Values

STEREO1_MASK

public static final int STEREO1_MASK

Single bond stereo mask. It equals UP | DOWN.

See Also:

UP, DOWN, Constant Field Values

STEREO2_CARE

public static final int STEREO2_CARE

Cis/trans info of this bond is taken care of during the SSS process if this flag is set - used only for query bonds.

See Also:

STEREO_MASK, Constant Field Values

STEREO_MASK

public static final int STEREO_MASK

Single and double bond stereo mask. It equals STEREO1_MASK | CTUMASK | STEREO2_CARE.

See Also:

STEREO1_MASK, StereoConstants.CTUMASK, STEREO2_CARE, Constant Field Values

TOPOLOGY_RING

public static final int TOPOLOGY_RING

Bond is in a ring.

See Also:

TOPOLOGY_MASK, Constant Field Values

TOPOLOGY_CHAIN

public static final int TOPOLOGY_CHAIN

Bond is in a chain.

See Also:

TOPOLOGY_MASK, Constant Field Values

TOPOLOGY_MASK

public static final int TOPOLOGY_MASK

Bond topology mask. It equals TOPOLOGY_CHAIN | TOPOLOGY_RING

See Also:

TOPOLOGY_CHAIN, TOPOLOGY_RING, Constant Field Values

RC_REACTING_CENTER

public static final int RC_REACTING_CENTER

The bond is a reacting center.

Since:

Marvin 4.1

See Also:

REACTING_CENTER_MASK, Constant Field Values

RC_MAKE_OR_BREAK

public static final int RC_MAKE_OR_BREAK

The bond is made or broken in the reaction.

Since:

Marvin 4.1

See Also:

REACTING_CENTER_MASK, Constant Field Values

RC_CHANGE

public static final int RC_CHANGE

The bond (order) has changed in the reaction.

Since:

Marvin 4.1

See Also:

REACTING_CENTER_MASK, Constant Field Values

RC_MAKE_AND_CHANGE

public static final int RC_MAKE_AND_CHANGE

The bond is created and changed.

Since:

Marvin 4.1

See Also:

REACTING_CENTER_MASK, Constant Field Values

RC_NOT_CENTER

public static final int RC_NOT_CENTER

The bond is not a reacting center. This is an additional ChemDraw feature (value 15 in RXN file).

Since:

Marvin 4.1

See Also:

REACTING_CENTER_MASK, Constant Field Values

RC_NOT_MODIFIED

public static final int RC_NOT_MODIFIED

The bond is not modified in the reaction.

Since:

Marvin 4.1

See Also:

REACTING_CENTER_MASK, Constant Field Values

RC_UNMAPPED

public static final int RC_UNMAPPED

Unmapped bond in reacting center. This is a ChemDraw feature that is not represented in neither standard nor ChemDraw generated RXN files (likely only in .cdx)

Since:

Marvin 4.1

See Also:

REACTING_CENTER_MASK, Constant Field Values

REACTING_CENTER_MASK

public static final int REACTING_CENTER_MASK

Mask for reacting center bits.

Since:

Marvin 4.1

See Also:

Constant Field Values

SETSEQ_OFF

public static final int SETSEQ_OFF

Bond set sequence number offset in flags.

Since:

Marvin 3.3

See Also:

SETSEQ_MAX, Constant Field Values

SETSEQ_MAX

public static final int SETSEQ_MAX

Maximum bond set sequence number.

Since:

Marvin 3.3

See Also:

SETSEQ_OFF, Constant Field Values

BOLD

public static final int BOLD

"Bold" attribute of the bond. Recognized only for single and double bonds

See Also:

Constant Field Values

HASHED

public static final int HASHED

"Hashed" attribute of the bond.

See Also:

Constant Field Values

Constructor Detail

MolBond

public MolBond(MolAtom a1,
       MolAtom a2,
       int f)

Construct a bond between two atoms.

Parameters:

a1 - the first atom

a2 - the second atom

f - bond type and other flags

MolBond

protected MolBond(MolBond b)

Copy constructor.

Parameters:

b - the original bond

Since:

3.5.2, 12/15/2004

MolBond

public MolBond(MolAtom a1,
       MolAtom a2)

Construct a single bond between two atoms.

Parameters:

a1 - the first atom

a2 - the second atom

Method Detail

getParent

public final MoleculeGraph getParent()

Gets the parent graph.

Returns:

the parent graph

swap

public void swap()

Change orientation.

getAtom1

public MolAtom getAtom1()

Gets the first endpoint.

Returns:

the first endpoint

getAtom2

public MolAtom getAtom2()

Gets the second endpoint.

Returns:

the second endpoint

getOtherAtom

public final MolAtom getOtherAtom(MolAtom atom)

Gets the other end of the bond.

Parameters:

atom - one of the bond endpoints

Returns:

the other endpoint, or null if the given atom is not an endpoint for this bond

Since:

Marvin 3.0

getLength

public final double getLength()

Gets the actual length of the bond.

Returns:

the distance between the two atoms

getFlags

public final int getFlags()

Gets bond type (4 bits), stereo (2+2+1 bits), topology (2 bits), bond set (5 bits) and reacting center (7 bits) information.

Returns:

the flags

See Also:

TYPE_MASK, STEREO_MASK, TOPOLOGY_MASK, SETSEQ_OFF, REACTING_CENTER_MASK

setFlags

public void setFlags(int f)

Sets bond type (4 bit), stereo (2+2+1 bit), topology (2 bit) bond set (5 bit) and reacting center (7 bits) information. Bond type can be set by calling

 b.setFlags((b.getFlags() & ~MolBond.TYPE_MASK) | type);
 

Valence checking is omitted if you set the bond type this way, without setType.

Parameters:

f - the flags

Since:

Marvin 2.5

See Also:

TYPE_MASK, STEREO_MASK, TOPOLOGY_MASK, SETSEQ_OFF, REACTING_CENTER_MASK, setType(int)

setFlags

public void setFlags(int f,
            int mask)

Sets bond type (3 bit), stereo (2+2+1 bit), and topology (2 bit) information. Bond type can be set by calling

 b.setFlags(type, MolBond.TYPE_MASK);
 

Valence checking is omitted if you set the bond type this way, without setType.

Parameters:

f - new value of the specified bits

mask - bits to set

See Also:

TYPE_MASK, STEREO_MASK, TOPOLOGY_MASK, setFlags(int), setType(int)

getType

public final int getType()

Gets the bond type. Possible values: 1 (single), 2 (double), 3 (triple), aromatic, coordinate, conjugated and query bond types.

Returns:

the bond type

See Also:

AROMATIC, SINGLE_OR_DOUBLE, SINGLE_OR_AROMATIC, DOUBLE_OR_AROMATIC, COORDINATE, CONJUGATED, ANY

getBondType

public final chemaxon.struc.BondType getBondType()

Gets the type of the bond.

Returns:

the bond type of the bond

setType

public void setType(int t)

Sets bond type and does valence checking for the endpoints.

Parameters:

t - the new bond type

See Also:

getType()

getSetSeq

public final int getSetSeq()

Gets the bond set.

Returns:

a number between 0 and SETSEQ_MAX

Since:

Marvin 3.3

setSetSeq

public final void setSetSeq(int g)

Sets the bond set.

Parameters:

g - a number between 0 and SETSEQ_MAX

Since:

Marvin 3.3

isConjugated

public final boolean isConjugated()

Gets the conjugation state of the bond set by the conjugation modul.

Returns:

true if the bond is a member of a conjugated system, false otherwise

Since:

Marvin 4.1, 06/13/2006

isCoordinate

public final boolean isCoordinate()

Tests whether the bond is coordinate.

Returns:

true if it is coordinate bond, false otherwise

Since:

Marvin 5.0, 12/04/2007

isPositionVariation

public final boolean isPositionVariation()

Decides whether this bond is a position variation bond.

Returns:

true if this is a position variation bond, false otherwise

Since:

Marvin 5.3, 01/05/2010

isBold

public final boolean isBold()

Decides whether this bond is bold or not.

Returns:

true if this bond is bold, false otherwise

Since:

Marvin 5.3, 09/24/2009

See Also:

BOLD

isHashed

public final boolean isHashed()

Decides whether this bond is hashed or not.

Returns:

true if this bond is hashed, false otherwise

Since:

Marvin 5.7

See Also:

HASHED

calcOrderFromLength

public int calcOrderFromLength()

Calculate the bond order from the atomic distances. The returned value should only be considered as an approximation.

Returns:

the bond order

calcOrderFromValence

public final int calcOrderFromValence()

Calculate bond order from the types and charges of the two atoms.

Returns:

the bond order

cloneBond

public MolBond cloneBond(MolAtom a1,
                MolAtom a2)

Clones this bond. The parent molecule and the end atoms are not cloned.

Parameters:

a1 - new end atom 1

a2 - new end atom 2

Returns:

the clone

Since:

Marvin 4.1, 09/22/2005

clone

public Object clone()

Make a copy of this object. These are not cloned:

• End Atoms;
• Parent molecule;
• MDocument: Although the bondset information is cloned, when the cloned bond is taken to another MDocument, the format (color, font type) will be lost.

Overrides:

clone in class Object

Returns:

the clone

getDesiredLength

@Deprecated
public double getDesiredLength()

Deprecated. since 5.11, replaced by desiredLength(int, int, int, int).

Desired length of a bond between two atoms in Angstroms. Works only for bonds in a molecule.

Returns:

the desired length

getDesiredLength

@Deprecated
public double getDesiredLength(boolean shortenHbonds)

Deprecated. since 5.11, replaced by desiredLength(int, int, int, int).

Desired length of a bond between two atoms in Angstroms. Works only for bonds in a molecule.

Parameters:

shortenHbonds - use 1.0 as bond length for explicit H bonds in 2D.

Returns:

the desired length

desiredLength

public static double desiredLength(int atno1,
                   int atno2,
                   int type,
                   int dim)

Desired length of a bond between two atoms in Angstroms.

Parameters:

atno1 - atomic number of the first atom

atno2 - atomic number of the second atom

type - bond order

dim - space dimension, 2 or 3

Returns:

the desired length

getStereo1

public final int getStereo1(MolAtom o)

Gets wedge bond type relative to the specified chiral atom.

Parameters:

o - the chiral atom

Returns:

the wedge bond type or zero

See Also:

UP, DOWN, STEREO1_MASK, getFlags()

getCTAtom1

public final MolAtom getCTAtom1()

Gets the first atom for cis/trans stereo calculation.

Returns:

atom a1 from a1-a2=a3-a4, or null in other configurations

See Also:

calcStereo2()

getCTAtom4

public final MolAtom getCTAtom4()

Gets the fourth atom for cis/trans stereo calculation.

Returns:

atom a4 from a1-a2=a3-a4, or null in other configurations

See Also:

calcStereo2()

setStereo2Flags

public void setStereo2Flags(MolAtom a1,
                   MolAtom a4,
                   int stereo2)

Sets double bond stereo information. Normally invoked by the SMILES import process.

Parameters:

a1 - atom number 1 in scheme a1-a2=a3-a4

a4 - atom number 4

stereo2 - CIS/TRANS information

See Also:

StereoConstants.CIS, StereoConstants.TRANS, StereoConstants.CTUNSPEC, StereoConstants.CTUMASK, calcStereo2(MolAtom, MolAtom)

transformCT

public int transformCT(MolAtom a1,
              MolAtom a4,
              int f)

Transform cis/trans stereo information into the `reference frame' of this bond. a1 == null and/or a4 == null is also accepted, null corresponds to any neighbor of a2 or a4 that is different than the reference atoms (the first ligands).

Parameters:

a1 - atom connected to atom1

a4 - atom connected to atom2

f - original flags

Returns:

the transformed flags

calcStereo2

public int calcStereo2()

Computes the stereochemistry of the bond based on the atomic coordinates. Note that this member function does not change the stereo flags. Bond type is not checked.

Returns:

0, CIS, TRANS, or CIS|TRANS

See Also:

StereoConstants, getCTAtom1(), getCTAtom4(), calcStereo2(MolAtom, MolAtom)

calcStereo2

public int calcStereo2(MolAtom atom1,
              MolAtom atom4)

Computes the stereochemistry of the bond based on the atomic coordinates. Note that this member function does not change the stereo flags. Bond type and connectivity are not checked (thus being bound to this bond is not a requirement for atoms a1 and a4).

Parameters:

atom1 - atom number 1 in scheme a1-a2=a3-a4

atom4 - atom number 4

Returns:

0, CIS, TRANS, or CIS|TRANS

See Also:

StereoConstants

calcStereo2

public static int calcStereo2(MolAtom atom1,
              MolAtom atom2,
              MolAtom atom3,
              MolAtom atom4)

Computes the stereochemistry of the atom sequence (scheme a1-a2=a3-a4) based on the atomic coordinates. Note that this member function does not change any stereo flags. Connectivity are not checked.

Parameters:

atom1 - atom number 1 in scheme a1-a2=a3-a4

atom2 - atom number 2 in scheme a1-a2=a3-a4

atom3 - atom number 3 in scheme a1-a2=a3-a4

atom4 - atom number 4 in scheme a1-a2=a3-a4

Returns:

0, CIS, TRANS, or CIS|TRANS

See Also:

StereoConstants

stepWedge

public boolean stepWedge()

Set the bond from 0 to UP or UP to DOWN.

Returns:

true if the initial state was 0 or UP, false after DOWN.

stepWedge

public static boolean stepWedge(MolBond[] bs)

Flip the given bonds to the next state ONLY 1 bond is set to chiral starting from the last bond

Parameters:

bs - bond array which elements can be flipped

Returns:

true if flipping can be continued, false after last step

getQuerystr

public String getQuerystr()

Gets the query properties.

Returns:

the query string

Since:

Marvin 3.4

haveEqualProperties

public boolean haveEqualProperties(MolBond b)

Tests whether two bonds have the same properties. Two bonds have equal properties if their flags are equal.

Returns:

true if they have the same properties, false otherwise

Since:

Marvin 3.4.1, 07/06/2004

overridesAtMerge

protected boolean overridesAtMerge(MolBond e)

Checks if this bond should override another one when two structures are merged. Aromatic bonds override non-aromatic bonds, higher order bonds override lower order bonds.

Parameters:

e - the other bond

Returns:

true if it overrides e, false otherwise

Since:

Marvin 3.5, 09/30/2004

isQuery

public final boolean isQuery()

Tests whether it is query bond or has query property:

• any
• single or double
• single or aromatic
• double or aromatic
• smarts bond
• ring or chain topology

For more information on smarts bond and query bonds, see The JChem Query Guide

Returns:

true if the bond has a query bond type or property, false otherwise

Since:

Marvin 3.4

See Also:

ANY, SINGLE_OR_DOUBLE, SINGLE_OR_AROMATIC, DOUBLE_OR_AROMATIC, TOPOLOGY_MASK, TOPOLOGY_CHAIN, TOPOLOGY_RING

isCollinear

public boolean isCollinear(MolAtom atom)

Returns whether atom is collinear with the bond or not. (Calculates from coordinates.)

Parameters:

atom - Atom to decide about.

Returns:

true if atom and the atoms of the bond lie on the same line

Since:

Marvin 4.0 12/16/2004

getLock

protected final Object getLock()

Gets lock object for synchronization.

Returns:

reference to the top parent graph

toString

public String toString()

Overrides Object.toString() to ease debugging.

Overrides:

toString in class Object

Returns:

a string representation of the object

Since:

Marvin 5.0 12/10/2007

propertySet

public Set<Map.Entry<String,Object>> propertySet()

Returns a set view of the properties (property key - property value mappings) of this bond. Each element in the returned set is a Map.Entry. Changes to the properties are reflected in the set, and vice-versa. The set supports element removal, which removes the corresponding property from this, via the Iterator.remove, Set.remove, removeAll, retainAll, and clear operations. It does not support the add or addAll operations.

Returns:

set view of the properties of this bond.

Since:

Marvin 5.10

propertyKeySet

public Set<String> propertyKeySet()

Returns a set view of the property keys of this bond. Changes to the properties of this bond are reflected in the set, and vice-versa. The set supports element removal, which removes the corresponding property from this atom, via the Iterator.remove, Set.remove, removeAll, retainAll, and clear operations. It does not support the add or addAll operations.

Returns:

set view of the property keys of this bond.

Since:

Marvin 5.10

containsPropertyKey

public boolean containsPropertyKey(String key)

Returns true if this bond has a mapping for the specified property key.

Parameters:

key - the property key which is to be searched for.

Returns:

true if this map contains a mapping for the specified property key.

Since:

Marvin 5.10

removeProperty

public Object removeProperty(String key)

Removes the mapping for this property key from this bond if present.

Parameters:

key - property key whose mapping is to be removed from the bond.

Returns:

previous poperty value associated with specified property key, or null if there was no mapping for property key. A null return can also indicate that the property mapping previously associated null with the specified property key.

Since:

Marvin 5.10

propertyCount

public int propertyCount()

Returns the number of property (property key - property value) mappings of this bond.

Returns:

the number of property mappings of this bond.

Since:

Marvin 5.10

getProperty

public Object getProperty(String key)

Returns the property value to which the specified property key is mapped at this bond, or null if this bond has no mapping for this property key. A return value of null does not necessarily indicate that the bond has no mapping for the property key; it is also possible that the bond explicitly maps the property key to null. The containsKey method may be used to distinguish these two cases.

Parameters:

key - the property key whose associated property value is to be returned.

Returns:

the property value to which this bond maps the specified property key, or null if the bond has no mapping for this property key.

Since:

Marvin 5.10

putProperty

public void putProperty(String key,
               Object value)

Associates the specified value with the specified key at this bond. If this bond previously had a mapping for this property key, the old property value is replaced.

Parameters:

key - property key with which the specified value is to be associated.

value - property value to be associated with the specified property key.

Since:

Marvin 5.10

clearProperties

public void clearProperties()

Removes all properties from this bond.

Since:

Marvin 5.10

isRemovable

@Deprecated
public boolean isRemovable()

Deprecated. As of Marvin 6.2, no replacement.
Not supported feature.

Decides whether the bond can be removed from the molecule. It depends on its end atoms. If one of the end atom is LeavingGroupAtom and not removable then the bond itself is not removable.

Returns:

true