chemaxon.struc
Class MolBond

java.lang.Object
  chemaxon.struc.CEdge
      chemaxon.struc.MolBond

All Implemented Interfaces:

java.io.Serializable, StereoConstants

public class MolBond

extends CEdge

implements StereoConstants

Chemical bond.

Version:

3.3, 08/26/2003

Author:

Peter Csizmadia, Tamas Karpati, Andras Volford

See Also:

Serialized Form

Field Summary

static int	ANY Any bond type.
static int	AROMATIC Aromatic bond type.
static int	ARROW Reaction arrow.
static double	CCLENGTH Default bond length.
static int	DOUBLE_OR_AROMATIC Double or aromatic query bond type.
static int	DOWN Single bond down.
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.

Fields inherited from class chemaxon.struc.CEdge

node1, node2

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

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.

Method Summary

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.
java.lang.Object	clone() Make a copy of this object.
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.
MolAtom	getCTAtom1() Gets the first atom for cis/trans stereo calculation.
MolAtom	getCTAtom4() Gets the fourth atom for cis/trans stereo calculation.
int	getFlags() Gets bond type (3 bit), stereo (2+2+1 bit), topology (2 bit) and bond set (5 bit) information.
double	getLength() Gets the actual length of the bond.
MolAtom	getOtherAtom(MolAtom atom) Gets the other end of the bond.
int	getSetSeq() Gets the bond set.
int	getStereo1(CNode o) Gets wedge bond type relative to the specified chiral atom.
int	getType() Gets the bond type.
boolean	isArrow() Checks if this edge represents a reaction arrow or not.
void	setFlags(int f) Sets bond type (3 bit), stereo (2+2+1 bit), topology (2 bit) and bond set (5 bit) 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(CNode a1, CNode 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
int	transformCT(CNode a1, CNode a4, int f) Transform cis/trans stereo information into the `reference frame' of this bond.

Methods inherited from class chemaxon.struc.CEdge

equals, getLock, getNode1, getNode2, getOtherNode, getParent, swap, toString

Methods inherited from class java.lang.Object

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

Field Detail

CCLENGTH

public static final double CCLENGTH

Default bond length.

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

ANY

public static final int ANY

Any bond type.

See Also:

Constant Field Values

UP

public static final int UP

Single bond up.

See Also:

Constant Field Values

DOWN

public static final int DOWN

Single bond down.

See Also:

Constant Field Values

ARROW

public static final int ARROW

Reaction arrow.

See Also:

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

SETSEQ_OFF

public static final int SETSEQ_OFF

Bond set sequence number offset in flags.

Since:

3.3

See Also:

SETSEQ_MAX, Constant Field Values

SETSEQ_MAX

public static final int SETSEQ_MAX

Maximum bond set sequence number.

Since:

3.3

See Also:

SETSEQ_OFF, 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

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

public MolBond(MolAtom a1,
               MolAtom a2)

Construct a single bond between two atoms.

Parameters:

a1 - the first atom

a2 - the second atom

Method Detail

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 edge endpoints

Returns:

the other end

Since:

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 (3 bit), stereo (2+2+1 bit), topology (2 bit) and bond set (5 bit) information.

Returns:

the flags

See Also:

TYPE_MASK, STEREO_MASK, TOPOLOGY_MASK, SETSEQ_OFF

setFlags

public final void setFlags(int f)

Sets bond type (3 bit), stereo (2+2+1 bit), topology (2 bit) and bond set (5 bit) 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:

2.5

See Also:

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

setFlags

public final 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), query bond types.

Returns:

the bond type

See Also:

AROMATIC, SINGLE_OR_DOUBLE, SINGLE_OR_AROMATIC, DOUBLE_OR_AROMATIC, ANY

setType

public final void setType(int t)

Sets bond type and does valence checking for the endpoints.

See Also:

getType()

getSetSeq

public final int getSetSeq()

Gets the bond set.

Returns:

a number between 0 and SETSEQ_MAX

Since:

3.3

setSetSeq

public final void setSetSeq(int g)

Sets the bond set.

Parameters:

g - a number between 0 and SETSEQ_MAX

Since:

3.3

isArrow

public final boolean isArrow()

Checks if this edge represents a reaction arrow or not.

Returns:

true if this edge represents a reaction arrow, false otherwise

See Also:

ARROW

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

clone

public java.lang.Object clone()

Make a copy of this object.

Overrides:

clone in class CEdge

Returns:

the clone

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(CNode 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(CNode a1,
                            CNode 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(CNode a1,
                       CNode 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 node1

a4 - atom connected to node2

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 CTUNKNOWN

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 CTUNKNOWN

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