chemaxon.struc

Class QueryBond

java.lang.Object

chemaxon.struc.MolBond

chemaxon.struc.QueryBond

All Implemented Interfaces:

StereoConstants, java.io.Serializable

@PublicAPI
public class QueryBond
extends MolBond

Chemical bond.

Since:

Marvin 3.4, 06/04/2004

Version:

5.3, 04/27/2009

Author:

Peter Csizmadia, Andras Volford

See Also:

Serialized Form

Field Summary

Fields inherited from class chemaxon.struc.MolBond

ANY, AROMATIC, BOLD, CCLENGTH, CONJUGATED, COORDINATE, DOUBLE_OR_AROMATIC, DOWN, HASHED, HYDROGEN, RC_CHANGE, RC_MAKE_AND_CHANGE, RC_MAKE_OR_BREAK, RC_NOT_CENTER, RC_NOT_MODIFIED, RC_REACTING_CENTER, RC_UNMAPPED, REACTING_CENTER_MASK, SETSEQ_MAX, SETSEQ_OFF, SINGLE_OR_AROMATIC, SINGLE_OR_DOUBLE, STEREO_MASK, STEREO1_MASK, STEREO2_CARE, TOPOLOGY_CHAIN, TOPOLOGY_MASK, TOPOLOGY_RING, TYPE_MASK, UP, WAVY

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_ALL_POSSIBLE, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CIS_TRANS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_NONE, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS

Constructor Summary

Constructors

Constructor and Description
QueryBond(MolAtom a1, MolAtom a2) Construct an any bond between two atoms.
QueryBond(MolAtom a1, MolAtom a2, int flags) Construct an any bond between two atoms.
QueryBond(MolAtom a1, MolAtom a2, java.lang.String s) Construct a query bond between two atoms.
QueryBond(QueryBond b) Copy constructor.

Method Summary

Modifier and Type	Method and Description
java.lang.Object	clone() Make a copy of this object.
MolBond	cloneBond(MolAtom a1, MolAtom a2) Clones this bond.
java.lang.String	getQuerystr() Gets the query properties.
boolean	haveEqualProperties(MolBond e) Checks if two bonds have the same properties.
void	setQuerystr(java.lang.String s) Sets the query string.

Methods inherited from class chemaxon.struc.MolBond

calcOrderFromLength, calcOrderFromValence, calcStereo2, calcStereo2, calcStereo2, clearProperties, containsPropertyKey, desiredLength, getAtom1, getAtom2, getBondType, getCTAtom1, getCTAtom4, getDesiredLength, getDesiredLength, getFlags, getLength, getLock, getOtherAtom, getParent, getProperty, getSetSeq, getStereo1, getType, isBold, isCollinear, isConjugated, isCoordinate, isHashed, isPositionVariation, isQuery, isRemovable, overridesAtMerge, propertyCount, propertyKeySet, propertySet, putProperty, removeProperty, setFlags, setFlags, setSetSeq, setStereo2Flags, setType, stepWedge, swap, toString, transformCT

Methods inherited from class java.lang.Object

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

Constructor Detail

QueryBond

public QueryBond(MolAtom a1,
                 MolAtom a2)

Construct an any bond between two atoms.

Parameters:

a1 - the first atom

a2 - the second atom

QueryBond

public QueryBond(MolAtom a1,
                 MolAtom a2,
                 int flags)

Construct an any bond between two atoms.

Parameters:

a1 - the first atom

a2 - the second atom

flags - bond type and other flags

QueryBond

public QueryBond(MolAtom a1,
                 MolAtom a2,
                 java.lang.String s)

Construct a query bond between two atoms.

Parameters:

a1 - the first atom

a2 - the second atom

s - the query string

QueryBond

public QueryBond(QueryBond b)

Copy constructor.

Parameters:

b - the original bond

Since:

3.5.2, 12/15/2004

Method Detail

getQuerystr

public java.lang.String getQuerystr()

Gets the query properties.

Overrides:

getQuerystr in class MolBond

Returns:

the query string

setQuerystr

public void setQuerystr(java.lang.String s)

Sets the query string.

Parameters:

s - the query string

haveEqualProperties

public boolean haveEqualProperties(MolBond e)

Checks if two bonds have the same properties.

Overrides:

haveEqualProperties in class MolBond

Returns:

true if they have the same properties, false otherwise

Since:

Marvin 3.4.1, 07/21/2004

cloneBond

public MolBond cloneBond(MolAtom a1,
                         MolAtom a2)

Clones this bond. Query string, bond type, stereo, topology and reacting center information are cloned with the bond.

Overrides:

cloneBond in class MolBond

Parameters:

a1 - new end atom 1

a2 - new end atom 2

Returns:

the clone

Since:

Marvin 4.1, 09/22/2005

clone

public java.lang.Object clone()

Make a copy of this object. Query string, bond type, stereo, topology and reacting center information are cloned with the bond.

Overrides:

clone in class MolBond

Returns:

the clone