org.openscience.cdk.geometry

Class BondTools

java.lang.Object

org.openscience.cdk.geometry.BondTools

public class BondTools
extends Object

A set of static utility classes for geometric calculations on IBonds. The methods for detecting stereo configurations are described in CDK news, vol 2, p. 64 - 66.

Author:

shk3

Source code:

master

Belongs to CDK module:

standard

Created on:

2005-08-04

Constructor Summary

Constructors

Constructor and Description
BondTools()

Method Summary

Methods

Modifier and Type	Method and Description
static boolean	closeEnoughToBond(IAtom atom1, IAtom atom2, double distanceFudgeFactor) Returns true if the two atoms are within the distance fudge factor of each other.
static double	giveAngle(IAtom from, IAtom to1, IAtom to2) Calls giveAngleBothMethods with bool = true.
static double	giveAngleBothMethods(IAtom from, IAtom to1, IAtom to2, boolean bool) Gives the angle between two lines starting at atom from and going to to1 and to2.
static double	giveAngleBothMethods(javax.vecmath.Point2d from, javax.vecmath.Point2d to1, javax.vecmath.Point2d to2, boolean bool)
static double	giveAngleFromMiddle(IAtom from, IAtom to1, IAtom to2) Calls giveAngleBothMethods with bool = false.
static boolean	isCisTrans(IAtom firstOuterAtom, IAtom firstInnerAtom, IAtom secondInnerAtom, IAtom secondOuterAtom, IAtomContainer ac) Says if two atoms are in cis or trans position around a double bond.
static boolean	isLeft(IAtom whereIs, IAtom viewFrom, IAtom viewTo) Says if an atom is on the left side of a another atom seen from a certain atom or not.
static boolean	isSquarePlanar(IAtomContainer container, IAtom atom) Says if an atom as a center of a square planar chirality.
static boolean	isStereo(IAtomContainer container, IAtom stereoAtom) Says if an atom as a center of any valid stereo configuration or not.
static int	isTetrahedral(IAtomContainer container, IAtom atom, boolean strict) Says if an atom as a center of a tetrahedral chirality.
static int	isTrigonalBipyramidalOrOctahedral(IAtomContainer container, IAtom atom) Says if an atom as a center of a trigonal-bipyramidal or actahedral chirality.
static boolean	isValidDoubleBondConfiguration(IAtomContainer container, IBond bond) Tells if a certain bond is center of a valid double bond configuration.
static void	makeUpDownBonds(IAtomContainer container)
static boolean	stereosAreOpposite(IAtomContainer container, IAtom atom) Says if of four atoms connected two one atom the up and down bonds are opposite or not, i.

Methods inherited from class java.lang.Object

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

Constructor Detail

BondTools

public BondTools()

Method Detail

isValidDoubleBondConfiguration

public static boolean isValidDoubleBondConfiguration(IAtomContainer container,
                                     IBond bond)

Tells if a certain bond is center of a valid double bond configuration.

Parameters:

container - The atomcontainer.

bond - The bond.

Returns:

true=is a potential configuration, false=is not.

isCisTrans

public static boolean isCisTrans(IAtom firstOuterAtom,
                 IAtom firstInnerAtom,
                 IAtom secondInnerAtom,
                 IAtom secondOuterAtom,
                 IAtomContainer ac)
                          throws CDKException

Says if two atoms are in cis or trans position around a double bond. The atoms have to be given to the method like this: firstOuterAtom - firstInnerAtom = secondInnterAtom - secondOuterAtom

Parameters:

firstOuterAtom - See above.

firstInnerAtom - See above.

secondInnerAtom - See above.

secondOuterAtom - See above.

ac - The atom container the atoms are in.

Returns:

true=trans, false=cis.

Throws:

CDKException - The atoms are not in a double bond configuration (no double bond in the middle, same atoms on one side)

isLeft

public static boolean isLeft(IAtom whereIs,
             IAtom viewFrom,
             IAtom viewTo)

Says if an atom is on the left side of a another atom seen from a certain atom or not.

Parameters:

whereIs - The atom the position of which is returned

viewFrom - The atom from which to look

viewTo - The atom to which to look

Returns:

true=is left, false = is not

closeEnoughToBond

public static boolean closeEnoughToBond(IAtom atom1,
                        IAtom atom2,
                        double distanceFudgeFactor)

Returns true if the two atoms are within the distance fudge factor of each other.

Parameters:

atom1 - Description of Parameter

atom2 - Description of Parameter

distanceFudgeFactor - Description of Parameter

Returns:

Description of the Returned Value

Keywords:

join-the-dots, bond creation

giveAngleBothMethods

public static double giveAngleBothMethods(IAtom from,
                          IAtom to1,
                          IAtom to2,
                          boolean bool)

Gives the angle between two lines starting at atom from and going to to1 and to2. If bool=false the angle starts from the middle line and goes from 0 to PI or 0 to -PI if the to2 is on the left or right side of the line. If bool=true the angle goes from 0 to 2PI.

Parameters:

from - the atom to view from.

to1 - first direction to look in.

to2 - second direction to look in.

bool - true=angle is 0 to 2PI, false=angel is -PI to PI.

Returns:

The angle in rad.

giveAngleBothMethods

public static double giveAngleBothMethods(javax.vecmath.Point2d from,
                          javax.vecmath.Point2d to1,
                          javax.vecmath.Point2d to2,
                          boolean bool)

isTetrahedral

public static int isTetrahedral(IAtomContainer container,
                IAtom atom,
                boolean strict)

Says if an atom as a center of a tetrahedral chirality. This method uses wedge bonds. 3D coordinates are not taken into account. If there are no wedge bonds around a potential stereo center, it will not be found.

Parameters:

atom - The atom which is the center

container - The atomContainer the atom is in

Returns:

0=is not tetrahedral; >1 is a certain depiction of tetrahedrality (evaluated in parse chain)

isTrigonalBipyramidalOrOctahedral

public static int isTrigonalBipyramidalOrOctahedral(IAtomContainer container,
                                    IAtom atom)

Says if an atom as a center of a trigonal-bipyramidal or actahedral chirality. This method uses wedge bonds. 3D coordinates are not taken into account. If there are no wedge bonds around a potential stereo center, it will not be found.

Parameters:

atom - The atom which is the center

container - The atomContainer the atom is in

Returns:

true=is square planar, false=is not

isStereo

public static boolean isStereo(IAtomContainer container,
               IAtom stereoAtom)

Says if an atom as a center of any valid stereo configuration or not. This method uses wedge bonds. 3D coordinates are not taken into account. If there are no wedge bonds around a potential stereo center, it will not be found.

Parameters:

stereoAtom - The atom which is the center

container - The atomContainer the atom is in

Returns:

true=is a stereo atom, false=is not

isSquarePlanar

public static boolean isSquarePlanar(IAtomContainer container,
                     IAtom atom)

Says if an atom as a center of a square planar chirality. This method uses wedge bonds. 3D coordinates are not taken into account. If there are no wedge bonds around a potential stereo center, it will not be found.

Parameters:

atom - The atom which is the center

container - The atomContainer the atom is in

Returns:

true=is square planar, false=is not

stereosAreOpposite

public static boolean stereosAreOpposite(IAtomContainer container,
                         IAtom atom)

Says if of four atoms connected two one atom the up and down bonds are opposite or not, i. e.if it's tetrehedral or square planar. The method does not check if there are four atoms and if two or up and two are down

Parameters:

atom - The atom which is the center

container - The atomContainer the atom is in

Returns:

true=are opposite, false=are not

giveAngle

public static double giveAngle(IAtom from,
               IAtom to1,
               IAtom to2)

Calls giveAngleBothMethods with bool = true.

Parameters:

from - the atom to view from

to1 - first direction to look in

to2 - second direction to look in

Returns:

The angle in rad from 0 to 2*PI

giveAngleFromMiddle

public static double giveAngleFromMiddle(IAtom from,
                         IAtom to1,
                         IAtom to2)

Calls giveAngleBothMethods with bool = false.

Parameters:

from - the atom to view from

to1 - first direction to look in

to2 - second direction to look in

Returns:

The angle in rad from -PI to PI

makeUpDownBonds

public static void makeUpDownBonds(IAtomContainer container)