Package org.openscience.cdk.tools.manipulator

Class BondManipulator

java.lang.Object

org.openscience.cdk.tools.manipulator.BondManipulator

public class BondManipulator
extends Object

Class with convenience methods that provide methods to manipulate AtomContainer's. For example:

 AtomContainerManipulator.replaceAtomByAtom(container, atom1, atom2);
 

will replace the Atom in the AtomContainer, but in all the ElectronContainer's it participates too.

Author:

Egon Willighagen

Source code:

main

Belongs to CDK module:

core

Created on:

2003-08-07

Constructor Summary

Constructors

Constructor	Description
BondManipulator()

Method Summary

Modifier and Type	Method	Description
static IBond.Order	createBondOrder(double bondOrder)	Convenience method to convert a double into an IBond.Order.
static void	decreaseBondOrder(IBond bond)	Decrease the order of a bond.
static IBond.Order	decreaseBondOrder(IBond.Order oldOrder)	Returns the IBond.Order one lower.
static double	destroyBondOrder(IBond.Order bondOrder)	Deprecated. use IBond.Order.numeric().doubleValue() instead
static IAtom[]	getAtomArray(IBond container)	Constructs an array of Atom objects from Bond.
static IBond.Order	getMaximumBondOrder(Iterator<IBond> bonds)	Returns the maximum bond order for a List of bonds, given an iterator to the list.
static IBond.Order	getMaximumBondOrder(List<IBond> bonds)	Returns the maximum bond order for a List of bonds.
static IBond.Order	getMaximumBondOrder(IBond.Order firstOrder, IBond.Order secondOrder)	Returns the maximum bond order for the two bond orders.
static IBond.Order	getMaximumBondOrder(IBond firstBond, IBond secondBond)	Returns the maximum bond order for the two bonds.
static IBond.Order	getMinimumBondOrder(Iterator<IBond> bonds)	Returns the minimum bond order for a List of bonds, given an iterator to the list.
static IBond.Order	getMinimumBondOrder(List<IBond> bonds)	Returns the minimum bond order for a List of bonds.
static int	getSingleBondEquivalentSum(Iterator<IBond> bonds)	Get the single bond equivalent (SBE) of a list of bonds, given an iterator to the list.
static int	getSingleBondEquivalentSum(List<IBond> bonds)	Get the single bond equivalent (SBE) of a list of bonds.
static void	increaseBondOrder(IBond bond)	Increment the bond order of this bond.
static IBond.Order	increaseBondOrder(IBond.Order oldOrder)	Returns the IBond.Order one higher.
static boolean	isHigherOrder(IBond.Order first, IBond.Order second)	Returns true if the first bond has a higher bond order than the second bond.
static boolean	isLowerOrder(IBond.Order first, IBond.Order second)	Returns true if the first bond has a lower bond order than the second bond.

Methods inherited from class java.lang.Object

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

Constructor Details

BondManipulator

public BondManipulator()

Method Details

getAtomArray

public static IAtom[] getAtomArray(IBond container)

Constructs an array of Atom objects from Bond.

Parameters:

container - The Bond object.

Returns:

The array of Atom objects.

isLowerOrder

public static boolean isLowerOrder(IBond.Order first,
 IBond.Order second)

Returns true if the first bond has a lower bond order than the second bond. It returns false if the bond order is equal, and if the order of the first bond is larger than that of the second. Also returns false if either bond order is unset.

Parameters:

first - The first bond order object

second - The second bond order object

Returns:

true if the first bond order is lower than the second one, false otherwise

See Also:

• isHigherOrder(org.openscience.cdk.interfaces.IBond.Order, org.openscience.cdk.interfaces.IBond.Order)

isHigherOrder

public static boolean isHigherOrder(IBond.Order first,
 IBond.Order second)

Returns true if the first bond has a higher bond order than the second bond. It returns false if the bond order is equal, and if the order of the first bond is lower than that of the second. Also returns false if either bond order is unset.

Parameters:

first - The first bond order object

second - The second bond order object

Returns:

true if the first bond order is higher than the second one, false otherwise

See Also:

• isLowerOrder(org.openscience.cdk.interfaces.IBond.Order, org.openscience.cdk.interfaces.IBond.Order)

increaseBondOrder

public static IBond.Order increaseBondOrder(IBond.Order oldOrder)

Returns the IBond.Order one higher. Does not increase the bond order beyond the QUADRUPLE bond order.

Parameters:

oldOrder - the old order

Returns:

The incremented bond order

See Also:

• increaseBondOrder(org.openscience.cdk.interfaces.IBond)
• decreaseBondOrder(org.openscience.cdk.interfaces.IBond.Order)
• decreaseBondOrder(org.openscience.cdk.interfaces.IBond)

increaseBondOrder

public static void increaseBondOrder(IBond bond)

Increment the bond order of this bond.

Parameters:

bond - The bond whose order is to be incremented

See Also:

• increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order)
• decreaseBondOrder(org.openscience.cdk.interfaces.IBond.Order)
• decreaseBondOrder(org.openscience.cdk.interfaces.IBond)

decreaseBondOrder

public static IBond.Order decreaseBondOrder(IBond.Order oldOrder)

Returns the IBond.Order one lower. Does not decrease the bond order lower the QUADRUPLE bond order.

Parameters:

oldOrder - the old order

Returns:

the decremented order

See Also:

• decreaseBondOrder(org.openscience.cdk.interfaces.IBond)
• increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order)
• increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order)

decreaseBondOrder

public static void decreaseBondOrder(IBond bond)

Decrease the order of a bond.

Parameters:

bond - The bond in question

See Also:

• decreaseBondOrder(org.openscience.cdk.interfaces.IBond.Order)
• increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order)
• increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order)

createBondOrder

public static IBond.Order createBondOrder(double bondOrder)

Convenience method to convert a double into an IBond.Order. Returns NULL if the bond order is not 1.0, 2.0, 3.0 and 4.0.

Parameters:

bondOrder - The numerical bond order

Returns:

An instance of IBond.Order

See Also:

• destroyBondOrder(org.openscience.cdk.interfaces.IBond.Order)

destroyBondOrder

public static double destroyBondOrder(IBond.Order bondOrder)

Deprecated.

use IBond.Order.numeric().doubleValue() instead

Convert a IBond.Order to a numeric value. Single, double, triple and quadruple bonds are converted to 1.0, 2.0, 3.0 and 4.0 respectively.

Parameters:

bondOrder - The bond order object

Returns:

The numeric value

See Also:

• createBondOrder(double)

getMaximumBondOrder

public static IBond.Order getMaximumBondOrder(List<IBond> bonds)

Returns the maximum bond order for a List of bonds.

Parameters:

bonds - The list of bonds to search through

Returns:

The maximum bond order found

See Also:

• getMaximumBondOrder(java.util.Iterator)

getMaximumBondOrder

public static IBond.Order getMaximumBondOrder(Iterator<IBond> bonds)

Returns the maximum bond order for a List of bonds, given an iterator to the list.

Parameters:

bonds - An iterator for the list of bonds

Returns:

The maximum bond order found

See Also:

• getMaximumBondOrder(java.util.List)

getMaximumBondOrder

public static IBond.Order getMaximumBondOrder(IBond firstBond,
 IBond secondBond)

Returns the maximum bond order for the two bonds.

Parameters:

firstBond - first bond to compare

secondBond - second bond to compare

Returns:

The maximum bond order found

getMaximumBondOrder

public static IBond.Order getMaximumBondOrder(IBond.Order firstOrder,
 IBond.Order secondOrder)

Returns the maximum bond order for the two bond orders.

Parameters:

firstOrder - first bond order to compare

secondOrder - second bond order to compare

Returns:

The maximum bond order found

getMinimumBondOrder

public static IBond.Order getMinimumBondOrder(List<IBond> bonds)

Returns the minimum bond order for a List of bonds.

Parameters:

bonds - The list of bonds to search through

Returns:

The maximum bond order found

See Also:

• getMinimumBondOrder(java.util.Iterator)

getMinimumBondOrder

public static IBond.Order getMinimumBondOrder(Iterator<IBond> bonds)

Returns the minimum bond order for a List of bonds, given an iterator to the list.

Parameters:

bonds - An iterator for the list of bonds

Returns:

The minimum bond order found

See Also:

• getMinimumBondOrder(java.util.List)

getSingleBondEquivalentSum

public static int getSingleBondEquivalentSum(List<IBond> bonds)

Get the single bond equivalent (SBE) of a list of bonds. This sums the bond orders of all the bonds.

Parameters:

bonds - The list of bonds

Returns:

The SBE sum

See Also:

• getSingleBondEquivalentSum(java.util.Iterator)

getSingleBondEquivalentSum

public static int getSingleBondEquivalentSum(Iterator<IBond> bonds)

Get the single bond equivalent (SBE) of a list of bonds, given an iterator to the list.

Parameters:

bonds - An iterator to the list of bonds

Returns:

The SBE sum