org.openscience.cdk.modeling.builder3d

Class AtomPlacer3D

java.lang.Object

org.openscience.cdk.modeling.builder3d.AtomPlacer3D

public class AtomPlacer3D
extends Object

Place aliphatic chains with Z matrix method. Please use ModelBuilder3D to place general molecules.

Author:

chhoppe

See Also:

ModelBuilder3D

Source code:

master

Belongs to CDK module:

builder3d

Keywords:

AtomPlacer3D

Created on:

2004-10-8

Method Summary

Modifier and Type	Method and Description
boolean	allHeavyAtomsPlaced(IAtomContainer ac) True is all the atoms in the given AtomContainer have been placed.
int[]	findHeavyAtomsInChain(IAtomContainer molecule, IAtomContainer chain) Count and find first heavy atom(s) (non Hydrogens) in a chain.
javax.vecmath.Point3d	geometricCenterAllPlacedAtoms(IAtomContainer molecule) Calculates the geometric center of all placed atoms in the atomcontainer.
double	getAngleValue(String id1, String id2, String id3) Gets the angleKey attribute of the AtomPlacer3D object.
double	getBondLengthValue(String id1, String id2) Gets the distanceValue attribute of the parameter set.
IAtom	getFarthestAtom(javax.vecmath.Point3d refAtomPoint, IAtomContainer ac) Gets the farthestAtom attribute of the AtomPlacer3D object.
IAtom	getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule) Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule.
IAtom	getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule) Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object.
IAtom	getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule) Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule.
IAtom	getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom) Returns a placed atom connected to a given atom.
IAtom	getPlacedHeavyAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB) Gets the first placed Heavy Atom around atomA which is not atomB.
IAtomContainer	getPlacedHeavyAtoms(IAtomContainer molecule, IAtom atom) Gets the placed Heavy Atoms connected to an atom.
IAtom	getUnplacedRingHeavyAtom(IAtomContainer molecule, IAtom atom) Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.
void	initilize(Map parameterSet) Initialize the atomPlacer class.
IAtomContainer	markPlaced(IAtomContainer ac) Mark all atoms in chain as placed.
int	numberOfUnplacedHeavyAtoms(IAtomContainer ac) Gets numberOfUnplacedHeavyAtoms (no Flag ISPLACED, no Hydrogens)
void	placeAliphaticHeavyChain(IAtomContainer molecule, IAtomContainer chain) Method assigns 3D coordinates to the heavy atoms in an aliphatic chain.
void	zmatrixChainToCartesian(IAtomContainer molecule, boolean flagBranched) Takes the given Z Matrix coordinates and converts them to cartesian coordinates.

Methods inherited from class java.lang.Object

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

Method Detail

initilize

public void initilize(Map parameterSet)

Initialize the atomPlacer class.

Parameters:

parameterSet - Force Field parameter as Hashtable

findHeavyAtomsInChain

public int[] findHeavyAtomsInChain(IAtomContainer molecule,
                                   IAtomContainer chain)

Count and find first heavy atom(s) (non Hydrogens) in a chain.

Parameters:

molecule - the reference molecule for searching the chain

chain - chain to be searched

Returns:

the atom number of the first heavy atom the number of heavy atoms in the chain

markPlaced

public IAtomContainer markPlaced(IAtomContainer ac)

Mark all atoms in chain as placed. (CDKConstant ISPLACED)

Parameters:

ac - chain

Returns:

chain all atoms marked as placed

placeAliphaticHeavyChain

public void placeAliphaticHeavyChain(IAtomContainer molecule,
                                     IAtomContainer chain)
                              throws CDKException

Method assigns 3D coordinates to the heavy atoms in an aliphatic chain.

Parameters:

molecule - the reference molecule for the chain

chain - the atoms to be assigned, must be connected

Throws:

CDKException - the 'chain' was not a chain

zmatrixChainToCartesian

public void zmatrixChainToCartesian(IAtomContainer molecule,
                                    boolean flagBranched)

Takes the given Z Matrix coordinates and converts them to cartesian coordinates. The first Atom end up in the origin, the second on on the x axis, and the third one in the XY plane. The rest is added by applying the Zmatrix distances, angles and dihedrals. Assign coordinates directly to the atoms.

Parameters:

molecule - the molecule to be placed in 3D

flagBranched - marks branched chain author: egonw,cho

getBondLengthValue

public double getBondLengthValue(String id1,
                                 String id2)

Gets the distanceValue attribute of the parameter set.

Parameters:

id1 - atom1 id

id2 - atom2 id

Returns:

The distanceValue value from the force field parameter set

getAngleValue

public double getAngleValue(String id1,
                            String id2,
                            String id3)

Gets the angleKey attribute of the AtomPlacer3D object.

Parameters:

id1 - Description of the Parameter

id2 - Description of the Parameter

id3 - Description of the Parameter

Returns:

The angleKey value

getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour

public IAtom getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule)

Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule.

Parameters:

molecule -

Returns:

The nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour value author: steinbeck,cho

getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour

public IAtom getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule)

Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule.

Parameters:

molecule -

Returns:

The nextUnplacedHeavyAtomWithUnplacedAliphaticNeigbor author: steinbeck,cho

getNextPlacedHeavyAtomWithUnplacedRingNeighbour

public IAtom getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule)

Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object.

Parameters:

molecule - The atom container under consideration

Returns:

The nextPlacedHeavyAtomWithUnplacedRingNeighbour value

getFarthestAtom

public IAtom getFarthestAtom(javax.vecmath.Point3d refAtomPoint,
                             IAtomContainer ac)

Gets the farthestAtom attribute of the AtomPlacer3D object.

Parameters:

refAtomPoint - Description of the Parameter

ac - Description of the Parameter

Returns:

The farthestAtom value

getUnplacedRingHeavyAtom

public IAtom getUnplacedRingHeavyAtom(IAtomContainer molecule,
                                      IAtom atom)

Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.

Parameters:

molecule -

atom - Description of the Parameter

Returns:

The unplacedRingHeavyAtom value

geometricCenterAllPlacedAtoms

public javax.vecmath.Point3d geometricCenterAllPlacedAtoms(IAtomContainer molecule)

Calculates the geometric center of all placed atoms in the atomcontainer.

Parameters:

molecule -

Returns:

Point3d the geometric center

getPlacedHeavyAtom

public IAtom getPlacedHeavyAtom(IAtomContainer molecule,
                                IAtom atom)

Returns a placed atom connected to a given atom.

Parameters:

molecule -

atom - The Atom whose placed bonding partners are to be returned

Returns:

a placed heavy atom connected to a given atom author: steinbeck

getPlacedHeavyAtom

public IAtom getPlacedHeavyAtom(IAtomContainer molecule,
                                IAtom atomA,
                                IAtom atomB)

Gets the first placed Heavy Atom around atomA which is not atomB.

Parameters:

molecule -

atomA - Description of the Parameter

atomB - Description of the Parameter

Returns:

The placedHeavyAtom value

getPlacedHeavyAtoms

public IAtomContainer getPlacedHeavyAtoms(IAtomContainer molecule,
                                          IAtom atom)

Gets the placed Heavy Atoms connected to an atom.

Parameters:

molecule -

atom - The atom the atoms must be connected to.

Returns:

The placed heavy atoms.

numberOfUnplacedHeavyAtoms

public int numberOfUnplacedHeavyAtoms(IAtomContainer ac)

Gets numberOfUnplacedHeavyAtoms (no Flag ISPLACED, no Hydrogens)

Parameters:

ac - AtomContainer

Returns:

#UnplacedAtoms

allHeavyAtomsPlaced

public boolean allHeavyAtomsPlaced(IAtomContainer ac)

True is all the atoms in the given AtomContainer have been placed.

Parameters:

ac - The AtomContainer to be searched

Returns:

True is all the atoms in the given AtomContainer have been placed