org.openscience.cdk.layout

Class AtomPlacer

java.lang.Object

org.openscience.cdk.layout.AtomPlacer

public class AtomPlacer
extends Object

Methods for generating coordinates for atoms in various situations. They can be used for Automated Structure Diagram Generation or in the interactive buildup of molecules by the user.

Author:

steinbeck

Source code:

master

Belongs to CDK module:

sdg

Created on:

2003-08-29

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	debug
static String	PRIORITY

Constructor Summary

Constructors

Constructor and Description
AtomPlacer() Constructor for the AtomPlacer object

Method Summary

Methods

Modifier and Type	Method and Description
static boolean	allPlaced(IAtomContainer ac) True is all the atoms in the given AtomContainer have been placed
static void	breadthFirstSearch(IAtomContainer ac, List<IAtom> sphere, IAtomContainer[] pathes) Performs a breadthFirstSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom, and searches for the longest aliphatic chain which is yet unplaced.
void	distributePartners(IAtom atom, IAtomContainer placedNeighbours, javax.vecmath.Point2d sharedAtomsCenter, IAtomContainer unplacedNeighbours, double bondLength) Distribute the bonded atoms (neighbours) of an atom such that they fill the remaining space around an atom in a geometrically nice way.
static IAtomContainer	getInitialLongestChain(IAtomContainer molecule) Search an aliphatic molecule for the longest chain.
static IAtomContainer	getLongestUnplacedChain(IAtomContainer molecule, IAtom startAtom) Search a molecule for the longest unplaced, aliphatic chain in it.
IAtomContainer	getMolecule() Return the molecule the AtomPlacer currently works with
javax.vecmath.Vector2d	getNextBondVector(IAtom atom, IAtom previousAtom, javax.vecmath.Point2d distanceMeasure, boolean trans) Returns the next bond vector needed for drawing an extended linear chain of atoms.
static IAtomContainer	getPlacedAtoms(IAtomContainer ac) Get all the placed atoms in an AtomContainer
static String	listNumbers(IAtomContainer mol, IAtomContainer ac) Returns a string with the numbers of all atoms in an AtomContainer relative to a given molecule.
static String	listNumbers(IAtomContainer mol, List<IAtom> ac) Returns a string with the numbers of all atoms in a Vector relative to a given molecule.
String	listPlaced(IAtomContainer ac) Returns a string with the numbers of all placed atoms in an AtomContainer
static void	markNotPlaced(IAtomContainer ac) Marks all the atoms in the given AtomContainer as not placed
static void	markPlaced(IAtomContainer ac) Marks all the atoms in the given AtomContainer as placed
void	partitionPartners(IAtom atom, IAtomContainer unplacedPartners, IAtomContainer placedPartners) Partition the bonding partners of a given atom into placed (coordinates assinged) and not placed.
void	placeLinearChain(IAtomContainer atomContainer, javax.vecmath.Vector2d initialBondVector, double bondLength) Places the atoms in a linear chain.
void	populatePolygonCorners(List<IAtom> atoms, javax.vecmath.Point2d center, double thetaBeg, double thetaStep, double radius) Populates the corners of a polygon with atoms.
void	setMolecule(IAtomContainer molecule) Sets the molecule the AtomPlacer currently works with
static boolean	shouldBeLinear(IAtom atom, IAtomContainer molecule) Deprecated.

Methods inherited from class java.lang.Object

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

Field Detail

debug

public static final boolean debug

See Also:

Constant Field Values

PRIORITY

public static final String PRIORITY

See Also:

Constant Field Values

Constructor Detail

AtomPlacer

public AtomPlacer()

Constructor for the AtomPlacer object

Method Detail

getMolecule

public IAtomContainer getMolecule()

Return the molecule the AtomPlacer currently works with

Returns:

the molecule the AtomPlacer currently works with

setMolecule

public void setMolecule(IAtomContainer molecule)

Sets the molecule the AtomPlacer currently works with

Parameters:

molecule - the molecule the AtomPlacer currently works with

distributePartners

public void distributePartners(IAtom atom,
                      IAtomContainer placedNeighbours,
                      javax.vecmath.Point2d sharedAtomsCenter,
                      IAtomContainer unplacedNeighbours,
                      double bondLength)

Distribute the bonded atoms (neighbours) of an atom such that they fill the remaining space around an atom in a geometrically nice way. IMPORTANT: This method is not supposed to handle the case of one or no place neighbor. In the case of one placed neigbor, the chain placement methods should be used.

Parameters:

atom - The atom whose partners are to be placed

placedNeighbours - The atoms which are already placed

unplacedNeighbours - The partners to be placed

bondLength - The standared bond length for the newly placed Atoms

sharedAtomsCenter - The 2D centre of the placed Atoms

placeLinearChain

public void placeLinearChain(IAtomContainer atomContainer,
                    javax.vecmath.Vector2d initialBondVector,
                    double bondLength)

Places the atoms in a linear chain.

Expects the first atom to be placed and places the next atom according to initialBondVector. The rest of the chain is placed such that it is as linear as possible (in the overall result, the angles in the chain are set to 120 Deg.)

Parameters:

atomContainer - The IAtomContainer containing the chain atom to be placed

initialBondVector - The Vector indicating the direction of the first bond

bondLength - The factor used to scale the initialBondVector

getNextBondVector

public javax.vecmath.Vector2d getNextBondVector(IAtom atom,
                                       IAtom previousAtom,
                                       javax.vecmath.Point2d distanceMeasure,
                                       boolean trans)

Returns the next bond vector needed for drawing an extended linear chain of atoms. It assumes an angle of 120 deg for a nice chain layout and calculates the two possible placments for the next atom. It returns the vector pointing farmost away from a given start atom.

Parameters:

atom - An atom for which the vector to the next atom to draw is calculated

previousAtom - The preceding atom for angle calculation

distanceMeasure - A point from which the next atom is to be farmost away

trans - if true E (trans) configurations are built, false makes Z (cis) configurations

Returns:

A vector pointing to the location of the next atom to draw

populatePolygonCorners

public void populatePolygonCorners(List<IAtom> atoms,
                          javax.vecmath.Point2d center,
                          double thetaBeg,
                          double thetaStep,
                          double radius)

Populates the corners of a polygon with atoms. Used to place atoms in a geometrically regular way around a ring center or another atom. If this is used to place the bonding partner of an atom (and not to draw a ring) we want to place the atoms such that those with highest "weight" are placed furthermost away from the rest of the molecules. The "weight" mentioned here is calculated by a modified morgan number algorithm.

Parameters:

atoms - All the atoms to draw

thetaBeg - A start angle (in radians), giving the angle of the most clockwise atom which has already been placed

thetaStep - An angle (in radians) to be added for each atom from atomsToDraw

center - The center of a ring, or an atom for which the partners are to be placed

radius - The radius of the polygon to be populated: bond length or ring radius

partitionPartners

public void partitionPartners(IAtom atom,
                     IAtomContainer unplacedPartners,
                     IAtomContainer placedPartners)

Partition the bonding partners of a given atom into placed (coordinates assinged) and not placed.

Parameters:

atom - The atom whose bonding partners are to be partitioned

unplacedPartners - A vector for the unplaced bonding partners to go in

placedPartners - A vector for the placed bonding partners to go in

getInitialLongestChain

public static IAtomContainer getInitialLongestChain(IAtomContainer molecule)
                                             throws CDKException

Search an aliphatic molecule for the longest chain. This is the method to be used if there are no rings in the molecule and you want to layout the longest chain in the molecule as a starting point of the structure diagram generation.

Parameters:

molecule - The molecule to be search for the longest unplaced chain

Returns:

An AtomContainer holding the longest chain.

Throws:

NoSuchAtomException - Description of the Exception

CDKException

getLongestUnplacedChain

public static IAtomContainer getLongestUnplacedChain(IAtomContainer molecule,
                                     IAtom startAtom)
                                              throws CDKException

Search a molecule for the longest unplaced, aliphatic chain in it. If an aliphatic chain encounters an unplaced ring atom, the ring atom is also appended to allow for it to be laid out. This gives us a vector for attaching the unplaced ring later.

Parameters:

molecule - The molecule to be search for the longest unplaced chain

startAtom - A start atom from which the chain search starts

Returns:

An AtomContainer holding the longest unplaced chain.

Throws:

CDKException - Description of the Exception

breadthFirstSearch

public static void breadthFirstSearch(IAtomContainer ac,
                      List<IAtom> sphere,
                      IAtomContainer[] pathes)
                               throws CDKException

Performs a breadthFirstSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom, and searches for the longest aliphatic chain which is yet unplaced. If the search encounters an unplaced ring atom, it is also appended to the chain so that this last bond of the chain can also be laid out. This gives us the orientation for the attachment of the ring system.

Parameters:

ac - The AtomContainer to be searched

sphere - A sphere of atoms to start the search with

pathes - A vector of N pathes (N = no of heavy atoms).

Throws:

CDKException - Description of the Exception

listPlaced

public String listPlaced(IAtomContainer ac)

Returns a string with the numbers of all placed atoms in an AtomContainer

Parameters:

ac - The AtomContainer for which the placed atoms are to be listed

Returns:

A string with the numbers of all placed atoms in an AtomContainer

listNumbers

public static String listNumbers(IAtomContainer mol,
                 IAtomContainer ac)
                          throws CDKException

Returns a string with the numbers of all atoms in an AtomContainer relative to a given molecule. I.e. the number the is listesd is the position of each atom in the molecule.

Parameters:

ac - The AtomContainer for which the placed atoms are to be listed

mol - Description of the Parameter

Returns:

A string with the numbers of all placed atoms in an AtomContainer

Throws:

CDKException - Description of the Exception

listNumbers

public static String listNumbers(IAtomContainer mol,
                 List<IAtom> ac)

Returns a string with the numbers of all atoms in a Vector relative to a given molecule. I.e. the number the is listesd is the position of each atom in the molecule.

Parameters:

ac - The Vector for which the placed atoms are to be listed

mol - Description of the Parameter

Returns:

A string with the numbers of all placed atoms in an AtomContainer

allPlaced

public static boolean allPlaced(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

markNotPlaced

public static void markNotPlaced(IAtomContainer ac)

Marks all the atoms in the given AtomContainer as not placed

Parameters:

ac - The AtomContainer whose atoms are to be marked

markPlaced

public static void markPlaced(IAtomContainer ac)

Marks all the atoms in the given AtomContainer as placed

Parameters:

ac - The AtomContainer whose atoms are to be marked

getPlacedAtoms

public static IAtomContainer getPlacedAtoms(IAtomContainer ac)

Get all the placed atoms in an AtomContainer

Parameters:

ac - The AtomContainer to be searched for placed atoms

Returns:

An AtomContainer containing all the placed atoms

shouldBeLinear

@Deprecated
public static boolean shouldBeLinear(IAtom atom,
                                IAtomContainer molecule)

Deprecated.