A B C D G H J L M O P R S T

A

addMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler

Adds a Molecule to the list of templates use by this TemplateHandler.

allPlaced(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

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

allPlaced(IRingSet) - Method in class org.openscience.cdk.layout.RingPlacer

True if coordinates have been assigned to all atoms in all rings.

areIntersected(IBond, IBond) - Method in class org.openscience.cdk.layout.OverlapResolver

Deprecated.

Checks if two bonds cross each other.

AtomPlacer - Class in org.openscience.cdk.layout

Methods for generating coordinates for atoms in various situations.

AtomPlacer() - Constructor for class org.openscience.cdk.layout.AtomPlacer

Constructor for the AtomPlacer object

B

breadthFirstSearch(IAtomContainer, List<IAtom>, IAtomContainer[]) - Static method in class org.openscience.cdk.layout.AtomPlacer

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.

C

checkAndMarkPlaced(IRingSet) - Method in class org.openscience.cdk.layout.RingPlacer

Walks throught the atoms of each ring in a ring set and marks a ring as PLACED if all of its atoms have been placed.

createFromSubstructure(Pattern, Iterable<IAtomContainer>) - Static method in class org.openscience.cdk.layout.TemplateHandler

Create a template from a substructure pattern.

createFromSubstructure(Pattern, IAtomContainer) - Static method in class org.openscience.cdk.layout.TemplateHandler

Create a template from a substructure pattern.

createSingleton(IAtomContainer) - Static method in class org.openscience.cdk.layout.TemplateHandler

Singleton template instance, mainly useful for aligning molecules.

D

debug - Static variable in class org.openscience.cdk.layout.AtomPlacer

DEFAULT_BOND_LENGTH - Static variable in class org.openscience.cdk.layout.StructureDiagramGenerator

DEFAULT_BOND_VECTOR - Static variable in class org.openscience.cdk.layout.StructureDiagramGenerator

defaultAngles - Static variable in class org.openscience.cdk.layout.RingPlacer

Default ring start angles.

displace(IAtomContainer, Vector, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver

Deprecated.

Makes a small displacement to some atoms or rings in the given atomcontainer.

distributePartners(IAtom, IAtomContainer, Point2d, IAtomContainer, double) - Method in class org.openscience.cdk.layout.AtomPlacer

Distribute the bonded atoms (neighbours) of an atom such that they fill the remaining space around an atom in a geometrically nice way.

G

generateCoordinates(IAtomContainer) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Convenience method for generating 2D coordinates.

generateCoordinates(IReaction) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Convenience method to generate 2D coordinates for a reaction.

generateCoordinates(Vector2d) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

The main method of this StructurDiagramGenerator.

generateCoordinates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

The main method of this StructurDiagramGenerator.

generateExperimentalCoordinates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Deprecated.

use StructureDiagramGenerator.generateCoordinates()

generateExperimentalCoordinates(Vector2d) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Deprecated.

use StructureDiagramGenerator.generateCoordinates()

getAtomOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver

Deprecated.

Calculates a score based on the overlap of atoms.

getAtomPlacer() - Method in class org.openscience.cdk.layout.RingPlacer

getBondLength() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Returns the bond length used for laying out the molecule.

getBondOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver

Deprecated.

Calculates a score based on the intersection of bonds.

getInitialLongestChain(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

Search an aliphatic molecule for the longest chain.

getLongestUnplacedChain(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.layout.AtomPlacer

Search a molecule for the longest unplaced, aliphatic chain in it.

getMappedSubstructures(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler

Checks if one of the loaded templates is a substructure in the given Molecule and returns all matched substructures in a IAtomContainerSet.

getMolecule() - Method in class org.openscience.cdk.layout.AtomPlacer

Return the molecule the AtomPlacer currently works with

getMolecule() - Method in class org.openscience.cdk.layout.RingPlacer

getMolecule() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Returns the molecule, usually used after a call of generateCoordinates()

getNativeRingRadius(IRing, double) - Method in class org.openscience.cdk.layout.RingPlacer

Returns the ring radius of a perfect polygons of size ring.getAtomCount() The ring radius is the distance of each atom to the ringcenter.

getNextBondVector(IAtom, IAtom, Point2d, boolean) - Method in class org.openscience.cdk.layout.AtomPlacer

Returns the next bond vector needed for drawing an extended linear chain of atoms.

getOtherBondAtom(IAtom, IBond) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Returns the other atom of the bond.

getOverlapScore(IAtomContainer, Vector, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver

Deprecated.

Calculates a score based on the overlap of atoms and intersection of bonds.

getPlacedAtoms(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

Get all the placed atoms in an AtomContainer

getTemplateAt(int) - Method in class org.openscience.cdk.layout.TemplateHandler

Gets the templateAt attribute of the TemplateHandler object

getTemplateCount() - Method in class org.openscience.cdk.layout.TemplateHandler

Gets the templateCount attribute of the TemplateHandler object

getTemplateHandler() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Deprecated.

always null, substructure templates are not used anymore

getUseTemplates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Deprecated.

always false, substructure templates are not used anymore

H

HydrogenPlacer - Class in org.openscience.cdk.layout

This is a wrapper class for some existing methods in AtomPlacer.

HydrogenPlacer() - Constructor for class org.openscience.cdk.layout.HydrogenPlacer

J

jcpAngles - Static variable in class org.openscience.cdk.layout.RingPlacer

Suggested ring start angles for JChempaint, different due to Y inversion of canvas.

L

listNumbers(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

Returns a string with the numbers of all atoms in an AtomContainer relative to a given molecule.

listNumbers(IAtomContainer, List<IAtom>) - Static method in class org.openscience.cdk.layout.AtomPlacer

Returns a string with the numbers of all atoms in a Vector relative to a given molecule.

listPlaced(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer

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

loadTemplates(IChemObjectBuilder) - Method in class org.openscience.cdk.layout.TemplateHandler

Loads all existing templates into memory.

M

mapTemplateExact(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler

Checks if one of the loaded templates is isomorph to the given Molecule.

mapTemplates(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler

Checks if one of the loaded templates is a substructure in the given Molecule.

markNotPlaced(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

Marks all the atoms in the given AtomContainer as not placed

markPlaced(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

Marks all the atoms in the given AtomContainer as placed

O

org.openscience.cdk.layout - package org.openscience.cdk.layout

OverlapPair(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.layout.OverlapResolver.OverlapPair

Deprecated.

Constructor for the OverlapPair object.

OverlapResolver - Class in org.openscience.cdk.layout

Deprecated.

does not resolve overlaps correctly

OverlapResolver() - Constructor for class org.openscience.cdk.layout.OverlapResolver

Deprecated.

OverlapResolver.OverlapPair - Class in org.openscience.cdk.layout

Deprecated.

A little helper class to store pairs of overlapping atoms.

P

partitionNonRingPartners(IAtom, IRing, IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.layout.RingPlacer

Partition the bonding partners of a given atom into ring atoms and non-ring atoms

partitionPartners(IAtom, IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer

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

placeFusedRing(IRing, IAtomContainer, Vector2d, double) - Method in class org.openscience.cdk.layout.RingPlacer

Generated coordinates for a given ring, which is fused to another ring.

placeHydrogens2D(IAtomContainer, double) - Method in class org.openscience.cdk.layout.HydrogenPlacer

Place all hydrogens connected to atoms which have already been laid out.

placeHydrogens2D(IAtomContainer, IAtom) - Method in class org.openscience.cdk.layout.HydrogenPlacer

Place hydrogens connected to the given atom using the average bond length in the container.

placeHydrogens2D(IAtomContainer, IAtom, double) - Method in class org.openscience.cdk.layout.HydrogenPlacer

Place hydrogens connected to the provided atom atom using the specified bondLength.

placeLinearChain(IAtomContainer, Vector2d, double) - Method in class org.openscience.cdk.layout.AtomPlacer

Places the atoms in a linear chain.

placeRing(IRing, IAtomContainer, Point2d, Vector2d, double) - Method in class org.openscience.cdk.layout.RingPlacer

Generated coordinates for a given ring.

placeRing(IRing, Point2d, double) - Method in class org.openscience.cdk.layout.RingPlacer

Place ring with default start angles, using RingPlacer.defaultAngles.

placeRing(IRing, Point2d, double, Map<Integer, Double>) - Method in class org.openscience.cdk.layout.RingPlacer

Place ring with user provided angles.

placeRingSubstituents(IRingSet, double) - Method in class org.openscience.cdk.layout.RingPlacer

Positions the aliphatic substituents of a ring system

placeSpiroRing(IRing, IAtomContainer, Point2d, Vector2d, double) - Method in class org.openscience.cdk.layout.RingPlacer

Generated coordinates for a given ring, which is connected to a spiro ring.

populatePolygonCorners(List<IAtom>, Point2d, double, double, double) - Method in class org.openscience.cdk.layout.AtomPlacer

Populates the corners of a polygon with atoms.

PRIORITY - Static variable in class org.openscience.cdk.layout.AtomPlacer

R

RAD_30 - Static variable in class org.openscience.cdk.layout.RingPlacer

RAD_30 - Static variable in class org.openscience.cdk.layout.StructureDiagramGenerator

removeMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler

resolveOverlap(IAtomContainer, IRingSet) - Method in class org.openscience.cdk.layout.OverlapResolver

Deprecated.

Main method to be called to resolve overlap situations.

RingPlacer - Class in org.openscience.cdk.layout

Class providing methods for generating coordinates for ring atoms.

RingPlacer() - Constructor for class org.openscience.cdk.layout.RingPlacer

The empty constructor.

S

setAlignMappedReaction(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Set whether reaction reactants should be allignned to their product.

setAtomPlacer(AtomPlacer) - Method in class org.openscience.cdk.layout.RingPlacer

setBondLength(double) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Deprecated.

use GeometryUtil.scaleMolecule(IAtomContainer, double)

setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer

Sets the molecule the AtomPlacer currently works with

setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.RingPlacer

setMolecule(IAtomContainer, boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

setMolecule(IAtomContainer, boolean, Set<IAtom>, Set<IBond>) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Assigns a molecule to be laid out.

setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Assings a molecule to be layed out.

setTemplateHandler(TemplateHandler) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Deprecated.

substructure templates are no longer used for layout but those provided here will be converted to identity templates

setUseIdentityTemplates(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Set whether identity templates are used.

setUseTemplates(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Deprecated.

always false, substructure templates are not used anymore

shouldBeLinear(IAtom, IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

Deprecated.

StructureDiagramGenerator - Class in org.openscience.cdk.layout

Generates 2D coordinates for a molecule for which only connectivity is known or the coordinates have been discarded for some reason.

StructureDiagramGenerator() - Constructor for class org.openscience.cdk.layout.StructureDiagramGenerator

The empty constructor.

StructureDiagramGenerator(IAtomContainer) - Constructor for class org.openscience.cdk.layout.StructureDiagramGenerator

Creates an instance of this class while assigning a molecule to be layed out.

T

TemplateHandler - Class in org.openscience.cdk.layout

Helper class for Structure Diagram Generation.

TemplateHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.layout.TemplateHandler

Creates a new TemplateHandler with default templates loaded.

TemplateHandler() - Constructor for class org.openscience.cdk.layout.TemplateHandler

Creates a new TemplateHandler without any default templates.

A B C D G H J L M O P R S T