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A

addBasePath(String) - Method in class org.molwind.chemical.io.SDFileLocator

Adds a path to the base paths

addFile(File) - Method in class org.molwind.chemical.model.ChemicalWorld

Adds the file to this chemical world.

addRelationship(Relationship) - Method in class org.molwind.chemical.model.ChemicalEntity

Adds a new relationship if it is not existing already.

analyze(EntityGraph, EntityVertex) - Method in class org.molwind.chemical.model.SubstructureResolver

Analyzes an entity graph.

C

calculatePositions() - Method in class org.molwind.chemical.view.ChemicalTopologyManager

ChemicalEntity - Class in org.molwind.chemical.model

ChemicalEntity represents a chemical entity in a Molwind world.

ChemicalEntity() - Constructor for class org.molwind.chemical.model.ChemicalEntity

Creates a new empty chemical entity.

ChemicalEntity(IMolecule) - Constructor for class org.molwind.chemical.model.ChemicalEntity

Creates a new empty chemical entity.

ChemicalTile - Class in org.molwind.chemical.view

ChemicalTile contains chemical entities and allows to visualize them.

ChemicalTile(LayeredPosition) - Constructor for class org.molwind.chemical.view.ChemicalTile

Creates a new tile containing chemical entities.

ChemicalTileGenerator - Class in org.molwind.chemical.view

ChemicalTileGenerator generates tiles containing chemical compounds.

ChemicalTileGenerator(ChemicalWorld) - Constructor for class org.molwind.chemical.view.ChemicalTileGenerator

Create a new tile generator based on the given chemical world.

ChemicalTopologyManager - Class in org.molwind.chemical.view

ChemicalTopologyManager determines and places visible chemical structures.

ChemicalTopologyManager() - Constructor for class org.molwind.chemical.view.ChemicalTopologyManager

Creates a new topology manager to place chemical entities.

ChemicalWorld - Class in org.molwind.chemical.model

ChemicalWorld represents a world of chemicals.

ChemicalWorld(String, File) - Constructor for class org.molwind.chemical.model.ChemicalWorld

Creates a new chemical world.

ChemicalWorld(String) - Constructor for class org.molwind.chemical.model.ChemicalWorld

Creates a new chemical world.

D

DEFAULT_ID_ATTRIBUTE - Static variable in class org.molwind.chemical.io.SDFileLocator

The default name of the attribute denoting the id.

DEFAULT_PARENT_ATTRIBUTE - Static variable in class org.molwind.chemical.io.SDFileLocator

The default name of the attribute denoting the parent.

DEFAULT_PATH_SEPARATOR - Static variable in class org.molwind.chemical.io.SDFileLocator

The default value for seperating a path

DEFAULT_SDF_SUFFIX - Static variable in class org.molwind.chemical.io.SDFileLocator

The default file extensions recognized by this locator.

E

equals(Object) - Method in class org.molwind.chemical.model.ChemicalEntity

Tests whether two objects are identical by using the Identity strategy which has been provided (optionally).

G

generateTile(LayeredPosition) - Method in class org.molwind.chemical.view.ChemicalTileGenerator

Generates a tile from the given position.

getAttribute(String) - Method in class org.molwind.chemical.model.ChemicalEntity

Returns the value of the attribute with the given name.

getDefaultEntityGraph() - Method in class org.molwind.chemical.io.SDFileIterator

Returns the Graph for the given file

getDimension() - Method in class org.molwind.chemical.model.ChemicalEntity

Returns int for the bigness of the entity

getDrawing() - Method in class org.molwind.chemical.model.ChemicalEntity

Renders an image representation of this entity.

getEntityIterator() - Method in class org.molwind.chemical.model.ChemicalWorld

Returns an iterator over the world's entities.

getIdAttributeName() - Method in class org.molwind.chemical.io.SDFileLocator

Get the idAttributeName value.

getIdentity() - Method in class org.molwind.chemical.model.ChemicalEntity

Get the Identity value.

getImage(ChemicalEntity) - Method in interface org.molwind.chemical.view.MoleculeRenderer

Returns a graphical representation of a molecule.

getImage(ChemicalEntity) - Method in class org.molwind.chemical.view.SubstructureRenderer

Returns a graphical representation of a molecule.

getInstance() - Static method in class org.molwind.chemical.view.MoleculeRendererFactory

Returns the renderer factory instance.

getMolecule() - Method in class org.molwind.chemical.model.ChemicalEntity

Return the molecule object

getMoleculeRenderer() - Method in class org.molwind.chemical.model.ChemicalEntity

Get the MoleculeRenderer value.

getParentAttributeName() - Method in class org.molwind.chemical.io.SDFileLocator

Get the parentAttributeName value.

getParentName() - Method in class org.molwind.chemical.model.SubstructureResolver

Get the ParentName value.

getPathNames() - Method in class org.molwind.chemical.io.SDFileLocator

Get the worldpaths

getRenderer(String) - Static method in class org.molwind.chemical.view.MoleculeRendererFactory

Returns the default molecule renderer.

getRenderer() - Static method in class org.molwind.chemical.view.MoleculeRendererFactory

Returns the default molecule renderer.

getTempDir() - Method in class org.molwind.chemical.view.ChemicalTile

Get the TempDir value.

getTileGenerator() - Method in class org.molwind.chemical.model.ChemicalWorld

Returns an instance of a tile generator.

getVisibleEntities(LayeredPosition) - Method in class org.molwind.chemical.view.ChemicalTopologyManager

Determines the visible entities for the given position.

getWorldName() - Method in class org.molwind.chemical.view.ChemicalTile

Get the WorldName value.

getWorldNames() - Method in class org.molwind.chemical.io.SDFileLocator

getX() - Method in class org.molwind.chemical.model.ChemicalEntity

Get the X value.

getY() - Method in class org.molwind.chemical.model.ChemicalEntity

Get the Y value.

getZoom() - Method in class org.molwind.chemical.view.SubstructureRenderer

Get the Zoom value.

GraphMain2 - Class in org.molwind.chemical.io

GraphMain2() - Constructor for class org.molwind.chemical.io.GraphMain2

H

hashCode() - Method in class org.molwind.chemical.model.ChemicalEntity

Returns a hash code value for this relationship.

hasNext() - Method in class org.molwind.chemical.io.SDFileIterator

Returns true if the iteration has more elements.

hasRelationship(ChemicalEntity) - Method in class org.molwind.chemical.model.ChemicalEntity

Tests whether there are relationships between this entity and the given entity.

I

identical(WorldEntity, WorldEntity) - Method in class org.molwind.chemical.model.SubstructureResolver

Tests whether two entities are identical.

L

locateByFileName(String) - Method in class org.molwind.chemical.io.SDFileLocator

Locates the world by the given name by iteraring all world names

locateWorld(String) - Method in class org.molwind.chemical.io.SDFileLocator

Locates a world with the given name.

M

main(String[]) - Static method in class org.molwind.chemical.io.GraphMain2

MoleculeRenderer - Interface in org.molwind.chemical.view

MoleculeRenderer implementations create drawings of molecules.

MoleculeRendererFactory - Class in org.molwind.chemical.view

MoleculeRendererFactory is a factory to produce default instances of a molecule rendering strategy.

N

next() - Method in class org.molwind.chemical.io.SDFileIterator

Returns the next element in the iteration.

O

org.molwind.chemical.io - package org.molwind.chemical.io

org.molwind.chemical.model - package org.molwind.chemical.model

org.molwind.chemical.view - package org.molwind.chemical.view

P

pathNames - Static variable in class org.molwind.chemical.io.SDFileLocator

The relativ adress for looking up the worlds

R

registerRenderer(String, MoleculeRenderer) - Static method in class org.molwind.chemical.view.MoleculeRendererFactory

Registers a named molecule renderer.

related(WorldEntity, WorldEntity) - Method in class org.molwind.chemical.model.SubstructureResolver

Augments the relationship between two entities.

remove() - Method in class org.molwind.chemical.io.SDFileIterator

Removes from the underlying collection the last element returned by the iterator.

removeBasePath(String) - Method in class org.molwind.chemical.io.SDFileLocator

Removes the given path from the base paths

resolve() - Method in class org.molwind.chemical.model.SubstructureResolver

Resolves the relationships by creating a graph of entity vertices and relationship edges.

S

SDFileIterator - Class in org.molwind.chemical.io

SDFileIterator reads sdf formatted files of chemical compounds.

SDFileIterator(File[], RelationshipResolver) - Constructor for class org.molwind.chemical.io.SDFileIterator

Creates a new chemical entity iterator based on the underlying SD files using the given relationship resolver.

SDFileLocator - Class in org.molwind.chemical.io

SDFileLocator implements a locator to find worlds based on SDF chemical file format.

SDFileLocator() - Constructor for class org.molwind.chemical.io.SDFileLocator

Creates an SDFilelocator instance.

setAttribute(String, Object) - Method in class org.molwind.chemical.model.ChemicalEntity

Sets the value of the attribute with the given name.

setFileReader(File) - Method in class org.molwind.chemical.io.SDFileIterator

Sets the file reader

setFileReader(String) - Method in class org.molwind.chemical.io.SDFileIterator

Sets the file reader

setIdAttributeName(String) - Method in class org.molwind.chemical.io.SDFileLocator

Set the idAttributeName value.

setIdentity(Identity) - Method in class org.molwind.chemical.model.ChemicalEntity

Set the Identity value.

setMolecule(IMolecule) - Method in class org.molwind.chemical.model.ChemicalEntity

Sets the molecule object

setMoleculeRenderer(MoleculeRenderer) - Method in class org.molwind.chemical.model.ChemicalEntity

Set the MoleculeRenderer value.

setParentAttributeName(String) - Method in class org.molwind.chemical.io.SDFileLocator

Set the ParentAttributeName value.

setParentName(String) - Method in class org.molwind.chemical.model.SubstructureResolver

Set the ParentName value.

setPathNames(String) - Method in class org.molwind.chemical.io.SDFileLocator

Set the pathNames

setTempDir(File) - Method in class org.molwind.chemical.view.ChemicalTile

Set the TempDir value.

setWorldName(String) - Method in class org.molwind.chemical.view.ChemicalTile

Set the WorldName value.

setX(double) - Method in class org.molwind.chemical.model.ChemicalEntity

Set the X value.

setY(double) - Method in class org.molwind.chemical.model.ChemicalEntity

Set the Y value.

setZoom(double) - Method in class org.molwind.chemical.view.SubstructureRenderer

Set the Zoom value.

SubstructureRenderer - Class in org.molwind.chemical.view

SubstructureRenderer implements a strategy to render molecules with parent substructures to be highlighted.

SubstructureRenderer() - Constructor for class org.molwind.chemical.view.SubstructureRenderer

SubstructureResolver - Class in org.molwind.chemical.model

SubstructureResolver resolves substructure relationships.

SubstructureResolver(String, String) - Constructor for class org.molwind.chemical.model.SubstructureResolver

Creates a new Substructure resolver which uses the given attributes to decide whether there is a relationship.

W

writeTo(OutputStream) - Method in class org.molwind.chemical.view.ChemicalTile

Writes the tile's image to the given output stream.

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