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Public Member Functions | Private Member Functions | Private Attributes | Static Private Attributes

org::openscience::cdk::layout::StructureDiagramGenerator Class Reference

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Public Member Functions

void generateCoordinates (Vector2d firstBondVector) throws java.lang.Exception
void generateCoordinates () throws java.lang.Exception
void generateExperimentalCoordinates (Vector2d firstBondVector) throws java.lang.Exception
void generateExperimentalCoordinates () throws java.lang.Exception
IMolecule getMolecule ()
IAtom getOtherBondAtom (IAtom atom, IBond bond)
TemplateHandler getTemplateHandler ()
boolean getUseTemplates ()
void setBondLength (double bondLength)
void setMolecule (IMolecule mol, boolean clone)
void setMolecule (IMolecule molecule)
void setTemplateHandler (TemplateHandler templateHandler)
void setUseTemplates (boolean useTemplates)
 StructureDiagramGenerator (IMolecule molecule)
 StructureDiagramGenerator ()

Private Member Functions

boolean allPlaced (IRingSet rings)
IMolecule fixMol (IMolecule molecule)
void fixRest ()
IAtom getNextAtomWithAliphaticUnplacedNeigbors ()
IBond getNextBondWithUnplacedRingAtom ()
IAtomContainer getPlacedAtoms (IAtom atom)
IAtom getRingAtom (IBond bond)
IRingSet getRingSystemOfAtom (List ringSystems, IAtom ringAtom)
IAtomContainer getUnplacedAtoms (IAtom atom)
void handleAliphatics () throws CDKException
void layoutNextRingSystem () throws Exception
void layoutRingSet (Vector2d firstBondVector, IRingSet rs) throws Exception
void markRingAtoms (IRingSet rings)
IAtomContainer placeFirstBond (IBond bond, Vector2d bondVector)
void resetUnplacedRings ()

Private Attributes

AtomPlacer atomPlacer = new AtomPlacer()
double bondLength = 1.5
final String disconnectedMessage = "Molecule not connected. Use ConnectivityChecker.partitionIntoMolecules() and do the layout for every single component."
Vector2d firstBondVector
LoggingTool logger = new LoggingTool(StructureDiagramGenerator.class)
IAtomContainerSet mappedSubstructures
IMolecule molecule
RingPlacer ringPlacer = new RingPlacer()
List ringSystems = null
IRingSet sssr
TemplateHandler templateHandler = null
boolean useTemplates = true

Static Private Attributes

static TemplateHandler DEFAULT_TEMPLATE_HANDLER = null

Detailed Description

Generates 2D coordinates for a molecule for which only connectivity is known or the coordinates have been discarded for some reason. Usage: Create an instance of this class, thereby assigning a molecule, call generateCoordinates() and get your molecule back:

 StructureDiagramGenerator sdg = new StructureDiagramGenerator();
 sdg.setMolecule(someMolecule);
 sdg.generateCoordinates();
 Molecule layedOutMol = sdg.getMolecule();
 

The method will fail if the molecule is disconnected. The partitionIntoMolecules(AtomContainer) can help here.

Author:
steinbeck .created 2004-02-02
See also:
org.openscience.cdk.graph.ConnectivityChecker::partitionIntoMolecules(IAtomContainer) .keyword Layout .keyword Structure Diagram Generation (SDG) .keyword 2D-coordinates .keyword Coordinate generation, 2D .dictref blue-obelisk:layoutMolecule .module sdg .githash .bug 1536561 .bug 1788686

Definition at line 79 of file StructureDiagramGenerator.java.


The documentation for this class was generated from the following file:

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