Package org.openscience.cdk.layout

Class RingPlacer

java.lang.Object
org.openscience.cdk.layout.RingPlacer
public class RingPlacer extends Object
Class providing methods for generating coordinates for ring atoms. Various situations are supported, like condensation, spiro-attachment, etc. They can be used for Automated Structure Diagram Generation or in the interactive buildup of ringsystems by the user.

  • Field Details

    • RAD_30

      public static final double RAD_30

    • defaultAngles

      public static final Map<Integer,Double> defaultAngles
      Default ring start angles. Map contains pairs: ring size with start angle.

    • jcpAngles

      public static final Map<Integer,Double> jcpAngles
      Suggested ring start angles for JChempaint, different due to Y inversion of canvas.

  • Constructor Details

    • RingPlacer

      public RingPlacer()
      The empty constructor.

  • Method Details

    • placeRing

      public void placeRing(IRing ring, IAtomContainer sharedAtoms, javax.vecmath.Point2d sharedAtomsCenter, javax.vecmath.Vector2d ringCenterVector, double bondLength)
      Generated coordinates for a given ring. Multiplexes to special handlers for the different possible situations (spiro-, fusion-, bridged attachement)
      Parameters:
      ring - The ring to be placed
      sharedAtoms - The atoms of this ring, also members of another ring, which are already placed
      sharedAtomsCenter - The geometric center of these atoms
      ringCenterVector - A vector pointing the the center of the new ring
      bondLength - The standard bondlength

    • placeRing

      public void placeRing(IRing ring, javax.vecmath.Point2d ringCenter, double bondLength)
      Place ring with default start angles, using defaultAngles.
      Parameters:
      ring - the ring to place.
      ringCenter - center coordinates of the ring.
      bondLength - given bond length.

    • placeRing

      public void placeRing(IRing ring, javax.vecmath.Point2d ringCenter, double bondLength, Map<Integer,Double> startAngles)
      Place ring with user provided angles.
      Parameters:
      ring - the ring to place.
      ringCenter - center coordinates of the ring.
      bondLength - given bond length.
      startAngles - a map with start angles when drawing the ring.

    • placeRingSubstituents

      public IAtomContainer placeRingSubstituents(IRingSet rs, double bondLength)
      Positions the aliphatic substituents of a ring system
      Parameters:
      rs - The RingSystem for which the substituents are to be laid out
      Returns:
      A list of atoms that where laid out

    • placeSpiroRing

      public void placeSpiroRing(IRing ring, IAtomContainer sharedAtoms, javax.vecmath.Point2d sharedAtomsCenter, javax.vecmath.Vector2d ringCenterVector, double bondLength)
      Generated coordinates for a given ring, which is connected to a spiro ring. The rings share exactly one atom.
      Parameters:
      ring - The ring to be placed
      sharedAtoms - The atoms of this ring, also members of another ring, which are already placed
      sharedAtomsCenter - The geometric center of these atoms
      ringCenterVector - A vector pointing the the center of the new ring
      bondLength - The standard bondlength

    • placeFusedRing

      public void placeFusedRing(IRing ring, IAtomContainer sharedAtoms, javax.vecmath.Vector2d ringCenterVector, double bondLength)
      Generated coordinates for a given ring, which is fused to another ring. The rings share exactly one bond.
      Parameters:
      ring - The ring to be placed
      sharedAtoms - The atoms of this ring, also members of another ring, which are already placed
      ringCenterVector - A vector pointing the the center of the new ring
      bondLength - The standard bondlength

    • allPlaced

      public boolean allPlaced(IRingSet rs)
      True if coordinates have been assigned to all atoms in all rings.
      Parameters:
      rs - The ringset to be checked
      Returns:
      True if coordinates have been assigned to all atoms in all rings.

    • checkAndMarkPlaced

      public void checkAndMarkPlaced(IRingSet rs)
      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.
      Parameters:
      rs - The ringset to be checked

    • partitionNonRingPartners

      public void partitionNonRingPartners(IAtom atom, IRing ring, IAtomContainer ringAtoms, IAtomContainer nonRingAtoms)
      Partition the bonding partners of a given atom into ring atoms and non-ring atoms
      Parameters:
      atom - The atom whose bonding partners are to be partitioned
      ring - The ring against which the bonding partners are checked
      ringAtoms - An AtomContainer to store the ring bonding partners
      nonRingAtoms - An AtomContainer to store the non-ring bonding partners

    • getNativeRingRadius

      public double getNativeRingRadius(IRing ring, double bondLength)
      Returns the ring radius of a perfect polygons of size ring.getAtomCount() The ring radius is the distance of each atom to the ringcenter.
      Parameters:
      ring - The ring for which the radius is to calculated
      bondLength - The bond length for each bond in the ring
      Returns:
      The radius of the ring.

    • getMolecule

      public IAtomContainer getMolecule()

    • setMolecule

      public void setMolecule(IAtomContainer molecule)

    • getAtomPlacer

      public AtomPlacer getAtomPlacer()

    • setAtomPlacer

      public void setAtomPlacer(AtomPlacer atomPlacer)