Package chemaxon.struc

Class SelectionMolecule

java.lang.Object
chemaxon.struc.MoleculeGraph
chemaxon.struc.SelectionMolecule
All Implemented Interfaces:
MoleculeWithValence<MolAtom>, chemaxon.core.structure.MoleculeForBuilder, MTransformable, StereoConstants, Serializable
@PublicApi public class SelectionMolecule extends MoleculeGraph
A selection object which can contain atoms and bonds without real parent relationship (the real parent of atoms and bonds is another MoleculeGraph ancestor).
Since:
Marvin 3.0
See Also:

  • Constructor Details

    • SelectionMolecule

      public SelectionMolecule()

  • Method Details

    • isRealAtomParent

      protected boolean isRealAtomParent()
      Selection molecules are not real atom parents. However, in some special cases a selection molecule can be an atom parent.
      Overrides:
      isRealAtomParent in class MoleculeGraph
      Returns:
      false
      Since:
      Marvin 3.0

    • setBond

      @Deprecated public void setBond(int i, MolBond bond)
      Deprecated.
      as of Marvin 6.2. Use removeBond(MolBond) for bond removal and add(MolBond) for adding a new bond to the molecule.
      Sets the bond at the specified index.
      Overrides:
      setBond in class MoleculeGraph
      Parameters:
      i - bond index
      bond - the bond reference

    • add

      public void add(MolBond bond)
      Adds a bond to the graph. If the bond doesn't have parent molecule then the bond is also added to its end-points.
      Overrides:
      add in class MoleculeGraph
      Parameters:
      bond - the bond object

    • add

      public void add(MolBond bond, boolean checkParallel)
      Add a bond to the molecule. If the second parameter is true, there an exception thrown when there is already a bond between the given MolAtoms. There is no checking if either is SgroupAtom. If the molecule graph is a superGraph, the bond is also added to its endpoints (two MolAtom objects).
      Overrides:
      add in class MoleculeGraph
      Parameters:
      bond - the bond object

    • add

      public void add(MolAtom atom)
      Adds an atom to the molecule. It doesn't add the bonds of the atom to the molecule.
      Overrides:
      add in class MoleculeGraph
      Parameters:
      atom - the atom object

    • add

      public void add(MolAtom atom, boolean addBonds)
      Adds an atom to the molecule. It the second parameter is true, then adds the bonds of the atom to the molecule, if the bond's other atom is already added.
      Since:
      Marvin 6.1, 04/30/2013

    • addAtomWithBonds

      protected void addAtomWithBonds(MolAtom atom)
      Adds an atom to the molecule. Adds the bonds of the atom to the molecule, if the bond's other atom is already added.
      Since:
      Marvin 6.1, 04/30/2013

    • swapAtoms

      public void swapAtoms(int i, int j)
      Swap two atoms.
      Parameters:
      i - index of the first atom
      j - index of the second atom
      Since:
      Marvin 3.3, 11/04/2003

    • removeAtom

      public void removeAtom(MolAtom atom)
      Removes an atom and its bonds.
      Overrides:
      removeAtom in class MoleculeGraph
      Parameters:
      atom - the atom

    • removeAtom

      public void removeAtom(int i)
      Removes an atom and its bonds from the graph.
      Overrides:
      removeAtom in class MoleculeGraph
      Parameters:
      i - the atom index

    • removeBond

      public void removeBond(MolBond bond)
      Removes a bond by reference.
      Overrides:
      removeBond in class MoleculeGraph
      Parameters:
      bond - the bond

    • removeBond

      public void removeBond(int i)
      Removes a bond from the graph.
      Overrides:
      removeBond in class MoleculeGraph
      Parameters:
      i - the bond index

    • addAtom0

      protected void addAtom0(MolAtom atom)
      Adds an atom.
      Overrides:
      addAtom0 in class MoleculeGraph
      Parameters:
      atom - the atom reference

    • setAtom0

      protected void setAtom0(int i, MolAtom atom)
      Sets the atom at the specified index.
      Overrides:
      setAtom0 in class MoleculeGraph
      Parameters:
      i - atom index
      atom - new atom reference

    • addBond0

      protected void addBond0(MolBond bond)
      Adds a bond.
      Overrides:
      addBond0 in class MoleculeGraph
      Parameters:
      bond - the bond reference

    • regenCtab

      protected void regenCtab()
      Regenerates the connection table.
      Overrides:
      regenCtab in class MoleculeGraph
      Since:
      Marvin 3.5.2, 12/16/2004

    • regenBtab

      protected void regenBtab()
      Regenerates the bond table.
      Overrides:
      regenBtab in class MoleculeGraph
      Since:
      Marvin 16.06.06.

    • fuse0

      protected void fuse0(MoleculeGraph g, boolean check)
      Adds those atoms and bonds of a graph to this one that are not already elements.
      Overrides:
      fuse0 in class MoleculeGraph
      Parameters:
      g - the graph
      check - true if a containment check should be performed to ensure that only those atoms and bonds are added that are not already elements - false if the graph is known to be disjoint from this graph and this check can be safely skipped
      Since:
      Marvin 5.0

    • transform

      public void transform(CTransform3D t)
      Apply a transformation matrix to the atomic coordinates.
      Specified by:
      transform in interface MTransformable
      Overrides:
      transform in class MoleculeGraph
      Parameters:
      t - the transformation matrix

    • clonecopy

      public void clonecopy(MoleculeGraph graph)
      Copies the clones of atoms and bonds of this graph to another one.
      Overrides:
      clonecopy in class MoleculeGraph
      Parameters:
      graph - the target graph

    • clonecopyMoleculeGraphWithoutSgroups

      protected boolean clonecopyMoleculeGraphWithoutSgroups(int[] iatoms, MolBond[] cbonds, int nb, MoleculeGraph g)
      Copies the specified atoms and bonds of this graph to another one.
      Overrides:
      clonecopyMoleculeGraphWithoutSgroups in class MoleculeGraph
      Parameters:
      iatoms - array of atoms indices to copy
      cbonds - array of bonds to copy or null to copy bonds in cbonds only
      nb - number of bonds
      g - the target graph
      Returns:
      false if the bonds array contains all bond end points, true if there is at least one external bond
      Since:
      Marvin 5.0.2, 03/07/2008

    • clone

      public SelectionMolecule clone()
      Create a clone of this SelectionMolecule.
      Overrides:
      clone in class MoleculeGraph
      Returns:
      the cloned SelectionMolecule

    • isGrinvCCValid

      protected boolean isGrinvCCValid()
      Tests whether the graph invariant change count is valid.
      Overrides:
      isGrinvCCValid in class MoleculeGraph
      Returns:
      false
      Since:
      Marvin 5.0, 11/30/2007

    • checkBondConsistency

      protected void checkBondConsistency()
      Empty implementation, bond consistency is not checked in case of selections.
      Overrides:
      checkBondConsistency in class MoleculeGraph
      Since:
      Marvin 5.0, 11/06/2007

    • createGearch

      protected chemaxon.struc.gearch.MoleculeGraphGearch createGearch()
      Overrides:
      createGearch in class MoleculeGraph

    • getLigands

      public Integer[] getLigands(Integer atom)

    • addAtomWithoutChangingIt

      protected final int addAtomWithoutChangingIt(MolAtom atom)
      Adds an atom without setting its parentGraph and index fields.
      Overrides:
      addAtomWithoutChangingIt in class MoleculeGraph
      Parameters:
      atom - the atom reference
      Returns:
      the new atom index