Package chemaxon.struc.sgroup

Class SgroupAtom

java.lang.Object
chemaxon.struc.MolAtom
chemaxon.struc.sgroup.SgroupAtom
All Implemented Interfaces:
StereoConstants, Serializable
@PublicApi public class SgroupAtom extends MolAtom
S-group superatom.
Since:
Marvin 3.0, 11/05/2002
See Also:

  • Field Details

  • Constructor Details

    • SgroupAtom

      public SgroupAtom(SuperatomSgroup sg)
      Constructs a superatom for a superatom type S-group.
      Parameters:
      sg - the S-group

  • Method Details

    • getSgroup

      public SuperatomSgroup getSgroup()
      Gets the S-group corresponding to this superatom.
      Returns:
      the S-group

    • getAtomSymbol

      public String getAtomSymbol(int style, int flags, int[] lcenter, CTransform3D preTransform)
      Gets the string representation of the atom symbol.
      Overrides:
      getAtomSymbol in class MolAtom
      Parameters:
      style - neglected
      flags - neglected
      lcenter - neglected
      preTransform - neglected
      Returns:
      the S-group name with the numbers subscripted
      See Also:

    • clone

      public SgroupAtom clone()
      Clones the S-group superatom and it's SuperatomSgroup as well.
      Overrides:
      clone in class MolAtom
      Returns:
      the clone

    • set

      public void set(MolAtom atom)
      Set properties of this S-group superatom.
      Overrides:
      set in class MolAtom
      Parameters:
      atom - the target atom
      Since:
      Marvin 4.1, 01/01/2006

    • cloneFromSgroupCopy

      public SgroupAtom cloneFromSgroupCopy()
      Clones the S-group superatom partially. This method is needed to prevent infinite recursion when cloning from SuperatomSgroup.copy. Use it only for this purpose.
      Returns:
      the clone

    • transform

      public void transform(CTransform3D t, boolean incg)
      Apply a transformation matrix to the coordinates.
      Overrides:
      transform in class MolAtom
      Parameters:
      t - the transformation matrix
      incg - graph invariants are changed (true) or not (false)
      Since:
      Marvin 4.0.2, 10/26/2005

    • getSymbol

      public String getSymbol()
      Gets the abbreviated group symbol.
      Overrides:
      getSymbol in class MolAtom
      Returns:
      the symbol

    • getLeftName

      public String getLeftName()
      Gets the string that will be shown at the left side of the molecule.
      Returns:
      the left name string
      Since:
      Marvin 4.1

    • setLeftName

      public void setLeftName(String s)
      Set the string that will be shown at the left side of the molecule.
      Since:
      Marvin 4.1

    • getRightName

      public String getRightName()
      Set the string that will be shown at the right side of the molecule.
      Since:
      Marvin 4.1

    • setRightName

      public void setRightName(String s)
      Set the string that will be shown at the right side of the molecule.
      Since:
      Marvin 4.1

    • hasAlternativeName

      public boolean hasAlternativeName()
      Checks whether there is an alternative name at all.
      Returns:
      true if an alternative name is available for the (s)group
      Since:
      Marvin 4.1

    • hasValenceError

      public boolean hasValenceError()
      Checks if any atom of the Sgroup has a valence error.
      Overrides:
      hasValenceError in class MolAtom
      Returns:
      true if at least one atom of this Sgroup has a valence error
      See Also:

    • getLabelCenter

      public int getLabelCenter()
      Gets the index of the character in the label the bonds should point to.
      Returns:
      character index + 1, or LABEL_DEFAULT for default behavior (geometrical center unless alternative name is specified), or LABEL_AUTO for automatic calculation
      Since:
      Marvin 4.1

    • setLabelCenter

      public void setLabelCenter(int k)
      Sets the index of the character in the label the bonds should point to.
      Parameters:
      k - character index + 1, or LABEL_DEFAULT for default behavior (geometrical center unless alternative name is specified), or LABEL_AUTO for automatic calculation
      Since:
      Marvin 4.1

    • setFromSgroupCopy

      protected void setFromSgroupCopy(SgroupAtom sa)
      Make a copy of this S-group superatom. Clones the S-group superatom partially. This method is needed to prevent infinite recursion when cloning from SuperatomSgroup.copy.
      Parameters:
      sa - the target atom
      Since:
      Marvin 4.1, 01/01/2006

    • add

      protected boolean add(MolBond edge)
      Add an edge if it had not been already added. Overridden to enable access from other classes of this package.
      Overrides:
      add in class MolAtom
      Parameters:
      edge - the edge to add
      Returns:
      true if valence check needed
      Throws:
      chemaxon.struc.sgroup.NoFreeAttachmentPointException - if there is no free attachment point for the given edge.

    • add

      protected boolean add(MolBond edge, MolAtom atom)
      Add an edge to the given atom of the sgroup, if it had not been already added.
      Parameters:
      edge - the edge to add
      Throws:
      chemaxon.struc.sgroup.NoFreeAttachmentPointException - if there is no free attachment point for the given edge.

    • removeBond

      protected void removeBond(int i, boolean clearFromAttachmentPoints)
      Removes a bond.
      Overrides:
      removeBond in class MolAtom
      Parameters:
      i - bond index

    • removeBond

      protected void removeBond(MolBond bond, boolean clearFromAttachmentPoints)
      Removes a bond by reference.
      Overrides:
      removeBond in class MolAtom
      Parameters:
      bond - bond reference to remove

    • insertBond

      protected void insertBond(int index, MolBond bond)
      Description copied from class: MolAtom
      Inserts a bond at a specified index.
      Overrides:
      insertBond in class MolAtom
      Parameters:
      index - the index where to insert the bond
      bond - the bond reference to insert

    • setAtom1

      protected static void setAtom1(MolBond edge, MolAtom newnode)
      Sets the first node of an edge. Overridden to enable access from other classes of this package.
      Parameters:
      edge - the edge
      newnode - the new node value

    • setAtom2

      protected static void setAtom2(MolBond edge, MolAtom newnode)
      Sets the second node of an edge. Overridden to enable access from other classes of this package.
      Parameters:
      edge - the edge
      newnode - the new node value

    • removeAllBonds

      protected void removeAllBonds()
      Remove all edges.
      Overrides:
      removeAllBonds in class MolAtom

    • removeAllBonds

      protected void removeAllBonds(boolean clearFromAttachmentPoints)
      Removes all edges. If the parameter clearFromAttachmentPoints is true, then the bonds are cleared from the SgroupAtoms's s-group's attachment points
      Overrides:
      removeAllBonds in class MolAtom

    • countAllAtoms

      protected int countAllAtoms()
      Counts all atoms represented by this atom.
      Overrides:
      countAllAtoms in class MolAtom
      Returns:
      the number of atoms in the S-group

    • getCharge

      public int getCharge()
      Returns the sum of the charges in the corresponding superatom s-group.
      Overrides:
      getCharge in class MolAtom
      Returns:
      the formal charge as a signed integer, the default value is zero
      Since:
      Marvin 6.1, 2013.05.21.

    • indexOf

      public int indexOf(MolBond bond)
      Returns the index of the specified bond in this atom. This method uses == for the bond comparison.
      Overrides:
      indexOf in class MolAtom
      Parameters:
      bond - bond reference
      Returns:
      the bond index, or -1 if it not found
      Since:
      Marvin 6.1, 2013.06.23.
      See Also: