Package chemaxon.struc

Class Sgroup

java.lang.Object
chemaxon.struc.Sgroup
All Implemented Interfaces:
Serializable
Direct Known Subclasses:
DataSgroup, MulticenterSgroup, MultipleSgroup, RepeatingUnitSgroup, SuperatomSgroup
@PublicApi public class Sgroup extends Object implements Serializable
Structural group representation in the molecule.
A structural group is an entity in the molecule. Some of these entities has direct subclasses.
Some example use cases:
  • It can be an abbreviation of a molecule part represented as SuperatomSgroup.
  • A repeating unit in the molecule represented as RepeatingUnitSgroup.
  • Data assigned to a part of the molecule represented as DataSgroup .
  • A bond which has connection to multiple atom in the molecule is represented as multicenter S-group type.
  • Components in the molecule can be represented as component S-groups.

See also the possible return values of getType() method which describes the possible S-group types.
Some relevant functions in the molecule to handle these structural elements:

Since:
Marvin 3.0
See Also:

  • Field Details

    • SGROUP_TYPE_COUNT

      public static final int SGROUP_TYPE_COUNT
      Number of S-group types. @see #getType()
      See Also:

    • ST_SUPERATOM

      public static final int ST_SUPERATOM
      Superatom S-group type. @see #getType()
      See Also:

    • ST_MULTIPLE

      public static final int ST_MULTIPLE
      Multiple group S-group type. @see #getType()
      See Also:

    • ST_SRU

      public static final int ST_SRU
      SRU (Structural Repeating Unit: polymers and repeating units with repetition ranges) S-group type.
      See Also:

    • ST_MONOMER

      public static final int ST_MONOMER
      Monomer S-group type. @see #getType()
      See Also:

    • ST_MER

      public static final int ST_MER
      Mer S-group type. @see #getType()
      See Also:

    • ST_COPOLYMER

      public static final int ST_COPOLYMER
      Copolymer S-group type. @see #getType()
      See Also:

    • ST_MODIFICATION

      public static final int ST_MODIFICATION
      Modification S-group type. @see #getType()
      See Also:

    • ST_MIXTURE

      public static final int ST_MIXTURE
      Mixture S-group type. Mixture S-groups are composed from unordered component S-groups.
      See Also:

    • ST_FORMULATION

      public static final int ST_FORMULATION
      Formulation S-group type. Formulation S-groups are composed from ordered component S-groups.
      See Also:

    • ST_DATA

      public static final int ST_DATA
      Data S-group type. @see #getType()
      See Also:

    • ST_ANY

      public static final int ST_ANY
      Any polymer S-group type. @see #getType()
      See Also:

    • ST_GENERIC

      public static final int ST_GENERIC
      Generic S-group type. @see #getType()
      See Also:

    • ST_COMPONENT

      public static final int ST_COMPONENT
      Component S-group type. A component here is a set of atoms contained by a component bracket. There are two kind of component S-group: ordered and unordered. The subscript of an unordered S-group contains a simple "c". The subscript of an ordered component S-group contains an additional integer e.g.: "c1" where "1" is the order of the ordered component S-group. Ordered component S-groups can be embedded into formulation S-groups. Unordered component S-groups can be embedded into mixture S-groups.
      See Also:

    • ST_MULTICENTER

      public static final int ST_MULTICENTER
      Multicenter S-group type. @see #getSubType()
      See Also:

    • ST_GRAFT

      public static final int ST_GRAFT
      Graft S-group type. @see #getType()
      See Also:

    • ST_AMINOACID

      public static final int ST_AMINOACID
      Amino acid S-group type. @see #getType()
      See Also:

    • SST_ALTERNATING

      public static final int SST_ALTERNATING
      Alternating polymer S-group subtype. @see #getSubType()
      See Also:

    • SST_RANDOM

      public static final int SST_RANDOM
      Random polymer S-group subtype. @see #getSubType()
      See Also:

    • SST_BLOCK

      public static final int SST_BLOCK
      Block polymer S-group subtype. @see #getSubType()
      See Also:

    • SCN_EITHER_UNKNOWN

      public static final int SCN_EITHER_UNKNOWN
      Either unknown S-group connectivity. @see #getConnectivity()
      See Also:

    • SCN_HEAD_TO_HEAD

      public static final int SCN_HEAD_TO_HEAD
      Head-to-head S-group connectivity. @see #getConnectivity()
      See Also:

    • SCN_HEAD_TO_TAIL

      public static final int SCN_HEAD_TO_TAIL
      Head-to-tail S-group connectivity. @see #getConnectivity()
      See Also:

    • XSTATE_NONE

      public static final int XSTATE_NONE
      S-group is in an undetermined state.
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • XSTATE_X

      public static final int XSTATE_X
      S-group is expanded.
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • XSTATE_C

      public static final int XSTATE_C
      S-group is contracted.
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • XSTATE_XC

      public static final int XSTATE_XC
      S-group is expanded, but its atoms have the same coordinates as in contracted state.
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • SORT_PARENT_CHILD

      public static final int SORT_PARENT_CHILD
      Parent-child sort order.
      Since:
      Marvin 3.4
      See Also:

    • SORT_CHILD_PARENT

      public static final int SORT_CHILD_PARENT
      Parent-child sort order.
      Since:
      Marvin 3.4
      See Also:

    • PR_ATSYMS

      public static final int PR_ATSYMS
      Print atom symbols.
      Since:
      Marvin 4.1, 07/26/2006
      See Also:

    • RA_IN_EXPAND

      protected static final int RA_IN_EXPAND
      Atom removal in expand.
      Since:
      Marvin 4.1, 07/27/2006
      See Also:

    • RA_REMOVE_EXCEPT_RU

      protected static final int RA_REMOVE_EXCEPT_RU
      Replace without duplicating.
      Since:
      Marvin 4.1, 07/27/2006
      See Also:

    • CHARGE_ON_ATOMS

      public static final int CHARGE_ON_ATOMS
      Charge is located on atoms and displayed on atoms.
      Since:
      Marvin 5.2, 01/22/2009
      See Also:

    • CHARGE_ON_GROUP

      public static final int CHARGE_ON_GROUP
      Charge is located on atoms but displayed on the whole group (bracket).
      Since:
      Marvin 5.2, 01/22/2009
      See Also:

    • parentSgroup

      protected transient Sgroup parentSgroup

    • sgroupType

      protected transient int sgroupType
      The S-group type.

    • sgroupGraph

      protected transient SelectionMolecule sgroupGraph
      The S-group's internal structure.

    • brackets

      protected transient ArrayList<MBracket> brackets

    • atomSet

      protected Set<MolAtom> atomSet
      Set for storing the atoms of the S-group's graph.

  • Constructor Details

    • Sgroup

      @Deprecated public Sgroup(Molecule parent, int t)
      Deprecated.
      As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType).
      Creates an S-group with the specified parent and type.
      Parameters:
      parent - the parent molecule
      t - S-group type

    • Sgroup

      @Deprecated public Sgroup(Molecule parent, int t, int xstate)
      Deprecated.
      As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType) and setXState(int).
      Creates an S-group with the specified parent and type.
      Parameters:
      parent - the parent molecule
      t - S-group type
      xstate - the expanded state
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • Sgroup

      protected Sgroup(Molecule parent, SgroupType type)

    • Sgroup

      protected Sgroup(Molecule parent, SgroupType type, int xstate)

    • Sgroup

      protected Sgroup(Sgroup sg, Molecule m, Sgroup psg)
      Copy constructor.
      Parameters:
      sg - the S-group to copy
      m - the new parent molecule
      psg - the new parent S-group or null
      Since:
      Marvin 3.4

    • Sgroup

      protected Sgroup(Sgroup sg, Molecule m, Sgroup psg, int[] iatoms)
      Copy constructor.
      Parameters:
      sg - the S-group to copy
      m - the new parent molecule
      psg - the new parent S-group or null
      iatoms - indices of cloned atoms in the original molecule or null* @since Marvin 3.4

  • Method Details

    • getId

      public String getId()

    • setId

      public void setId(String id)

    • setSgroupGraph

      public void setSgroupGraph(SelectionMolecule smol)
      Sets the molecule graph.
      Parameters:
      smol - the molecule graph
      Since:
      Marvin 3.3, 11/03/2003

    • getSgroupGraph

      public SelectionMolecule getSgroupGraph()
      Gets a COPY of the molecule graph. WARNING! If the returned selection molecule is changed then the graph of the S-group remains unchanged!
      Returns:
      the molecule graph
      Since:
      Marvin 3.3, 11/03/2003

    • setParentMolecule

      protected final void setParentMolecule(Molecule p)
      Sets the parent molecule.
      Parameters:
      p - the parent molecule

    • getParentMolecule

      public final Molecule getParentMolecule()
      Gets the parent molecule.
      Returns:
      the parent molecule

    • getChildSgroupCount

      public final int getChildSgroupCount()
      Gets the number of child S-groups.
      Returns:
      the number of children
      Since:
      Marvin 3.4

    • getChildSgroup

      public final Sgroup getChildSgroup(int i)
      Gets a child S-group.
      Parameters:
      i - the child index
      Returns:
      the child
      Since:
      Marvin 3.4

    • addChildSgroup

      public final void addChildSgroup(Sgroup sg)
      Adds a child S-group.
      Parameters:
      sg - the child
      Since:
      Marvin 3.4

    • removeChildSgroup

      public final void removeChildSgroup(Sgroup sg)
      Removes an S-group from the children list.
      Parameters:
      sg - the child to remove
      Since:
      Marvin 4.0.4, 01/04/2006

    • findSmallestSgroupContaining

      public final Sgroup findSmallestSgroupContaining(MolAtom a)
      Finds the smallest S-group containing the specified atom. If this S-group contains the atom, then it searches its children recursively.
      Parameters:
      a - the atom
      Returns:
      the S-group or null if not found
      Since:
      Marvin 3.4, 05/05/2004

    • contains

      public boolean contains(MolAtom atom)
      Is this atom contained by the S-group?
      Parameters:
      atom - the atom that's may be part of this S-group
      Returns:
      true it the referenced atom is contained by this S-group, false otherwise

    • findSmallestSgroupOf

      public final Sgroup findSmallestSgroupOf(MolAtom a)
      Finds the smallest S-group that has the specified node. If this parent has the node, then it searches the children recursively.
      Parameters:
      a - the node
      Returns:
      the S-group or null if not found
      Since:
      Marvin 3.4, 05/05/2004

    • getParentSgroup

      public final Sgroup getParentSgroup()
      Gets the parent S-group.
      Returns:
      the parent S-group
      Since:
      Marvin 3.4

    • getXState

      public final int getXState()
      Gets the expanded/contracted state.
      Returns:
      the expanded/contracted state
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • setXState

      public final void setXState(int state)
      Sets the expanded/contracted state.
      Parameters:
      state - the expanded/contracted state
      Throws:
      IllegalArgumentException - if the group is invisible (it has a non-expanded parent)
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • setXState

      @Deprecated public final void setXState(int state, int opts) throws IllegalArgumentException
      Deprecated.
      as of Marvin 6.2, use setXState(int) instead
      Sets the expanded/contracted state.
      Parameters:
      state - the expanded/contracted state
      opts - option for updating coordinates
      Throws:
      IllegalArgumentException - if the group is invisible (it has a non-expanded parent)
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • setXState0

      protected void setXState0(int state)

    • setGUIStateRecursively

      @Deprecated public boolean setGUIStateRecursively(boolean v)
      Deprecated.
      as of Marvin 6.2, use Molecule.setGUIContracted(boolean) for such functionality
      Sets the expanded/contracted state recursively.
      Parameters:
      v - true sets XSTATE_C if previous state was XSTATE_XC, false sets XSTATE_XC if previous state was XSTATE_C, no operation in other cases
      Returns:
      true if at least one S-group's state was changed, false otherwise
      Throws:
      IllegalArgumentException - if the group is invisible (it has a non-expanded parent)
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • setGUIStateRecursively

      @Deprecated public boolean setGUIStateRecursively(boolean contract, int opts) throws IllegalArgumentException
      Deprecated.
      as of Marvin 6.2, use Molecule.setGUIContracted(boolean) for such functionality
      Sets the expanded/contracted state recursively.
      Parameters:
      contract - true sets XSTATE_C if previous state was XSTATE_XC, false sets XSTATE_XC if previous state was XSTATE_C, no operation in other cases
      opts - the expansion/contraction options
      Returns:
      true if at least one S-group's state was changed, false otherwise
      Throws:
      IllegalArgumentException - if the group is invisible (it has a non-expanded parent)
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • expand

      protected boolean expand(int f) throws IllegalArgumentException
      Sets the state to XSTATE_X or XSTATE_XC.
      Parameters:
      f - options, only the Expandable.LEAVE_COORDS_UNCHANGED and the Expandable.MDL_EXPAND flags are taken into account
      Returns:
      true
      Throws:
      IllegalArgumentException - if the group is invisible (it has a non-expanded parent)
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • contract

      protected boolean contract(int opts) throws IllegalArgumentException
      Sets the state to XSTATE_C.
      Parameters:
      opts - neglected
      Returns:
      true
      Throws:
      IllegalArgumentException - if the group is invisible (it has a non-expanded parent)
      Since:
      Marvin 3.4, 05/04/2004
      See Also:

    • getSuperscript

      public String getSuperscript()
      Gets the superscript for non-superatom S-groups.
      Returns:
      the superscript

    • isOrderedComponentSgroup

      public boolean isOrderedComponentSgroup()
      Returns if the Sgroup is ordered component Sgroup.
      Since:
      Marvin 4.1.1, 08/30/2006

    • getSubscript

      public String getSubscript()
      Gets the subscript for non-superatom S-groups.
      Returns:
      the subscript

    • setSubscript

      public void setSubscript(String s)
      Sets the subscript for non-superatom S-groups.
      Parameters:
      s - the subscript

    • getType

      public int getType()
      Gets S-group type.

      Warning: as of Marvin 6.3, getSgroupType() is suggested to be used instead, but the two methods have important differences. In the case of AminoAcidSgroups, this method returns ST_SUPERATOM, but getSgroupType() returns SgroupType.AMINOACID. Furthermore, when this method returns ST_COPOLYMER, getSgroupType() returns either SgroupType.COPOLYMER or one of SgroupType.COPOLYMER_ALT, SgroupType.COPOLYMER_RAN, SgroupType.COPOLYMER_BLK.

      Returns:
      the type
      See Also:

    • getSgroupType

      public SgroupType getSgroupType()
      Gets the S-group type.
      Returns:
      the type of the S-group
      See Also:

    • getSubType

      public int getSubType()
      Gets polymer S-group subtype.
      Returns:
      the type
      See Also:

    • setSubType

      public void setSubType(int t)
      Sets polymer S-group subtype.
      Parameters:
      t - the type
      See Also:

    • getConnectivity

      public int getConnectivity()
      Gets S-group connectivity.
      Returns:
      the connectivity
      See Also:

    • setConnectivity

      public void setConnectivity(int c)
      Sets S-group connectivity.
      Parameters:
      c - the connectivity
      See Also:

    • hasBrackets

      public boolean hasBrackets()
      Checks if brackets should be painted or not.
      Returns:
      always true in the default implementation
      Since:
      Marvin 3.3

    • cloneStructure

      public final SelectionMolecule cloneStructure()
      Gets the clone of the structure stored.
      Returns:
      the clone

    • createMolecule

      public Molecule createMolecule()
      Creates a molecule object that contains only this group.
      Returns:
      the molecule

    • createMolecule

      public Sgroup createMolecule(Molecule m)
      Creates a cloned S-group instance and a molecule object that contains only this S-group.
      Parameters:
      m - the molecule object
      Returns:
      the cloned S-group
      Since:
      Marvin 5.0, 09/01/2008

    • getAtomArray

      public final MolAtom[] getAtomArray()
      Gets the array of atoms in the S-group.
      Returns:
      the atom array

    • getAtom

      public final MolAtom getAtom(int i)
      Gets an atom in the S-group.
      Parameters:
      i - the atom index
      Returns:
      the atom

    • countAllAtoms

      public final int countAllAtoms()
      Counts the total number of atoms recursively.
      Returns:
      the number of atoms

    • isEmpty

      public final boolean isEmpty()
      Is it an empty S-group?
      Returns:
      true if the S-group does not contain any atoms, false otherwise

    • cloneSgroup

      public final Sgroup cloneSgroup(Molecule m, Sgroup psg)
      Gets a new Sgroup instance.
      Parameters:
      m - the new parent molecule
      psg - the new parent S-group
      Returns:
      the new object
      Since:
      Marvin 3.4

    • cloneSgroup

      protected Sgroup cloneSgroup(Molecule m, Sgroup psg, int[] atomIndexMap)
      Gets a new Sgroup instance.
      Parameters:
      m - the new parent molecule
      psg - the new parent S-group
      atomIndexMap - indices of cloned atoms in the original molecule or null
      Returns:
      the new object
      Since:
      Marvin 5.0.2, 03/07/2008

    • getAtomCount

      public final int getAtomCount()
      Gets the number of atoms in the S-group.
      Returns:
      the number of atoms

    • indexOf

      public int indexOf(MolAtom a)
      Gets the atom index in the S-group graph.
      Parameters:
      a - the atom
      Returns:
      the index or -1 if not found

    • indexOf

      public int indexOf(MolBond b)
      Gets the bond index in the S-group graph.
      Parameters:
      b - the bond
      Returns:
      the index or -1 if not found
      Since:
      Marvin 5.3.2

    • hasAtom

      public boolean hasAtom(MolAtom a)
      Is the specified atom an element of this group?
      Parameters:
      a - the atom
      Returns:
      true if it contains the atom, false otherwise
      Since:
      Marvin 3.4

    • containsAllAtomsOf

      public boolean containsAllAtomsOf(Sgroup sg)
      Checks if the S-group contains the atoms of another S-group.
      Returns:
      true if this S-group contains the specified one
      Since:
      Marvin 3.4

    • add

      public void add(MolAtom a)
      Adds a new atom to the S-group.
      Parameters:
      a - the atom

    • setAtom

      public void setAtom(int i, MolAtom a)
      Sets the specified atom in the S-group graph. For internal use only.
      Parameters:
      i - the index
      a - the atom

    • removeBonds

      public void removeBonds()
      Removes the edge references.

    • removeAtom

      public final void removeAtom(MolAtom a)
      Removes an atom and its bonds from the S-group.
      Parameters:
      a - the atom

    • removeAtom

      protected void removeAtom(MolAtom a, int opts)
      Removes an atom and its bonds from the S-group.
      Parameters:
      a - the atom
      opts - 0 or RA_IN_EXPAND
      Since:
      Marvin 4.1, 07/27/2006

    • removeAtom

      protected static void removeAtom(Sgroup sg, MolAtom a, int opts)
      Wrapper method that calls removeAtom(MolAtom, int) of sg. Needed by subclasses because they cannot call the protected removeAtom(MolAtom, int) method of another Sgroup.
      Parameters:
      sg - the other S-group
      a - the atom
      opts - 0 or RA_IN_EXPAND
      Since:
      Marvin 4.1, 07/27/2006

    • removeBond

      protected void removeBond(MolBond b)
      Removes a bond from the S-group.
      Parameters:
      b - the bond

    • replaceAtom

      public final void replaceAtom(MolAtom olda, MolAtom newa)
      Replace an existing atom by a new one in this S-group and its parent(recursively). For internal use only.
      Parameters:
      olda - the original atom
      newa - the new atom
      Since:
      3.5.2, 12/15/2004

    • replaceAtom

      public void replaceAtom(MolAtom olda, MolAtom newa, int opts)
      Replace an existing atom by a new one in this S-group and its parent (recursively). For internal use only.
      Parameters:
      olda - the original atom
      newa - the new atom
      opts - options
      Since:
      4.1, 07/25/2006
      See Also:

    • findCrossingBonds

      public MolBond[] findCrossingBonds()
      Finds the crossing bonds. Use only when the S-group is expanded.
      Returns:
      the attachment bonds
      Since:
      Marvin 3.3

    • isBracketCrossingBond

      public boolean isBracketCrossingBond(MolBond bond)

    • getCrossingAtoms

      public MolAtom[] getCrossingAtoms(MolBond[] xbonds) throws IllegalArgumentException
      Gets the atoms that have crossing bonds.
      Parameters:
      xbonds - the crossing bonds
      Returns:
      the attachment atoms
      Throws:
      IllegalArgumentException - if a bond in the specified array is not a crossing bond
      Since:
      Marvin 3.3

    • removeGroupedAtom

      protected static void removeGroupedAtom(MoleculeGraph m, MolAtom a, MolBond[] v, int opts)
      Removes an atom from the molecule and removes its specified bonds.
      Parameters:
      m - the molecule graph
      a - the atom
      v - bonds to remove from the atom, remove all bonds if null
      opts - the removal options
      See Also:

    • areChildSgroupsVisible

      public boolean areChildSgroupsVisible()
      Checks whether the child S-groups are visible.
      Returns:
      true if children are visible, false otherwise
      Since:
      Marvin 3.4

    • isVisible

      public final boolean isVisible()
      Checks whether this group is 'visible' (all parents are expanded in case of superatom S-groups) or not.
      Returns:
      true if the group is visible, false otherwise
      Since:
      Marvin 3.4

    • isBracketVisible

      public boolean isBracketVisible()
      Tests whether the bracket is visible.
      Returns:
      true if visible, false otherwise
      Since:
      Marvin 3.5.1, 11/12/2004

    • transformByParent

      protected void transformByParent(CTransform3D t, boolean incg)
      Applies a transformation matrix to the coordinates. This method is called by the parent molecule's Molecule.transform(CTransform3D, boolean) method, thus only those atom coordinates are transformed here that are not handled in MoleculeGraph.transform(CTransform3D, boolean).
      Parameters:
      t - the transformation matrix
      incg - graph invariants are changed (true) or not (false)
      Since:
      Marvin 4.0.2, 10/26/2005

    • sort

      public static void sort(Sgroup[] sgroups, int orderType)
      Sorts S-groups in parent-child or child-parent order.
      Parameters:
      sgroups - the array to sort
      orderType - the sort order
      Since:
      Marvin 3.4
      See Also:

    • toString

      public final String toString()
      Overrides Object.toString() to ease debugging. Returns a string consisting of the classname (without the package name!), the at-sign character `@', and the unsigned hexadecimal representation of the hash code of the object.
      Overrides:
      toString in class Object
      Returns:
      a string representation of the object
      Since:
      Marvin 3.4

    • toString

      public String toString(int opts)
      Gets a string representation of the S-group. Returns a string consisting of the classname (without the package name!), the at-sign character ` @', and the unsigned hexadecimal representation of the hash code of the object.
      Parameters:
      opts - options or 0
      Returns:
      a string representation of the object
      Since:
      Marvin 4.1, 07/26/2006
      See Also:

    • getAtomSymbolListAsString

      protected static String getAtomSymbolListAsString(MolAtom[] atoms)

    • isDescendantOf

      public boolean isDescendantOf(Sgroup psg)
      Decides whether this is a descendant of another S-group.
      Parameters:
      psg - the other S-group
      Returns:
      true if this is a descendant of the other S-group, false otherwise.
      Since:
      Marvin 5.0

    • isRemovable

      public boolean isRemovable()
      Decides whether an S-group should be ungrouped if its structure changes.
      Returns:
      is true if the S-group is removable, false otherwise.
      See Also:

    • isSelected

      public boolean isSelected(MoleculeGraph sel)
      Is the S-group or part of the S-group selected?
      Parameters:
      sel - the molecule that contains the selected atoms
      Returns:
      true if the S-group contains at least one selected atom false otherwise.
      Since:
      Marvin 5.0, 04/02/2007

    • isTotalSelected

      public boolean isTotalSelected(MoleculeGraph sel)
      Decides if the whole S-group is selected or not.
      Parameters:
      sel - molecule graph that contains the selection
      Returns:
      true if the whole S-group is selected
      Since:
      Marvin 5.3.2, 10/01/2010

    • isPartSelected

      public boolean isPartSelected(MoleculeGraph sel)
      Decides if part of the S-group is selected or not.
      Parameters:
      sel - molecule graph that contains the selection
      Returns:
      true if at least one of the S-group atoms is selected, but the whole group is not
      Since:
      Marvin 5.3.2, 10/01/2010

    • clearObjects

      public void clearObjects()
      Clears all MObject-s that belong to this S-groups.
      Since:
      Marvin 5.3, 11/30/2009

    • removeObject

      public void removeObject(MObject mo)
      Removes the specified MObject from this Sgroup.
      Parameters:
      mo - the MObject to remove.
      Since:
      Marvin 5.3, 11/30/2009

    • selectAllObjects

      public void selectAllObjects(boolean s)
      Sets the selection state of the MObject-s that belong to this Sgroup.
      Parameters:
      s - the state value to set
      Since:
      Marvin 5.3, 11/30/2009

    • addBracket

      public void addBracket(MBracket bracket)
      Adds a bracket to this S-group.
      Parameters:
      bracket - the bracket to add
      Since:
      Marvin 5.3, 11/30/2009
      See Also:

    • initBrackets

      public void initBrackets()
      Initializes the list of brackets in this S-group. Creates an empty list of brackets if no brackets were added previously to the S-group, otherwise deletes the brackets from the existing list.
      Since:
      Marvin 5.3, 11/30/2009
      See Also:

    • getBracketCount

      public int getBracketCount()
      Gets the number of brackets in this S-group.
      Returns:
      the number of brackets in this S-group.
      Since:
      Marvin 5.3, 11/30/2009
      See Also:

    • getBrackets

      public ArrayList<MBracket> getBrackets()
      Gets all graphic brackets from this Sgroup
      Returns:
      the list of brackets
      Since:
      Marvin 5.3, 11/30/2009
      See Also:

    • getChargeLocation

      public int getChargeLocation()
      Returns the charge location attribute of the S-group.
      Returns:
      charge location type: CHARGE_ON_ATOMS or CHARGE_ON_GROUP.
      Since:
      Marvin 5.2, 01/22/2009
      See Also:

    • setChargeLocation

      public void setChargeLocation(int location)
      Sets the charge location attribute of the S-group. Possible charge location types: CHARGE_ON_ATOMS or CHARGE_ON_GROUP.
      Parameters:
      location - the charge location type to set
      Since:
      Marvin 5.2, 01/22/2009
      See Also:

    • getTotalCharge

      public int getTotalCharge()
      Calculates the sum of the charge values on the atoms in this S-group.
      Returns:
      the sum charge
      Since:
      Marvin 5.2, 01/22/2009
      See Also:

    • checkBonds

      protected void checkBonds(MolAtom atom)
      Add the bonds of the given atom to the S-group if the given atom and the other atom of the selected bond are both in the S-group.
      Parameters:
      atom - the given atom

    • getAttach

      protected static int getAttach(MolAtom atom)
      Gets the attachment point information from the ExtraAtomProperties
      Parameters:
      atom - that attachment point is question.
      Returns:
      the attachment point information from ExtraAtomProperties
      Since:
      Marvin 6.0, Dec 12, 2012

    • getBondArray

      public MolBond[] getBondArray()
      Gets all bonds connecting two atoms that are both in the Sgroup
      Returns:
      S-group's MolBond object array
      Since:
      Marvin 6.1, 04/29/2013

    • checkConsistencyInEmbeddings

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2026) public boolean checkConsistencyInEmbeddings()
      Deprecated, for removal: This API element is subject to removal in a future version.
      replaced by checkConsistency()
      For internal use only. Checks if the S-group contains all child S-group's atoms and checks consistency between atom and bond references.
      Returns:
      true if the S-group is consistent

    • checkConsistency

      public void checkConsistency()
      For internal use only. Checks if the S-group contains all atoms of its children atoms and checks consistency between atom and bond references.
      Throws:
      IllegalStateException - if inconsistency found

    • checkSgroupGraphConsistency

      protected boolean checkSgroupGraphConsistency(Sgroup parentSgroup)
      Checks whether the parameter S-group contains the atoms of this S-group. It checks also that the parent molecule (if exists) contains these atoms as well.
      Parameters:
      parentSgroup - parent of Sgroup
      Returns:
      true if the S-group is consistent

    • getChildSgroups

      protected Sgroup[] getChildSgroups()
      Gets the children of this S-group.
      Returns:
      Child S-groups as an array.