Package org.openscience.cdk.interfaces

Interface IAtomContainer

All Superinterfaces:
Cloneable, ICDKObject, IChemObject, IChemObjectListener
All Known Subinterfaces:
IAminoAcid, IBioPolymer, ICrystal, IMonomer, IPDBMonomer, IPDBPolymer, IPolymer, IQueryAtomContainer, IRing, IStrand
All Known Implementing Classes:
AminoAcid, AminoAcid, AtomContainer, AtomContainer, AtomContainerLegacy, AtomContainerLegacy, BioPolymer, BioPolymer, ChargeGroup, Crystal, Crystal, DebugAminoAcid, DebugAtomContainer, DebugBioPolymer, DebugCrystal, DebugMonomer, DebugPDBMonomer, DebugPDBPolymer, DebugPolymer, DebugRing, DebugStrand, MDMolecule, Monomer, Monomer, PDBMonomer, PDBMonomer, PDBPolymer, PDBPolymer, PDBStrand, PharmacophoreQuery, Polymer, Polymer, QueryAtomContainer, Residue, Ring, Ring, Strand, Strand
public interface IAtomContainer extends IChemObject, IChemObjectListener
Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.

Looping over all IBonds in the IAtomContainer is typically done like: 

  for (IBond bond : atomContainer.bonds()) {
    // do something
  }
If you do need an explicit Iterator then use 

 Iterator<IBond> bondIter = atomContainer.bonds().iterator();
Author:
steinbeck
Created on:
2000-10-02

  • Method Details

    • addStereoElement

      void addStereoElement(IStereoElement element)
      Adds a stereo element to this container.
      Parameters:
      element - The new IStereoElement for this container
      See Also:

    • setStereoElements

      void setStereoElements(List<IStereoElement> elements)
      Set the stereo elements - this will replace the existing instance with a new instance.
      Parameters:
      elements - the new stereo elements

    • stereoElements

      Iterable<IStereoElement> stereoElements()
      Returns the stereo elements defined for this atom container.
      Returns:
      An Iterable of IStereoElements.
      See Also:

    • setAtoms

      void setAtoms(IAtom[] atoms)
      Sets the array of atoms of this AtomContainer.
      Parameters:
      atoms - The array of atoms to be assigned to this AtomContainer
      See Also:

    • setBonds

      void setBonds(IBond[] bonds)
      Sets the array of bonds of this AtomContainer.
      Parameters:
      bonds - The array of bonds to be assigned to this AtomContainer
      See Also:

    • setAtom

      void setAtom(int idx, IAtom atom)
      Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
      Parameters:
      idx - The index of the atom to be set.
      atom - The atom to be stored at position idx
      Throws:
      IndexOutOfBoundsException - index is out of bounds
      IllegalArgumentException - the atom could not be set
      See Also:

    • getAtom

      IAtom getAtom(int idx)
      Get the atom at the specified idx, the index should be in the range 0 ≤ idx < getAtomCount().
      Parameters:
      idx - atom index
      Returns:
      the atom stored at the index
      Throws:
      IndexOutOfBoundsException - the index is out of range
      See Also:

    • getBond

      IBond getBond(int idx)
      Get the bond at the specified idx, the index should be in the range 0 ≤ idx < getBondCount().
      Parameters:
      idx - bond index
      Returns:
      the bond stored at the index
      Throws:
      IndexOutOfBoundsException - the index is out of range

    • getLonePair

      ILonePair getLonePair(int idx)
      Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < getLonePairCount().
      Parameters:
      idx - lone pair index
      Returns:
      the lone pair stored at the index
      Throws:
      IndexOutOfBoundsException - the index is out of range

    • getSingleElectron

      ISingleElectron getSingleElectron(int idx)
      Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < getSingleElectronCount().
      Parameters:
      idx - single electron index
      Returns:
      the single electron stored at the index
      Throws:
      IndexOutOfBoundsException - the index is out of range

    • atoms

      Iterable<IAtom> atoms()
      Returns an Iterable for looping over all atoms in this container.
      Returns:
      An Iterable with the atoms in this container

    • bonds

      Iterable<IBond> bonds()
      Returns an Iterable for looping over all bonds in this container.
      Returns:
      An Iterable with the bonds in this container

    • lonePairs

      Iterable<ILonePair> lonePairs()
      Returns an Iterable for looping over all lone pairs in this container.
      Returns:
      An Iterable with the lone pairs in this container

    • singleElectrons

      Iterable<ISingleElectron> singleElectrons()
      Returns an Iterable for looping over all single electrons in this container.
      Returns:
      An Iterable with the single electrons in this container

    • electronContainers

      Iterable<IElectronContainer> electronContainers()
      Returns an Iterable for looping over all electron containers in this container.
      Returns:
      An Iterable with the electron containers in this container

    • getFirstAtom

      @Deprecated IAtom getFirstAtom()
      Deprecated.
      use getAtom(int)
      Returns the atom at position 0 in the container.
      Returns:
      The atom at position 0 .

    • getLastAtom

      @Deprecated IAtom getLastAtom()
      Deprecated.
      use getAtom(int)
      Returns the atom at the last position in the container.
      Returns:
      The atom at the last position

    • getAtomNumber

      @Deprecated int getAtomNumber(IAtom atom)
      Deprecated.
      use indexOf(IAtom)
      Returns the position of a given atom in the atoms array. It returns -1 if the atom atom does not exist.
      Parameters:
      atom - The atom to be sought
      Returns:
      The Position of the atom in the atoms array in [0,..].

    • getBondNumber

      @Deprecated int getBondNumber(IAtom atom1, IAtom atom2)
      Deprecated.
      use indexOf(IBond)
      Returns the position of the bond between two given atoms in the electronContainers array. It returns -1 if the bond does not exist.
      Parameters:
      atom1 - The first atom
      atom2 - The second atom
      Returns:
      The Position of the bond between a1 and a2 in the electronContainers array.

    • getBondNumber

      @Deprecated int getBondNumber(IBond bond)
      Deprecated.
      use indexOf(IBond)
      Returns the position of a given bond in the electronContainers array. It returns -1 if the bond does not exist.
      Parameters:
      bond - The bond to be sought
      Returns:
      The Position of the bond in the electronContainers array in [0,..].

    • getLonePairNumber

      @Deprecated int getLonePairNumber(ILonePair lonePair)
      Deprecated.
      use indexOf(ILonePair)
      Returns the position of a given lone pair in the lone pair array. It returns -1 if the lone pair does not exist.
      Parameters:
      lonePair - The lone pair to be sought
      Returns:
      The Position of the lone pair in the array..

    • getSingleElectronNumber

      int getSingleElectronNumber(ISingleElectron singleElectron)
      Deprecated.
      use indexOf(ISingleElectron)
      Returns the position of a given single electron in the single electron array. It returns -1 if the single electron does not exist.
      Parameters:
      singleElectron - The single electron to be sought
      Returns:
      The Position of the single electron in the array.

    • indexOf

      int indexOf(IAtom atom)
      Access the storage index of an atom.
      Parameters:
      atom - atom instance to find
      Returns:
      the index, -1 if not found

    • indexOf

      int indexOf(IBond bond)
      Access the storage index of a bond.
      Parameters:
      bond - bond instance to find
      Returns:
      the index, -1 if not found

    • indexOf

      int indexOf(ISingleElectron electron)
      Access the storage index of a single electron (radical).
      Parameters:
      electron - the electron
      Returns:
      the index, -1 if not found

    • indexOf

      int indexOf(ILonePair pair)
      Access the storage index of a long pair.
      Parameters:
      pair - the long pair
      Returns:
      the index, -1 if not found

    • getElectronContainer

      IElectronContainer getElectronContainer(int number)
      Returns the ElectronContainer at position number in the container.
      Parameters:
      number - The position of the ElectronContainer to be returned.
      Returns:
      The ElectronContainer at position number.
      See Also:

    • getBond

      IBond getBond(IAtom atom1, IAtom atom2)
      Returns the bond that connects the two given atoms.
      Parameters:
      atom1 - The first atom
      atom2 - The second atom
      Returns:
      The bond that connects the two atoms

    • getAtomCount

      int getAtomCount()
      Returns the number of Atoms in this Container.
      Returns:
      The number of Atoms in this Container

    • getBondCount

      int getBondCount()
      Returns the number of Bonds in this Container.
      Returns:
      The number of Bonds in this Container

    • getLonePairCount

      int getLonePairCount()
      Returns the number of LonePairs in this Container.
      Returns:
      The number of LonePairs in this Container

    • getSingleElectronCount

      int getSingleElectronCount()
      Returns the number of the single electrons in this container.
      Returns:
      The number of SingleElectron objects of this AtomContainer

    • getElectronContainerCount

      int getElectronContainerCount()
      Returns the number of ElectronContainers in this Container.
      Returns:
      The number of ElectronContainers in this Container

    • getConnectedAtomsList

      List<IAtom> getConnectedAtomsList(IAtom atom)
      Returns the atoms connected connected to the specified atom by a bond.
      Parameters:
      atom - the atom
      Returns:
      connected atoms
      Throws:
      NoSuchElementException - the atom is not present

    • getConnectedBondsList

      List<IBond> getConnectedBondsList(IAtom atom)
      Returns the bonds connected connected to the specified atom.
      Parameters:
      atom - the atom
      Returns:
      connected bonds
      Throws:
      NoSuchElementException - the atom is not present

    • getConnectedLonePairsList

      List<ILonePair> getConnectedLonePairsList(IAtom atom)
      Returns the lone pairs connected connected to the specified atom.
      Parameters:
      atom - the atom
      Returns:
      connected lone pairs
      Throws:
      NoSuchElementException - the atom is not present

    • getConnectedSingleElectronsList

      List<ISingleElectron> getConnectedSingleElectronsList(IAtom atom)
      Returns the single electrons connected connected to the specified atom.
      Parameters:
      atom - the atom
      Returns:
      connected lone pairs
      Throws:
      NoSuchElementException - the atom is not present

    • getConnectedElectronContainersList

      List<IElectronContainer> getConnectedElectronContainersList(IAtom atom)
      Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
      Parameters:
      atom - the atom
      Returns:
      connected lone pairs
      Throws:
      NoSuchElementException - the atom is not present

    • getConnectedAtomsCount

      @Deprecated int getConnectedAtomsCount(IAtom atom)
      Deprecated.
      use getConnectedBondsCount(IAtom)
      Returns the number of connected atoms (explicit degree) to the specified atom. This does not include bonds to implicit hydrogens.
      Parameters:
      atom - the atom
      Returns:
      number of connected bonds
      Throws:
      NoSuchElementException - the atom is not present

    • getConnectedBondsCount

      int getConnectedBondsCount(IAtom atom)
      Returns the number of connected bonds (explicit degree) to the specified atom. This does not include bonds to implicit hydrogens.
      Parameters:
      atom - the atom
      Returns:
      number of connected bonds
      Throws:
      NoSuchElementException - the atom is not present

    • getConnectedBondsCount

      int getConnectedBondsCount(int idx)
      Returns the number of connected bonds (explicit degree) to atom at the specified index. This does not include bonds to implicit hydrogens.
      Parameters:
      idx - the atom idx
      Returns:
      number of connected bonds
      Throws:
      IndexOutOfBoundsException - the index is not in range

    • getConnectedLonePairsCount

      int getConnectedLonePairsCount(IAtom atom)
      Returns the number of lone pairs connected to the specified atom.
      Parameters:
      atom - the atom
      Returns:
      number of connected bonds
      Throws:
      NoSuchElementException - the atom is not present

    • getConnectedSingleElectronsCount

      int getConnectedSingleElectronsCount(IAtom atom)
      Returns the number of single electrons connected to the specified atom.
      Parameters:
      atom - the atom
      Returns:
      number of connected bonds
      Throws:
      NoSuchElementException - the atom is not present

    • getBondOrderSum

      double getBondOrderSum(IAtom atom)
      Returns the sum of the bond orders for a given Atom.
      Parameters:
      atom - The atom
      Returns:
      The number of bondorders for this atom

    • getMaximumBondOrder

      IBond.Order getMaximumBondOrder(IAtom atom)
      Returns the maximum bond order that this atom currently has in the context of this AtomContainer. If the atom has no bonds but does have implicit hydrogens the minimum bond order is IBond.Order.SINGLE, otherwise the bond is unset IBond.Order.UNSET.
      Parameters:
      atom - The atom
      Returns:
      The maximum bond order that this atom currently has
      Throws:
      NoSuchElementException - atom does not belong to this container

    • getMinimumBondOrder

      IBond.Order getMinimumBondOrder(IAtom atom)
      Returns the minimum bond order that this atom currently has in the context of this AtomContainer. If the atom has no bonds but does have implicit hydrogens the minimum bond order is IBond.Order.SINGLE, otherwise the bond is unset IBond.Order.UNSET.
      Parameters:
      atom - The atom
      Returns:
      The minimum bond order that this atom currently has
      Throws:
      NoSuchElementException - atom does not belong to this container

    • add

      void add(IAtomContainer atomContainer)
      Adds all atoms and electronContainers of a given atomcontainer to this container.
      Parameters:
      atomContainer - The atomcontainer to be added

    • newAtom

      default IAtom newAtom()
      Create a new carbon atom in this container, it will have the implicit hydrogen count initialized to 0.
      Returns:
      thew new atom

    • newAtom

      default IAtom newAtom(int element)
      Create a new atom in this container of the specified element, it will have the implicit hydrogen count initialized to 0.
      Parameters:
      element - the atomic number
      Returns:
      thew new atom

    • newAtom

      default IAtom newAtom(int element, int numImplH)
      Create a new atom in this container of the specified element and implicit hydrogen count.
      Parameters:
      element - the atomic number
      numImplH - the number of implicit hydrogens
      Returns:
      thew new atom

    • newAtom

      default IAtom newAtom(IAtom atom)
      Create a new atom in the container based on properties of the provided atom. The new atom will have the same properties as the original but is distinct.
      Parameters:
      atom - the original atom
      Returns:
      the new atom

    • newBond

      default IBond newBond(IAtom beg, IAtom end)
      Create a new single bond between two atoms.
      Parameters:
      beg - the begin atom
      end - the end atom
      Returns:
      the new bond

    • newBond

      default IBond newBond(IAtom beg, IAtom end, IBond.Order order)
      Create a new bond between two atoms.
      Parameters:
      beg - the begin atom
      end - the end atom
      order - the bond order
      Returns:
      the new bond

    • addAtom

      void addAtom(IAtom atom)
      Adds an atom to this container.
      Parameters:
      atom - The atom to be added to this container

    • addBond

      void addBond(IBond bond)
      Adds a Bond to this AtomContainer.
      Parameters:
      bond - The bond to added to this container
      Throws:
      NoSuchAtomException - optionally thrown if the atoms of the bond have not yet been added

    • addLonePair

      void addLonePair(ILonePair lonePair)
      Adds a lone pair to this AtomContainer.
      Parameters:
      lonePair - The LonePair to added to this container

    • addSingleElectron

      void addSingleElectron(ISingleElectron singleElectron)
      Adds a single electron to this AtomContainer.
      Parameters:
      singleElectron - The SingleElectron to added to this container

    • addElectronContainer

      void addElectronContainer(IElectronContainer electronContainer)
      Adds a ElectronContainer to this AtomContainer.
      Parameters:
      electronContainer - The ElectronContainer to added to this container

    • remove

      void remove(IAtomContainer atomContainer)
      Removes all atoms and electronContainers of a given atomcontainer from this container.
      Parameters:
      atomContainer - The atomcontainer to be removed

    • removeAtomOnly

      void removeAtomOnly(int position)
      Unsafely remove atom at index.
      Removes the atom at the given position from the AtomContainer. Note that the electronContainers are unaffected: you also have to take care of removing all electronContainers to this atom from the container manually.
      Parameters:
      position - The position of the atom to be removed.

    • removeAtomOnly

      void removeAtomOnly(IAtom atom)
      Unsafely remove atom.
      Removes the given atom from the AtomContainer. Note that the electronContainers are unaffected: you also have to take care of removeing all electronContainers to this atom from the container.
      Parameters:
      atom - The atom to be removed

    • removeBond

      IBond removeBond(int position)
      Removes the bond at the given position from the AtomContainer.
      Parameters:
      position - The position of the bond to be removed.
      Returns:
      the bond at the given position

    • removeBond

      IBond removeBond(IAtom atom1, IAtom atom2)
      Removes the bond that connects the two given atoms.
      Parameters:
      atom1 - The first atom
      atom2 - The second atom
      Returns:
      The bond that connects the two atoms

    • removeBond

      void removeBond(IBond bond)
      Removes the bond from this container.
      Parameters:
      bond - The bond to be removed.

    • removeLonePair

      ILonePair removeLonePair(int position)
      Removes the lone pair at the given position from the AtomContainer.
      Parameters:
      position - The position of the LonePair to be removed.
      Returns:
      The removed ILonePair.

    • removeLonePair

      void removeLonePair(ILonePair lonePair)
      Removes the lone pair from the AtomContainer.
      Parameters:
      lonePair - The LonePair to be removed.

    • removeSingleElectron

      ISingleElectron removeSingleElectron(int position)
      Removes the single electron at the given position from the AtomContainer.
      Parameters:
      position - The position of the SingleElectron to be removed.
      Returns:
      The removed ISingleElectron

    • removeSingleElectron

      void removeSingleElectron(ISingleElectron singleElectron)
      Removes the single electron from the AtomContainer.
      Parameters:
      singleElectron - The SingleElectron to be removed.

    • removeElectronContainer

      IElectronContainer removeElectronContainer(int position)
      Removes the bond at the given position from this container.
      Parameters:
      position - The position of the bond in the electronContainers array
      Returns:
      the IElectronContainer that was removed

    • removeElectronContainer

      void removeElectronContainer(IElectronContainer electronContainer)
      Removes this ElectronContainer from this container.
      Parameters:
      electronContainer - The electronContainer to be removed

    • removeAtom

      void removeAtom(IAtom atom)
      Safely remove an atom from the container.
      Removes a single atom from the container updating all internal state to be consistent. All bonds connected to the atom will be deleted as well as all stereo elements. If multiple atoms/bonds are being deleted they should be gathered into a single transaction and removed with remove(IAtomContainer).
      If you are removing hydrogens one of the utility methods (e.g. AtomContainerManipulator.removeHydrogens(IAtomContainer)) is preferable.
      Parameters:
      atom - the atom to be removed

    • removeAtom

      void removeAtom(int pos)
      Safely remove an atom from the container.
      Removes a single atom from the container updating all internal state to be consistent. All bonds connected to the atom will be deleted as well as all stereo elements. If multiple atoms/bonds are being deleted they should be gathered into a single transaction and removed with remove(IAtomContainer).
      If you are removing hydrogens one of the utility methods (e.g. AtomContainerManipulator.removeHydrogens(IAtomContainer)) is preferable.
      Parameters:
      pos - the position of the atom to be removed

    • removeAtomAndConnectedElectronContainers

      @Deprecated void removeAtomAndConnectedElectronContainers(IAtom atom)
      Deprecated.
      Method has be renamed removeAtom(IAtom).
      Safely remove an atom from the container.
      See Also:

    • removeAllElements

      void removeAllElements()
      Removes all atoms, bonds and stereo elements from this container.

    • removeAllElectronContainers

      void removeAllElectronContainers()
      Removes electronContainers from this container.

    • removeAllBonds

      void removeAllBonds()
      Removes all Bonds from this container.

    • addBond

      void addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo)
      Adds a bond to this container.
      Parameters:
      atom1 - Id of the first atom of the Bond in [0,..]
      atom2 - Id of the second atom of the Bond in [0,..]
      order - Bondorder
      stereo - Stereochemical orientation

    • addBond

      void addBond(int atom1, int atom2, IBond.Order order, IBond.Display display)
      Adds a bond to this container.
      Parameters:
      atom1 - idx of the first atom of the Bond in [0,..]
      atom2 - idx of the second atom of the Bond in [0,..]
      order - the bond order
      display - the display type of the bond

    • addBond

      default void addBond(int atom1, int atom2, IBond.Order order)
      Adds a bond to this container.
      Parameters:
      atom1 - Id of the first atom of the Bond in [0,..]
      atom2 - Id of the second atom of the Bond in [0,..]
      order - Bondorder

    • addLonePair

      void addLonePair(int atomID)
      Adds a LonePair to this Atom.
      Parameters:
      atomID - The atom number to which the LonePair is added in [0,..]

    • addSingleElectron

      void addSingleElectron(int atomID)
      Adds a SingleElectron to this Atom.
      Parameters:
      atomID - The atom number to which the SingleElectron is added in [0,..]

    • contains

      boolean contains(IAtom atom)
      True, if the AtomContainer contains the given atom object.
      Parameters:
      atom - the atom this AtomContainer is searched for
      Returns:
      True, if the AtomContainer contains the given atom object

    • contains

      boolean contains(IBond bond)
      True, if the AtomContainer contains the given bond object.
      Parameters:
      bond - the bond this AtomContainer is searched for
      Returns:
      True, if the AtomContainer contains the given bond object

    • contains

      boolean contains(ILonePair lonePair)
      True, if the AtomContainer contains the given LonePair object.
      Parameters:
      lonePair - the LonePair this AtomContainer is searched for
      Returns:
      True, if the AtomContainer contains the given LonePair object

    • contains

      boolean contains(ISingleElectron singleElectron)
      True, if the AtomContainer contains the given SingleElectron object.
      Parameters:
      singleElectron - the SingleElectron this AtomContainer is searched for
      Returns:
      True, if the AtomContainer contains the given SingleElectron object

    • contains

      boolean contains(IElectronContainer electronContainer)
      True, if the AtomContainer contains the given ElectronContainer object.
      Parameters:
      electronContainer - ElectronContainer that is searched for
      Returns:
      True, if the AtomContainer contains the given bond object

    • isEmpty

      boolean isEmpty()
      Indicates whether this container is empty. The container is considered empty if there are no atoms. Bonds are not checked as a graph with no vertexes can not have edges.
      Returns:
      whether the container is empty

    • getTitle

      String getTitle()
      Access the title of the record.
      Returns:
      the title

    • setTitle

      void setTitle(String title)
      Modify the title of the record.
      Parameters:
      title - the title

    • clone

      IAtomContainer clone() throws CloneNotSupportedException
      Returns a deep clone of this IChemObject.
      Specified by:
      clone in interface IChemObject
      Returns:
      Object the clone of this IChemObject.
      Throws:
      CloneNotSupportedException - if the IChemObject cannot be cloned