Interface IAtomContainer

    • Method Detail

      • 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
      • 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:
        atoms()
      • 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:
        bonds()
      • 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(int)
      • 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.
        Returns the atom at position 0 in the container.
        Returns:
        The atom at position 0 .
      • getLastAtom

        @Deprecated
        IAtom getLastAtom()
        Deprecated.
        Returns the atom at the last position in the container.
        Returns:
        The atom at the last position
      • getAtomNumber

        @Deprecated
        int getAtomNumber​(IAtom atom)
        Deprecated.
        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.
        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.
        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.
        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.
        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:
        addElectronContainer(IElectronContainer)
      • 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)
        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
      • 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
      • 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)
        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