Package chemaxon.struc

Interface Smolecule

All Superinterfaces:
Incomplecule
All Known Subinterfaces:
WSmolecule
@PublicAPI public interface Smolecule extends Incomplecule
Array-based abstract molecule class.

PLEASE DO NOT IMPLEMENT THIS INTERFACE! It may get more abstract methods in later versions.

Since:
Marvin 5.2.2, 04/24/2009

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    A_ALL
    Use all atom and bond property arrays.
    static final int
    A_ASTEREO
    Use atom stereo properties arrays, equals A_PARITY|A_CHIRALITY.
    static final int
    A_ATOMMAP
    Use atom type array.
    static final int
    A_BOND
    Use arrays to store bonds.
    static final int
    A_CHARGE
    Use charge array.
    static final int
    A_CHIRALITY
    Chirality.
    static final int
    A_EXPLH
    Use explicit Hydrogen count array.
    static final int
    A_HYBRIDIZATION
    Use hybridization state array.
    static final int
    A_IMPLH
    Use implicit Hydrogen count array.
    static final int
    A_MASSNO
    Use mass number array.
    static final int
    A_PARITY
    Atom parity.
    static final int
    A_RADICAL
    Use radical array.
    static final int
    A_RGROUP
    Use R-group ID array.
    static final int
    A_VALENCE
    Use valence array.
    static final int
    RGROUP_MAX
    Maximum R-group index (32767).

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    areNeighbors(int atom1, int atom2)
    Tests whether two atoms are connected.
    chemaxon.struc.Gearch
    gearch()
    Gets graph search algorithms.
    int
    getArrayFlags()
    Gets info about the used arrays.
    int
    getAtom1(int i)
    Gets the index of the first atom of the specified bond.
    int
    getAtom2(int i)
    Gets the index of the second atom of the specified bond.
    int
    getAtomMap(int atom)
    Gets the atom-atom mapping number.
    int
    getAtomStereo(int atom)
    Gets atom stereo properties as an integer.
    int
    getAtomType(int atom)
    Gets the type of an atom.
    int
    getBondFlags(int i)
    Gets the bond descriptor flags.
    int
    getBondIndex(int atom1, int atom2)
    Gets the index of the bond between the specified atoms.
    int
    getBondType(int i)
    Gets the type of a bond.
    int
    getBondType(int atom1, int atom2)
    Gets the type of a bond between the two specified atoms.
    int
    getCharge(int atom)
    Gets the charge of an ion.
    int
    getChirality(int atom)
    Gets the chirality of an atom.
    int
    getExplicitHcount(int atom)
    Gets the number of explicit hydrogen atom neighbors of the given atom.
    int
    getHcount(int atom)
    Gets the total number of hydrogens of an atom.
    int
    getHybridizationState(int atom)
    Gets the hybridization state of an atom.
    int
    getImplicitHcount()
    Gets the total number of implicit Hydrogens.
    int
    getImplicitHcount(int atom)
    Gets the number of implicit Hydrogens of an atom.
    int
    getMassno(int atom)
    Gets the mass number of an atom.
    int
    getNeighbor(int atom, int i)
    Gets the index of a neighbor of an atom.
    int
    getNeighborCount(int atom)
    Gets the number of neighbors of an atom.
    int
    getParity(int atom)
    Gets the parity of an atom.
    int
    getQPropAsInt(int atom, String name)
    Gets a query property as an integer.
    default int
    getRadical(int atom)
    Deprecated.
    Use getRadicalValue(int) instead.
    AtomProperty.Radical
    getRadicalValue(int atom)
    Gets the radical value of an atom.
    int
    getRgroupId(int atom)
    Gets the R-group identifier of an atom.
    int
    getValence(int atom)
    Gets the valence.
    boolean
    inAtomList(int atom, int atno)
    Tests whether the specified element is in the atom list.

    Methods inherited from interface chemaxon.struc.Incomplecule

    getAtomCount, getBondCount, getName, properties

  • Field Details

  • Method Details

    • getArrayFlags

      int getArrayFlags()
      Gets info about the used arrays.
      Returns:
      the array info

    • getAtomType

      int getAtomType(int atom)
      Gets the type of an atom.
      Parameters:
      atom - the atom index
      Returns:
      the atom type

    • getCharge

      int getCharge(int atom)
      Gets the charge of an ion.
      Parameters:
      atom - the atom index
      Returns:
      the charge
      See Also:

    • getRadical

      @Deprecated default int getRadical(int atom)
      Deprecated.
      Use getRadicalValue(int) instead.
      Gets the radical value of an atom.
      Parameters:
      atom - the atom index
      Returns:
      the radical value
      See Also:

    • getRadicalValue

      AtomProperty.Radical getRadicalValue(int atom)
      Gets the radical value of an atom.
      Parameters:
      atom - the atom index
      Returns:
      the radical value
      See Also:

    • getMassno

      int getMassno(int atom)
      Gets the mass number of an atom. In the case of an element it returns 0, because it is a mix of isotopes having different mass numbers.
      Parameters:
      atom - the atom index
      Returns:
      the mass number, or zero if not specified
      See Also:

    • getHybridizationState

      int getHybridizationState(int atom)
      Gets the hybridization state of an atom.
      Parameters:
      atom - the atom index
      Returns:
      the hybridization state
      See Also:

    • getQPropAsInt

      int getQPropAsInt(int atom, String name)
      Gets a query property as an integer.
      Parameters:
      atom - the atom index
      name - the property name
      Returns:
      the property's value

    • inAtomList

      boolean inAtomList(int atom, int atno)
      Tests whether the specified element is in the atom list.
      Parameters:
      atom - the atom index
      atno - the atomic number of the element to check
      Returns:
      true if the atom list contains the element, false otherwise

    • getImplicitHcount

      int getImplicitHcount(int atom)
      Gets the number of implicit Hydrogens of an atom.
      Parameters:
      atom - the atom index
      Returns:
      the number of Hydrogens
      See Also:

    • getImplicitHcount

      int getImplicitHcount()
      Gets the total number of implicit Hydrogens.
      Returns:
      the number of implicit Hydrogens
      See Also:

    • getExplicitHcount

      int getExplicitHcount(int atom)
      Gets the number of explicit hydrogen atom neighbors of the given atom.
      Parameters:
      atom - the atom index
      Returns:
      the number of Hydrogens
      See Also:

    • getHcount

      int getHcount(int atom)
      Gets the total number of hydrogens of an atom. This method should return getImplicitHcount(atom)|getExplicitHcount(atom)
      Parameters:
      atom - the atom index
      Returns:
      sum of the number of implicit and explicit Hydrogens

    • getValence

      int getValence(int atom)
      Gets the valence. If valence is set as a property, returns that. Otherwise the valence is the sum of bond orders plus the number of implicit hydrogens or query hydrogen atoms.
      Parameters:
      atom - the atom index
      Returns:
      the valence
      See Also:

    • getAtomMap

      int getAtomMap(int atom)
      Gets the atom-atom mapping number.
      Parameters:
      atom - the atom index
      Returns:
      the map value (positive integer) or 0
      See Also:

    • getRgroupId

      int getRgroupId(int atom)
      Gets the R-group identifier of an atom.
      Parameters:
      atom - the atom index
      Returns:
      the R-group identifier (between 0 and RGROUP_MAX) or 0 for normal atoms
      See Also:

    • getParity

      int getParity(int atom)
      Gets the parity of an atom.
      Parameters:
      atom - the atom index
      Returns:
      the parity or 0
      See Also:

    • getChirality

      int getChirality(int atom)
      Gets the chirality of an atom.
      Parameters:
      atom - the atom index
      Returns:
      the chirality or 0 if the atom is not chiral
      See Also:

    • getAtomStereo

      int getAtomStereo(int atom)
      Gets atom stereo properties as an integer.
      Returns:
      getParity(atom)|getChirality(atom)
      See Also:

    • getNeighborCount

      int getNeighborCount(int atom)
      Gets the number of neighbors of an atom.
      Parameters:
      atom - the atom index
      Returns:
      the number of neighbors
      See Also:

    • getNeighbor

      int getNeighbor(int atom, int i)
      Gets the index of a neighbor of an atom.
      Parameters:
      atom - the atom index
      i - the neighbor index
      Returns:
      the atom index of the i-th neighbor of atom k
      See Also:

    • areNeighbors

      boolean areNeighbors(int atom1, int atom2)
      Tests whether two atoms are connected.
      Parameters:
      atom1 - first atom index
      atom2 - second atom index
      Returns:
      true if they are connected, false otherwise
      See Also:

    • getAtom1

      int getAtom1(int i)
      Gets the index of the first atom of the specified bond.
      Parameters:
      i - the bond index
      Returns:
      an atom index
      See Also:

    • getAtom2

      int getAtom2(int i)
      Gets the index of the second atom of the specified bond.
      Parameters:
      i - the bond index
      Returns:
      an atom index
      See Also:

    • gearch

      chemaxon.struc.Gearch gearch()
      Gets graph search algorithms.
      Returns:
      graph searches

    • getBondIndex

      int getBondIndex(int atom1, int atom2)
      Gets the index of the bond between the specified atoms.
      Parameters:
      atom1 - first atom index
      atom2 - second atom index
      Returns:
      the bond index or -1
      See Also:

    • getBondType

      int getBondType(int i)
      Gets the type of a bond.
      Parameters:
      i - the bond index
      Returns:
      the bond type
      See Also:

    • getBondType

      int getBondType(int atom1, int atom2)
      Gets the type of a bond between the two specified atoms.
      Parameters:
      atom1 - first atom index
      atom2 - second atom index
      Returns:
      the bond type
      See Also:

    • getBondFlags

      int getBondFlags(int i)
      Gets the bond descriptor flags.
      Parameters:
      i - the bond index
      Returns:
      getBondType(i) | stereo1 | stereo2 | topology | reacting_center
      See Also: