comparison docs/modules/txt/Atom.txt @ 0:4816e4a8ae95 draft default tip

Uploaded

0:4816e4a8ae95

NAME
    Atom

SYNOPSIS
    use Atom;

DESCRIPTION
    Atom class provides the following methods:

    new, AddHydrogens, Copy, DeleteAtom, DeleteHydrogens,
    DoesAtomNeighborhoodMatch, GetAtomicInvariantValue, GetAtomicWeight,
    GetBondToAtom, GetBonds, GetBondsToHeavyAtoms, GetBondsToHydrogenAtoms,
    GetBondsToNonHydrogenAtoms, GetExactMass, GetExplicitHydrogens,
    GetFormalCharge, GetFreeRadicalElectrons, GetGroupNumber,
    GetHeavyAtomNeighbors, GetHeavyAtomNeighborsAtomInformation,
    GetHeavyAtomNeighborsBondformation, GetHighestCommonValence,
    GetHydrogenAtomNeighbors, GetHydrogens, GetImplicitHydrogens,
    GetLargestBondOrder, GetLargestBondOrderToHeavyAtoms,
    GetLargestBondOrderToNonHydrogenAtoms, GetLargestRing,
    GetLowestCommonValence, GetMassNumber, GetMissingHydrogens,
    GetNeighbors, GetNeighborsUsingAtomSpecification,
    GetNonHydrogenAtomNeighbors, GetNonHydrogenAtomNeighborsAtomInformation,
    GetNonHydrogenAtomNeighborsBondInformation,
    GetNonHydrogenNeighborOfHydrogenAtom, GetNumOfAromaticBondsToHeavyAtoms,
    GetNumOfAromaticBondsToNonHydrogenAtoms, GetNumOfBondTypesToHeavyAtoms,
    GetNumOfBondTypesToNonHydrogenAtoms, GetNumOfBonds,
    GetNumOfBondsToHeavyAtoms, GetNumOfBondsToHydrogenAtoms,
    GetNumOfBondsToNonHydrogenAtoms, GetNumOfDoubleBondsToHeavyAtoms,
    GetNumOfBondsAvailableForHeavyAtoms,
    GetNumOfBondsAvailableForNonHydrogenAtoms,
    GetNumOfDoubleBondsToNonHydrogenAtoms, GetNumOfExplicitHydrogens,
    GetNumOfHeavyAtomNeighbors, GetNumOfHydrogenAtomNeighbors,
    GetNumOfHydrogens, GetNumOfImplicitHydrogens, GetNumOfMissingHydrogens,
    GetNumOfNeighbors, GetNumOfNonHydrogenAtomNeighbors, GetNumOfRings,
    GetNumOfRingsWithEvenSize, GetNumOfRingsWithOddSize,
    GetNumOfRingsWithSize, GetNumOfRingsWithSizeGreaterThan,
    GetNumOfRingsWithSizeLessThan, GetNumOfSigmaAndPiBondsToHeavyAtoms,
    GetNumOfSigmaAndPiBondsToNonHydrogenAtoms,
    GetNumOfSingleBondsToHeavyAtoms, GetNumOfSingleBondsToNonHydrogenAtoms,
    GetNumOfTripleBondsToHeavyAtoms, GetNumOfTripleBondsToNonHydrogenAtoms,
    GetPeriodNumber, GetPotentialTotalCommonValence, GetRings,
    GetRingsWithEvenSize, GetRingsWithOddSize, GetRingsWithSize,
    GetRingsWithSizeGreaterThan, GetRingsWithSizeLessThan,
    GetSizeOfLargestRing, GetSizeOfSmallestRing, GetSmallestRing,
    GetSpinMultiplicity, GetSumOfBondOrders, GetSumOfBondOrdersToHeavyAtoms,
    GetSumOfBondOrdersToHydrogenAtoms, GetSumOfBondOrdersToNonHydrogenAtoms,
    GetValence, GetValenceElectrons, GetValenceFreeElectrons, GetX, GetXYZ,
    GetXYZVector, GetY, GetZ, IsAmideCarbon, IsAmideNitrogen, IsAromatic,
    IsArsenic, IsBondedToAtom, IsBromine, IsCarbon, IsCarboxylCarbon,
    IsCarboxylOxygen, IsCarboxylateCarbon, IsCarboxylateOxygen, IsChlorine,
    IsFluorine, IsFunctionalClassType, IsGuadiniumCarbon,
    IsGuadiniumNitrogen, IsHBondAcceptor, IsHBondDonor, IsHalogen,
    IsHeteroAtom, IsHydrogen, IsHydrogenBondAcceptor, IsHydrogenBondDonor,
    IsHydrophobic, IsInRing, IsInRingOfSize, IsIodine, IsIsotope,
    IsLipophilic, IsMetallic, IsNegativelyIonizable, IsNitrogen,
    IsNonCarbonOrHydrogen, IsNotInRing, IsOnlyInOneRing, IsOxygen,
    IsPhosphateOxygen, IsPhosphatePhosphorus, IsPhosphorus, IsPolarAtom,
    IsPolarHydrogen, IsPositivelyIonizable, IsSaturated, IsSelenium,
    IsSilicon, IsStereoCenter, IsSulfur, IsSulphur, IsTellurium, IsTerminal,
    IsTopologicalPharmacophoreType, IsUnsaturated, SetAtomSymbol,
    SetAtomicNumber, SetExplicitHydrogens, SetMassNumber, SetStereoCenter,
    SetStereochemistry, SetX, SetXYZ, SetY, SetZ, StringifyAtom

    Atom class is derived from ObjectProperty base class which provides
    methods not explicitly defined in Atom or ObjectProperty class using
    Perl's AUTOLOAD functionality. These methods are generated on-the-fly
    for a specified object property:

        Set<PropertyName>(<PropertyValue>);
        $PropertyValue = Get<PropertyName>();
        Delete<PropertyName>();

  METHODS
    new
            $NewAtom = new Atom([%PropertyNameAndValues]);

        Using specified *Atom* property names and values hash, new method
        creates a new object and returns a reference to newly created Atom
        object. By default, following properties are initialized:

            ID = SequentialObjectID
            Name = "Atom <SequentialObjectID>"
            AtomSymbol = ""
            AtomicNumber = 0
            XYZ = ZeroVector

        Except for *ID* property, all other default properties and other
        additional properties can be set during invocation of this method.

        Examples:

            $Atom = new Atom();
            $CarbonAtom = new Atom('AtomSymbol' => 'C', 'XYZ' => (0.0, 1.0,
                          0.0));
            $OxygenAtom = new Atom('AtomName' => 'Oxygen', AtomSymbol' => 'O',
                          'XYZ' => (1.0, 1.0, 1.0));

    AddHydrogens
            $NumOfHydrogensAdded = $Atom->AddHydrogens();

        Adds hydrogens to an Atom present in a Molecule object and returns
        the number of added hydrogens. The current release of MayaChemTools
        doesn't assign hydrogen positions.

    Copy
            $AtomCopy = $Atom->Copy();

        Copy *Atom* and its associated data using Storable::dclone and
        return a new Atom object.

    DeleteAtom
            $Atom->DeleteAtom();

        Delete *Atom* from a molecule.

    DoesAtomNeighborhoodMatch
            $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec);
            $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec,
                                      $NbrAtomSpecsRef);
            $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec,
                                      $NbrAtomSpecsRef, $AllowedNbrBondSpecsRef);
            $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec,
                                      $NbrAtomSpecsRef, $NbrBondSpecsRef,
                                      $AllowedNbrOfNbrAtomSpecsRef);

        Returns 1 or 0 based on whether atom matches central atom and its
        neighborhood using specified atom and bonds specifications.
        Neighborhood atom and bond specifications are specified as array
        references containing neighbor atom and bond specifications.

        Let:

            AS = Atom symbol corresponding to element symbol, atomic number (#n)
                 or any atom (A)

            X<n>  = Number of non-hydrogen atom neighbors or heavy atoms
                    attached to atom
            T<n>  = Total number of atom neighbors including implicit and explicit
                    hydrogens
            BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy
                    atoms attached to atom
            LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy
                     atoms attached to atom
            SB<n> = Number of single bonds to non-hydrogen atom neighbors or
                    heavy atoms attached to atom
            TSB<n> = Total number of single bonds to atom neighbors including implicit
                     and explicit hydrogens
            DB<n> = Number of double bonds to non-hydrogen atom neighbors or
                    heavy atoms attached to atom
            TB<n> = Number of triple bonds to non-hydrogen atom neighbors or
                    heavy atoms attached to atom
            AB<n> = Number of aromatic bonds to non-hydrogen atom neighbors or
                    heavy atoms attached to atom
            H<n>   = Number of implicit and explicit hydrogens for atom
            Ar     = Aromatic annotation indicating whether atom is aromatic
            RA or RA<n>  = Ring atom annotation indicating whether atom
                           is a ring
            TR<n>  = Total number of rings containing atom
            FC<+n/-n> = Formal charge assigned to atom
            MN<n> = Mass number indicating isotope other than most abundant isotope
            SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet),
                    2 (doublet) or 3 (triplet)

        Then, atom specification corresponds to:

            AS.X<n>.T<n>.BO<n>.LBO<n>.<SB><n>.TSB<n>.<DB><n>.<TB><n>.AB<n>.H<n>.Ar.
            RA<n>.TR<n>FC<+n/-n>.MN<n>.SM<n>

        Except for AS which is a required atomic invariant in atom
        specification, all other atomic invariants are optional. For an atom
        specification to match an atom, the values of all specified atomic
        invariants must match. Exclamation in from of atomic invariant can
        be used to negate its effect during the match.

        For *FC* value matching, the following value operators are also
        supported:

            o +* : Any positive value
            o -* : Any negative value
            o > ValidNumber or >= ValidNumber
            o < ValidNumber or <= ValidNumber

        A comma delimited atom specification string is used to match any one
        of the specified atom specification.

        Notes:

            o During atom specification match to an atom, the first atomic invariant is always assumed to
              atom symbol.

        Examples:

            o ('N', 'N', 'N')
            o ('N.FC0', 'N.FC0', 'N,N.FC+1.H1')
            o ('N.H2', 'N.H2', 'N.H1')
            o ('C,N', '!N', '!H')
            o ('C,N', 'N.Ar', 'N.R5')

        Let:

            -|1|s|Single = Single bond
            =|2|d|Double = Double bond
            #|3|t|Triple  = Triple bond
            :|1.5|a|Ar|Aromatic = Aromatic bond

            @|RB|Ring = Ring bond
            ~|*|Any = Any bond

        Then, bond specification corresponds to:

            -.:
            =.@
            Double.Aromatic

        For a bond specification to match bond between two atoms, the values
        of all specified bond symbols must match. Exclamation in from of
        bond symbol can be used to negate its effect during the match.

        A comma delimited bond specification string is used to match any one
        of the specified atom specification.

        Notes:

            o During atom neighborhood match for central atom neighborhood atom and bond specifications,
              implicit or missing hydrogens are automatically checked for any matches to unmatched
              specifications.

        Examples:

            Aromatic carbon in a 5 membered ring:
                                      $Atom->DoesAtomNeighborhoodMatch('C.Ar.RA5');

            AcetylenicCarbon: $Atom->DoesAtomNeighborhoodMatch('C.T2.TB1'); or
                               $Atom->DoesAtomNeighborhoodMatch('C.T2.TB1',
                                      ['*', '*'], ['#', '-']);

            GuadiniumCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4',
                                      ['N.FC0', 'N.FC0', 'N.FC0,N.FC+1'],
                                      ['-', '-', '='],
                                      ['C,H', 'C,H', 'C,H']);

            AmideCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3',
                                      ['C,H', 'O', 'N'],
                                      ['-', '=', '-'],
                                      ['C,H', 'C', 'C,H,N,O,S,P,F,Cl,Br,I']);

            CarboxylCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3',
                                      ['C,H', 'O', 'O.X1.FC0'],
                                      ['-', '=', '-'],
                                      ['C,H', 'C', 'C']);

            CarboxylateCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3',
                                      ['C,H', 'O', 'O.X1.FC-1'],
                                      ['-', '=', '-'],
                                      ['C,H', 'C', 'C']);

    DeleteHydrogens
            $NumOfHydrogensDeleted = $Atom->AddHydrogens();

        Delete hydrogens from an Atom present in a Molecule object and
        returns the number of deleted hydrogens.

    GetAtomicInvariantValue
            $Value = $Atom->GetAtomicInvariantValue($AtomicInvariant);

        Returns atomic invariant value for a specified *AtomicInvariant*.
        The current release of MayaChemTools supports following
        abbreviations and descriptive names for *AtomicInvarints*:

            AS : Atom or element symbol
            X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
            T : TotalNumOfAtomNeighbors
            BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
            LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
            SB :  NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
            TSB :  TotalNumOfSingleBonds
            DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
            TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
            AB : NumOfAromaticBondsToNonHydrogenAtoms or NumOfAromaticBondsToHeavyAtoms
            H :  NumOfImplicitAndExplicitHydrogens
            Ar : Aromatic
            Str : Stereochemistry
            RA : RingAtom
            FC : FormalCharge
            AN : AtomicNumber
            AM : AtomicMass
            MN : MassNumber
            SM : SpinMultiplicity

    GetAtomicWeight
            $Value = $Aom->GetAtomicWeight();

        Returns atomic weight of an Atom which corresponds to either
        explicity set *AtomicWeight* atom property or atomic weight of the
        corresponding element in the periodic table available by
        PeriodicTable module.

    GetBondToAtom
            $Bond = $Atom->GetBondToAtom($OtherAtom);

        Returns a Bond object corresponding to bond between *Atom* and
        *OtherAtom* in a molecule.

    GetBonds
            @Bonds = $Aoto->GetBonds();

        Returns an array of Bond objects corresponding to all bonds from
        *Atom* to other bonded atoms in a molecule.

    GetBondsToHeavyAtoms
            @Bonds = $Atom->GetBondsToHeavyAtoms();

        Returns an array of Bond objects corresponding to bonds from *Atom*
        to other bonded non-hydrogen atoms in a molecule.

    GetBondsToHydrogenAtoms
            @Bonds = $Atom->GetBondsToHydrogenAtoms();

        Returns an array of Bond objects corresponding to bonds from *Atom*
        to any other hydrogen atom in a molecule.

    GetBondsToNonHydrogenAtoms
            @Bonds = $Atom->GetBondsToNonHydrogenAtoms();

        Returns an array of Bond objects corresponding to bonds from *Atom*
        to other bonded non-hydrogen atoms in a molecule.

    GetExactMass
            $ExactMass = $Atom->GetExactMass();

        Returns exact mass of an *Atom* which correspond to one of these
        three values: explicity set *ExactMass* property; mass of natural
        isotope for an explicty set value of *MassNumber*; most abundant
        natural isotope mass for *Atom* with valid atomic number value
        available by PerodicTable module.

    GetExplicitHydrogens
            $NumOfExplicitHydrogens = $Atom->GetExplicitHydrogens();

        Returns number of hydrogens explicity bonded to an *Atom* in a
        molecule.

    GetFormalCharge
            $FormalCharge = $Atom->GetFormalCharge();

        Returns formal charge of an *Atom* in a molecule.

    GetFreeRadicalElectrons
            $FreeRadicalElectrons = $Atom->GetFreeRadicalElectrons();

        Returns number of free radical electrons corresponding to to one of
        these three values: *FreeRadicalElectrons* property;
        *SpinMultiplicity* property; value of 0.

        For atoms with explicit assignment of *SpinMultiplicity* atom
        property values,

            Singlet  - two unparied electrons corresponding to one spin state
            Doublet - free radical; an unpaired electron corresponding to two
                      spin states
            Triplet - two unparied electrons corresponding to three spin states
                      (divalent carbon atoms: carbenes)

        FreeRadicalElectrons are calculated as follows:

            Doublet: 1 (one valence electron not available for bonding)
            Singlet: 2 (two valence electrons not available for bonding)
            Triplet: 2 (two valence electrons not available for bonding)

    GetGroupNumber
            $GroupNumber = $Atom->GetGroupNumber();

        Returns group number of an *Atom* in a molecule with a valid atomic
        number.

    GetHeavyAtomNeighbors
            $NumOfHeavyAtoms = $Atom->GetHeavyAtomNeighbors();
            @HeavyAtoms = $Atom->GetHeavyAtomNeighbors();

        Return number of heavy atoms or an array of Atom objects
        corresponding to heavy atoms bonded to an *Atom* in a molecule.

    GetHeavyAtomNeighborsAtomInformation
            ($NumOfAtomNeighbors, $AtomNeighborsRef,
             $NumOfAtomNeighborsType, $AtomNeighborsTypeMapRef) = $Atom->
                                      GetHeavyAtomNeighborsAtomInformation();

        Returns atoms information for all non-hydrogen atoms attached to an
        *Atom* in a molecule.

        The following values are returned:

            o Number of non-hydrogen atom neighbors
            o A reference to an array containing atom objects corresponding to
              non-hydrogen atom neighbors
            o Number of different types of non-hydrogen atom neighbors
            o A reference to a hash containing atom symbol as key with value
              corresponding to its count for non-hydrogen atom neighbors

    GetHeavyAtomNeighborsBondformation
            ($NumOfBonds, $BondTypeCountMapRef,
            $AtomsBondTypesCountMapRef,
            $AtomsBondTypeAtomsMap) = $Atom->
                                      GetHeavyAtomNeighborsBondformation();

        Returns bonds information for all non-hydrogen atoms attached to an
        *Atom* in a molecule.

        The following values are returned:

            o Number of bonds to non-hydrogen atom neighbors
            o A reference to an array containing bond objects corresponding to
              non-hydrogen atom neighbors
            o A reference to a hash containing bond type as key with value
              corresponding to its count for non-hydrogen atom neighbors. Bond
              types are: Single, Double or Triple
            o A reference to a hash containing atom symbol as key pointing to bond
              type as second key with values corresponding to count of bond types for atom
              symbol for non-hydrogen atom neighbors
            o A reference to a hash containing atom symbol as key pointing to bond
              type as second key with values corresponding to atom objects array involved
              in corresponding bond type for atom symbol for non-hydrogen atom neighbors

    GetHighestCommonValence
            $HighestCommonValence = $Atom->GetHighestCommonValence();

        Returns highest common valence of an *Atom* which corresponds to
        either explicity set *HighestCommonValence* atom property or highest
        common valence of the corresponding element in the periodic table
        available by PerodicTable module.

    GetHydrogens
            $NumOfHydrogens = $Atom->GetHydrogens();

        Returns total number of hydrogens for an *Atom* in a molecule
        including both hydrogen atom neighbors and implicit hydrogens.

    GetHydrogenAtomNeighbors
            $NumOfHydrogenAtomNeighbors = $Atom->GetHydrogenAtomNeighbors();
            @HydrogenAtomNeighbors = $Atom->GetHydrogenAtomNeighbors();

        Return number of hydrogen atoms or an array of *Atom* objects
        corresponding to hydrogen atoms bonded to an *Atom* in a molecule.

    GetImplicitHydrogens
            $NumOfImplicitHydrogens = $Atom->GetImplicitHydrogens();

        Returns number of implicit hydrogens for an *Atom* in a molecule.
        This value either corresponds to explicitly set *ImplicitHydrogens*
        atom property or calculated as the difference between the value of
        potential total valence and sum of bond orders to both hydrogen and
        non-hydrogen atom neighbors.

    GetPotentialTotalCommonValence
            $PotentialTotalValence = $Atom->GetPotentialTotalCommonValence();

        Returns potential total common valence of an *Atom* in a molecule
        corresponding to a specific valence model set for the molecule using
        its SetValenceModel method or default internal valence model. It is
        used during the calculation of missing or implicit hydrogens.

        The current release of MayaChemTools supports three valence models:
        *MDLValenceModel, DaylightValenceModel, InternalValenceModel or
        MayaChemToolsValenceModel*.

        For *MDLValenceModel* and *DaylightValenceModel*, the following data
        files, distributed with the package, are used to calculate potential
        total valence:

            lib/data/MDLValenceModelData.csv
            lib/data/DaylightValenceModelData.csv

        The calculation of potential total common valence for these two
        models is performed as follows: Calculate current effective total
        valence of the *Atom* by adding up the bond order of its neighbors
        and number of free radical electrons; Find available common valence
        for the *Atom*, corresponding to any specified formal charge, higher
        than the effective total valence, and return it as
        *PotentialTotalValence*.

        The calculation of potential total common valence For
        *InternalValenceModel* or *MayaChenToolsValenceModel* doesn't uses
        PeriodicTable module to retrieve values for common valence, which in
        turn reads in PeriodicTableElements.csv file distributed with the
        package.

        For elements with one one common valence, potential total common
        valence corresponds to:

            CommonValence + FormalCharge - FreeRadicalElectrons

        For elements with multiple common valences, each common valence is
        used to calculate total potential common valence as shown above, and
        the first total potential common valence greater than the sum of
        bond orders to all neighbors is selected as the final total common
        valence.

        FormalCharge sign is reversed for electropositive elements with
        positive formal charge during common valence calculations.
        Electropositive elements, metals and transition elements, have
        usually plus formal charge and it leads to decrease in common
        valence; the negative formal charge should result in the decrease of
        common valence.

        The sign of formal charge is adjusted as follows.

        Group numbers > 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He):

        Formal charge sign is not adjusted. Positive and negative values
        result in the increase and decrease of valence.

        Group 14 containing C, Si, Ge, Sn, Pb...:

        Formal charge sign is reversed for positive values. Both positive
        and negative values result in the decrease of valence.

        Group 13 containing B, Al, Ga, In, Tl...:

        Formal charge sign is always reversed. Positive and negative values
        result in the decrease and increase of valence.

        Groups 1 (H) through 12 (Zn)...:

        Formal charge sign is reversed for positive values. Both positive
        and negative values result in the decrease of valence.

        Lanthanides and actinides:

        Formal charge sign is reversed for positive values. Both positive
        and negative values result in the decrease of valence.

    GetLargestBondOrder
            $LargestBO =$Atom->GetLargestBondOrder();

        Returns largest bond order for an *Atom* among the bonds to other
        atoms in a molecule.

    GetLargestBondOrderToHeavyAtoms
            $LargestBO =$Atom->GetLargestBondOrderToHeavyAtoms();

        Returns largest bond order for an *Atom* among the bonds to other
        heavy atoms in a molecule.

    GetLargestBondOrderToNonHydrogenAtoms
            $LargestBO =$Atom->GetLargestBondOrderToNonHydrogenAtoms();

        Returns largest bond order for an *Atom* among the bonds to other
        non-hydrogen atoms in a molecule.

    GetLargestRing
            @RingAtoms = $Atom->GetLargestRing();

        Returns an array of ring *Atom* objects corresponding to the largest
        ring containing *Atom* in a molecule.

    GetLowestCommonValence
            $LowestCommonValence = $Atom->GetLowestCommonValence();

        Returns lowest common valence of an *Atom* which corresponds to
        either explicity set *LowestCommonValence* atom property or highest
        common valence of the corresponding element in the periodic table
        available by PerodicTable module.

    GetMassNumber
            $MassNumber = $Aom->GetMassNumber();

        Returns atomic weight of an Atom which corresponds to either
        explicity set *MassNumber* atom property or mass number of the most
        abundant natural isotope of the corresponding element in the
        periodic table available by PeriodicTable module.

    GetMissingHydrogens
            $NumOfMissingHydrogens = $Atom->GetMissingHydrogens();

        Returns number of missing hydrogens for an *Atom* in a molecule.
        This value either corresponds to explicitly set *ImplicitHydrogens*
        atom property or calculated as the difference between the value of
        potential total valence and sum of bond orders to both hydrogen and
        non-hydrogen atom neighbors.

    GetNeighbors
            $NumOfNeighbors = $Atom->GetNeighbors();
            @Neighbors = $Atom->GetNeighbors();

        Returns number of neighbor atoms or an array of *Atom* objects
        corresponding to all atoms bonded to an *Atom* in a molecule.

    GetNeighborsUsingAtomSpecification
            @AtomNeighbors = $Atom->GetNeighborsUsingAtomSpecification($AtomSpec);
            $NumOfNeighbors = $Atom->GetNeighborsUsingAtomSpecification($AtomSpec);

            @AtomNeighbors = $Atom->GetNeighborsUsingAtomSpecification($AtomSpec,
                             @ExcludeNeighbors);

        Returns number of neighbor atoms or an array of *Atom* objects
        matching atom specification corresponding to atom neighbors of an
        *Atom* in a molecule. Optionally, *Atom* neighbors can be excluded
        from the neighbors list using *ExcludeNeighbors*.

        Notes:

            o AtomSpecification correspond to any valid AtomicInvariant based atomic specifications
              as supported by DoesAtomNeighborhoodMatch method
            o Multiple atom specifications can be used in a string delimited by comma

    GetNonHydrogenAtomNeighbors
            $NumOfNeighbors = $Atom->GetNonHydrogenAtomNeighbors();
            @Neighbors = $Atom->GetNonHydrogenAtomNeighbors();

        Returns number of non-hydrogen atoms or an array of Atom objects
        corresponding to non-hydrogen atoms bonded to an *Atom* in a
        molecule.

    GetNonHydrogenAtomNeighborsAtomInformation
            ($NumOfAtomNeighbors, $AtomNeighborsRef,
             $NumOfAtomNeighborsType, $AtomNeighborsTypeMapRef) = $Atom->
                                      GetNonHydrogenAtomNeighborsAtomInformation();

        Returns atoms information for all non-hydrogen atoms attached to an
        *Atom* in a molecule.

        The following values are returned:

            o Number of non-hydrogen atom neighbors
            o A reference to an array containing atom objects corresponding to
              non-hydrogen atom neighbors
            o Number of different types of non-hydrogen atom neighbors
            o A reference to a hash containing atom symbol as key with value
              corresponding to its count for non-hydrogen atom neighbors

    GetNonHydrogenAtomNeighborsBondInformation
            ($NumOfBonds, $BondTypeCountMapRef,
            $AtomsBondTypesCountMapRef,
            $AtomsBondTypeAtomsMap) = $Atom->
                                      GetNonHydrogenAtomNeighborsBondInformation();

        Returns bonds information for all non-hydrogen atoms attached to an
        *Atom* in a molecule.

        The following values are returned:

            o Number of bonds to non-hydrogen atom neighbors
            o A reference to an array containing bond objects corresponding to
              non-hydrogen atom neighbors
            o A reference to a hash containing bond type as key with value
              corresponding to its count for non-hydrogen atom neighbors. Bond
              types are: Single, Double or Triple
            o A reference to a hash containing atom symbol as key pointing to bond
              type as second key with values corresponding to count of bond types for atom
              symbol for non-hydrogen atom neighbors
            o A reference to a hash containing atom symbol as key pointing to bond
              type as second key with values corresponding to atom objects array involved
              in corresponding bond type for atom symbol for non-hydrogen atom neighbors

    GetNonHydrogenNeighborOfHydrogenAtom
            $Atom = $Atom->GetNonHydrogenNeighborOfHydrogenAtom();

        Returns non-hydrogen or heavy atom neighbor of a hydrogen atom in a
        molecule..

    GetNumOfAromaticBondsToHeavyAtoms
            $NumOfBonds = $Atom->GetNumOfAromaticBondsToHeavyAtoms();

        Returns number of aromatic bonds from an *Atom* to other
        non-hydrogen or heavy atoms in a molecule.

    GetNumOfAromaticBondsToNonHydrogenAtoms
            $NumOfBonds = $Atom->GetNumOfAromaticBondsToNonHydrogenAtoms();

        Returns number of aromatic bonds from an *Atom* to other
        non-hydrogen or heavy atoms in a molecule.

    GetNumOfBonds
            $NumOfBonds = $Atom->GetNumOfBonds();

        Returns number of bonds from an *Atom* to other atoms in a molecule.

    GetNumOfBondsAvailableForHeavyAtoms
            $NumOfBonds = $Atom->GetNumOfBondsAvailableForHeavyAtoms();

        Get number of bonds available to form additional bonds with heavy
        atoms, excluding any implicit bonds to hydrogens set using
        *ImplicitHydrogens* property.

        It's different from number of implicit or missing hydrogens, both of
        which are equivalent.

        For example, in a SMILES string, [nH] ring atom corresponds to an
        aromatic nitrogen. Although the hydrogen specified for n is treated
        internally as implicit hydrogen and shows up in missing hydrogen
        count, it's not available to participate in double bonds to
        additional heavy atoms.

    GetNumOfBondsAvailableForNonHydrogenAtoms
            $NumOfBonds = $Atom->GetNumOfBondsAvailableForNonHydrogenAtoms();

        Get number of bonds available to form additional bonds with heavy
        atoms, excluding any implicit bonds to hydrogens set using
        ImplicitHydrogens property.

    GetNumOfBondsToHeavyAtoms
            $NumOfBondsToHeavyAtoms = $Atom->GetNumOfBondsToHeavyAtoms();

        Returns number of bonds from an *Atom* to other heavy atoms in a
        molecule.

    GetNumOfBondsToHydrogenAtoms
            $NumOfBonds = $Atom->GetNumOfBondsToHydrogenAtoms();

        Returns number of bonds from an *Atom* to other hydrogen atoms in a
        molecule.

    GetNumOfBondsToNonHydrogenAtoms
            $NumOfBonds = $Atom->GetNumOfBondsToNonHydrogenAtoms();

        Returns number of bonds from an *Atom* to other non-hydrogen atoms
        in a molecule.

    GetNumOfBondTypesToHeavyAtoms
            ($NumOfSingleBonds, $NumOfDoubleBonds,
             $NumOfTripleBonds, $NumOfAromaticBonds) = $Atom->
                           GetNumOfBondTypesToHeavyAtoms($CountAromaticBonds);

        Get number of single, double, triple, and aromatic bonds from an
        *Atom* to all other non-hydrogen atoms in a molecule.

        Value of *CountAtomaticBonds* parameter controls whether number of
        aromatic bonds is returned; default is not to count aromatic bonds.
        During counting of aromatic bonds, the bond marked aromatic is not
        included in the count of other bond types.

    GetNumOfBondTypesToNonHydrogenAtoms
            ($NumOfSingleBonds, $NumOfDoubleBonds,
             $NumOfTripleBonds, $NumOfAromaticBonds) = $Atom->
                     GetNumOfBondTypesToNonHydrogenAtoms($CountAromaticBonds);

        Get number of single, double, triple, and aromatic bonds from an
        *Atom* to all other non-hydrogen atoms in a molecule.

        Value of *CountAtomaticBonds* parameter controls whether number of
        aromatic bonds is returned; default is not to count aromatic bonds.
        During counting of aromatic bonds, the bond marked aromatic is not
        included in the count of other bond types.

    GetNumOfDoubleBondsToHeavyAtoms
            $NumOfDoubleBonds = $Atom->GetNumOfDoubleBondsToHeavyAtoms();

        Returns number of double bonds from an *Atom* to other heavy atoms
        or non-hydrogen atoms in a molecule.

    GetNumOfDoubleBondsToNonHydrogenAtoms
            $NumOfDoubleBonds =$Atom->GetNumOfDoubleBondsToNonHydrogenAtoms();

        Returns number of double bonds from an *Atom* to other heavy atoms
        or non-hydrogen atoms in a molecule.

    GetNumOfHeavyAtomNeighbors
            $NumOfNeighbors = $Atom->GetNumOfHeavyAtomNeighbors();

        Returns number heavy atom neighbors for an *Atom* in a molecule.

    GetNumOfHydrogenAtomNeighbors
            $NumOfNeighbors = $Atom->GetNumOfHydrogenAtomNeighbors();

        Returns number hydrogens atom neighbors for an *Atom* in a molecule.

    GetNumOfMissingHydrogens
            $NumOfMissingHydrogens = $Atom->GetNumOfMissingHydrogens();

        Returns number of implicit hydrogens for an *Atom* in a molecule.
        This value either corresponds to explicitly set *ImplicitHydrogens*
        atom property or calculated as the difference between the value of
        potential total valence and sum of bond orders to both hydrogen and
        non-hydrogen atom neighbors.

    GetNumOfExplicitHydrogens
            $NumOfExplicitHydrogens = $Atom->GetNumOfExplicitHydrogens();

        Returns number hydrogens atom neighbors for an *Atom* in a molecule.

    GetNumOfHydrogens
            $NumOfHydrogens = $Atom->GetNumOfHydrogens();

        Returns total number of hydrogens for an *Atom* in a molecule
        including both hydrogen atom neighbors and implicit hydrogens.

    GetNumOfImplicitHydrogens
            $NumOfImplicitHydrogens = $Atom->GetNumOfImplicitHydrogens();

        Returns number of implicit hydrogens for an *Atom* in a molecule.
        This value either corresponds to explicitly set *ImplicitHydrogens*
        atom property or calculated as the difference between the value of
        potential total valence and sum of bond orders to both hydrogen and
        non-hydrogen atom neighbors.

    GetNumOfNeighbors
            $NumOfNeighbors = $Atom->GetNumOfNeighbors();

        Returns number atom neighbors for an *Atom* in a molecule.

    GetNumOfNonHydrogenAtomNeighbors
            $NumNeighbors = $This->GetNumOfNonHydrogenAtomNeighbors();

        Returns number non-hydrogens atom neighbors for an *Atom* in a
        molecule.

    GetNumOfRings
            $NumOfRings = $Atom->GetNumOfRings();

        Returns number of rings containing *Atom* in a molecule.

    GetNumOfRingsWithEvenSize
            $NumOfRings = $Atom->GetNumOfRingsWithEvenSize();

        Returns number of rings with even size containing *Atom* in a
        molecule.

    GetNumOfRingsWithOddSize
            $NumOfRings = $Atom->GetNumOfRingsWithOddSize();

        Returns number of rings with odd size containing *Atom* in a
        molecule.

    GetNumOfRingsWithSize
            $NumOfRings = $Atom->GetNumOfRingsWithSize($RingSize);

        Returns number of rings with specific *RingSize* containing *Atom*
        in a molecule.

    GetNumOfRingsWithSizeGreaterThan
            $NumOfRings = $Atom->GetNumOfRingsWithSizeGreaterThan($RingSize);

        Returns number of rings with size greater than specific *RingSize*
        containing *Atom* in a molecule.

    GetNumOfRingsWithSizeLessThan
            $NumOfRings = $Atom->GetNumOfRingsWithSizeLessThan($RingSize);

        Returns number of rings with size less than specific *RingSize*
        containing *Atom* in a molecule.

    GetNumOfSigmaAndPiBondsToHeavyAtoms
            ($NumOfSigmaBonds, $NumOfPiBonds) = $Atom->
                                      GetNumOfSigmaAndPiBondsToHeavyAtoms();

        Get number of sigma and pi bonds from an *Atom* to all other
        non-hydrogen atoms in a molecule.

        Sigma and pi bonds are counted using the following methodology: a
        single bond correspond to one sigma bond; a double bond contributes
        one to sigma bond count and one to pi bond count; a triple bond
        contributes one to sigma bond count and two to pi bond count.

    GetNumOfSigmaAndPiBondsToNonHydrogenAtoms
            ($NumOfSigmaBonds, $NumOfPiBonds) = $Atom->
                                      GetNumOfSigmaAndPiBondsToNonHydrogenAtoms();

        Get number of sigma and pi bonds from an *Atom* to all other
        non-hydrogen atoms in a molecule.

        Sigma and pi bonds are counted using the following methodology: a
        single bond correspond to one sigma bond; a double bond contributes
        one to sigma bond count and one to pi bond count; a triple bond
        contributes one to sigma bond count and two to pi bond count.

    GetNumOfSingleBondsToNonHydrogenAtoms
            $NumOfSingleBonds =$Atom->GetNumOfSingleBondsToNonHydrogenAtoms();

        Returns number of single bonds from an *Atom* to other heavy atoms
        or non-hydrogen atoms in a molecule.

    GetNumOfSingleBondsToHeavyAtoms
            $NumOfSingleBonds = $Atom->GetNumOfSingleBondsToHeavyAtoms();

        Returns number of single bonds from an *Atom* to other heavy atoms
        or non-hydrogen atoms in a molecule.

    GetNumOfTripleBondsToNonHydrogenAtoms
            $NumOfTripleBonds =$Atom->GetNumOfTripleBondsToNonHydrogenAtoms();

        Returns number of triple bonds from an *Atom* to other heavy atoms
        or non-hydrogen atoms in a molecule.

    GetNumOfTripleBondsToHeavyAtoms
            $NumOfTripleBonds = $Atom->GetNumOfTripleBondsToHeavyAtoms();

        Returns number of triple bonds from an *Atom* to other heavy atoms
        or non-hydrogen atoms in a molecule.

    GetPeriodNumber
            $PeriodNumber = $Atom->GetPeriodNumber();

        Returns periodic table period number for an *Atom* in a molecule
        with a valid atomic number .

    GetRings
            @Rings = $Aotm->GetRings();

        Returns an array of references to arrays containing ring atoms
        corressponding to all rings containing *Atom* in a molecule.

    GetRingsWithEvenSize
            @Rings = $Aotm->GetRingsWithEvenSize();

        Returns an array of references to arrays containing ring atoms
        corressponding to all rings with even size containing *Atom* in a
        molecule.

    GetRingsWithOddSize
            @Rings = $Aotm->GetRingsWithOddSize();

        Returns an array of references to arrays containing ring atoms
        corressponding to all rings with odd size containing *Atom* in a
        molecule.

    GetRingsWithSize
            @Rings = $Aotm->GetRingsWithSize($RingSize);

        Returns an array of references to arrays containing ring atoms
        corressponding to all rings with specific *RingSize *containing
        *Atom* in a molecule.

    GetRingsWithSizeGreaterThan
            @Rings = $Aotm->GetRingsWithSizeGreaterThan($RingSize);

        Returns an array of references to arrays containing ring atoms
        corressponding to all rings with size greater than specific
        *RingSize *containing *Atom* in a molecule.

    GetRingsWithSizeLessThan
            @Rings = $Aotm->GetRingsWithSizeLessThan($RingSize);

        Returns an array of references to arrays containing ring atoms
        corressponding to all rings with size less than specific *RingSize
        *containing *Atom* in a molecule.

    GetSizeOfLargestRing
            $Size = $Atom->GetSizeOfLargestRing();

        Returns size of the largest ring containing *Atom* in a molecule.

    GetSizeOfSmallestRing
            $Size = $Atom->GetSizeOfSmallestRing();

        Returns size of the smallest ring containing *Atom* in a molecule.

    GetSmallestRing
            @RingAtoms = $Atom->GetSmallestRing();

        Returns an array of ring *Atom* objects corresponding to the largest
        ring containing *Atom* in a molecule.

    GetSpinMultiplicity
            $SpinMultiplicity = $Atom->GetSpinMultiplicity();

        Returns spin multiplicity of an *Atom* corresponding to one of these
        three values: explicitly set SpinMultiplicity property value;
        calculated from FreeRadicalElectrons property; value of 0.

        The SpinMultiplicity is calculate from *FreeRadicalElectrons*
        property as follows:

            FreeRadicalElectrons: 1; SpinMultiplicity: 2
            FreeRadicalElectrons: 2; SpinMultiplicity: 1
            FreeRadicalElectrons: other; SpinMultiplicity: 0

    GetSumOfBondOrders
            $SumBondOrders = $Atom->GetSumOfBondOrders();

        Returns sum of bond orders corresponding to all atoms bonded to an
        *Atom* in a molecule.

    GetSumOfBondOrdersToHeavyAtoms
            $SumBondOrders = $Atom->GetSumOfBondOrdersToHeavyAtoms();

        Returns sum of bond orders corresponding to all heavy atoms bonded
        to an *Atom* in a molecule.

    GetSumOfBondOrdersToHydrogenAtoms
            $SumBondOrders = $Atom->GetSumOfBondOrdersToHydrogenAtoms();

        Returns sum of bond orders corresponding to all hydrogen atoms
        bonded to an *Atom* in a molecule.

    GetSumOfBondOrdersToNonHydrogenAtoms
            $SumBondOrders = $Atom->GetSumOfBondOrdersToNonHydrogenAtoms();

        Returns sum of bond orders corresponding to all non-hydrogen atoms
        bonded to an *Atom* in a molecule.

    GetValence
            $Valence = $Atom->GetValence();

        Returns valence of an *Atom* in a molecule. Valence corresponds to
        number of electrons used by an atom in bonding:

            Valence = ValenceElectrons - ValenceFreeElectrons = BondingElectrons

        Single, double and triple bonds with bond orders of 1, 2, and 3
        correspond to contribution of 1, 2, and 3 bonding electrons. So:

            Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge

        where positive and negative values of FormalCharge increase and
        decrease the number of bonding electrons, respectively.

        The current release of MayaChemTools supports the following three
        valence models, which are used during calculation of implicit
        hydrogens: MDLValenceModel, DaylightValenceModel,
        InternalValenceModel or MayaChemToolsValenceModel.

        Notes:

            . Missing hydrogens are included in the valence.
            . For neutral molecules, valence and sum of bond orders are equal.
            . For molecules containing only single bonds, SumOfBondOrders and
              NumOfBonds are equal.
            . Free radical electrons lead to the decrease in valence. For atoms with
              explicit assignment of SpinMultiplicity property values corresponding to
              Singlet (two unparied electrons corresponding to one spin state), Doublet
              (free radical; an unpaired electron corresponding to two spin states),
              and Triplet (two unparied electrons corresponding to three spin states;
              divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:

               SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1 (one valence
                   electron not available for bonding)
               SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2 (two
                   valence electrons not available for bonding)

    GetValenceElectrons
            $ValenceElectrons = $Atom->GetValenceElectrons();

        Returns valence electrons for an Atom which corresponds to either
        explicity set *ValenceElectrons* atom property or valence electrons
        for the corresponding element in the periodic table available by
        PeriodicTable module.

    GetValenceFreeElectrons
            $ValenceFreeElectrons = $Atom->GetValenceFreeElectrons();
            $ValenceFreeElectrons = $Atom->GetValenceFreeElectrons(
                                    $ExcludeFreeRadicalElectrons);

        Returns valence frees electrons for an Atom in a molecule. It
        corresponds to:

            ValenceElectrons - Valence
            or
            ValenceElectrons - NumOfMissingHydrogens - SumOfBondOrders - FormalCharge

        Free radical electrons are included in the valence free electrons
        count by default.

        Examples:

            NH3: ValenceFreeElectrons = 5 - 3 = 5 - 3 - 0 - 0 = 2
            NH2: ValenceFreeElectrons = 5 - 3 = 5 - 2 - 1 - 0 = 2
            NH4+; ValenceFreeElectrons = 5 - 5 = 5 - 4 - 0 - 1 = 0
            NH3+; ValenceFreeElectrons = 5 - 5 = 5 - 3 - 1 - 1 = 0
            C(=O)O- : ValenceFreeElectrons on O- = 6 - 0 = 6 - 1 - 0 - (-1) = 6
            C(=O)O- : ValenceFreeElectrons on =O = 6 - 2 = 6 - 2 - 0 - 0 = 4

    GetX
            $X = $Atom->GetX();

        Returns value of X-coordinate for an *Atom*.

    GetXYZ
            @XYZ = $Atom->GetXYZ();
            $XYZRef = $Atom->GetXYZ();

        Returns an array or a reference to an array containing values for
        *Atom* coordinates.

    GetXYZVector
            $XYZVector = $Atom->GetXYZVector();

        Returns a *Vector* object containing values for *Atom* coordinates

    GetY
            $Y = $Atom->GetY();

        Returns value of Y-coordinate for an *Atom*.

    GetZ
            $Z = $Atom->GetZ();

        Returns value of Z-coordinate for an *Atom*.

    IsAmideCarbon
            $Status = $Atom->IsAmideCarbon();

        Returns 1 or 0 based on whether it's amide carbon *Atom*.

        An amide group is defineds as:

            R-C(=O)-N(-R')-R''

        where:

            o R = Hydrogen or groups of atoms attached through carbon
            o R' = Hydrogens or groups of atoms attached through carbon or
                   hetro atoms
            o R'' = Hydrogens or groups of atoms attached through carbon or
                   hetro atoms

    IsAmideNitrogen
            $Status = $Atom->IsAmideNitrogen();

        Returns 1 or 0 based on whether it's amide nitrogen *Atom*.

    IsAromatic
            $Status = $Atom->IsAromatic();

        Returns 1 or 0 based on whether it's an aromatic *Atom*.

    IsArsenic
            $Status = $Atom->IsArsenic();

        Returns 1 or 0 based on whether it's an arsenic *Atom*.

    IsBondedToAtom
            $Status = $Atom->IsBondedToAtom($OtherAtom);

        Returns 1 or 0 based on whether *Atom* is bonded to *OtherAtom*.

    IsBromine
            $Status = $Atom->IsBromine();

        Returns 1 or 0 based on whether it's a bromine *Atom*.

    IsCarbon
            $Status = $Atom->IsCarbon();

        Returns 1 or 0 based on whether it's a carbon *Atom*.

    IsCarboxylCarbon
            $Status = $Atom->IsCarboxylCarbon();

        Returns 1 or 0 based on whether it's a carboxyl carbon atom in
        carboxyl group: R-C(=O)-OH.

    IsCarboxylOxygen
            $Status = $Atom->IsCarboxylOxygen();

        Returns 1 or 0 based on whether it's a carboxyl oxygen atom in
        carboxyl group: R-C(=O)-OH.

    IsCarboxylateCarbon
            $Status = $Atom->IsCarboxylateCarbon();

        Returns 1 or 0 based on whether it's a carboxylate carbon atom in
        carboxyl group: R-C(=O)-O-.

    IsCarboxylateOxygen
            $Status = $Atom->IsCarboxylateOxygen();

        Returns 1 or 0 based on whether it's a carboxylate oxygen atom in
        carboxyl group: R-C(=O)-O-.

    IsChlorine
            $Status = $Atom->IsChlorine();

        Returns 1 or 0 based on whether it's a chlorine *Atom*.

    IsFluorine
            $Status = $Atom->IsFluorine();

        Returns 1 or 0 based on whether it's a fluorine *Atom*.

    IsFunctionalClassType
            $Status =$Atom->IsFunctionalClassType($Type);

        Returns 1 or 0 based on whether it's a specified functional class
        *Type*.

        The current release of MayaChemTools supports following
        abbreviations and descriptive names for *FunctionalClassType*:

            HBD: HydrogenBondDonor
            HBA: HydrogenBondAcceptor
            PI :  PositivelyIonizable
            NI : NegativelyIonizable
            Ar : Aromatic
            Hal : Halogen
            H : Hydrophobic
            RA : RingAtom
            CA : ChainAtom

        The following definitions are used to determine functional class
        types: [ Ref 60-61, Ref 65-66 ]:

            HydrogenBondDonor: NH, NH2, OH
            HydrogenBondAcceptor: N[!H], O
            PositivelyIonizable: +, NH2
            NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH

    IsGuadiniumCarbon
            $Status = $Atom->IsGuadiniumCarbon();

        Returns 1 or 0 based on whether it's a guadinium carbon in guadinium
        group by checking its neighbors for a nitrogen in guadinium group.

    IsGuadiniumNitrogen
            $Status = $Atom->IsGuadiniumNitrogen();

        Returns 1 or 0 based on whether it's a guadinium nitrogen in
        guadinium group.

        A guadinium group is defined as:

            R2N-C(=NR)-(NR2) or R2N-C(=NR2+)-(NR2)

        where:

            o R = Hydrogens or group of atoms attached through carbon
            o Only one of the three nitrogens has a double bond to carbon
              and has optional formal charge allowing it to be neutral or charged state

    IsHBondAcceptor
            $Status =$Atom->IsHBondAcceptor();
            $Status =$Atom->IsHBondAcceptor($HydrogenBondsType);

        Returns 1 or 0 based on whether it's a hydrogen bond acceptor
        *Atom*.

    IsHBondDonor
            $Status =$Atom->IsHBondDonor();
            $Status =$Atom->IsHBondDonor($HydrogenBondsType);

        Returns 1 or 0 based on whether it's a hydrogen bond donor *Atom*.

    IsHydrogenBondAcceptor
            $Status =$Atom->IsHydrogenBondAcceptor();
            $Status =$Atom->IsHydrogenBondAcceptor($HydrogenBondsType);

        Returns 1 or 0 based on whether it's a hydrogen bond acceptor
        *Atom*.

    IsHydrogenBondDonor
            $Status =$Atom->IsHydrogenBondDonor();
            $Status =$Atom->IsHydrogenBondDonor($HydrogenBondsType);

        Returns 1 or 0 based on whether it's a hydrogen bond donor *Atom*.

        The current release of MayaChemTools supports identification of two
        types of hydrogen bond donor and acceptor atoms with these names:

            HBondsType1 or HydrogenBondsType1
            HBondsType2 or HydrogenBondsType2

        The names of these hydrogen bond types are rather arbitrary.
        However, their definitions have specific meaning and are as follows:

            HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:

                Donor: NH, NH2, OH - Any N and O with available H
                Acceptor: N[!H], O - Any N without available H and any O

            HydrogenBondsType2 [ Ref 91 ]:

                Donor: NH, NH2, OH - N and O with available H
                Acceptor: N, O - And N and O

        By default, *HydrogenBondsType1* is used to calculate number
        hydrogen bond donor and acceptor atoms. *HydrogenBondsType2*
        corresponds to RuleOf5 definition of hydrogen bond donors and
        acceptors.

    IsHalogen
            $Status =$Atom->IsHalogen();

        Returns 1 or 0 based on whether it's a halogen *Atom*.

    IsHeteroAtom
            $Status = $Atom->IsHeteroAtom();

        Returns 0 or 1 based on whether it's a hetro *Atom*. Following atoms
        are considered hetro atoms: N, O, F, P, S, Cl, Br, I.

    IsHydrogen
            $Status = $Atom->IsHydrogen();

        Returns 1 or 0 based on whether it's a hydrogen *Atom*.

    IsHydrophobic
            $Status =$Atom->IsHydrophobic();

        Returns 1 or 0 based on whether it's a hydrophobic *Atom*.

    IsInRing
            $Status = $Atom->IsInRing();

        Returns 1 or 0 based on whether *Atom* is present in a ring.

    IsInRingOfSize
            $Status = $Atom->IsInRingOfSize($Size);

        Returns 1 or 0 based on whether *Atom* is present in a ring of
        specific *Size*.

    IsIodine
            $Status = $Atom->IsIodine();

        Returns 1 or 0 based on whether it's an iodine *Atom*.

    IsIsotope
            $Status =$Atom->IsIsotope();

        Returns 1 or 0 based on whether it's an isotope *Atom*.

    IsLipophilic
            $Status =$Atom->IsLipophilic();

        Returns 1 or 0 based on whether it's a lipophilic *Atom*.

    IsMetallic
            $Status = $Atom->IsMetallic();

        Returns 1 or 0 based on whether it's a metallic *Atom*.

    IsNegativelyIonizable
            $Status =$Atom->IsNegativelyIonizable();

        Returns 1 or 0 based on whether it's a negatively ionizable atom
        *Atom*.

    IsNitrogen
            $Status = $Atom->IsNitrogen();

        Returns 1 or 0 based on whether it's a nitrogen *Atom*.

    IsNonCarbonOrHydrogen
            $Status =$Atom->IsNonCarbonOrHydrogen();

        Returns 1 or 0 based on whether it's not a carbon or hydrogen
        *Atom*.

    IsNotInRing
            $Status = $Atom->IsNotInRing();

        Returns 1 or 0 based on whether *Atom* is not present in a ring.

    IsOnlyInOneRing
            $Status = $Atom->IsOnlyInOneRing();

        Returns 1 or 0 based on whether *Atom* is only present in one ring.

    IsOxygen
            $Status = $Atom->IsOxygen();

        Returns 0 or 1 based on whether it's an oxygen *Atom*.

    IsPhosphorus
            $Status = $Atom->IsPhosphorus();

        Returns 0 or 1 based on whether it's a phosphorus *Atom*.

    IsPhosphateOxygen
            $Status = $Atom->IsPhosphateOxygen();

        Returns 1 or 0 based on whether it's a phosphate oxygen in phosphate
        group.

        A phosphate group is defined as:

            AO-(O=)P(-OA)-OA

        Where:

           A - Any group of atoms including hydrogens

    IsPhosphatePhosphorus
            $Status = $Atom->IsPhosphatePhosphorus();

        Returns 1 or 0 based on whether it's a phosphate phosphorus in
        phosphate group.

    IsPolarAtom
            $Status = $Atom->IsPolarAtom();

        Returns 0 or 1 based on whether it's a polar *Atom*. Following atoms
        are considered polar atoms: N, O, P, S.

    IsPolarHydrogen
            $Status = $Atom->IsPolarHydrogen();

        Returns 0 or 1 based on whether it's a hydrogen *Atom* bonded to a
        polar atom.

    IsPositivelyIonizable
            $Status =$Atom->IsPositivelyIonizable();

        Returns 1 or 0 based on whether it's a positively ionizable *Atom*.

    IsSaturated
            $Status = $Atom->IsSaturated();

        Returns 1 or 0 based on whether it's a saturated *Atom*. An atom
        attached to other atoms with only single bonds is considered a
        saturated atom.

    IsSelenium
            $Status = $Atom->IsSelenium();

        Returns 0 or 1 based on whether it's a selenium *Atom*.

    IsStereoCenter
            $Status = $Atom->IsStereoCenter();

        Returns 0 or 1 based on whether it's marked as a stero center *Atom*
        by explicit setting of *StereoCenter* atom propert to value of *1*.

    IsSilicon
            $Status = $Atom->IsSilicon();

        Returns 0 or 1 based on whether it's a silicon *Atom*.

    IsSulfur
            $Status = $Atom->IsSulfur();

        Returns 0 or 1 based on whether it's a sulfur *Atom*.

    IsSulphur
            $Status = $Atom->IsSulphur();

        Returns 0 or 1 based on whether it's a sulfur *Atom*.

    IsTellurium
            $Status = $Atom->IsTellurium();

        Returns 0 or 1 based on whether it's a tellurium *Atom*.

    IsTerminal
            $Status = $Atom->IsTerminal();

        Returns 0 or 1 based on whether it's a terminal *Atom* attached to
        no more than one non-hydrogen atom.

    IsUnsaturated
            $Status = $Atom->IsUnsaturated();

        Returns 1 or 0 based on whether it's as unsaturated *Atom*. An atom
        attached to other atoms with at least one non-single bond is
        considered an unsaturated atom.

    IsTopologicalPharmacophoreType
            $Status =$Atom->IsTopologicalPharmacophoreType();

        Returns 1 or 0 based on whether it's any of the supportyed
        topological pharmacophore *Atom* type. See *IsFunctionalClassType*
        for a list of supported types.

    SetAtomSymbol
            $Atom->SetAtomSymbol($AtomicSymbol);

        Sets atom symbol for *Atom* and returns *Atom* object. The
        appropriate atomic number is also set automatically.

    SetAtomicNumber
            $Atom->SetAtomicNumber($AtomicNumber);

        Sets atomic number for *Atom* and returns *Atom* object. The
        appropriate atom symbol is also set automatically.

    SetMassNumber
            $Atom->SetMassNumber($MassNumber);

        Sets mass number for *Atom* and returns *Atom* object.

    SetStereoCenter
            $Atom->SetStereoCenter($StereoCenter);

        Sets stereo center for *Atom* and returns *Atom* object.

    SetStereochemistry
            $Atom->SetStereochemistry($Stereochemistry);

        Sets stereo chemistry for *Atom* and returns *Atom* object.

    SetX
            $Atom->SetX($Value);

        Sets X-coordinate value for *Atom* and returns *Atom* object.

    SetXYZ
            $Atom->SetXYZ(@XYZValues);
            $Atom->SetXYZ($XYZValuesRef);
            $Atom->SetXYZ($XYZVector);

        Sets *Atom* coordinates using an array, reference to an array or a
        *Vector* object and returns *Atom* object.

    SetY
            $Atom->SetY($Value);

        Sets Y-coordinate value for *Atom* and returns *Atom* object.

    SetZ
            $Atom->SetZ($Value);

        Sets Z-coordinate value for *Atom* and returns *Atom* object.

    StringifyAtom
            $AtomString = $Atom->StringifyAtom();

        Returns a string containing information about *Atom* object.

AUTHOR
    Manish Sud <[e-mail]>

SEE ALSO
    Bond.pm, Molecule.pm, MoleculeFileIO.pm

COPYRIGHT
    Copyright (C) 2015 Manish Sud. All rights reserved.

    This file is part of MayaChemTools.

    MayaChemTools is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License as published by
    the Free Software Foundation; either version 3 of the License, or (at
    your option) any later version.