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.\" ========================================================================
.\"
.IX Title "ATOM 1"
.TH ATOM 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Atom
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use Atom;
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBAtom\fR class provides the following methods:
.PP
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
.PP
\&\fBAtom\fR class is derived from \fBObjectProperty\fR base class which provides methods not explicitly
defined in \fBAtom\fR or \fBObjectProperty\fR class using Perl's \s-1AUTOLOAD\s0 functionality. These methods
are generated on-the-fly for a specified object property:
.PP
.Vb 3
\&    Set<PropertyName>(<PropertyValue>);
\&    $PropertyValue = Get<PropertyName>();
\&    Delete<PropertyName>();
.Ve
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.IP "\fBnew\fR" 4
.IX Item "new"
.Vb 1
\&    $NewAtom = new Atom([%PropertyNameAndValues]);
.Ve
.Sp
Using specified \fIAtom\fR property names and values hash, \fBnew\fR method creates a new object
and returns a reference to newly created \fBAtom\fR object. By default, following properties are
initialized:
.Sp
.Vb 5
\&    ID = SequentialObjectID
\&    Name = "Atom <SequentialObjectID>"
\&    AtomSymbol = ""
\&    AtomicNumber = 0
\&    XYZ = ZeroVector
.Ve
.Sp
Except for \fI\s-1ID\s0\fR property, all other default properties and other additional properties can
be set during invocation of this method.
.Sp
Examples:
.Sp
.Vb 5
\&    $Atom = new Atom();
\&    $CarbonAtom = new Atom(\*(AqAtomSymbol\*(Aq => \*(AqC\*(Aq, \*(AqXYZ\*(Aq => (0.0, 1.0,
\&                  0.0));
\&    $OxygenAtom = new Atom(\*(AqAtomName\*(Aq => \*(AqOxygen\*(Aq, AtomSymbol\*(Aq => \*(AqO\*(Aq,
\&                  \*(AqXYZ\*(Aq => (1.0, 1.0, 1.0));
.Ve
.IP "\fBAddHydrogens\fR" 4
.IX Item "AddHydrogens"
.Vb 1
\&    $NumOfHydrogensAdded = $Atom\->AddHydrogens();
.Ve
.Sp
Adds hydrogens to an \fBAtom\fR present in a \fBMolecule\fR object and returns
the number of added hydrogens. The current release of MayaChemTools doesn't
assign hydrogen positions.
.IP "\fBCopy\fR" 4
.IX Item "Copy"
.Vb 1
\&    $AtomCopy = $Atom\->Copy();
.Ve
.Sp
Copy \fIAtom\fR and its associated data using \fBStorable::dclone\fR and return a new
\&\fBAtom\fR object.
.IP "\fBDeleteAtom\fR" 4
.IX Item "DeleteAtom"
.Vb 1
\&    $Atom\->DeleteAtom();
.Ve
.Sp
Delete \fIAtom\fR from a molecule.
.IP "\fBDoesAtomNeighborhoodMatch\fR" 4
.IX Item "DoesAtomNeighborhoodMatch"
.Vb 8
\&    $Status = $Atom\->DoesAtomNeighborhoodMatch($CentralAtomSpec);
\&    $Status = $Atom\->DoesAtomNeighborhoodMatch($CentralAtomSpec,
\&                              $NbrAtomSpecsRef);
\&    $Status = $Atom\->DoesAtomNeighborhoodMatch($CentralAtomSpec,
\&                              $NbrAtomSpecsRef, $AllowedNbrBondSpecsRef);
\&    $Status = $Atom\->DoesAtomNeighborhoodMatch($CentralAtomSpec,
\&                              $NbrAtomSpecsRef, $NbrBondSpecsRef,
\&                              $AllowedNbrOfNbrAtomSpecsRef);
.Ve
.Sp
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.
.Sp
Let:
.Sp
.Vb 2
\&    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)
.Ve
.Sp
Then, atom specification corresponds to:
.Sp
.Vb 2
\&    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>
.Ve
.Sp
Except for \s-1AS\s0 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.
.Sp
For \fI\s-1FC\s0\fR value matching, the following value operators are also supported:
.Sp
.Vb 4
\&    o +* : Any positive value
\&    o \-* : Any negative value
\&    o > ValidNumber or >= ValidNumber
\&    o < ValidNumber or <= ValidNumber
.Ve
.Sp
A comma delimited atom specification string is used to match any one of the specified atom specification.
.Sp
Notes:
.Sp
.Vb 2
\&    o During atom specification match to an atom, the first atomic invariant is always assumed to
\&      atom symbol.
.Ve
.Sp
Examples:
.Sp
.Vb 5
\&    o (\*(AqN\*(Aq, \*(AqN\*(Aq, \*(AqN\*(Aq)
\&    o (\*(AqN.FC0\*(Aq, \*(AqN.FC0\*(Aq, \*(AqN,N.FC+1.H1\*(Aq)
\&    o (\*(AqN.H2\*(Aq, \*(AqN.H2\*(Aq, \*(AqN.H1\*(Aq)
\&    o (\*(AqC,N\*(Aq, \*(Aq!N\*(Aq, \*(Aq!H\*(Aq)
\&    o (\*(AqC,N\*(Aq, \*(AqN.Ar\*(Aq, \*(AqN.R5\*(Aq)
.Ve
.Sp
Let:
.Sp
.Vb 4
\&    \-|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
.Ve
.Sp
Then, bond specification corresponds to:
.Sp
.Vb 3
\&    \-.:
\&    =.@
\&    Double.Aromatic
.Ve
.Sp
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.
.Sp
A comma delimited bond specification string is used to match any one of the specified atom specification.
.Sp
Notes:
.Sp
.Vb 3
\&    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.
.Ve
.Sp
Examples:
.Sp
.Vb 2
\&    Aromatic carbon in a 5 membered ring:
\&                              $Atom\->DoesAtomNeighborhoodMatch(\*(AqC.Ar.RA5\*(Aq);
\&
\&    AcetylenicCarbon: $Atom\->DoesAtomNeighborhoodMatch(\*(AqC.T2.TB1\*(Aq); or
\&                       $Atom\->DoesAtomNeighborhoodMatch(\*(AqC.T2.TB1\*(Aq,
\&                              [\*(Aq*\*(Aq, \*(Aq*\*(Aq], [\*(Aq#\*(Aq, \*(Aq\-\*(Aq]);
\&
\&    GuadiniumCarbon: $Atom\->DoesAtomNeighborhoodMatch(\*(AqC.X3.BO4\*(Aq,
\&                              [\*(AqN.FC0\*(Aq, \*(AqN.FC0\*(Aq, \*(AqN.FC0,N.FC+1\*(Aq],
\&                              [\*(Aq\-\*(Aq, \*(Aq\-\*(Aq, \*(Aq=\*(Aq],
\&                              [\*(AqC,H\*(Aq, \*(AqC,H\*(Aq, \*(AqC,H\*(Aq]);
\&
\&    AmideCarbon: $Atom\->DoesAtomNeighborhoodMatch(\*(AqC.X3.BO4,C.X2.BO3\*(Aq,
\&                              [\*(AqC,H\*(Aq, \*(AqO\*(Aq, \*(AqN\*(Aq],
\&                              [\*(Aq\-\*(Aq, \*(Aq=\*(Aq, \*(Aq\-\*(Aq],
\&                              [\*(AqC,H\*(Aq, \*(AqC\*(Aq, \*(AqC,H,N,O,S,P,F,Cl,Br,I\*(Aq]);
\&
\&    CarboxylCarbon: $Atom\->DoesAtomNeighborhoodMatch(\*(AqC.X3.BO4,C.X2.BO3\*(Aq,
\&                              [\*(AqC,H\*(Aq, \*(AqO\*(Aq, \*(AqO.X1.FC0\*(Aq],
\&                              [\*(Aq\-\*(Aq, \*(Aq=\*(Aq, \*(Aq\-\*(Aq],
\&                              [\*(AqC,H\*(Aq, \*(AqC\*(Aq, \*(AqC\*(Aq]);
\&
\&    CarboxylateCarbon: $Atom\->DoesAtomNeighborhoodMatch(\*(AqC.X3.BO4,C.X2.BO3\*(Aq,
\&                              [\*(AqC,H\*(Aq, \*(AqO\*(Aq, \*(AqO.X1.FC\-1\*(Aq],
\&                              [\*(Aq\-\*(Aq, \*(Aq=\*(Aq, \*(Aq\-\*(Aq],
\&                              [\*(AqC,H\*(Aq, \*(AqC\*(Aq, \*(AqC\*(Aq]);
.Ve
.IP "\fBDeleteHydrogens\fR" 4
.IX Item "DeleteHydrogens"
.Vb 1
\&    $NumOfHydrogensDeleted = $Atom\->AddHydrogens();
.Ve
.Sp
Delete hydrogens from an \fBAtom\fR present in a \fBMolecule\fR object and returns
the number of deleted hydrogens.
.IP "\fBGetAtomicInvariantValue\fR" 4
.IX Item "GetAtomicInvariantValue"
.Vb 1
\&    $Value = $Atom\->GetAtomicInvariantValue($AtomicInvariant);
.Ve
.Sp
Returns atomic invariant value for a specified \fIAtomicInvariant\fR. The current release
of MayaChemTools supports following abbreviations and descriptive names for
\&\fIAtomicInvarints\fR:
.Sp
.Vb 10
\&    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
.Ve
.IP "\fBGetAtomicWeight\fR" 4
.IX Item "GetAtomicWeight"
.Vb 1
\&    $Value = $Aom\->GetAtomicWeight();
.Ve
.Sp
Returns atomic weight of an \fBAtom\fR which corresponds to either explicity set \fIAtomicWeight\fR
atom property or atomic weight of the corresponding element in the periodic table available by
\&\fBPeriodicTable\fR module.
.IP "\fBGetBondToAtom\fR" 4
.IX Item "GetBondToAtom"
.Vb 1
\&    $Bond = $Atom\->GetBondToAtom($OtherAtom);
.Ve
.Sp
Returns a \fBBond\fR object corresponding to bond between \fIAtom\fR and \fIOtherAtom\fR in
a molecule.
.IP "\fBGetBonds\fR" 4
.IX Item "GetBonds"
.Vb 1
\&    @Bonds = $Aoto\->GetBonds();
.Ve
.Sp
Returns an array of \fBBond\fR objects corresponding to all bonds from \fIAtom\fR to other
bonded atoms in a molecule.
.IP "\fBGetBondsToHeavyAtoms\fR" 4
.IX Item "GetBondsToHeavyAtoms"
.Vb 1
\&    @Bonds = $Atom\->GetBondsToHeavyAtoms();
.Ve
.Sp
Returns an array of \fBBond\fR objects corresponding to bonds from \fIAtom\fR to other bonded
non-hydrogen atoms in a molecule.
.IP "\fBGetBondsToHydrogenAtoms\fR" 4
.IX Item "GetBondsToHydrogenAtoms"
.Vb 1
\&    @Bonds = $Atom\->GetBondsToHydrogenAtoms();
.Ve
.Sp
Returns an array of \fBBond\fR objects corresponding to bonds from \fIAtom\fR to any other
hydrogen atom in a molecule.
.IP "\fBGetBondsToNonHydrogenAtoms\fR" 4
.IX Item "GetBondsToNonHydrogenAtoms"
.Vb 1
\&    @Bonds = $Atom\->GetBondsToNonHydrogenAtoms();
.Ve
.Sp
Returns an array of \fBBond\fR objects corresponding to bonds from \fIAtom\fR to other bonded
non-hydrogen atoms in a molecule.
.IP "\fBGetExactMass\fR" 4
.IX Item "GetExactMass"
.Vb 1
\&    $ExactMass = $Atom\->GetExactMass();
.Ve
.Sp
Returns exact mass of an \fIAtom\fR which correspond to one of these three values: explicity set
\&\fIExactMass\fR property; mass of natural isotope for an explicty set value of \fIMassNumber\fR; most
abundant natural isotope mass for \fIAtom\fR with valid atomic number value available by
\&\fBPerodicTable\fR module.
.IP "\fBGetExplicitHydrogens\fR" 4
.IX Item "GetExplicitHydrogens"
.Vb 1
\&    $NumOfExplicitHydrogens = $Atom\->GetExplicitHydrogens();
.Ve
.Sp
Returns number of hydrogens explicity bonded to an \fIAtom\fR in a molecule.
.IP "\fBGetFormalCharge\fR" 4
.IX Item "GetFormalCharge"
.Vb 1
\&    $FormalCharge = $Atom\->GetFormalCharge();
.Ve
.Sp
Returns formal charge of an \fIAtom\fR in a molecule.
.IP "\fBGetFreeRadicalElectrons\fR" 4
.IX Item "GetFreeRadicalElectrons"
.Vb 1
\&    $FreeRadicalElectrons = $Atom\->GetFreeRadicalElectrons();
.Ve
.Sp
Returns number of free radical electrons corresponding to to one of these
three values: \fIFreeRadicalElectrons\fR property; \fISpinMultiplicity\fR property; value
of 0.
.Sp
For atoms with explicit assignment of \fISpinMultiplicity\fR atom property values,
.Sp
.Vb 5
\&    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)
.Ve
.Sp
\&\fBFreeRadicalElectrons\fR are calculated as follows:
.Sp
.Vb 3
\&    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)
.Ve
.IP "\fBGetGroupNumber\fR" 4
.IX Item "GetGroupNumber"
.Vb 1
\&    $GroupNumber = $Atom\->GetGroupNumber();
.Ve
.Sp
Returns group number of an \fIAtom\fR in a molecule with a valid atomic number.
.IP "\fBGetHeavyAtomNeighbors\fR" 4
.IX Item "GetHeavyAtomNeighbors"
.Vb 2
\&    $NumOfHeavyAtoms = $Atom\->GetHeavyAtomNeighbors();
\&    @HeavyAtoms = $Atom\->GetHeavyAtomNeighbors();
.Ve
.Sp
Return number of heavy atoms or an array of \fBAtom\fR objects corresponding to heavy atoms
bonded to an \fIAtom\fR in a molecule.
.IP "\fBGetHeavyAtomNeighborsAtomInformation\fR" 4
.IX Item "GetHeavyAtomNeighborsAtomInformation"
.Vb 3
\&    ($NumOfAtomNeighbors, $AtomNeighborsRef,
\&     $NumOfAtomNeighborsType, $AtomNeighborsTypeMapRef) = $Atom\->
\&                              GetHeavyAtomNeighborsAtomInformation();
.Ve
.Sp
Returns atoms information for all non-hydrogen atoms attached to an \fIAtom\fR
in a molecule.
.Sp
The following values are returned:
.Sp
.Vb 6
\&    o Number of non\-hydrogen atom neighbors
\&    o A reference to an array containing atom objects corresponding to
\&      non\-hydrogen atom neighbors
\&    o Number of different types of non\-hydrogen atom neighbors
\&    o A reference to a hash containing atom symbol as key with value
\&      corresponding to its count for non\-hydrogen atom neighbors
.Ve
.IP "\fBGetHeavyAtomNeighborsBondformation\fR" 4
.IX Item "GetHeavyAtomNeighborsBondformation"
.Vb 4
\&    ($NumOfBonds, $BondTypeCountMapRef,
\&    $AtomsBondTypesCountMapRef,
\&    $AtomsBondTypeAtomsMap) = $Atom\->
\&                              GetHeavyAtomNeighborsBondformation();
.Ve
.Sp
Returns bonds information for all non-hydrogen atoms attached to an \fIAtom\fR
in a molecule.
.Sp
The following values are returned:
.Sp
.Vb 12
\&    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
.Ve
.IP "\fBGetHighestCommonValence\fR" 4
.IX Item "GetHighestCommonValence"
.Vb 1
\&    $HighestCommonValence = $Atom\->GetHighestCommonValence();
.Ve
.Sp
Returns highest common valence of an \fIAtom\fR which corresponds to either explicity set
\&\fIHighestCommonValence\fR atom property or highest common valence of the corresponding
element in the periodic table available by \fBPerodicTable\fR module.
.IP "\fBGetHydrogens\fR" 4
.IX Item "GetHydrogens"
.Vb 1
\&    $NumOfHydrogens = $Atom\->GetHydrogens();
.Ve
.Sp
Returns total number of hydrogens for an \fIAtom\fR in a molecule including both hydrogen atom
neighbors and implicit hydrogens.
.IP "\fBGetHydrogenAtomNeighbors\fR" 4
.IX Item "GetHydrogenAtomNeighbors"
.Vb 2
\&    $NumOfHydrogenAtomNeighbors = $Atom\->GetHydrogenAtomNeighbors();
\&    @HydrogenAtomNeighbors = $Atom\->GetHydrogenAtomNeighbors();
.Ve
.Sp
Return number of hydrogen atoms or an array of \fIAtom\fR objects corresponding to hydrogen
atoms bonded to an \fIAtom\fR in a molecule.
.IP "\fBGetImplicitHydrogens\fR" 4
.IX Item "GetImplicitHydrogens"
.Vb 1
\&    $NumOfImplicitHydrogens = $Atom\->GetImplicitHydrogens();
.Ve
.Sp
Returns number of implicit hydrogens for an \fIAtom\fR in a molecule. This value either
corresponds to explicitly set \fIImplicitHydrogens\fR 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.
.IP "\fBGetPotentialTotalCommonValence\fR" 4
.IX Item "GetPotentialTotalCommonValence"
.Vb 1
\&    $PotentialTotalValence = $Atom\->GetPotentialTotalCommonValence();
.Ve
.Sp
Returns potential total common valence of an \fIAtom\fR in a molecule corresponding
to a specific valence model set for the molecule using its \fBSetValenceModel\fR method
or default internal valence model. It is used during the calculation of missing or
implicit hydrogens.
.Sp
The current release of MayaChemTools supports three valence models: \fIMDLValenceModel,
DaylightValenceModel, InternalValenceModel or MayaChemToolsValenceModel\fR.
.Sp
For \fIMDLValenceModel\fR and \fIDaylightValenceModel\fR, the following data files, distributed
with the package, are used to calculate potential total valence:
.Sp
.Vb 2
\&    lib/data/MDLValenceModelData.csv
\&    lib/data/DaylightValenceModelData.csv
.Ve
.Sp
The calculation of potential total common valence for these two models is performed as
follows: Calculate current effective total valence of the \fIAtom\fR by adding up the bond
order of its neighbors and number of free radical electrons; Find available common valence
for the \fIAtom\fR, corresponding to any specified formal charge, higher than the effective
total valence, and return it as \fIPotentialTotalValence\fR.
.Sp
The calculation of potential total common valence For \fIInternalValenceModel\fR or
\&\fIMayaChenToolsValenceModel\fR doesn't uses \fBPeriodicTable\fR module to retrieve values
for common valence, which in turn reads in PeriodicTableElements.csv file distributed with
the package.
.Sp
For elements with one one common valence, potential total common valence corresponds
to:
.Sp
.Vb 1
\&    CommonValence + FormalCharge \- FreeRadicalElectrons
.Ve
.Sp
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.
.Sp
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.
.Sp
The sign of formal charge is adjusted as follows.
.Sp
Group numbers > 14 \- Group numbers 15 (N), 16 (O), 17 (F), 18 (He):
.Sp
Formal charge sign is not adjusted. Positive and negative values result in the
increase and decrease of valence.
.Sp
Group 14 containing C, Si, Ge, Sn, Pb...:
.Sp
Formal charge sign is reversed for positive values. Both positive and negative
values result in the decrease of valence.
.Sp
Group 13 containing B, Al, Ga, In, Tl...:
.Sp
Formal charge sign is always reversed. Positive and negative values result in the
decrease and increase of valence.
.Sp
Groups 1 (H) through 12 (Zn)...:
.Sp
Formal charge sign is reversed for positive values. Both positive and negative
values result in the decrease of valence.
.Sp
Lanthanides and actinides:
.Sp
Formal charge sign is reversed for positive values. Both positive and negative
values result in the decrease of valence.
.IP "\fBGetLargestBondOrder\fR" 4
.IX Item "GetLargestBondOrder"
.Vb 1
\&    $LargestBO =$Atom\->GetLargestBondOrder();
.Ve
.Sp
Returns largest bond order for an \fIAtom\fR among the bonds to other atoms in a molecule.
.IP "\fBGetLargestBondOrderToHeavyAtoms\fR" 4
.IX Item "GetLargestBondOrderToHeavyAtoms"
.Vb 1
\&    $LargestBO =$Atom\->GetLargestBondOrderToHeavyAtoms();
.Ve
.Sp
Returns largest bond order for an \fIAtom\fR among the bonds to other heavy atoms in a molecule.
.IP "\fBGetLargestBondOrderToNonHydrogenAtoms\fR" 4
.IX Item "GetLargestBondOrderToNonHydrogenAtoms"
.Vb 1
\&    $LargestBO =$Atom\->GetLargestBondOrderToNonHydrogenAtoms();
.Ve
.Sp
Returns largest bond order for an \fIAtom\fR among the bonds to other non-hydrogen atoms
in a molecule.
.IP "\fBGetLargestRing\fR" 4
.IX Item "GetLargestRing"
.Vb 1
\&    @RingAtoms = $Atom\->GetLargestRing();
.Ve
.Sp
Returns an array of ring \fIAtom\fR objects corresponding to the largest ring containing \fIAtom\fR
in a molecule.
.IP "\fBGetLowestCommonValence\fR" 4
.IX Item "GetLowestCommonValence"
.Vb 1
\&    $LowestCommonValence = $Atom\->GetLowestCommonValence();
.Ve
.Sp
Returns lowest common valence of an \fIAtom\fR which corresponds to either explicity set
\&\fILowestCommonValence\fR atom property or highest common valence of the corresponding
element in the periodic table available by \fBPerodicTable\fR module.
.IP "\fBGetMassNumber\fR" 4
.IX Item "GetMassNumber"
.Vb 1
\&    $MassNumber = $Aom\->GetMassNumber();
.Ve
.Sp
Returns atomic weight of an \fBAtom\fR which corresponds to either explicity set \fIMassNumber\fR
atom property or mass number of the most abundant natural isotope of the corresponding element
in the periodic table available by \fBPeriodicTable\fR module.
.IP "\fBGetMissingHydrogens\fR" 4
.IX Item "GetMissingHydrogens"
.Vb 1
\&    $NumOfMissingHydrogens = $Atom\->GetMissingHydrogens();
.Ve
.Sp
Returns number of missing hydrogens for an \fIAtom\fR in a molecule. This value either
corresponds to explicitly set \fIImplicitHydrogens\fR 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.
.IP "\fBGetNeighbors\fR" 4
.IX Item "GetNeighbors"
.Vb 2
\&    $NumOfNeighbors = $Atom\->GetNeighbors();
\&    @Neighbors = $Atom\->GetNeighbors();
.Ve
.Sp
Returns number of neighbor atoms or an array of \fIAtom\fR objects corresponding to all
atoms bonded to an \fIAtom\fR in a molecule.
.IP "\fBGetNeighborsUsingAtomSpecification\fR" 4
.IX Item "GetNeighborsUsingAtomSpecification"
.Vb 2
\&    @AtomNeighbors = $Atom\->GetNeighborsUsingAtomSpecification($AtomSpec);
\&    $NumOfNeighbors = $Atom\->GetNeighborsUsingAtomSpecification($AtomSpec);
\&
\&    @AtomNeighbors = $Atom\->GetNeighborsUsingAtomSpecification($AtomSpec,
\&                     @ExcludeNeighbors);
.Ve
.Sp
Returns number of neighbor atoms or an array of \fIAtom\fR objects matching atom
specification corresponding to atom neighbors of an \fIAtom\fR in a molecule. Optionally,
\&\fIAtom\fR neighbors can be excluded from the neighbors list using \fIExcludeNeighbors\fR.
.Sp
Notes:
.Sp
.Vb 3
\&    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
.Ve
.IP "\fBGetNonHydrogenAtomNeighbors\fR" 4
.IX Item "GetNonHydrogenAtomNeighbors"
.Vb 2
\&    $NumOfNeighbors = $Atom\->GetNonHydrogenAtomNeighbors();
\&    @Neighbors = $Atom\->GetNonHydrogenAtomNeighbors();
.Ve
.Sp
Returns number of non-hydrogen atoms or an array of \fBAtom\fR objects corresponding to non-hydrogen
atoms bonded to an \fIAtom\fR in a molecule.
.IP "\fBGetNonHydrogenAtomNeighborsAtomInformation\fR" 4
.IX Item "GetNonHydrogenAtomNeighborsAtomInformation"
.Vb 3
\&    ($NumOfAtomNeighbors, $AtomNeighborsRef,
\&     $NumOfAtomNeighborsType, $AtomNeighborsTypeMapRef) = $Atom\->
\&                              GetNonHydrogenAtomNeighborsAtomInformation();
.Ve
.Sp
Returns atoms information for all non-hydrogen atoms attached to an \fIAtom\fR
in a molecule.
.Sp
The following values are returned:
.Sp
.Vb 6
\&    o Number of non\-hydrogen atom neighbors
\&    o A reference to an array containing atom objects corresponding to
\&      non\-hydrogen atom neighbors
\&    o Number of different types of non\-hydrogen atom neighbors
\&    o A reference to a hash containing atom symbol as key with value
\&      corresponding to its count for non\-hydrogen atom neighbors
.Ve
.IP "\fBGetNonHydrogenAtomNeighborsBondInformation\fR" 4
.IX Item "GetNonHydrogenAtomNeighborsBondInformation"
.Vb 4
\&    ($NumOfBonds, $BondTypeCountMapRef,
\&    $AtomsBondTypesCountMapRef,
\&    $AtomsBondTypeAtomsMap) = $Atom\->
\&                              GetNonHydrogenAtomNeighborsBondInformation();
.Ve
.Sp
Returns bonds information for all non-hydrogen atoms attached to an \fIAtom\fR
in a molecule.
.Sp
The following values are returned:
.Sp
.Vb 12
\&    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
.Ve
.IP "\fBGetNonHydrogenNeighborOfHydrogenAtom\fR" 4
.IX Item "GetNonHydrogenNeighborOfHydrogenAtom"
.Vb 1
\&    $Atom = $Atom\->GetNonHydrogenNeighborOfHydrogenAtom();
.Ve
.Sp
Returns non-hydrogen or heavy atom neighbor of a hydrogen atom in a molecule..
.IP "\fBGetNumOfAromaticBondsToHeavyAtoms\fR" 4
.IX Item "GetNumOfAromaticBondsToHeavyAtoms"
.Vb 1
\&    $NumOfBonds = $Atom\->GetNumOfAromaticBondsToHeavyAtoms();
.Ve
.Sp
Returns number of aromatic bonds from an \fIAtom\fR to other non-hydrogen or heavy atoms in
a molecule.
.IP "\fBGetNumOfAromaticBondsToNonHydrogenAtoms\fR" 4
.IX Item "GetNumOfAromaticBondsToNonHydrogenAtoms"
.Vb 1
\&    $NumOfBonds = $Atom\->GetNumOfAromaticBondsToNonHydrogenAtoms();
.Ve
.Sp
Returns number of aromatic bonds from an \fIAtom\fR to other non-hydrogen or heavy atoms in
a molecule.
.IP "\fBGetNumOfBonds\fR" 4
.IX Item "GetNumOfBonds"
.Vb 1
\&    $NumOfBonds = $Atom\->GetNumOfBonds();
.Ve
.Sp
Returns number of bonds from an \fIAtom\fR to other atoms in a molecule.
.IP "\fBGetNumOfBondsAvailableForHeavyAtoms\fR" 4
.IX Item "GetNumOfBondsAvailableForHeavyAtoms"
.Vb 1
\&    $NumOfBonds = $Atom\->GetNumOfBondsAvailableForHeavyAtoms();
.Ve
.Sp
Get number of bonds available to form additional bonds with heavy atoms, excluding
any implicit bonds to hydrogens set using \fIImplicitHydrogens\fR property.
.Sp
It's different from number of implicit or missing hydrogens, both of which are equivalent.
.Sp
For example, in a \s-1SMILES\s0 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.
.IP "\fBGetNumOfBondsAvailableForNonHydrogenAtoms\fR" 4
.IX Item "GetNumOfBondsAvailableForNonHydrogenAtoms"
.Vb 1
\&    $NumOfBonds = $Atom\->GetNumOfBondsAvailableForNonHydrogenAtoms();
.Ve
.Sp
Get number of bonds available to form additional bonds with heavy atoms, excluding
any implicit bonds to hydrogens set using ImplicitHydrogens property.
.IP "\fBGetNumOfBondsToHeavyAtoms\fR" 4
.IX Item "GetNumOfBondsToHeavyAtoms"
.Vb 1
\&    $NumOfBondsToHeavyAtoms = $Atom\->GetNumOfBondsToHeavyAtoms();
.Ve
.Sp
Returns number of bonds from an \fIAtom\fR to other heavy atoms in a molecule.
.IP "\fBGetNumOfBondsToHydrogenAtoms\fR" 4
.IX Item "GetNumOfBondsToHydrogenAtoms"
.Vb 1
\&    $NumOfBonds = $Atom\->GetNumOfBondsToHydrogenAtoms();
.Ve
.Sp
Returns number of bonds from an \fIAtom\fR to other hydrogen atoms in a molecule.
.IP "\fBGetNumOfBondsToNonHydrogenAtoms\fR" 4
.IX Item "GetNumOfBondsToNonHydrogenAtoms"
.Vb 1
\&    $NumOfBonds = $Atom\->GetNumOfBondsToNonHydrogenAtoms();
.Ve
.Sp
Returns number of bonds from an \fIAtom\fR to other non-hydrogen atoms in a molecule.
.IP "\fBGetNumOfBondTypesToHeavyAtoms\fR" 4
.IX Item "GetNumOfBondTypesToHeavyAtoms"
.Vb 3
\&    ($NumOfSingleBonds, $NumOfDoubleBonds,
\&     $NumOfTripleBonds, $NumOfAromaticBonds) = $Atom\->
\&                   GetNumOfBondTypesToHeavyAtoms($CountAromaticBonds);
.Ve
.Sp
Get number of single, double, triple, and aromatic bonds from an \fIAtom\fR to all other
non-hydrogen atoms in a molecule.
.Sp
Value of \fICountAtomaticBonds\fR 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.
.IP "\fBGetNumOfBondTypesToNonHydrogenAtoms\fR" 4
.IX Item "GetNumOfBondTypesToNonHydrogenAtoms"
.Vb 3
\&    ($NumOfSingleBonds, $NumOfDoubleBonds,
\&     $NumOfTripleBonds, $NumOfAromaticBonds) = $Atom\->
\&             GetNumOfBondTypesToNonHydrogenAtoms($CountAromaticBonds);
.Ve
.Sp
Get number of single, double, triple, and aromatic bonds from an \fIAtom\fR to all other
non-hydrogen atoms in a molecule.
.Sp
Value of \fICountAtomaticBonds\fR 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.
.IP "\fBGetNumOfDoubleBondsToHeavyAtoms\fR" 4
.IX Item "GetNumOfDoubleBondsToHeavyAtoms"
.Vb 1
\&    $NumOfDoubleBonds = $Atom\->GetNumOfDoubleBondsToHeavyAtoms();
.Ve
.Sp
Returns number of double bonds from an \fIAtom\fR to other heavy atoms or non-hydrogen
atoms in a molecule.
.IP "\fBGetNumOfDoubleBondsToNonHydrogenAtoms\fR" 4
.IX Item "GetNumOfDoubleBondsToNonHydrogenAtoms"
.Vb 1
\&    $NumOfDoubleBonds =$Atom\->GetNumOfDoubleBondsToNonHydrogenAtoms();
.Ve
.Sp
Returns number of double bonds from an \fIAtom\fR to other heavy atoms or non-hydrogen
atoms in a molecule.
.IP "\fBGetNumOfHeavyAtomNeighbors\fR" 4
.IX Item "GetNumOfHeavyAtomNeighbors"
.Vb 1
\&    $NumOfNeighbors = $Atom\->GetNumOfHeavyAtomNeighbors();
.Ve
.Sp
Returns number heavy atom neighbors for an \fIAtom\fR in a molecule.
.IP "\fBGetNumOfHydrogenAtomNeighbors\fR" 4
.IX Item "GetNumOfHydrogenAtomNeighbors"
.Vb 1
\&    $NumOfNeighbors = $Atom\->GetNumOfHydrogenAtomNeighbors();
.Ve
.Sp
Returns number hydrogens atom neighbors for an \fIAtom\fR in a molecule.
.IP "\fBGetNumOfMissingHydrogens\fR" 4
.IX Item "GetNumOfMissingHydrogens"
.Vb 1
\&    $NumOfMissingHydrogens = $Atom\->GetNumOfMissingHydrogens();
.Ve
.Sp
Returns number of implicit hydrogens for an \fIAtom\fR in a molecule. This value either
corresponds to explicitly set \fIImplicitHydrogens\fR 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.
.IP "\fBGetNumOfExplicitHydrogens\fR" 4
.IX Item "GetNumOfExplicitHydrogens"
.Vb 1
\&    $NumOfExplicitHydrogens = $Atom\->GetNumOfExplicitHydrogens();
.Ve
.Sp
Returns number hydrogens atom neighbors for an \fIAtom\fR in a molecule.
.IP "\fBGetNumOfHydrogens\fR" 4
.IX Item "GetNumOfHydrogens"
.Vb 1
\&    $NumOfHydrogens = $Atom\->GetNumOfHydrogens();
.Ve
.Sp
Returns total number of hydrogens for an \fIAtom\fR in a molecule including both hydrogen atom
neighbors and implicit hydrogens.
.IP "\fBGetNumOfImplicitHydrogens\fR" 4
.IX Item "GetNumOfImplicitHydrogens"
.Vb 1
\&    $NumOfImplicitHydrogens = $Atom\->GetNumOfImplicitHydrogens();
.Ve
.Sp
Returns number of implicit hydrogens for an \fIAtom\fR in a molecule. This value either
corresponds to explicitly set \fIImplicitHydrogens\fR 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.
.IP "\fBGetNumOfNeighbors\fR" 4
.IX Item "GetNumOfNeighbors"
.Vb 1
\&    $NumOfNeighbors = $Atom\->GetNumOfNeighbors();
.Ve
.Sp
Returns number atom neighbors for an \fIAtom\fR in a molecule.
.IP "\fBGetNumOfNonHydrogenAtomNeighbors\fR" 4
.IX Item "GetNumOfNonHydrogenAtomNeighbors"
.Vb 1
\&    $NumNeighbors = $This\->GetNumOfNonHydrogenAtomNeighbors();
.Ve
.Sp
Returns number non-hydrogens atom neighbors for an \fIAtom\fR in a molecule.
.IP "\fBGetNumOfRings\fR" 4
.IX Item "GetNumOfRings"
.Vb 1
\&    $NumOfRings = $Atom\->GetNumOfRings();
.Ve
.Sp
Returns number of rings containing \fIAtom\fR in a molecule.
.IP "\fBGetNumOfRingsWithEvenSize\fR" 4
.IX Item "GetNumOfRingsWithEvenSize"
.Vb 1
\&    $NumOfRings = $Atom\->GetNumOfRingsWithEvenSize();
.Ve
.Sp
Returns number of rings with even size containing \fIAtom\fR in a molecule.
.IP "\fBGetNumOfRingsWithOddSize\fR" 4
.IX Item "GetNumOfRingsWithOddSize"
.Vb 1
\&    $NumOfRings = $Atom\->GetNumOfRingsWithOddSize();
.Ve
.Sp
Returns number of rings with odd size containing \fIAtom\fR in a molecule.
.IP "\fBGetNumOfRingsWithSize\fR" 4
.IX Item "GetNumOfRingsWithSize"
.Vb 1
\&    $NumOfRings = $Atom\->GetNumOfRingsWithSize($RingSize);
.Ve
.Sp
Returns number of rings with specific \fIRingSize\fR containing \fIAtom\fR in a molecule.
.IP "\fBGetNumOfRingsWithSizeGreaterThan\fR" 4
.IX Item "GetNumOfRingsWithSizeGreaterThan"
.Vb 1
\&    $NumOfRings = $Atom\->GetNumOfRingsWithSizeGreaterThan($RingSize);
.Ve
.Sp
Returns number of rings with size greater than specific \fIRingSize\fR containing \fIAtom\fR
in a molecule.
.IP "\fBGetNumOfRingsWithSizeLessThan\fR" 4
.IX Item "GetNumOfRingsWithSizeLessThan"
.Vb 1
\&    $NumOfRings = $Atom\->GetNumOfRingsWithSizeLessThan($RingSize);
.Ve
.Sp
Returns number of rings with size less than specific \fIRingSize\fR containing \fIAtom\fR in a molecule.
.IP "\fBGetNumOfSigmaAndPiBondsToHeavyAtoms\fR" 4
.IX Item "GetNumOfSigmaAndPiBondsToHeavyAtoms"
.Vb 2
\&    ($NumOfSigmaBonds, $NumOfPiBonds) = $Atom\->
\&                              GetNumOfSigmaAndPiBondsToHeavyAtoms();
.Ve
.Sp
Get number of sigma and pi bonds from an \fIAtom\fR to all other non-hydrogen
atoms in a molecule.
.Sp
Sigma and pi bonds are counted using the following methodology: a single bond
correspond to one sigma bond; a double bond contributes one to sigma bond count
and one to pi bond count; a triple bond contributes one to sigma bond count and
two to pi bond count.
.IP "\fBGetNumOfSigmaAndPiBondsToNonHydrogenAtoms\fR" 4
.IX Item "GetNumOfSigmaAndPiBondsToNonHydrogenAtoms"
.Vb 2
\&    ($NumOfSigmaBonds, $NumOfPiBonds) = $Atom\->
\&                              GetNumOfSigmaAndPiBondsToNonHydrogenAtoms();
.Ve
.Sp
Get number of sigma and pi bonds from an \fIAtom\fR to all other non-hydrogen
atoms in a molecule.
.Sp
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.
.IP "\fBGetNumOfSingleBondsToNonHydrogenAtoms\fR" 4
.IX Item "GetNumOfSingleBondsToNonHydrogenAtoms"
.Vb 1
\&    $NumOfSingleBonds =$Atom\->GetNumOfSingleBondsToNonHydrogenAtoms();
.Ve
.Sp
Returns number of single bonds from an \fIAtom\fR to other heavy atoms or non-hydrogen
atoms in a molecule.
.IP "\fBGetNumOfSingleBondsToHeavyAtoms\fR" 4
.IX Item "GetNumOfSingleBondsToHeavyAtoms"
.Vb 1
\&    $NumOfSingleBonds = $Atom\->GetNumOfSingleBondsToHeavyAtoms();
.Ve
.Sp
Returns number of single bonds from an \fIAtom\fR to other heavy atoms or non-hydrogen
atoms in a molecule.
.IP "\fBGetNumOfTripleBondsToNonHydrogenAtoms\fR" 4
.IX Item "GetNumOfTripleBondsToNonHydrogenAtoms"
.Vb 1
\&    $NumOfTripleBonds =$Atom\->GetNumOfTripleBondsToNonHydrogenAtoms();
.Ve
.Sp
Returns number of triple bonds from an \fIAtom\fR to other heavy atoms or non-hydrogen
atoms in a molecule.
.IP "\fBGetNumOfTripleBondsToHeavyAtoms\fR" 4
.IX Item "GetNumOfTripleBondsToHeavyAtoms"
.Vb 1
\&    $NumOfTripleBonds = $Atom\->GetNumOfTripleBondsToHeavyAtoms();
.Ve
.Sp
Returns number of triple bonds from an \fIAtom\fR to other heavy atoms or non-hydrogen
atoms in a molecule.
.IP "\fBGetPeriodNumber\fR" 4
.IX Item "GetPeriodNumber"
.Vb 1
\&    $PeriodNumber = $Atom\->GetPeriodNumber();
.Ve
.Sp
Returns periodic table period number for an \fIAtom\fR in a molecule with a valid atomic number .
.IP "\fBGetRings\fR" 4
.IX Item "GetRings"
.Vb 1
\&    @Rings = $Aotm\->GetRings();
.Ve
.Sp
Returns an array of references to arrays containing ring atoms corressponding to all rings containing
\&\fIAtom\fR in a molecule.
.IP "\fBGetRingsWithEvenSize\fR" 4
.IX Item "GetRingsWithEvenSize"
.Vb 1
\&    @Rings = $Aotm\->GetRingsWithEvenSize();
.Ve
.Sp
Returns an array of references to arrays containing ring atoms corressponding to all rings with even size
containing \fIAtom\fR in a molecule.
.IP "\fBGetRingsWithOddSize\fR" 4
.IX Item "GetRingsWithOddSize"
.Vb 1
\&    @Rings = $Aotm\->GetRingsWithOddSize();
.Ve
.Sp
Returns an array of references to arrays containing ring atoms corressponding to all rings with odd size
containing \fIAtom\fR in a molecule.
.IP "\fBGetRingsWithSize\fR" 4
.IX Item "GetRingsWithSize"
.Vb 1
\&    @Rings = $Aotm\->GetRingsWithSize($RingSize);
.Ve
.Sp
Returns an array of references to arrays containing ring atoms corressponding to all rings with specific
\&\fIRingSize \fRcontaining \fIAtom\fR in a molecule.
.IP "\fBGetRingsWithSizeGreaterThan\fR" 4
.IX Item "GetRingsWithSizeGreaterThan"
.Vb 1
\&    @Rings = $Aotm\->GetRingsWithSizeGreaterThan($RingSize);
.Ve
.Sp
Returns an array of references to arrays containing ring atoms corressponding to all rings with size
greater than specific \fIRingSize \fRcontaining \fIAtom\fR in a molecule.
.IP "\fBGetRingsWithSizeLessThan\fR" 4
.IX Item "GetRingsWithSizeLessThan"
.Vb 1
\&    @Rings = $Aotm\->GetRingsWithSizeLessThan($RingSize);
.Ve
.Sp
Returns an array of references to arrays containing ring atoms corressponding to all rings with size
less than specific \fIRingSize \fRcontaining \fIAtom\fR in a molecule.
.IP "\fBGetSizeOfLargestRing\fR" 4
.IX Item "GetSizeOfLargestRing"
.Vb 1
\&    $Size = $Atom\->GetSizeOfLargestRing();
.Ve
.Sp
Returns size of the largest ring containing \fIAtom\fR in a molecule.
.IP "\fBGetSizeOfSmallestRing\fR" 4
.IX Item "GetSizeOfSmallestRing"
.Vb 1
\&    $Size = $Atom\->GetSizeOfSmallestRing();
.Ve
.Sp
Returns size of the smallest ring containing \fIAtom\fR in a molecule.
.IP "\fBGetSmallestRing\fR" 4
.IX Item "GetSmallestRing"
.Vb 1
\&    @RingAtoms = $Atom\->GetSmallestRing();
.Ve
.Sp
Returns an array of ring \fIAtom\fR objects corresponding to the largest ring containing \fIAtom\fR
in a molecule.
.IP "\fBGetSpinMultiplicity\fR" 4
.IX Item "GetSpinMultiplicity"
.Vb 1
\&    $SpinMultiplicity = $Atom\->GetSpinMultiplicity();
.Ve
.Sp
Returns spin multiplicity of an \fIAtom\fR corresponding to one of these three
values: explicitly set \fBSpinMultiplicity\fR property value; calculated from
\&\fBFreeRadicalElectrons\fR property; value of 0.
.Sp
The \fBSpinMultiplicity\fR is calculate from \fIFreeRadicalElectrons\fR property as
follows:
.Sp
.Vb 3
\&    FreeRadicalElectrons: 1; SpinMultiplicity: 2
\&    FreeRadicalElectrons: 2; SpinMultiplicity: 1
\&    FreeRadicalElectrons: other; SpinMultiplicity: 0
.Ve
.IP "\fBGetSumOfBondOrders\fR" 4
.IX Item "GetSumOfBondOrders"
.Vb 1
\&    $SumBondOrders = $Atom\->GetSumOfBondOrders();
.Ve
.Sp
Returns sum of bond orders corresponding to all atoms bonded to an \fIAtom\fR in a molecule.
.IP "\fBGetSumOfBondOrdersToHeavyAtoms\fR" 4
.IX Item "GetSumOfBondOrdersToHeavyAtoms"
.Vb 1
\&    $SumBondOrders = $Atom\->GetSumOfBondOrdersToHeavyAtoms();
.Ve
.Sp
Returns sum of bond orders corresponding to all heavy atoms bonded to an \fIAtom\fR in a molecule.
.IP "\fBGetSumOfBondOrdersToHydrogenAtoms\fR" 4
.IX Item "GetSumOfBondOrdersToHydrogenAtoms"
.Vb 1
\&    $SumBondOrders = $Atom\->GetSumOfBondOrdersToHydrogenAtoms();
.Ve
.Sp
Returns sum of bond orders corresponding to all hydrogen atoms bonded to an \fIAtom\fR in a molecule.
.IP "\fBGetSumOfBondOrdersToNonHydrogenAtoms\fR" 4
.IX Item "GetSumOfBondOrdersToNonHydrogenAtoms"
.Vb 1
\&    $SumBondOrders = $Atom\->GetSumOfBondOrdersToNonHydrogenAtoms();
.Ve
.Sp
Returns sum of bond orders corresponding to all non-hydrogen atoms bonded to an \fIAtom\fR
in a molecule.
.IP "\fBGetValence\fR" 4
.IX Item "GetValence"
.Vb 1
\&    $Valence = $Atom\->GetValence();
.Ve
.Sp
Returns valence of an \fIAtom\fR in a molecule. Valence corresponds to number of electrons used
by an atom in bonding:
.Sp
.Vb 1
\&    Valence = ValenceElectrons \- ValenceFreeElectrons = BondingElectrons
.Ve
.Sp
Single, double and triple bonds with bond orders of 1, 2, and 3 correspond to
contribution of 1, 2, and 3 bonding electrons. So:
.Sp
.Vb 1
\&    Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge
.Ve
.Sp
where positive and negative values of FormalCharge increase and decrease the number of bonding
electrons, respectively.
.Sp
The current release of MayaChemTools supports the following three valence models, which
are used during calculation of implicit hydrogens: MDLValenceModel, DaylightValenceModel,
InternalValenceModel or MayaChemToolsValenceModel.
.Sp
Notes:
.Sp
.Vb 10
\&    . 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)
.Ve
.IP "\fBGetValenceElectrons\fR" 4
.IX Item "GetValenceElectrons"
.Vb 1
\&    $ValenceElectrons = $Atom\->GetValenceElectrons();
.Ve
.Sp
Returns valence electrons for an \fBAtom\fR which corresponds to either explicity set \fIValenceElectrons\fR
atom property or valence electrons for the corresponding element in the periodic table available by
\&\fBPeriodicTable\fR module.
.IP "\fBGetValenceFreeElectrons\fR" 4
.IX Item "GetValenceFreeElectrons"
.Vb 3
\&    $ValenceFreeElectrons = $Atom\->GetValenceFreeElectrons();
\&    $ValenceFreeElectrons = $Atom\->GetValenceFreeElectrons(
\&                            $ExcludeFreeRadicalElectrons);
.Ve
.Sp
Returns valence frees electrons for an \fBAtom\fR in a molecule. It corresponds to:
.Sp
.Vb 3
\&    ValenceElectrons \- Valence
\&    or
\&    ValenceElectrons \- NumOfMissingHydrogens \- SumOfBondOrders \- FormalCharge
.Ve
.Sp
Free radical electrons are included in the valence free electrons count by default.
.Sp
Examples:
.Sp
.Vb 6
\&    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
.Ve
.IP "\fBGetX\fR" 4
.IX Item "GetX"
.Vb 1
\&    $X = $Atom\->GetX();
.Ve
.Sp
Returns value of X\-coordinate for an \fIAtom\fR.
.IP "\fBGetXYZ\fR" 4
.IX Item "GetXYZ"
.Vb 2
\&    @XYZ = $Atom\->GetXYZ();
\&    $XYZRef = $Atom\->GetXYZ();
.Ve
.Sp
Returns an array or a reference to an array containing values for \fIAtom\fR coordinates.
.IP "\fBGetXYZVector\fR" 4
.IX Item "GetXYZVector"
.Vb 1
\&    $XYZVector = $Atom\->GetXYZVector();
.Ve
.Sp
Returns a \fIVector\fR object containing values for \fIAtom\fR coordinates
.IP "\fBGetY\fR" 4
.IX Item "GetY"
.Vb 1
\&    $Y = $Atom\->GetY();
.Ve
.Sp
Returns value of Y\-coordinate for an \fIAtom\fR.
.IP "\fBGetZ\fR" 4
.IX Item "GetZ"
.Vb 1
\&    $Z = $Atom\->GetZ();
.Ve
.Sp
Returns value of Z\-coordinate for an \fIAtom\fR.
.IP "\fBIsAmideCarbon\fR" 4
.IX Item "IsAmideCarbon"
.Vb 1
\&    $Status = $Atom\->IsAmideCarbon();
.Ve
.Sp
Returns 1 or 0 based on whether it's amide carbon \fIAtom\fR.
.Sp
An amide group is defineds as:
.Sp
.Vb 1
\&    R\-C(=O)\-N(\-R\*(Aq)\-R\*(Aq\*(Aq
.Ve
.Sp
where:
.Sp
.Vb 5
\&    o R = Hydrogen or groups of atoms attached through carbon
\&    o R\*(Aq = Hydrogens or groups of atoms attached through carbon or
\&           hetro atoms
\&    o R\*(Aq\*(Aq = Hydrogens or groups of atoms attached through carbon or
\&           hetro atoms
.Ve
.IP "\fBIsAmideNitrogen\fR" 4
.IX Item "IsAmideNitrogen"
.Vb 1
\&    $Status = $Atom\->IsAmideNitrogen();
.Ve
.Sp
Returns 1 or 0 based on whether it's amide nitrogen \fIAtom\fR.
.IP "\fBIsAromatic\fR" 4
.IX Item "IsAromatic"
.Vb 1
\&    $Status = $Atom\->IsAromatic();
.Ve
.Sp
Returns 1 or 0 based on whether it's an aromatic \fIAtom\fR.
.IP "\fBIsArsenic\fR" 4
.IX Item "IsArsenic"
.Vb 1
\&    $Status = $Atom\->IsArsenic();
.Ve
.Sp
Returns 1 or 0 based on whether it's an arsenic \fIAtom\fR.
.IP "\fBIsBondedToAtom\fR" 4
.IX Item "IsBondedToAtom"
.Vb 1
\&    $Status = $Atom\->IsBondedToAtom($OtherAtom);
.Ve
.Sp
Returns 1 or 0 based on whether \fIAtom\fR is bonded to \fIOtherAtom\fR.
.IP "\fBIsBromine\fR" 4
.IX Item "IsBromine"
.Vb 1
\&    $Status = $Atom\->IsBromine();
.Ve
.Sp
Returns 1 or 0 based on whether it's a bromine \fIAtom\fR.
.IP "\fBIsCarbon\fR" 4
.IX Item "IsCarbon"
.Vb 1
\&    $Status = $Atom\->IsCarbon();
.Ve
.Sp
Returns 1 or 0 based on whether it's a carbon \fIAtom\fR.
.IP "\fBIsCarboxylCarbon\fR" 4
.IX Item "IsCarboxylCarbon"
.Vb 1
\&    $Status = $Atom\->IsCarboxylCarbon();
.Ve
.Sp
Returns 1 or 0 based on whether it's a carboxyl carbon atom in carboxyl group:
R\-C(=O)\-OH.
.IP "\fBIsCarboxylOxygen\fR" 4
.IX Item "IsCarboxylOxygen"
.Vb 1
\&    $Status = $Atom\->IsCarboxylOxygen();
.Ve
.Sp
Returns 1 or 0 based on whether it's a carboxyl oxygen atom in carboxyl group:
R\-C(=O)\-OH.
.IP "\fBIsCarboxylateCarbon\fR" 4
.IX Item "IsCarboxylateCarbon"
.Vb 1
\&    $Status = $Atom\->IsCarboxylateCarbon();
.Ve
.Sp
Returns 1 or 0 based on whether it's a carboxylate carbon atom in carboxyl group:
R\-C(=O)\-O\-.
.IP "\fBIsCarboxylateOxygen\fR" 4
.IX Item "IsCarboxylateOxygen"
.Vb 1
\&    $Status = $Atom\->IsCarboxylateOxygen();
.Ve
.Sp
Returns 1 or 0 based on whether it's a carboxylate oxygen atom in carboxyl group:
R\-C(=O)\-O\-.
.IP "\fBIsChlorine\fR" 4
.IX Item "IsChlorine"
.Vb 1
\&    $Status = $Atom\->IsChlorine();
.Ve
.Sp
Returns 1 or 0 based on whether it's a chlorine \fIAtom\fR.
.IP "\fBIsFluorine\fR" 4
.IX Item "IsFluorine"
.Vb 1
\&    $Status = $Atom\->IsFluorine();
.Ve
.Sp
Returns 1 or 0 based on whether it's a fluorine \fIAtom\fR.
.IP "\fBIsFunctionalClassType\fR" 4
.IX Item "IsFunctionalClassType"
.Vb 1
\&    $Status =$Atom\->IsFunctionalClassType($Type);
.Ve
.Sp
Returns 1 or 0 based on whether it's a specified functional class \fIType\fR.
.Sp
The current release of MayaChemTools supports following abbreviations and descriptive
names for \fIFunctionalClassType\fR:
.Sp
.Vb 9
\&    HBD: HydrogenBondDonor
\&    HBA: HydrogenBondAcceptor
\&    PI :  PositivelyIonizable
\&    NI : NegativelyIonizable
\&    Ar : Aromatic
\&    Hal : Halogen
\&    H : Hydrophobic
\&    RA : RingAtom
\&    CA : ChainAtom
.Ve
.Sp
The following definitions are used to determine functional class types: [ Ref 60\-61, Ref 65\-66 ]:
.Sp
.Vb 4
\&    HydrogenBondDonor: NH, NH2, OH
\&    HydrogenBondAcceptor: N[!H], O
\&    PositivelyIonizable: +, NH2
\&    NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
.Ve
.IP "\fBIsGuadiniumCarbon\fR" 4
.IX Item "IsGuadiniumCarbon"
.Vb 1
\&    $Status = $Atom\->IsGuadiniumCarbon();
.Ve
.Sp
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.
.IP "\fBIsGuadiniumNitrogen\fR" 4
.IX Item "IsGuadiniumNitrogen"
.Vb 1
\&    $Status = $Atom\->IsGuadiniumNitrogen();
.Ve
.Sp
Returns 1 or 0 based on whether it's a guadinium nitrogen in guadinium group.
.Sp
A guadinium group is defined as:
.Sp
.Vb 1
\&    R2N\-C(=NR)\-(NR2) or R2N\-C(=NR2+)\-(NR2)
.Ve
.Sp
where:
.Sp
.Vb 3
\&    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
.Ve
.IP "\fBIsHBondAcceptor\fR" 4
.IX Item "IsHBondAcceptor"
.Vb 2
\&    $Status =$Atom\->IsHBondAcceptor();
\&    $Status =$Atom\->IsHBondAcceptor($HydrogenBondsType);
.Ve
.Sp
Returns 1 or 0 based on whether it's a hydrogen bond acceptor \fIAtom\fR.
.IP "\fBIsHBondDonor\fR" 4
.IX Item "IsHBondDonor"
.Vb 2
\&    $Status =$Atom\->IsHBondDonor();
\&    $Status =$Atom\->IsHBondDonor($HydrogenBondsType);
.Ve
.Sp
Returns 1 or 0 based on whether it's a hydrogen bond donor \fIAtom\fR.
.IP "\fBIsHydrogenBondAcceptor\fR" 4
.IX Item "IsHydrogenBondAcceptor"
.Vb 2
\&    $Status =$Atom\->IsHydrogenBondAcceptor();
\&    $Status =$Atom\->IsHydrogenBondAcceptor($HydrogenBondsType);
.Ve
.Sp
Returns 1 or 0 based on whether it's a hydrogen bond acceptor \fIAtom\fR.
.IP "\fBIsHydrogenBondDonor\fR" 4
.IX Item "IsHydrogenBondDonor"
.Vb 2
\&    $Status =$Atom\->IsHydrogenBondDonor();
\&    $Status =$Atom\->IsHydrogenBondDonor($HydrogenBondsType);
.Ve
.Sp
Returns 1 or 0 based on whether it's a hydrogen bond donor \fIAtom\fR.
.Sp
The current release of MayaChemTools supports identification of two types of hydrogen bond
donor and acceptor atoms with these names:
.Sp
.Vb 2
\&    HBondsType1 or HydrogenBondsType1
\&    HBondsType2 or HydrogenBondsType2
.Ve
.Sp
The names of these hydrogen bond types are rather arbitrary. However, their definitions have
specific meaning and are as follows:
.Sp
.Vb 1
\&    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
.Ve
.Sp
By default, \fIHydrogenBondsType1\fR is used to calculate number hydrogen bond donor
and acceptor atoms. \fIHydrogenBondsType2\fR corresponds to \fBRuleOf5\fR definition
of hydrogen bond donors and acceptors.
.IP "\fBIsHalogen\fR" 4
.IX Item "IsHalogen"
.Vb 1
\&    $Status =$Atom\->IsHalogen();
.Ve
.Sp
Returns 1 or 0 based on whether it's a halogen \fIAtom\fR.
.IP "\fBIsHeteroAtom\fR" 4
.IX Item "IsHeteroAtom"
.Vb 1
\&    $Status = $Atom\->IsHeteroAtom();
.Ve
.Sp
Returns 0 or 1 based on whether it's a hetro \fIAtom\fR. Following atoms are considered hetro atoms:
\&\fBN, O, F, P, S, Cl, Br, I\fR.
.IP "\fBIsHydrogen\fR" 4
.IX Item "IsHydrogen"
.Vb 1
\&    $Status = $Atom\->IsHydrogen();
.Ve
.Sp
Returns 1 or 0 based on whether it's a hydrogen \fIAtom\fR.
.IP "\fBIsHydrophobic\fR" 4
.IX Item "IsHydrophobic"
.Vb 1
\&    $Status =$Atom\->IsHydrophobic();
.Ve
.Sp
Returns 1 or 0 based on whether it's a hydrophobic \fIAtom\fR.
.IP "\fBIsInRing\fR" 4
.IX Item "IsInRing"
.Vb 1
\&    $Status = $Atom\->IsInRing();
.Ve
.Sp
Returns 1 or 0 based on whether \fIAtom\fR is present in a ring.
.IP "\fBIsInRingOfSize\fR" 4
.IX Item "IsInRingOfSize"
.Vb 1
\&    $Status = $Atom\->IsInRingOfSize($Size);
.Ve
.Sp
Returns 1 or 0 based on whether \fIAtom\fR is present in a ring of specific \fISize\fR.
.IP "\fBIsIodine\fR" 4
.IX Item "IsIodine"
.Vb 1
\&    $Status = $Atom\->IsIodine();
.Ve
.Sp
Returns 1 or 0 based on whether it's an iodine \fIAtom\fR.
.IP "\fBIsIsotope\fR" 4
.IX Item "IsIsotope"
.Vb 1
\&    $Status =$Atom\->IsIsotope();
.Ve
.Sp
Returns 1 or 0 based on whether it's an isotope \fIAtom\fR.
.IP "\fBIsLipophilic\fR" 4
.IX Item "IsLipophilic"
.Vb 1
\&    $Status =$Atom\->IsLipophilic();
.Ve
.Sp
Returns 1 or 0 based on whether it's a lipophilic \fIAtom\fR.
.IP "\fBIsMetallic\fR" 4
.IX Item "IsMetallic"
.Vb 1
\&    $Status = $Atom\->IsMetallic();
.Ve
.Sp
Returns 1 or 0 based on whether it's a metallic \fIAtom\fR.
.IP "\fBIsNegativelyIonizable\fR" 4
.IX Item "IsNegativelyIonizable"
.Vb 1
\&    $Status =$Atom\->IsNegativelyIonizable();
.Ve
.Sp
Returns 1 or 0 based on whether it's a negatively ionizable atom \fIAtom\fR.
.IP "\fBIsNitrogen\fR" 4
.IX Item "IsNitrogen"
.Vb 1
\&    $Status = $Atom\->IsNitrogen();
.Ve
.Sp
Returns 1 or 0 based on whether it's a nitrogen \fIAtom\fR.
.IP "\fBIsNonCarbonOrHydrogen\fR" 4
.IX Item "IsNonCarbonOrHydrogen"
.Vb 1
\&    $Status =$Atom\->IsNonCarbonOrHydrogen();
.Ve
.Sp
Returns 1 or 0 based on whether it's not a carbon or hydrogen \fIAtom\fR.
.IP "\fBIsNotInRing\fR" 4
.IX Item "IsNotInRing"
.Vb 1
\&    $Status = $Atom\->IsNotInRing();
.Ve
.Sp
Returns 1 or 0 based on whether \fIAtom\fR is not present in a ring.
.IP "\fBIsOnlyInOneRing\fR" 4
.IX Item "IsOnlyInOneRing"
.Vb 1
\&    $Status = $Atom\->IsOnlyInOneRing();
.Ve
.Sp
Returns 1 or 0 based on whether \fIAtom\fR is only present in one ring.
.IP "\fBIsOxygen\fR" 4
.IX Item "IsOxygen"
.Vb 1
\&    $Status = $Atom\->IsOxygen();
.Ve
.Sp
Returns 0 or 1 based on whether it's an oxygen \fIAtom\fR.
.IP "\fBIsPhosphorus\fR" 4
.IX Item "IsPhosphorus"
.Vb 1
\&    $Status = $Atom\->IsPhosphorus();
.Ve
.Sp
Returns 0 or 1 based on whether it's a phosphorus \fIAtom\fR.
.IP "\fBIsPhosphateOxygen\fR" 4
.IX Item "IsPhosphateOxygen"
.Vb 1
\&    $Status = $Atom\->IsPhosphateOxygen();
.Ve
.Sp
Returns 1 or 0 based on whether it's a phosphate oxygen in phosphate group.
.Sp
A phosphate group is defined as:
.Sp
.Vb 1
\&    AO\-(O=)P(\-OA)\-OA
.Ve
.Sp
Where:
.Sp
.Vb 1
\&   A \- Any group of atoms including hydrogens
.Ve
.IP "\fBIsPhosphatePhosphorus\fR" 4
.IX Item "IsPhosphatePhosphorus"
.Vb 1
\&    $Status = $Atom\->IsPhosphatePhosphorus();
.Ve
.Sp
Returns 1 or 0 based on whether it's a phosphate phosphorus in phosphate group.
.IP "\fBIsPolarAtom\fR" 4
.IX Item "IsPolarAtom"
.Vb 1
\&    $Status = $Atom\->IsPolarAtom();
.Ve
.Sp
Returns 0 or 1 based on whether it's a polar \fIAtom\fR. Following atoms are considered polar atoms:
\&\fBN, O, P, S\fR.
.IP "\fBIsPolarHydrogen\fR" 4
.IX Item "IsPolarHydrogen"
.Vb 1
\&    $Status = $Atom\->IsPolarHydrogen();
.Ve
.Sp
Returns 0 or 1 based on whether it's a hydrogen \fIAtom\fR bonded to a polar atom.
.IP "\fBIsPositivelyIonizable\fR" 4
.IX Item "IsPositivelyIonizable"
.Vb 1
\&    $Status =$Atom\->IsPositivelyIonizable();
.Ve
.Sp
Returns 1 or 0 based on whether it's a positively ionizable \fIAtom\fR.
.IP "\fBIsSaturated\fR" 4
.IX Item "IsSaturated"
.Vb 1
\&    $Status = $Atom\->IsSaturated();
.Ve
.Sp
Returns 1 or 0 based on whether it's a saturated \fIAtom\fR. An atom attached
to other atoms with only single bonds is considered a saturated atom.
.IP "\fBIsSelenium\fR" 4
.IX Item "IsSelenium"
.Vb 1
\&    $Status = $Atom\->IsSelenium();
.Ve
.Sp
Returns 0 or 1 based on whether it's a selenium \fIAtom\fR.
.IP "\fBIsStereoCenter\fR" 4
.IX Item "IsStereoCenter"
.Vb 1
\&    $Status = $Atom\->IsStereoCenter();
.Ve
.Sp
Returns 0 or 1 based on whether it's marked as a stero center \fIAtom\fR by explicit setting
of \fIStereoCenter\fR atom propert to value of \fI1\fR.
.IP "\fBIsSilicon\fR" 4
.IX Item "IsSilicon"
.Vb 1
\&    $Status = $Atom\->IsSilicon();
.Ve
.Sp
Returns 0 or 1 based on whether it's a silicon \fIAtom\fR.
.IP "\fBIsSulfur\fR" 4
.IX Item "IsSulfur"
.Vb 1
\&    $Status = $Atom\->IsSulfur();
.Ve
.Sp
Returns 0 or 1 based on whether it's a sulfur \fIAtom\fR.
.IP "\fBIsSulphur\fR" 4
.IX Item "IsSulphur"
.Vb 1
\&    $Status = $Atom\->IsSulphur();
.Ve
.Sp
Returns 0 or 1 based on whether it's a sulfur \fIAtom\fR.
.IP "\fBIsTellurium\fR" 4
.IX Item "IsTellurium"
.Vb 1
\&    $Status = $Atom\->IsTellurium();
.Ve
.Sp
Returns 0 or 1 based on whether it's a tellurium \fIAtom\fR.
.IP "\fBIsTerminal\fR" 4
.IX Item "IsTerminal"
.Vb 1
\&    $Status = $Atom\->IsTerminal();
.Ve
.Sp
Returns 0 or 1 based on whether it's a terminal \fIAtom\fR attached to no
more than one non-hydrogen atom.
.IP "\fBIsUnsaturated\fR" 4
.IX Item "IsUnsaturated"
.Vb 1
\&    $Status = $Atom\->IsUnsaturated();
.Ve
.Sp
Returns 1 or 0 based on whether it's as unsaturated \fIAtom\fR. An atom attached
to other atoms with at least one non-single bond is considered an unsaturated atom.
.IP "\fBIsTopologicalPharmacophoreType\fR" 4
.IX Item "IsTopologicalPharmacophoreType"
.Vb 1
\&    $Status =$Atom\->IsTopologicalPharmacophoreType();
.Ve
.Sp
Returns 1 or 0 based on whether it's any of the supportyed topological pharmacophore
\&\fIAtom\fR type. See \fIIsFunctionalClassType\fR for a list of supported types.
.IP "\fBSetAtomSymbol\fR" 4
.IX Item "SetAtomSymbol"
.Vb 1
\&    $Atom\->SetAtomSymbol($AtomicSymbol);
.Ve
.Sp
Sets atom symbol for \fIAtom\fR and returns \fIAtom\fR object. The appropriate atomic number is also
set automatically.
.IP "\fBSetAtomicNumber\fR" 4
.IX Item "SetAtomicNumber"
.Vb 1
\&    $Atom\->SetAtomicNumber($AtomicNumber);
.Ve
.Sp
Sets atomic number for \fIAtom\fR and returns \fIAtom\fR object. The appropriate atom symbol is also
set automatically.
.IP "\fBSetMassNumber\fR" 4
.IX Item "SetMassNumber"
.Vb 1
\&    $Atom\->SetMassNumber($MassNumber);
.Ve
.Sp
Sets mass number for \fIAtom\fR and returns \fIAtom\fR object.
.IP "\fBSetStereoCenter\fR" 4
.IX Item "SetStereoCenter"
.Vb 1
\&    $Atom\->SetStereoCenter($StereoCenter);
.Ve
.Sp
Sets stereo center for \fIAtom\fR and returns \fIAtom\fR object.
.IP "\fBSetStereochemistry\fR" 4
.IX Item "SetStereochemistry"
.Vb 1
\&    $Atom\->SetStereochemistry($Stereochemistry);
.Ve
.Sp
Sets stereo chemistry for \fIAtom\fR and returns \fIAtom\fR object.
.IP "\fBSetX\fR" 4
.IX Item "SetX"
.Vb 1
\&    $Atom\->SetX($Value);
.Ve
.Sp
Sets X\-coordinate value for \fIAtom\fR and returns \fIAtom\fR object.
.IP "\fBSetXYZ\fR" 4
.IX Item "SetXYZ"
.Vb 3
\&    $Atom\->SetXYZ(@XYZValues);
\&    $Atom\->SetXYZ($XYZValuesRef);
\&    $Atom\->SetXYZ($XYZVector);
.Ve
.Sp
Sets \fIAtom\fR coordinates using an array, reference to an array or a \fIVector\fR object and
returns \fIAtom\fR object.
.IP "\fBSetY\fR" 4
.IX Item "SetY"
.Vb 1
\&    $Atom\->SetY($Value);
.Ve
.Sp
Sets Y\-coordinate value for \fIAtom\fR and returns \fIAtom\fR object.
.IP "\fBSetZ\fR" 4
.IX Item "SetZ"
.Vb 1
\&    $Atom\->SetZ($Value);
.Ve
.Sp
Sets Z\-coordinate value for \fIAtom\fR and returns \fIAtom\fR object.
.IP "\fBStringifyAtom\fR" 4
.IX Item "StringifyAtom"
.Vb 1
\&    $AtomString = $Atom\->StringifyAtom();
.Ve
.Sp
Returns a string containing information about \fIAtom\fR object.
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bond.pm, Molecule.pm, MoleculeFileIO.pm
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
Copyright (C) 2015 Manish Sud. All rights reserved.
.PP
This file is part of MayaChemTools.
.PP
MayaChemTools is free software; you can redistribute it and/or modify it under
the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option)
any later version.