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.IX Title "TOPOLOGICALATOMTRIPLETSFINGERPRINTS 1"
.TH TOPOLOGICALATOMTRIPLETSFINGERPRINTS 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"
TopologicalAtomTripletsFingerprints
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use Fingerprints::TopologicalAtomTripletsFingerprints;
.PP
use Fingerprints::TopologicalAtomTripletsFingerprints qw(:all);
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBTopologicalAtomTripletsFingerprints\fR  [ Ref 57, Ref 59, Ref 72 ] class provides the following methods:
.PP
new, GenerateFingerprints, GetAtomTripletIDs, GetDescription,
SetAtomIdentifierType, SetAtomicInvariantsToUse, SetFunctionalClassesToUse,
SetMaxDistance, SetMinDistance, StringifyTopologicalAtomTripletsFingerprints
.PP
\&\fBTopologicalAtomTripletsFingerprints\fR is derived from \fBFingerprints\fR class which in turn
is  derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
in \fBTopologicalAtomTripletsFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR classes 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
.PP
The current release of MayaChemTools supports generation of \fBTopologicalAtomTripletsFingerprints\fR
corresponding to following \fBAtomtomIdentifierTypes\fR:
.PP
.Vb 3
\&    AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
\&    FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
\&    SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
.Ve
.PP
Based on the values specified for \fBAtomIdentifierType\fR along with other specified
parameters such as \fBAtomicInvariantsToUse\fR and \fBFunctionalClassesToUse\fR, initial
atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance
matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom
triplets within \fBMinDistance\fR and \fBMaxDistance\fR are identified and counted. An atom triplet
identifier is generated for each unique atom triplet; the format of atom triplet identifier is:
.PP
.Vb 1
\&    <ATx>\-Dyz\-<ATy>\-Dxz\-<ATz>\-Dxy
\&
\&    ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z
\&    Dxy: Distance between atom x and atom y
\&    Dxz: Distance between atom x and atom z
\&    Dyz: Distance between atom y and atom z
\&
\&    where <AT1>\-D23 <= <AT2>\-D13 <= <AT3>\-D12
.Ve
.PP
The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute
topological atom triplets fingerprints of the molecule.
.PP
The current release of MayaChemTools generates the following types of topological atom triplets
fingerprints vector strings:
.PP
.Vb 7
\&    FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
\&    inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
\&    .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
\&    0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
\&    \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
\&    1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
\&    2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
\&
\&    FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
\&    inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
\&    ;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 1 C.X1.BO1.H3\-D1\-C.X2.BO
\&    2.H2\-D10\-C.X3.BO4\-D9 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 2 C.X
\&    1.BO1.H3\-D1\-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2
\&    \-D6\-C.X3.BO3.H1\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3.BO3.H1\-D7 2...
\&
\&    FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan
\&    ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2\-D1\-C_2\-D
\&    9\-C_3\-D10 C_2\-D1\-C_2\-D9\-C_R\-D10 C_2\-D1\-C_3\-D1\-C_3\-D2 C_2\-D1\-C_3\-D10\-C_
\&    3\-D9 C_2\-D1\-C_3\-D2\-C_3\-D3 C_2\-D1\-C_3\-D2\-C_R\-D3 C_2\-D1\-C_3\-D3\-C_3\-D4 C_
\&    2\-D1\-C_3\-D3\-N_R\-D4 C_2\-D1\-C_3\-D3\-O_3\-D2 C_2\-D1\-C_3\-D4\-C_3\-D5 C_2\-D...;
\&    1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2
\&    2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...
\&
\&    FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance
\&    1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH\-D1\-aaCH\-D
\&    1\-aaCH\-D2 aaCH\-D1\-aaCH\-D1\-aasC\-D2 aaCH\-D1\-aaCH\-D10\-aaCH\-D9 aaCH\-D1\-aaC
\&    H\-D10\-aasC\-D9 aaCH\-D1\-aaCH\-D2\-aaCH\-D3 aaCH\-D1\-aaCH\-D2\-aasC\-D1 aaCH\-D1\-
\&    aaCH\-D2\-aasC\-D3 aaCH\-D1\-aaCH\-D3\-aasC\-D2 aaCH\-D1\-aaCH\-D4\-aasC\-D5 aa...;
\&    6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2
\&    2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1
\&    2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...
\&
\&    FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi
\&    nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar\-D1
\&    \-Ar\-D1\-Ar\-D2 Ar\-D1\-Ar\-D1\-Ar.HBA\-D2 Ar\-D1\-Ar\-D10\-Ar\-D9 Ar\-D1\-Ar\-D10\-Hal
\&    \-D9 Ar\-D1\-Ar\-D2\-Ar\-D2 Ar\-D1\-Ar\-D2\-Ar\-D3 Ar\-D1\-Ar\-D2\-Ar.HBA\-D1 Ar\-D1\-Ar
\&    \-D2\-Ar.HBA\-D2 Ar\-D1\-Ar\-D2\-Ar.HBA\-D3 Ar\-D1\-Ar\-D2\-HBD\-D1 Ar\-D1\-Ar\-D2...;
\&    27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5
\&    2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3
\&    4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...
\&
\&    FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance
\&    1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A\-D1\-C5A\-D1\-
\&    N5\-D2 C5A\-D1\-C5A\-D2\-C5B\-D2 C5A\-D1\-C5A\-D3\-CB\-D2 C5A\-D1\-C5A\-D3\-CR\-D2 C5A
\&    \-D1\-C5B\-D1\-C5B\-D2 C5A\-D1\-C5B\-D2\-C=ON\-D1 C5A\-D1\-C5B\-D2\-CB\-D1 C5A\-D1\-C5B
\&    \-D3\-C=ON\-D2 C5A\-D1\-C5B\-D3\-CB\-D2 C5A\-D1\-C=ON\-D3\-NC=O\-D2 C5A\-D1\-C=ON\-D3\-
\&    O=CN\-D2 C5A\-D1\-C=ON\-D4\-NC=O\-D3 C5A\-D1\-C=ON\-D4\-O=CN\-D3 C5A\-D1\-CB\-D1\-...
\&
\&    FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1
\&    :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1\-D1\-C1\-D1\-C11
\&    \-D2 C1\-D1\-C1\-D1\-CS\-D2 C1\-D1\-C1\-D10\-C5\-D9 C1\-D1\-C1\-D3\-C10\-D2 C1\-D1\-C1\-D
\&    3\-C5\-D2 C1\-D1\-C1\-D3\-CS\-D2 C1\-D1\-C1\-D3\-CS\-D4 C1\-D1\-C1\-D4\-C10\-D5 C1\-D1\-C
\&    1\-D4\-C11\-D5 C1\-D1\-C1\-D5\-C10\-D4 C1\-D1\-C1\-D5\-C5\-D4 C1\-D1\-C1\-D6\-C11\-D7 C1
\&    \-D1\-C1\-D6\-CS\-D5 C1\-D1\-C1\-D6\-CS\-D7 C1\-D1\-C1\-D8\-C11\-D9 C1\-D1\-C1\-D8\-CS...
\&
\&    FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
\&    :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
\&    .3\-D10 C.2\-D1\-C.2\-D9\-C.ar\-D10 C.2\-D1\-C.3\-D1\-C.3\-D2 C.2\-D1\-C.3\-D10\-C.3\-
\&    D9 C.2\-D1\-C.3\-D2\-C.3\-D3 C.2\-D1\-C.3\-D2\-C.ar\-D3 C.2\-D1\-C.3\-D3\-C.3\-D4 C.2
\&    \-D1\-C.3\-D3\-N.ar\-D4 C.2\-D1\-C.3\-D3\-O.3\-D2 C.2\-D1\-C.3\-D4\-C.3\-D5 C.2\-D1\-C.
\&    3\-D5\-C.3\-D6 C.2\-D1\-C.3\-D5\-O.3\-D4 C.2\-D1\-C.3\-D6\-C.3\-D7 C.2\-D1\-C.3\-D7...
\&
\&    FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1:
\&    MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21\-D1\-N7\-D3\-Non
\&    e\-D4 N21\-D1\-N7\-D5\-None\-D4 N21\-D1\-None\-D1\-None\-D2 N21\-D1\-None\-D2\-None\-D
\&    2 N21\-D1\-None\-D2\-None\-D3 N21\-D1\-None\-D3\-None\-D4 N21\-D1\-None\-D4\-None\-D5
\&     N21\-D1\-None\-D4\-O3\-D3 N21\-D1\-None\-D4\-O4\-D3 N21\-D1\-None\-D5\-None\-D6 N21\-
\&    D1\-None\-D6\-None\-D7 N21\-D1\-None\-D6\-O4\-D5 N21\-D1\-None\-D7\-None\-D8 N21\-...
\&
\&    FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M
\&    axDistance10;2377;NumericalValues;IDsAndValuesString;C_2\-D1\-C_2\-D9\-C_3
\&    \-D10 C_2\-D1\-C_2\-D9\-C_R\-D10 C_2\-D1\-C_3\-D1\-C_3\-D2 C_2\-D1\-C_3\-D10\-C_3\-D9 
\&    C_2\-D1\-C_3\-D2\-C_3\-D3 C_2\-D1\-C_3\-D2\-C_R\-D3 C_2\-D1\-C_3\-D3\-C_3\-D4 C_2\-D1\-
\&    C_3\-D3\-N_R\-D4 C_2\-D1\-C_3\-D3\-O_3\-D2 C_2\-D1\-C_3\-D4\-C_3\-D5 C_2\-D1\-C_3\-D5\-
\&    C_3\-D6 C_2\-D1\-C_3\-D5\-O_3\-D4 C_2\-D1\-C_3\-D6\-C_3\-D7 C_2\-D1\-C_3\-D7\-C_3\-...
.Ve
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.IP "\fBnew\fR" 4
.IX Item "new"
.Vb 2
\&    $NewTopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
\&                                                   %NamesAndValues);
.Ve
.Sp
Using specified \fITopologicalAtomTripletsFingerprints\fR property names and values hash, \fBnew\fR
method creates a new object and returns a reference to newly created \fBTopologicalAtomTripletsFingerprints\fR
object. By default, the following properties are initialized:
.Sp
.Vb 8
\&    Molecule = \*(Aq\*(Aq
\&    Type = \*(AqTopologicalAtomTriplets\*(Aq
\&    MinDistance = 1
\&    MaxDistance = 10
\&    UseTriangleInequality = 1
\&    AtomIdentifierType = \*(Aq\*(Aq
\&    AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq]
\&    FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]
.Ve
.Sp
Examples:
.Sp
.Vb 4
\&    $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
\&                              \*(AqMolecule\*(Aq => $Molecule,
\&                              \*(AqAtomIdentifierType\*(Aq =>
\&                                              \*(AqAtomicInvariantsAtomTypes\*(Aq);
\&
\&    $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
\&                              \*(AqMolecule\*(Aq => $Molecule,
\&                              \*(AqMinDistance\*(Aq => 1,
\&                              \*(AqMaxDistance\*(Aq => 10,
\&                              \*(AqAtomIdentifierType\*(Aq =>
\&                                              \*(AqAtomicInvariantsAtomTypes\*(Aq,
\&                              \*(AqAtomicInvariantsToUse\*(Aq =>
\&                                              [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] );
\&
\&    $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
\&                              \*(AqMolecule\*(Aq => $Molecule,
\&                              \*(AqAtomIdentifierType\*(Aq =>
\&                                              \*(AqDREIDINGAtomTypes\*(Aq);
\&
\&    $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
\&                              \*(AqMolecule\*(Aq => $Molecule,
\&                              \*(AqAtomIdentifierType\*(Aq =>
\&                                              \*(AqMMFF94AtomTypes\*(Aq);
\&
\&    $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
\&                              \*(AqMolecule\*(Aq => $Molecule,
\&                              \*(AqAtomIdentifierType\*(Aq =>
\&                                              \*(AqTPSAAtomTypes\*(Aq);
\&
\&    $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
\&                              \*(AqMolecule\*(Aq => $Molecule,
\&                              \*(AqMinDistance\*(Aq => 1,
\&                              \*(AqMaxDistance\*(Aq => 10,
\&                              \*(AqAtomIdentifierType\*(Aq =>
\&                                              \*(AqFunctionalClassAtomTypes\*(Aq,
\&                              \*(AqFunctionalClassesToUse\*(Aq =>
\&                                              [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]);
\&
\&    $TopologicalAtomTripletsFingerprints\->GenerateFingerprints();
\&    print "$TopologicalAtomTripletsFingerprints\en";
.Ve
.IP "\fBGetDescription\fR" 4
.IX Item "GetDescription"
.Vb 1
\&    $Return = $TopologicalAtomTripletsFingerprints\->GetDescription();
.Ve
.Sp
Returns a string containing description of topological atom triplets fingerprints.
.IP "\fBGenerateFingerprints\fR" 4
.IX Item "GenerateFingerprints"
.Vb 1
\&    $TopologicalAtomTripletsFingerprints\->GenerateFingerprints();
.Ve
.Sp
Generates topological atom triplets fingerprints and returns \fITopologicalAtomTripletsFingerprints\fR.
.IP "\fBGetAtomTripletIDs\fR" 4
.IX Item "GetAtomTripletIDs"
.Vb 2
\&    $AtomTripletIDsRef = $TopologicalAtomTripletsFingerprints\->GetAtomTripletIDs();
\&    @AtomTripletIDs = $TopologicalAtomTripletsFingerprints\->GetAtomTripletIDs();
.Ve
.Sp
Returns atom triplet IDs corresponding to atom triplets count values in topological atom triplets
fingerprints vector as an array or reference to an array.
.IP "\fBSetAtomIdentifierType\fR" 4
.IX Item "SetAtomIdentifierType"
.Vb 1
\&    $TopologicalAtomTripletsFingerprints\->SetAtomIdentifierType($IdentifierType);
.Ve
.Sp
Sets atom \fIIdentifierType\fR to use during atom triplets fingerprints generation and
returns \fITopologicalAtomTripletsFingerprints\fR.
.Sp
Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
TPSAAtomTypes, UFFAtomTypes\fR.
.IP "\fBSetAtomicInvariantsToUse\fR" 4
.IX Item "SetAtomicInvariantsToUse"
.Vb 2
\&    $TopologicalAtomTripletsFingerprints\->SetAtomicInvariantsToUse($ValuesRef);
\&    $TopologicalAtomTripletsFingerprints\->SetAtomicInvariantsToUse(@Values);
.Ve
.Sp
Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR
for topological atom triplets fingerprints generation and returns \fITopologicalAtomTripletsFingerprints\fR.
.Sp
Possible values for atomic invariants are: \fI\s-1AS\s0, X, \s-1BO\s0,  \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0,
H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value: \fI\s-1AS\s0,X,BO,H,FC\fR.
.Sp
The atomic invariants abbreviations correspond to:
.Sp
.Vb 1
\&    AS = Atom symbol corresponding to element symbol
\&
\&    X<n>   = Number of non\-hydrogen atom neighbors or heavy atoms
\&    BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
\&    LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
\&    SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
\&    DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
\&    TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
\&    H<n>   = Number of implicit and explicit hydrogens for atom
\&    Ar     = Aromatic annotation indicating whether atom is aromatic
\&    RA     = Ring atom annotation indicating whether atom is a ring
\&    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
Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
.Sp
.Vb 1
\&    AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
.Ve
.Sp
Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
.Sp
In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
are also allowed:
.Sp
.Vb 12
\&    X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
\&    BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
\&    LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
\&    SB :  NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
\&    DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
\&    TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
\&    H :  NumOfImplicitAndExplicitHydrogens
\&    Ar : Aromatic
\&    RA : RingAtom
\&    FC : FormalCharge
\&    MN : MassNumber
\&    SM : SpinMultiplicity
.Ve
.Sp
\&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
atom types.
.IP "\fBSetFunctionalClassesToUse\fR" 4
.IX Item "SetFunctionalClassesToUse"
.Vb 2
\&    $TopologicalTripletsFingerprints\->SetFunctionalClassesToUse($ValuesRef);
\&    $TopologicalTripletsFingerprints\->SetFunctionalClassesToUse(@Values);
.Ve
.Sp
Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR
for topological atom triplets fingerprints generation and returns \fITopologicalAtomTripletsFingerprints\fR.
.Sp
Possible values for atom functional classes are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR.
Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
.Sp
The functional class abbreviations correspond to:
.Sp
.Vb 9
\&    HBD: HydrogenBondDonor
\&    HBA: HydrogenBondAcceptor
\&    PI :  PositivelyIonizable
\&    NI : NegativelyIonizable
\&    Ar : Aromatic
\&    Hal : Halogen
\&    H : Hydrophobic
\&    RA : RingAtom
\&    CA : ChainAtom
\&
\& Functional class atom type specification for an atom corresponds to:
\&
\&    Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
.Ve
.Sp
\&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
types. It uses following definitions [ 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 "\fBSetMaxDistance\fR" 4
.IX Item "SetMaxDistance"
.Vb 1
\&    $TopologicalAtomTripletsFingerprints\->SetMaxDistance($Distance);
.Ve
.Sp
Sets maximum distance to use during topological atom triplets fingerprints generation and
returns \fITopologicalAtomTripletsFingerprints\fR.
.IP "\fBSetMinDistance\fR" 4
.IX Item "SetMinDistance"
.Vb 1
\&    $TopologicalAtomTripletsFingerprints\->SetMinDistance($Distance);
.Ve
.Sp
Sets minimum distance to use during topological atom triplets fingerprints generation and
returns \fITopologicalAtomTripletsFingerprints\fR.
.IP "\fBStringifyTopologicalAtomTripletsFingerprints\fR" 4
.IX Item "StringifyTopologicalAtomTripletsFingerprints"
.Vb 2
\&    $String = $TopologicalAtomTripletsFingerprints\->
\&                  StringifyTopologicalAtomTripletsFingerprints();
.Ve
.Sp
Returns a string containing information about \fITopologicalAtomTripletsFingerprints\fR object.
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
MACCSKeys.pm, PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
TopologicalPharmacophoreAtomTripletsFingerprints.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.