diff mayachemtools/docs/modules/man3/TopologicalPharmacophoreAtomPairsFingerprints.3 @ 0:73ae111cf86f draft

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+.\" ========================================================================
+.\"
+.IX Title "TOPOLOGICALPHARMACOPHOREATOMPAIRSFINGERPRINTS 1"
+.TH TOPOLOGICALPHARMACOPHOREATOMPAIRSFINGERPRINTS 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"
+TopologicalPharmacophoreAtomPairsFingerprints
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+use Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints;
+.PP
+use Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints qw(:all);
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+\&\fBTopologicalPharmacophoreAtomPairsFingerprints\fR [ Ref 60\-62, Ref 65, Ref 68 ] class provides
+the following methods:
+.PP
+new, GenerateFingerprints, GetDescription, GetAtomPairIDs, SetAtomTypesToUse,
+SetAtomTypesWeight, SetFuzzFactor, SetFuzzificationMethodology,
+SetFuzzificationMode, SetMaxDistance, SetMinDistance,
+SetNormalizationMethodology, SetValuesPrecision,
+StringifyTopologicalPharmacophoreAtomPairsFingerprints
+.PP
+\&\fBTopologicalPharmacophoreAtomPairsFingerprints\fR is derived from \fBFingerprints\fR class which in turn
+is  derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
+in \fBTopologicalPharmacophoreAtomPairsFingerprints\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
+Based on the values specified for \fBAtomTypesToUse\fR, pharmacophore atom types are
+assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
+A pharmacophore atom pairs basis set is initialized for all unique possible pairs within
+\&\fBMinDistance\fR and \fBMaxDistance\fR range.
+.PP
+.Vb 1
+\&    Let:
+\&
+\&    P = Valid pharmacophore atom type
+\&
+\&    Px = Pharmacophore atom type x
+\&    Py = Pharmacophore atom type y
+\&
+\&    Dmin = Minimum distance corresponding to number of bonds between two atoms
+\&    Dmax = Maximum distance corresponding to number of bonds between two atoms
+\&    D = Distance corresponding to number of bonds between two atoms
+\&
+\&    Px\-Dn\-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn
+\&
+\&    P = Number of pharmacophore atom types to consider
+\&    PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn
+\&
+\&    PPT = Total number of possible pharmacophore atom pairs at all distances between Dmin and Dmax
+\&
+\&    Then:
+\&
+\&    PPD =  (P * (P \- 1))/2 + P
+\&
+\&    PPT = ((Dmax \- Dmin) + 1) * ((P * (P \- 1))/2 + P)
+\&        = ((Dmax \- Dmin) + 1) * PPD
+\&
+\&    So for default values of Dmin = 1, Dmax = 10 and P = 5,
+\&
+\&    PPD =  (5 * (5 \- 1))/2 + 5 = 15
+\&    PPT = ((10 \- 1) + 1) * 15 = 150
+\&
+\&    The pharmacophore atom pairs bais set includes 150 values.
+\&
+\&    The atom pair IDs correspond to:
+\&
+\&    Px\-Dn\-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn
+\&
+\&    For example: H\-D1\-H, H\-D2\-HBA, PI\-D5\-PI and so on
+.Ve
+.PP
+Using distance matrix and pharmacohore atom types, occurrence of unique pharmacohore atom
+pairs is counted. The contribution of each atom type to atom pair interaction is optionally
+weighted by specified \fBAtomTypesWeight\fR before assigning its count to appropriate distance
+bin. Based on \fBNormalizationMethodology\fR option, pharmacophore atom pairs count is optionally
+normalized. Additionally, pharmacohore atom pairs count is optionally fuzzified before or after
+the normalization controlled by values of \fBFuzzifyAtomPairsCount\fR, \fBFuzzificationMode\fR,
+\&\fBFuzzificationMethodology\fR and \fBFuzzFactor\fR.
+.PP
+The final pharmacophore atom pairs count along with atom pair identifiers involving all non-hydrogen
+atoms, with optional normalization and fuzzification, constitute pharmacophore topological atom pairs
+fingerprints of the molecule.
+.PP
+For \fIArbitrarySize\fR value of \fBAtomPairsSetSizeToUse\fR, the fingerprint vector correspond to
+only those topological pharmacophore atom pairs which are present and have non-zero count. However,
+for \fIFixedSize\fR value of \fBAtomPairsSetSizeToUse\fR, the fingerprint vector contains all possible
+valid topological pharmacophore atom pairs with both zero and non-zero count values.
+.PP
+The current release of MayaChemTools generates the following types of topological pharmacophore
+atom pairs fingerprints vector strings:
+.PP
+.Vb 7
+\&    FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
+\&    Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
+\&    \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
+\&    HBD H\-D3\-H H\-D3\-HBA H\-D3\-HBD H\-D3\-NI HBA\-D3\-NI HBD\-D3\-NI H\-D4\-H H\-D4\-H
+\&    BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
+\&    18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
+\&    3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
+\&
+\&    FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
+\&    ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
+\&    0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
+\&    0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
+\&    0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
+\&    0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...
+\&
+\&    FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
+\&    ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H\-D1
+\&    \-H H\-D1\-HBA H\-D1\-HBD H\-D1\-NI H\-D1\-PI HBA\-D1\-HBA HBA\-D1\-HBD HBA\-D1\-NI H
+\&    BA\-D1\-PI HBD\-D1\-HBD HBD\-D1\-NI HBD\-D1\-PI NI\-D1\-NI NI\-D1\-PI PI\-D1\-PI H\-D
+\&    2\-H H\-D2\-HBA H\-D2\-HBD H\-D2\-NI H\-D2\-PI HBA\-D2\-HBA HBA\-D2\-HBD HBA\-D2...;
+\&    18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
+\&    1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
+\&    1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0
+.Ve
+.SS "\s-1METHODS\s0"
+.IX Subsection "METHODS"
+.IP "\fBnew\fR" 4
+.IX Item "new"
+.Vb 2
+\&    $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
+\&                                                   %NamesAndValues);
+.Ve
+.Sp
+Using specified \fITopologicalPharmacophoreAtomPairsFingerprints\fR property names and
+values hash, \fBnew\fR method creates a new object and returns a reference to newly created
+\&\fBTopologicalPharmacophoreAtomPairsFingerprints\fR object. By default, the following properties
+are initialized:
+.Sp
+.Vb 6
+\&    Molecule = \*(Aq\*(Aq
+\&    Type = \*(AqTopologicalPharmacophoreAtomPairs\*(Aq
+\&    MinDistance = 1
+\&    MaxDistance = 10
+\&    NormalizationMethodology = \*(AqNone\*(Aq
+\&    AtomTypesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq]
+\&
+\&    FuzzifyAtomPairsCount = 0
+\&    FuzzificationMode = \*(AqAfterNormalization\*(Aq
+\&    FuzzificationMethodology =  \*(AqFuzzyBinning\*(Aq
+\&    FuzzFactor = 0.15
+\&
+\&    ValuesPrecision = 2
+.Ve
+.Sp
+Examples:
+.Sp
+.Vb 2
+\&    $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
+\&                              \*(AqMolecule\*(Aq => $Molecule);
+\&
+\&    $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
+\&                              \*(AqMolecule\*(Aq => $Molecule,
+\&                              \*(AqAtomPairsSetSizeToUse\*(Aq => \*(AqArbitrarySize\*(Aq,
+\&                              \*(AqMinDistance\*(Aq => 1,
+\&                              \*(AqMaxDistance\*(Aq => 10,
+\&                              \*(AqNormalizationMethodology\*(Aq => \*(AqNone\*(Aq,
+\&                              \*(AqAtomTypesToUse\*(Aq => [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq],
+\&                              \*(AqFuzzifyAtomPairsCount\*(Aq => 0);
+\&
+\&    $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
+\&                              \*(AqMolecule\*(Aq => $Molecule,
+\&                              \*(AqAtomPairsSetSizeToUse\*(Aq => \*(AqFizedSize\*(Aq,
+\&                              \*(AqMinDistance\*(Aq => 1,
+\&                              \*(AqMaxDistance\*(Aq => 10,
+\&                              \*(AqNormalizationMethodology\*(Aq => \*(AqNone\*(Aq,
+\&                              \*(AqAtomTypesToUse\*(Aq => [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq],
+\&                              \*(AqFuzzifyAtomPairsCount\*(Aq => 1,
+\&                              \*(AqFuzzificationMethodology\*(Aq => \*(AqFuzzyBinning\*(Aq,
+\&                              \*(AqFuzzFactor\*(Aq => 0.15,
+\&                              \*(AqValuesPrecision\*(Aq => 2);
+\&
+\&    $TPAPFP\->GenerateFingerprints();
+\&    print "$TPAPFP\en";
+.Ve
+.IP "\fBGetDescription\fR" 4
+.IX Item "GetDescription"
+.Vb 1
+\&    $Description = $TopologicalPharmacophoreAtomPairsFP\->GetDescription();
+.Ve
+.Sp
+Returns a string containing description of topological pharmacophore atom pairs fingerprints.
+.IP "\fBGenerateFingerprints\fR" 4
+.IX Item "GenerateFingerprints"
+.Vb 1
+\&    $TopologicalPharmacophoreAtomPairsFP\->GenerateFingerprints();
+.Ve
+.Sp
+Generates topological pharmacophore atom pairs fingerprints and returns
+\&\fITopologicalPharmacophoreAtomPairsFP\fR.
+.IP "\fBGetAtomPairIDs\fR" 4
+.IX Item "GetAtomPairIDs"
+.Vb 2
+\&    $AtomPairIDsRef = $TopologicalPharmacophoreAtomPairsFP\->GetAtomPairIDs();
+\&    @AtomPairIDs = $TopologicalPharmacophoreAtomPairsFP\->GetAtomPairIDs();
+.Ve
+.Sp
+Returns atom pair IDs corresponding to atom pairs count values in topological pharmacophore
+atom pairs fingerprints vector as an array or reference to an array.
+.IP "\fBSetAtomPairsSetSizeToUse\fR" 4
+.IX Item "SetAtomPairsSetSizeToUse"
+.Vb 1
+\&    $TopologicalPharmacophoreAtomPairsFP\->SetAtomPairsSetSizeToUse($Values);
+.Ve
+.Sp
+Sets pharmacophore atom pairs set size to use for topological pharmacophore fingerprints
+generation and returns \fITopologicalPharmacophoreAtomPairsFingerprints\fR.
+.Sp
+Possible values for pharmacophore atom pairs set size are: \fIArbitrarySize, FizedSize\fR.
+Default value: \fIArbitrarySize\fR.
+.Sp
+For \fIArbitrarySize\fR value of \fBAtomPairsSetSizeToUse\fR, the fingerprint vector correspond to
+only those topological pharmacophore atom pairs which are present and have non-zero count. However,
+for \fIFixedSize\fR value of \fBAtomPairsSetSizeToUse\fR, the fingerprint vector contains all possible
+valid topological pharmacophore atom pairs with both zero and non-zero count values.
+.IP "\fBSetAtomTypesToUse\fR" 4
+.IX Item "SetAtomTypesToUse"
+.Vb 2
+\&    $TopologicalPharmacophoreAtomPairsFP\->SetAtomTypesToUse($ValuesRef);
+\&    $TopologicalPharmacophoreAtomPairsFP\->SetAtomTypesToUse(@Values);
+.Ve
+.Sp
+Sets pharmacophore atom types to use for topological pharmacophore fingerprints
+generation and returns \fITopologicalPharmacophoreAtomPairsFingerprints\fR.
+.Sp
+Possible values for pharmacophore atom types 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 60\-62 ] : \fI\s-1HBD\s0,HBA,PI,NI,H\fR.
+.Sp
+The pharmacophore atom types abbreviations correspond to:
+.Sp
+.Vb 9
+\&    HBD: HydrogenBondDonor
+\&    HBA: HydrogenBondAcceptor
+\&    PI :  PositivelyIonizable
+\&    NI : NegativelyIonizable
+\&    Ar : Aromatic
+\&    Hal : Halogen
+\&    H : Hydrophobic
+\&    RA : RingAtom
+\&    CA : ChainAtom
+.Ve
+.Sp
+\&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign pharmacophore 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 "\fBSetAtomTypesWeight\fR" 4
+.IX Item "SetAtomTypesWeight"
+.Vb 2
+\&    $TopologicalPharmacophoreAtomPairsFP\->SetAtomTypesWeight(
+\&        %AtomTypesToWeight);
+.Ve
+.Sp
+Sets weights of specified pharmacophore atom types to use during calculation of their contribution
+to atom pair count and returns \fITopologicalPharmacophoreAtomPairsFP\fR.  Default values: \fI1 for
+each atom type\fR.
+.Sp
+The weight values allow to increase the importance of specific pharmacophore atom type
+in the generated fingerprints. A weight value of 0 for an atom type eliminates its contribution to
+atom pair count where as weight value of 2 doubles its contribution.
+.IP "\fBSetFuzzFactor\fR" 4
+.IX Item "SetFuzzFactor"
+.Vb 1
+\&    $TopologicalPharmacophoreAtomPairsFP\->SetFuzzFactor($Value);
+.Ve
+.Sp
+Sets fuzz factor value to use during fuzzification of atom pairs count and returns
+\&\fITopologicalPharmacophoreAtomPairsFP\fR. Default value: \fI0.15\fR.
+.Sp
+Valid values: For \fIFuzzyBinning\fR value of \fBFuzzificationMethodology\fR: \fIbetween 0 and 1.0\fR; For
+\&\fIFuzzyBinSmoothing\fR value of \fBFuzzificationMethodology\fR: \fIbetween 0 and 0.5\fR.
+.IP "\fBSetFuzzificationMethodology\fR" 4
+.IX Item "SetFuzzificationMethodology"
+.Vb 1
+\&    $TopologicalPharmacophoreAtomPairsFP\->SetFuzzificationMethodology($Value);
+.Ve
+.Sp
+Sets fuzzification methodology to use for fuzzification of atom pairs count and returns
+\&\fITopologicalPharmacophoreAtomPairsFP\fR. Default value: \fIFuzzyBinning\fR.  Possible values:
+\&\fIFuzzyBinning | FuzzyBinSmoothing\fR.
+.Sp
+In conjunction with values for options \fBFuzzifyAtomPairsCount\fR, \fBFuzzificationMode\fR and
+\&\fBFuzzFactor\fR, \fBFuzzificationMethodology\fR option is used to fuzzify pharmacophore atom
+pairs count.
+.Sp
+Let:
+.Sp
+.Vb 3
+\&    Px = Pharmacophore atom type x
+\&    Py = Pharmacophore atom type y
+\&    PPxy = Pharmacophore atom pair between atom type Px and Py
+\&
+\&    PPxyDn = Pharmacophore atom pairs count between atom type Px and Py
+\&             at distance Dn
+\&    PPxyDn\-1 = Pharmacophore atom pairs count between atom type Px and Py
+\&               at distance Dn \- 1
+\&    PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py
+\&               at distance Dn + 1
+\&
+\&    FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing
+.Ve
+.Sp
+Then:
+.Sp
+For \fIFuzzyBinning\fR:
+.Sp
+.Vb 1
+\&    PPxyDn = PPxyDn (Unchanged)
+\&
+\&    PPxyDn\-1 = PPxyDn\-1 + PPxyDn * FF
+\&    PPxyDn+1 = PPxyDn+1 + PPxyDn * FF
+.Ve
+.Sp
+For \fIFuzzyBinSmoothing\fR:
+.Sp
+.Vb 2
+\&    PPxyDn = PPxyDn \- PPxyDn * 2FF for Dmin < Dn < Dmax
+\&    PPxyDn = PPxyDn \- PPxyDn * FF for Dn = Dmin or Dmax
+\&
+\&    PPxyDn\-1 = PPxyDn\-1 + PPxyDn * FF
+\&    PPxyDn+1 = PPxyDn+1 + PPxyDn * FF
+.Ve
+.Sp
+In both fuzzification schemes, a value of 0 for \s-1FF\s0 implies no fuzzification of occurrence counts.
+A value of 1 during \fIFuzzyBinning\fR corresponds to maximum fuzzification of occurrence counts;
+however, a value of 1 during \fIFuzzyBinSmoothing\fR ends up completely distributing the value over
+the previous and next distance bins.
+.Sp
+So for default value of \fBFuzzFactor\fR (\s-1FF\s0) 0.15, the occurrence count of pharmacohore atom pairs
+at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn \-1 and Dn + 1
+are incremented by PPxyDn * 0.15.
+.Sp
+And during \fIFuzzyBinSmoothing\fR the occurrence counts at Distance Dn is scaled back using multiplicative
+factor of (1 \- 2*0.15) and the occurrence counts at distances Dn \-1 and Dn + 1 are incremented by
+PPxyDn * 0.15. In other words, occurrence bin count is smoothed out by distributing it over the
+previous and next distance value.
+.IP "\fBSetFuzzificationMode\fR" 4
+.IX Item "SetFuzzificationMode"
+.Vb 1
+\&    $TopologicalPharmacophoreAtomPairsFP\->SetFuzzificationMode($Value);
+.Ve
+.Sp
+Sets fuzzification mode to use for fuzzification of atom pairs count and returns
+\&\fITopologicalPharmacophoreAtomPairsFP\fR. Default value: \fIAfterNormalization\fR.  Possible values:
+\&\fIBeforeNormalization | AfterNormalization\fR.
+.IP "\fBSetMaxDistance\fR" 4
+.IX Item "SetMaxDistance"
+.Vb 1
+\&    $TopologicalPharmacophoreAtomPairsFP\->SetMaxDistance($Value);
+.Ve
+.Sp
+Sets maximum bond distance between atom pairs for generating topological pharmacophore atom
+pairs fingerprints and returns \fITopologicalPharmacophoreAtomPairsFP\fR.
+.IP "\fBSetMinDistance\fR" 4
+.IX Item "SetMinDistance"
+.Vb 1
+\&    $TopologicalPharmacophoreAtomPairsFP\->SetMinDistance($Value);
+.Ve
+.Sp
+Sets minimum bond distance between atom pairs for generating topological pharmacophore atom
+pairs fingerprints and returns \fITopologicalPharmacophoreAtomPairsFP\fR.
+.IP "\fBSetNormalizationMethodology\fR" 4
+.IX Item "SetNormalizationMethodology"
+.Vb 1
+\&    $TopologicalPharmacophoreAtomPairsFP\->SetNormalizationMethodology($Value);
+.Ve
+.Sp
+Sets normalization methodology to use for scaling the occurrence count of pharmacophore atom
+pairs within specified distance range and returns \fITopologicalPharmacophoreAtomPairsFP\fR.
+Default value: \fINone\fR. Possible values: \fINone, ByHeavyAtomsCount or ByAtomTypesCount\fR.
+.IP "\fBSetValuesPrecision\fR" 4
+.IX Item "SetValuesPrecision"
+.Vb 1
+\&    $TopologicalPharmacophoreAtomPairsFP\->SetValuesPrecision($Value);
+.Ve
+.Sp
+Sets precision of atom pairs count real values which might be generated after normalization
+or fuzzification  and returns \fITopologicalPharmacophoreAtomPairsFP\fR. Default: up to \fI2\fR decimal
+places.
+.IP "\fBStringifyTopologicalPharmacophoreAtomPairsFingerprints\fR" 4
+.IX Item "StringifyTopologicalPharmacophoreAtomPairsFingerprints"
+.Vb 2
+\&    $String = $TopologicalPharmacophoreAtomPairsFP\->
+\&                  StringifyTopologicalPharmacophoreAtomPairsFingerprints();
+.Ve
+.Sp
+Returns a string containing information about \fITopologicalPharmacophoreAtomPairsFingerprints\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,
+TopologicalAtomTripletsFingerprints.pm, TopologicalAtomTorsionsFingerprints.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.