diff docs/modules/txt/Fingerprints.txt @ 0:4816e4a8ae95 draft default tip

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+NAME
+    Fingerprints - Fingerprints class
+
+SYNOPSIS
+    use Fingerprints::Fingerprints;
+
+    use Fingerprints::Fingerprints qw(:all);
+
+DESCRIPTION
+    Fingerprints class provides the following methods:
+
+    new, FoldFingerprintsByBitDensity, FoldFingerprintsBySize,
+    GetFingerprintBitsAsBinaryString, GetFingerprintBitsAsHexadecimalString,
+    GetFingerprintBitsAsRawBinaryString, GetFingerprintsVectorValueIDs,
+    GetFingerprintsVectorValues, IsFingerprintsGenerationSuccessful,
+    SetFingerprintsBitVector, SetFingerprintsVector,
+    SetFingerprintsVectorType, SetMolecule, SetSize, SetType, SetVectorType
+
+    Fingerprints class is used as a base class for various specific
+    fingerprint classes such as AtomNeighborhoodsFingerprints,
+    AtomTypesFingerprints, EStateIndiciesFingerprints,
+    PathLengthFingerprints, ExtendedConnectivityFingerprints, MACCSKeys and
+    so on. It implements functionality common to fingerprint classes.
+
+    Fingerprints class is derived from ObjectProperty base class which
+    provides methods not explicitly defined in Fingerprints or
+    ObjectProperty classes using Perl's AUTOLOAD functionality. These
+    methods are generated on-the-fly for a specified object property:
+
+        Set<PropertyName>(<PropertyValue>);
+        $PropertyValue = Get<PropertyName>();
+        Delete<PropertyName>();
+
+    Fingerprints class uses FingerprintsBitVector class to provide bits
+    manipulation functionality.
+
+  METHODS
+    new
+            $NewFingerprints = new Fingerprints(%NamesAndValues);
+
+        Using specified *Fingerprints* property names and values hash, new
+        method creates a new object and returns a reference to newly created
+        Fingerprints object. By default, following properties are
+        initialized:
+
+            Molecule = '';
+            Type = '';
+            VectorType = '';
+            Size = '';
+            MinSize = '';
+            MaxSize = '';
+            FingerprintsBitVector = '';
+            FingerprintsVectorType = '';
+            FingerprintsVector = '';
+
+    FoldFingerprintsByBitDensity
+            $Fingerprints->FoldFingerprintsByBitDensity($BitDensity);
+
+        Folds fingerprints by recursively reducing its size by half until
+        bit density is greater than or equal to specified *BitDensity* and
+        returns *Fingerprints*.
+
+    FoldFingerprintsBySize
+            $Fingerprints->FoldFingerprintsBySize($Size, [$CheckSizeValue]);
+
+        Fold fingerprints by recursively reducing its size by half until
+        size is less than or equal to specified *Size* and returns
+        *Fingerprints*. By default, value *Size* is checked to make sure
+        it's:
+
+            >= MinSize and < Size and IsPowerOfTwo
+
+    GetFingerprintBitsAsBinaryString
+            $BinaryASCIIString =
+               $Fingerprints->GetFingerprintBitsAsBinaryString();
+
+        Returns fingerprints as a binary ASCII string containing 0s and 1s.
+
+    GetFingerprintBitsAsHexadecimalString
+            $HexadecimalString =
+               $Fingerprints->GetFingerprintBitsAsHexadecimalString();
+
+        Returns fingerprints as a hexadecimal string
+
+    GetFingerprintBitsAsRawBinaryString
+            $RawBinaryString =
+               $Fingerprints->GetFingerprintBitsAsRawBinaryString();
+
+        Returns fingerprints as a raw binary string containing packed bit
+        values for each byte.
+
+    GetFingerprintsVectorValueIDs
+            $ValueIDsRef = $Fingerprints->GetFingerprintsVectorValueIDs();
+            @ValueIDs = $Fingerprints->GetFingerprintsVectorValueIDs();
+
+        Returns fingerprints vector value IDs as an array or reference to an
+        array.
+
+    GetFingerprintsVectorValues
+            $ValuesRef = $Fingerprints->GetFingerprintsVectorValues();
+            @Values = $Fingerprints->GetFingerprintsVectorValues();
+
+        Returns fingerprints vector values as an array or reference to an
+        array.
+
+    IsFingerprintsGenerationSuccessful
+            $Return = $Fingerprints->IsFingerprintsGenerationSuccessful();
+
+        Returns 1 or 0 based on whether fingerprints were successfully
+        generated.
+
+    SetFingerprintsBitVector
+            $Fingerprints->SetFingerprintsBitVector($FingerprintsBitVector);
+
+        Sets *FingerprintsBitVector* object for *Fingerprints* and returns
+        *Fingerprints*.
+
+    SetFingerprintsVector
+            $Fingerprints->SetFingerprintsVector();
+
+        Sets *FingerprintsVector* object for *Fingerprints* and returns
+        *Fingerprints*.
+
+    SetFingerprintsVectorType
+            $Fingerprints->SetFingerprintsVectorType($VectorType);
+
+        Sets *FingerprintsVector* type for *Fingerprints* and returns
+        *Fingerprints*. Possible *VectorType* values:
+        *OrderedNumericalValues, NumericalValues or AlphaNumericalValues*.
+
+    SetMolecule
+            $Fingerprints->SetMolecule($Molecule);
+
+        Sets *Molecule* object for *Fingerprints* and returns
+        *Fingerprints*.
+
+    SetSize
+            $Fingerprints->SetSize($Size);
+
+        Sets *Size* of fingerprints and returns *Fingerprints*.
+
+    SetType
+            $Fingerprints->SetType($Type);
+
+        Sets *Type* of fingerprints and returns *Fingerprints*.
+
+    SetVectorType
+            $Fingerprints->SetVectorType($Type);
+
+        Sets *Type* of fingerprints vector and returns *Fingerprints*.
+        Possible *Type* values: *FingerprintsBitVector or
+        FingerprintsVector*.
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
+    AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm,
+    ExtendedConnectivityFingerprints.pm, MACCSKeys.pm,
+    PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
+    TopologicalAtomTripletsFingerprints.pm,
+    TopologicalAtomTorsionsFingerprints.pm,
+    TopologicalPharmacophoreAtomPairsFingerprints.pm,
+    TopologicalPharmacophoreAtomTripletsFingerprints.pm
+
+COPYRIGHT
+    Copyright (C) 2015 Manish Sud. All rights reserved.
+
+    This file is part of MayaChemTools.
+
+    MayaChemTools is free software; you can redistribute it and/or modify it
+    under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or (at
+    your option) any later version.
+