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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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NAME PathLengthFingerprints SYNOPSIS use Fingerprints::PathLengthFingerprints; use Fingerprints::PathLengthFingerprints qw(:all); DESCRIPTION PathLengthFingerprints class provides the following methods: new, GenerateFingerprints, , GetDescription, SetAtomIdentifierType, SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetMaxLength, SetMinLength, SetNumOfBitsToSetPerPath, SetType, StringifyPathLengthFingerprints PathLengthFingerprints is derived from Fingerprints class which in turn is derived from ObjectProperty base class that provides methods not explicitly defined in PathLengthFingerprints, 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>(); The current release of MayaChemTools supports generation of AtomTypesFingerpritns corresponding to following AtomtomIdentifierTypes: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes Based on the values specified for Type, AtomtomIdentifierTypes, MinPathLength and MaxPathLength, all appropriate atom paths are generated for each atom in the molecule and collected in a list and the list is filtered to remove any structurally duplicate paths as indicated by the value of UseUniquePaths. For molecules containing rings, atom paths starting from each atom can be traversed in four different ways: o Atom paths without any rings and sharing of bonds in traversed paths. o Atom paths containing rings and without any sharing of bonds in traversed paths o All possible atom paths without any rings and sharing of bonds in traversed paths o All possible atom paths containing rings and with sharing of bonds in traversed paths. Atom path traversal is terminated at the last ring atom. For molecules containing no rings, first two and last two types described above are equivalent. AllowSharedBonds and AllowRings allow generation of different types of paths to be used for fingerprints generation. The combination of AllowSharedBonds, AllowRings, and UseBondSymbols allows generation of 8 different types of path length fingerprints: AllowSharedBonds AllowRings UseBondSymbols 0 0 1 - AtomPathsNoCyclesWithBondSymbols 0 1 1 - AtomPathsWithCyclesWithBondSymbols 1 0 1 - AllAtomPathsNoCyclesWithBondSymbols 1 1 1 - AllAtomPathsWithCyclesWithBondSymbols [ DEFAULT ] 0 0 0 - AtomPathsNoCyclesNoBondSymbols 0 1 0 - AtomPathsWithCyclesNoBondSymbols 1 0 0 - AllAtomPathsNoCyclesNoBondSymbols 1 1 0 - AllAtomPathsWithCyclesNoWithBondSymbols Additionally, possible values for option --AtomIdentifierType in conjunction with corresponding specified values for AtomicInvariantsToUse and FunctionalClassesToUse changes the nature of atom path length strings and the fingerprints. For each atom path in the filtered atom paths list, an atom path string is created using value of AtomIdentifierType and specified values to use for a particular atom identifier type. Value of UseBondSymbols controls whether bond order symbols are used during generation of atom path string. Atom symbol corresponds to element symbol and characters used to represent bond order are: *1 - None; 2 - '='; 3 - '#'; 1.5 or aromatic - ':'; others: bond order value*. By default, bond symbols are included in atom path strings. Exclusion of bond symbols in atom path strings results in fingerprints which correspond purely to atom paths without considering bonds. UseUniquePaths controls the removal of structurally duplicate atom path strings are removed from the list. For *PathLengthBits* value of Type, each atom path is hashed to a 32 bit unsigned integer key using TextUtil::HashCode function. Using the hash key as a seed for a random number generator, a random integer value between 0 and Size is used to set corresponding bits in the fingerprint bit-vector string. Value of NumOfBitsToSetPerPaths option controls the number of time a random number is generated to set corresponding bits. For * PathLengthCount* value of Typen, the number of times an atom path appears is tracked and a fingerprints count-string corresponding to count of atom paths is generated. The current release of MayaChemTools generates the following types of path length fingerprints bit-vector and vector strings: FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110 0100010101011000101001011100110001000010001001101000001001001001001000 0010110100000111001001000001001010100100100000000011000000101001011100 0010000001000101010100000100111100110111011011011000000010110111001101 0101100011000000010001000011000010100011101100001000001000100000000... FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d 6ea05280140069c780290c43 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2 C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C.... FingerprintsVector;PathLengthCount:DREIDINGAtomTypes:MinLength1:MaxLen gth8;410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ 1 N_3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 1 C_3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C _RF_ 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C _2O_3 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R ... FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH: aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1 sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a... FingerprintsVector;PathLengthCount:FunctionalClassAtomTypes:MinLength1 :MaxLength8;404;NumericalValues;IDsAndValuesPairsString;Ar 22 Ar.HBA 1 HBA 2 HBA.HBD 3 HBD 1 Hal 1 NI 1 None 10 Ar.HBA:Ar 2 Ar.HBANone 1 Ar: Ar 21 ArAr 2 ArHBD 1 ArHal 1 ArNone 2 HBA.HBDNI 1 HBA.HBDNone 2 HBA=NI 1 HBA=None 1 HBDNone 1 NINone 1 NoneNone 7 Ar.HBA:Ar:Ar 2 Ar.HBA:ArAr 1 Ar.HBA:ArNone 1 Ar.HBANoneNone 1 Ar:Ar.HBA:Ar 1 Ar:Ar.HBANone 2 ... FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1 CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ... FingerprintsVector;PathLengthCount:SLogPAtomTypes:MinLength1:MaxLength 8;518;NumericalValues;IDsAndValuesPairsString;C1 5 C10 1 C11 1 C14 1 C 18 14 C20 4 C21 2 C22 1 C5 2 CS 2 F 1 N11 1 N4 1 O10 1 O2 3 O9 1 C10C1 1 C10N11 1 C11C1 2 C11C21 1 C14:C18 2 C14F 1 C18:C18 10 C18:C20 4 C18 :C22 2 C1C5 1 C1CS 4 C20:C20 1 C20:C21 1 C20:N11 1 C20C20 2 C21:C21 1 C21:N11 1 C21C5 1 C22N4 1 C5=O10 1 C5=O9 1 C5N4 1 C5O2 1 CSO2 2 C10... FingerprintsVector;PathLengthCount:SYBYLAtomTypes:MinLength1:MaxLength 8;412;NumericalValues;IDsAndValuesPairsString;C.2 2 C.3 9 C.ar 22 F 1 N.am 1 N.ar 1 O.2 1 O.3 2 O.co2 2 C.2=O.2 1 C.2=O.co2 1 C.2C.3 1 C.2C. ar 1 C.2N.am 1 C.2O.co2 1 C.3C.3 7 C.3C.ar 1 C.3N.ar 1 C.3O.3 2 C.ar:C .ar 21 C.ar:N.ar 2 C.arC.ar 2 C.arF 1 C.arN.am 1 C.2C.3C.3 1 C.2C.ar:C .ar 2 C.2N.amC.ar 1 C.3C.2=O.co2 1 C.3C.2O.co2 1 C.3C.3C.3 5 C.3C.3... FingerprintsVector;PathLengthCount:TPSAAtomTypes:MinLength1:MaxLength8 ;331;NumericalValues;IDsAndValuesPairsString;N21 1 N7 1 None 34 O3 2 O 4 3 N21:None 2 N21None 1 N7None 2 None:None 21 None=O3 2 NoneNone 13 N oneO4 3 N21:None:None 2 N21:NoneNone 2 N21NoneNone 1 N7None:None 2 N7N one=O3 1 N7NoneNone 1 None:N21:None 1 None:N21None 2 None:None:None 20 None:NoneNone 12 NoneN7None 1 NoneNone=O3 2 NoneNoneNone 8 NoneNon... FingerprintsVector;PathLengthCount:UFFAtomTypes:MinLength1:MaxLength8; 410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ 1 N_ 3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 1 C_ 3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C_RF_ 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C_2O_3 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R 1 C_3... METHODS new $NewPathLengthFingerprints = new PathLengthFingerprints( %NamesAndValues); Using specified *PathLengthFingerprints* property names and values hash, new method creates a new object and returns a reference to newly created PathLengthFingerprints object. By default, the following properties are initialized: Molecule = ''; Type = '' Size = 1024 MinSize = 32 MaxSize = 2**32 NumOfBitsToSetPerPath = 1 MinLength = 1 MaxLength = 8 AllowSharedBonds = 1 AllowRings = 1 UseBondSymbols = 1 UseUniquePaths = '' AtomIdentifierType = '' SetAtomicInvariantsToUse = ['AS'] FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] Examples: $PathLengthFingerprints = new PathLengthFingerprints( 'Molecule' => $Molecule, 'Type' => 'PathLengthBits', 'AtomIdentifierType' = 'AtomicInvariantsAtomTypes'); $PathLengthFingerprints = new PathLengthFingerprints( 'Molecule' => $Molecule, 'Type' => 'PathLengthBits', 'Size' => 1024, 'MinLength' => 1, 'MaxLength' => 8, 'AllowRings' => 1, 'AllowSharedBonds' => 1, 'UseBondSymbols' => 1, 'UseUniquePaths' => 1, 'AtomIdentifierType' = 'AtomicInvariantsAtomTypes', 'AtomicInvariantsToUse' => ['AS']); $PathLengthFingerprints = new PathLengthFingerprints( 'Molecule' => $Molecule, 'Type' => 'PathLengthCount', 'MinLength' => 1, 'MaxLength' => 8, 'AllowRings' => 1, 'AllowSharedBonds' => 1, 'UseBondSymbols' => 1, 'UseUniquePaths' => 1, 'AtomIdentifierType' => 'AtomicInvariantsAtomTypes', 'AtomicInvariantsToUse' => ['AS']); $PathLengthFingerprints = new PathLengthFingerprints( 'Molecule' => $Molecule, 'Type' => 'PathLengthBits', 'AtomIdentifierType' = 'SLogPAtomTypes'); $PathLengthFingerprints = new PathLengthFingerprints( 'Molecule' => $Molecule, 'Type' => 'PathLengthCount', 'AtomIdentifierType' = 'SYBYLAtomTypes'); $PathLengthFingerprints = new PathLengthFingerprints( 'Molecule' => $Molecule, 'Type' => 'PathLengthBits', 'AtomIdentifierType' = 'FunctionalClassAtomTypes', 'FunctionalClassesToUse' => ['HBD', 'HBA', 'Ar']); $PathLengthFingerprints->GenerateFingerprints(); print "$PathLengthFingerprints\n"; GetDescription $Description = $PathLengthFingerprints->GetDescription(); Returns a string containing description of path length fingerprints. GenerateFingerprints $PathLengthFingerprints->GenerateFingerprints(); Generates path length fingerprints and returns *PathLengthFingerprints*. SetMaxLength $PathLengthFingerprints->SetMaxLength($Length); Sets maximum value of atom path length to be used during atom path length fingerprints generation and returns *PathLengthFingerprints* SetAtomIdentifierType $PathLengthFingerprints->SetAtomIdentifierType(); Sets atom *IdentifierType* to use during path length fingerprints generation and returns *PathLengthFingerprints*. Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. SetAtomicInvariantsToUse $PathLengthFingerprints->SetAtomicInvariantsToUse($ValuesRef); $PathLengthFingerprints->SetAtomicInvariantsToUse(@Values); Sets atomic invariants to use during *AtomicInvariantsAtomTypes* value of *AtomIdentifierType* for path length fingerprints generation and returns *PathLengthFingerprints*. Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB, TB, H, Ar, RA, FC, MN, SM*. Default value: *AS*. The atomic invariants abbreviations correspond to: 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) Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to: AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n> Except for AS 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. In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words are also allowed: 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 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign atomic invariant atom types. SetFunctionalClassesToUse $PathLengthFingerprints->SetFunctionalClassesToUse($ValuesRef); $PathLengthFingerprints->SetFunctionalClassesToUse(@Values); Sets functional classes invariants to use during *FunctionalClassAtomTypes* value of *AtomIdentifierType* for path length fingerprints generation and returns *PathLengthFingerprints*. Possible values for atom functional classes are: *Ar, CA, H, HBA, HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]: *HBD,HBA,PI,NI,Ar,Hal*. The functional class abbreviations correspond to: 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 *AtomTypes::FunctionalClassAtomTypes* module is used to assign functional class atom types. It uses following definitions [ Ref 60-61, Ref 65-66 ]: HydrogenBondDonor: NH, NH2, OH HydrogenBondAcceptor: N[!H], O PositivelyIonizable: +, NH2 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH SetMinLength $PathLengthFingerprints->SetMinLength($Length); Sets minimum value of atom path length to be used during atom path length fingerprints generation and returns *PathLengthFingerprints*. SetMaxLength $PathLengthFingerprints->SetMaxLength($Length); Sets maximum value of atom path length to be used during atom path length fingerprints generation and returns *PathLengthFingerprints*. SetNumOfBitsToSetPerPath $PathLengthFingerprints->SetNumOfBitsToSetPerPath($NumOfBits); Sets number of bits to set for each path during *PathLengthBits* Type during path length fingerprints generation and returns *PathLengthFingerprints*. SetType $PathLengthFingerprints->SetType($Type); Sets type of path length fingerprints and returns *PathLengthFingerprints*. Possible values: *PathLengthBits or PathLengthCount*. StringifyPathLengthFingerprints $String = $PathLengthFingerprints->StringifyPathLengthFingerprints(); Returns a string containing information about *PathLengthFingerprints* object. AUTHOR Manish Sud <msud@san.rr.com> SEE ALSO Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm, MACCSKeys.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.