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diff docs/modules/txt/PathLengthFingerprints.txt @ 0:4816e4a8ae95 draft default tip
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/modules/txt/PathLengthFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,444 @@ +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. +