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diff docs/modules/txt/TopologicalAtomPairsFingerprints.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/TopologicalAtomPairsFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,355 @@ +NAME + TopologicalAtomPairsFingerprints + +SYNOPSIS + use Fingerprints::TopologicalAtomPairsFingerprints; + + use Fingerprints::TopologicalAtomPairsFingerprints qw(:all); + +DESCRIPTION + TopologicalAtomPairsFingerprints [ Ref 57, Ref 59, Ref 72 ] class + provides the following methods: + + new, GenerateFingerprints, GetAtomPairIDs, GetDescription, + SetAtomIdentifierType, SetAtomicInvariantsToUse, + SetFunctionalClassesToUse, SetMaxDistance, SetMinDistance, + StringifyTopologicalAtomPairsFingerprints + + TopologicalAtomPairsFingerprints is derived from Fingerprints class + which in turn is derived from ObjectProperty base class that provides + methods not explicitly defined in TopologicalAtomPairsFingerprints, + 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 AtomIdentifierType along with other + specified parameters such as AtomicInvariantsToUse and + FunctionalClassesToUse, 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 pairs within MinDistance and MaxDistance are identified and + counted. An atom pair identifier is generated for each unique atom pair; + the format of atom pair identifier is: + + <AtomType1>-D<n>-<AtomType2> + + AtomType1, AtomType2: Atom types assigned to atom1 and atom2 + D: Distance between atom1 and atom2 + + where AtomType1 <= AtomType2 + + The atom pair identifiers for all unique atom pairs corresponding to + non-hydrogen atoms constitute topological atom pairs fingerprints of the + molecule. + + The current release of MayaChemTools generates the following types of + topological atom pairs fingerprints vector strings: + + FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD + istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1 + .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3. + H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...; + 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1 + 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1... + + FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD + istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X + 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1- + C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2 + .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X + 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO... + + FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1 + :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2-D1-C_3 C_2-D + 1-C_R C_2-D1-N_3 C_2-D1-O_2 C_2-D1-O_3 C_3-D1-C_3 C_3-D1-C_R C_3-D1-N_ + R C_3-D1-O_3 C_R-D1-C_R C_R-D1-F_ C_R-D1-N_3 C_R-D1-N_R C_2-D2-C_3 C_2 + 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3 + 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1... + + FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M + axDistance10;251;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH aaCH- + D1-aasC aasC-D1-aasC aasC-D1-aasN aasC-D1-dssC aasC-D1-sF aasC-D1-ssNH + aasC-D1-sssCH aasN-D1-ssCH2 dO-D1-dssC dssC-D1-sOH dssC-D1-ssCH2 d...; + 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1 + 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2... + + FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi + stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar + Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H + BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...; + 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4 + 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ... + + FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M + axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A-D1-C5B 2 + C5A-D1-CB 1 C5A-D1-CR 1 C5A-D1-N5 2 C5B-D1-C5B 1 C5B-D1-C=ON 1 C5B-D1- + CB 1 C=ON-D1-NC=O 1 C=ON-D1-O=CN 1 CB-D1-CB 18 CB-D1-F 1 CB-D1-NC=O 1 + COO-D1-CR 1 COO-D1-O=CO 1 COO-D1-OC=O 1 CR-D1-CR 7 CR-D1-N5 1 CR-D1-OR + 2 C5A-D2-C5A 1 C5A-D2-C5B 2 C5A-D2-C=ON 1 C5A-D2-CB 3 C5A-D2-CR 4 ... + + FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma + xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1-D1-C10 1 C1 + -D1-C11 2 C1-D1-C5 1 C1-D1-CS 4 C10-D1-N11 1 C11-D1-C21 1 C14-D1-C18 2 + C14-D1-F 1 C18-D1-C18 10 C18-D1-C20 4 C18-D1-C22 2 C20-D1-C20 3 C20-D + 1-C21 1 C20-D1-N11 1 C21-D1-C21 1 C21-D1-C5 1 C21-D1-N11 1 C22-D1-N4 1 + C5-D1-N4 1 C5-D1-O10 1 C5-D1-O2 1 C5-D1-O9 1 CS-D1-O2 2 C1-D2-C1 3... + + FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma + xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2-D1-C.3 1 C + .2-D1-C.ar 1 C.2-D1-N.am 1 C.2-D1-O.2 1 C.2-D1-O.co2 2 C.3-D1-C.3 7 C. + 3-D1-C.ar 1 C.3-D1-N.ar 1 C.3-D1-O.3 2 C.ar-D1-C.ar 23 C.ar-D1-F 1 C.a + r-D1-N.am 1 C.ar-D1-N.ar 2 C.2-D2-C.3 1 C.2-D2-C.ar 3 C.3-D2-C.3 5 C.3 + -D2-C.ar 5 C.3-D2-N.ar 2 C.3-D2-O.3 4 C.3-D2-O.co2 2 C.ar-D2-C.ar 2... + + FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max + Distance10;64;NumericalValues;IDsAndValuesPairsString;N21-D1-None 3 N7 + -D1-None 2 None-D1-None 34 None-D1-O3 2 None-D1-O4 3 N21-D2-None 5 N7- + D2-None 3 N7-D2-O3 1 None-D2-None 44 None-D2-O3 2 None-D2-O4 5 O3-D2-O + 4 1 N21-D3-None 7 N7-D3-None 4 None-D3-None 45 None-D3-O3 4 None-D3-O4 + 5 N21-D4-N7 1 N21-D4-None 5 N21-D4-O3 1 N21-D4-O4 1 N7-D4-None 4 N... + + FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD + istance10;157;NumericalValues;IDsAndValuesPairsString;C_2-D1-C_3 1 C_2 + -D1-C_R 1 C_2-D1-N_3 1 C_2-D1-O_2 2 C_2-D1-O_3 1 C_3-D1-C_3 7 C_3-D1-C + _R 1 C_3-D1-N_R 1 C_3-D1-O_3 2 C_R-D1-C_R 23 C_R-D1-F_ 1 C_R-D1-N_3 1 + C_R-D1-N_R 2 C_2-D2-C_3 1 C_2-D2-C_R 3 C_3-D2-C_3 5 C_3-D2-C_R 5 C_3-D + 2-N_R 2 C_3-D2-O_2 1 C_3-D2-O_3 5 C_R-D2-C_R 28 C_R-D2-F_ 2 C_R-D2-... + + METHODS + new + $NewTopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( + %NamesAndValues); + + Using specified *TopologicalAtomPairsFingerprints* property names + and values hash, new method creates a new object and returns a + reference to newly created TopologicalAtomPairsFingerprints object. + By default, the following properties are initialized: + + Molecule = '' + Type = 'TopologicalAtomPairs' + MinDistance = 1 + MaxDistance = 10 + AtomIdentifierType = '' + AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC'] + FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] + + Examples: + + $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes'); + + $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( + 'Molecule' => $Molecule, + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes', + 'AtomicInvariantsToUse' => + ['AS', 'X', 'BO', 'H', 'FC'] ); + + $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'EStateAtomTypes'); + + $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'SLogPAtomTypes'); + + $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( + 'Molecule' => $Molecule, + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'AtomIdentifierType' => + 'FunctionalClassAtomTypes', + 'FunctionalClassesToUse' => + ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']); + + + $TopologicalAtomPairsFingerprints->GenerateFingerprints(); + print "$TopologicalAtomPairsFingerprints\n"; + + GetDescription + $Description = $TopologicalAtomPairsFingerprints->GetDescription(); + + Returns a string containing description of topological atom pairs + fingerprints fingerprints. + + GenerateFingerprints + $TopologicalAtomPairsFingerprints->GenerateFingerprints(); + + Generates topological atom pairs fingerprints and returns + *TopologicalAtomPairsFingerprints*. + + GetAtomPairIDs + $AtomPairIDsRef = $TopologicalAtomPairsFingerprints->GetAtomPairIDs(); + @AtomPairIDs = $TopologicalAtomPairsFingerprints->GetAtomPairIDs(); + + Returns atom pair IDs corresponding to atom pairs count values in + topological atom pairs fingerprints vector as an array or reference + to an array. + + SetAtomIdentifierType + $TopologicalAtomPairsFingerprints->SetAtomIdentifierType($IdentifierType); + + Sets atom *IdentifierType* to use during atom pairs fingerprints + generation and returns *TopologicalAtomPairsFingerprints*. + + Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, + EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, + SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. + + SetAtomicInvariantsToUse + $TopologicalAtomPairsFingerprints->SetAtomicInvariantsToUse($ValuesRef); + $TopologicalAtomPairsFingerprints->SetAtomicInvariantsToUse(@Values); + + Sets atomic invariants to use during *AtomicInvariantsAtomTypes* + value of *AtomIdentifierType* for topological atom pairs + fingerprints generation and returns + *TopologicalAtomPairsFingerprints*. + + Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB, + TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*. + + 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 + $TopologicalAtomPairsFingerprints->SetFunctionalClassesToUse($ValuesRef); + $TopologicalAtomPairsFingerprints->SetFunctionalClassesToUse(@Values); + + Sets functional classes invariants to use during + *FunctionalClassAtomTypes* value of *AtomIdentifierType* for + topological atom pairs fingerprints generation and returns + *TopologicalAtomPairsFingerprints*. + + 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 + + SetMaxDistance + $TopologicalAtomPairsFingerprints->SetMaxDistance($Distance); + + Sets maximum distance to use during topological atom pairs + fingerprints generation and returns + *TopologicalAtomPairsFingerprints*. + + SetMinDistance + $TopologicalAtomPairsFingerprints->SetMinDistance($Distance); + + Sets minimum distance to use during topological atom pairs + fingerprints generation and returns + *TopologicalAtomPairsFingerprints*. + + StringifyTopologicalAtomPairsFingerprints + $String = $TopologicalAtomPairsFingerprints-> + StringifyTopologicalAtomPairsFingerprints(); + + Returns a string containing information about + *TopologicalAtomPairsFingerprints* object. + +AUTHOR + Manish Sud <msud@san.rr.com> + +SEE ALSO + Fingerprints.pm, FingerprintsStringUtil.pm, + AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm, + EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm, + MACCSKeys.pm, PathLengthFingerprints.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. +