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diff docs/modules/txt/TopologicalAtomTripletsFingerprints.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/TopologicalAtomTripletsFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,369 @@ +NAME + TopologicalAtomTripletsFingerprints + +SYNOPSIS + use Fingerprints::TopologicalAtomTripletsFingerprints; + + use Fingerprints::TopologicalAtomTripletsFingerprints qw(:all); + +DESCRIPTION + TopologicalAtomTripletsFingerprints [ Ref 57, Ref 59, Ref 72 ] class + provides the following methods: + + new, GenerateFingerprints, GetAtomTripletIDs, GetDescription, + SetAtomIdentifierType, SetAtomicInvariantsToUse, + SetFunctionalClassesToUse, SetMaxDistance, SetMinDistance, + StringifyTopologicalAtomTripletsFingerprints + + TopologicalAtomTripletsFingerprints is derived from Fingerprints class + which in turn is derived from ObjectProperty base class that provides + methods not explicitly defined in TopologicalAtomTripletsFingerprints, + 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 + TopologicalAtomTripletsFingerprints 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 triplets within MinDistance and MaxDistance are identified + and counted. An atom triplet identifier is generated for each unique + atom triplet; the format of atom triplet identifier is: + + <ATx>-Dyz-<ATy>-Dxz-<ATz>-Dxy + + ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z + Dxy: Distance between atom x and atom y + Dxz: Distance between atom x and atom z + Dyz: Distance between atom y and atom z + + where <AT1>-D23 <= <AT2>-D13 <= <AT3>-D12 + + The atom triplet identifiers for all unique atom triplets corresponding + to non-hydrogen atoms constitute topological atom triplets fingerprints + of the molecule. + + The current release of MayaChemTools generates the following types of + topological atom triplets fingerprints vector strings: + + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M + inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 + .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1 + 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1 + -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....; + 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 + 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8... + + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M + inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString + ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO + 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X + 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2 + -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2... + + FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan + ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D + 9-C_3-D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_ + 3-D9 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_ + 2-D1-C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D...; + 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2 + 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1... + + FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance + 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH-D + 1-aaCH-D2 aaCH-D1-aaCH-D1-aasC-D2 aaCH-D1-aaCH-D10-aaCH-D9 aaCH-D1-aaC + H-D10-aasC-D9 aaCH-D1-aaCH-D2-aaCH-D3 aaCH-D1-aaCH-D2-aasC-D1 aaCH-D1- + aaCH-D2-aasC-D3 aaCH-D1-aaCH-D3-aasC-D2 aaCH-D1-aaCH-D4-aasC-D5 aa...; + 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2 + 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1 + 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ... + + FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi + nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar-D1 + -Ar-D1-Ar-D2 Ar-D1-Ar-D1-Ar.HBA-D2 Ar-D1-Ar-D10-Ar-D9 Ar-D1-Ar-D10-Hal + -D9 Ar-D1-Ar-D2-Ar-D2 Ar-D1-Ar-D2-Ar-D3 Ar-D1-Ar-D2-Ar.HBA-D1 Ar-D1-Ar + -D2-Ar.HBA-D2 Ar-D1-Ar-D2-Ar.HBA-D3 Ar-D1-Ar-D2-HBD-D1 Ar-D1-Ar-D2...; + 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5 + 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3 + 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2... + + FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance + 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A-D1-C5A-D1- + N5-D2 C5A-D1-C5A-D2-C5B-D2 C5A-D1-C5A-D3-CB-D2 C5A-D1-C5A-D3-CR-D2 C5A + -D1-C5B-D1-C5B-D2 C5A-D1-C5B-D2-C=ON-D1 C5A-D1-C5B-D2-CB-D1 C5A-D1-C5B + -D3-C=ON-D2 C5A-D1-C5B-D3-CB-D2 C5A-D1-C=ON-D3-NC=O-D2 C5A-D1-C=ON-D3- + O=CN-D2 C5A-D1-C=ON-D4-NC=O-D3 C5A-D1-C=ON-D4-O=CN-D3 C5A-D1-CB-D1-... + + FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1 + :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1-D1-C1-D1-C11 + -D2 C1-D1-C1-D1-CS-D2 C1-D1-C1-D10-C5-D9 C1-D1-C1-D3-C10-D2 C1-D1-C1-D + 3-C5-D2 C1-D1-C1-D3-CS-D2 C1-D1-C1-D3-CS-D4 C1-D1-C1-D4-C10-D5 C1-D1-C + 1-D4-C11-D5 C1-D1-C1-D5-C10-D4 C1-D1-C1-D5-C5-D4 C1-D1-C1-D6-C11-D7 C1 + -D1-C1-D6-CS-D5 C1-D1-C1-D6-CS-D7 C1-D1-C1-D8-C11-D9 C1-D1-C1-D8-CS... + + FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1 + :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C + .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3- + D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2 + -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C. + 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7... + + FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1: + MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21-D1-N7-D3-Non + e-D4 N21-D1-N7-D5-None-D4 N21-D1-None-D1-None-D2 N21-D1-None-D2-None-D + 2 N21-D1-None-D2-None-D3 N21-D1-None-D3-None-D4 N21-D1-None-D4-None-D5 + N21-D1-None-D4-O3-D3 N21-D1-None-D4-O4-D3 N21-D1-None-D5-None-D6 N21- + D1-None-D6-None-D7 N21-D1-None-D6-O4-D5 N21-D1-None-D7-None-D8 N21-... + + FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M + axDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D9-C_3 + -D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_3-D9 + C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_2-D1- + C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D1-C_3-D5- + C_3-D6 C_2-D1-C_3-D5-O_3-D4 C_2-D1-C_3-D6-C_3-D7 C_2-D1-C_3-D7-C_3-... + + METHODS + new + $NewTopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + %NamesAndValues); + + Using specified *TopologicalAtomTripletsFingerprints* property names + and values hash, new method creates a new object and returns a + reference to newly created TopologicalAtomTripletsFingerprints + object. By default, the following properties are initialized: + + Molecule = '' + Type = 'TopologicalAtomTriplets' + MinDistance = 1 + MaxDistance = 10 + UseTriangleInequality = 1 + AtomIdentifierType = '' + AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC'] + FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] + + Examples: + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes'); + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes', + 'AtomicInvariantsToUse' => + ['AS', 'X', 'BO', 'H', 'FC'] ); + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'DREIDINGAtomTypes'); + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'MMFF94AtomTypes'); + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'TPSAAtomTypes'); + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'AtomIdentifierType' => + 'FunctionalClassAtomTypes', + 'FunctionalClassesToUse' => + ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']); + + $TopologicalAtomTripletsFingerprints->GenerateFingerprints(); + print "$TopologicalAtomTripletsFingerprints\n"; + + GetDescription + $Return = $TopologicalAtomTripletsFingerprints->GetDescription(); + + Returns a string containing description of topological atom triplets + fingerprints. + + GenerateFingerprints + $TopologicalAtomTripletsFingerprints->GenerateFingerprints(); + + Generates topological atom triplets fingerprints and returns + *TopologicalAtomTripletsFingerprints*. + + GetAtomTripletIDs + $AtomTripletIDsRef = $TopologicalAtomTripletsFingerprints->GetAtomTripletIDs(); + @AtomTripletIDs = $TopologicalAtomTripletsFingerprints->GetAtomTripletIDs(); + + Returns atom triplet IDs corresponding to atom triplets count values + in topological atom triplets fingerprints vector as an array or + reference to an array. + + SetAtomIdentifierType + $TopologicalAtomTripletsFingerprints->SetAtomIdentifierType($IdentifierType); + + Sets atom *IdentifierType* to use during atom triplets fingerprints + generation and returns *TopologicalAtomTripletsFingerprints*. + + Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, + EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, + SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. + + SetAtomicInvariantsToUse + $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse($ValuesRef); + $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse(@Values); + + Sets atomic invariants to use during *AtomicInvariantsAtomTypes* + value of *AtomIdentifierType* for topological atom triplets + fingerprints generation and returns + *TopologicalAtomTripletsFingerprints*. + + 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 + $TopologicalTripletsFingerprints->SetFunctionalClassesToUse($ValuesRef); + $TopologicalTripletsFingerprints->SetFunctionalClassesToUse(@Values); + + Sets functional classes invariants to use during + *FunctionalClassAtomTypes* value of *AtomIdentifierType* for + topological atom triplets fingerprints generation and returns + *TopologicalAtomTripletsFingerprints*. + + 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 + $TopologicalAtomTripletsFingerprints->SetMaxDistance($Distance); + + Sets maximum distance to use during topological atom triplets + fingerprints generation and returns + *TopologicalAtomTripletsFingerprints*. + + SetMinDistance + $TopologicalAtomTripletsFingerprints->SetMinDistance($Distance); + + Sets minimum distance to use during topological atom triplets + fingerprints generation and returns + *TopologicalAtomTripletsFingerprints*. + + StringifyTopologicalAtomTripletsFingerprints + $String = $TopologicalAtomTripletsFingerprints-> + StringifyTopologicalAtomTripletsFingerprints(); + + Returns a string containing information about + *TopologicalAtomTripletsFingerprints* 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, + TopologicalAtomPairsFingerprints.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. +