Mercurial > repos > deepakjadmin > mayatool3_test2
diff docs/modules/txt/TopologicalAtomTorsionsFingerprints.txt @ 0:4816e4a8ae95 draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/modules/txt/TopologicalAtomTorsionsFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,331 @@ +NAME + TopologicalAtomTorsionsFingerprints + +SYNOPSIS + use Fingerprints::TopologicalAtomTorsionsFingerprints; + + use Fingerprints::TopologicalAtomTorsionsFingerprints qw(:all); + +DESCRIPTION + TopologicalAtomTorsionsFingerprints class provides the following + methods: + + new, GenerateFingerprints, GetAtomTorsionsIDs, GetDescription, + SetAtomIdentifierType, SetAtomicInvariantsToUse, + SetFunctionalClassesToUse, StringifyTopologicalAtomTorsionsFingerprints + + TopologicalAtomTorsionsFingerprints is derived from Fingerprints class + which in turn is derived from ObjectProperty base class that provides + methods not explicitly defined in TopologicalAtomTorsionsFingerprints, + 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 + TopologicalAtomTorsionsFingerprints 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 in a molecule. All unique atom torsions are identified and + an atom torsion identifier is generated; the format of atom torsion + identifier is: + + <AtomType1>-<AtomType2>-<AtomType3>-<AtomType4> + + AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types + + where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4 + + The atom torsion identifiers for all unique atom torsions corresponding + to non-hydrogen atoms constitute topological atom torsions fingerprints + of the molecule. + + The current release of MayaChemTools generates the following types of + topological atom torsions fingerprints vector strings: + + FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 + 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4- + C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO + 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...; + 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1 + + FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 + 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3 + .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H + 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B + O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B + O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1... + + FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri + calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C + _R-C_3 C_2-C_R-C_R-C_R C_2-C_R-C_R-N_R C_2-N_3-C_R-C_R C_3-C_3-C_2-O_2 + C_3-C_3-C_2-O_3 C_3-C_3-C_3-C_3 C_3-C_3-C_3-N_R C_3-C_3-C_3-O_3 C_...; + 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1 + + FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica + lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC + H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC- + ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...; + 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2 + + FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26 + ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar- + Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar + -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...; + 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3 + + FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica + lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5 + B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5 + A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...; + 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1 + 1 1 2 1 1 3 1 3 + + FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical + Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1 + 1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS + 2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1 + C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20 + 2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C... + + FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical + Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2 + -C.ar-C.ar-C.3 1 C.2-C.ar-C.ar-C.ar 2 C.2-C.ar-C.ar-N.ar 1 C.2-N.am-C. + ar-C.ar 2 C.3-C.3-C.2-O.co2 2 C.3-C.3-C.3-C.3 3 C.3-C.3-C.3-N.ar 1 C.3 + -C.3-C.3-O.3 3 C.3-C.3-C.ar-C.ar 2 C.3-C.3-C.ar-N.ar 2 C.3-C.3-N.ar-C. + ar 2 C.3-C.ar-C.ar-C.ar 1 C.3-C.ar-N.ar-C.3 1 C.3-C.ar-N.ar-C.ar 1 ... + + FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa + lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4 + None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None- + None-None 44 None-None-None-O3 3 None-None-None-O4 5 + + FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa + lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C + _R-C_R-C_3 1 C_2-C_R-C_R-C_R 2 C_2-C_R-C_R-N_R 1 C_2-N_3-C_R-C_R 2 C_3 + -C_3-C_2-O_2 1 C_3-C_3-C_2-O_3 1 C_3-C_3-C_3-C_3 3 C_3-C_3-C_3-N_R 1 C + _3-C_3-C_3-O_3 3 C_3-C_3-C_R-C_R 2 C_3-C_3-C_R-N_R 2 C_3-C_3-N_R-C_R 2 + C_3-C_R-C_R-C_R 1 C_3-C_R-N_R-C_3 1 C_3-C_R-N_R-C_R 1 C_3-N_R-C_R-... + + METHODS + new + $NewTopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + %NamesAndValues); + + Using specified *TopologicalAtomTorsionsFingerprints* property names + and values hash, new method creates a new object and returns a + reference to newly created TopologicalAtomTorsionsFingerprints + object. By default, the following properties are initialized: + + Molecule = '' + Type = 'TopologicalAtomTorsions' + AtomIdentifierType = '' + AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC'] + FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] + + Examples: + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes'); + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes', + 'AtomicInvariantsToUse' => + ['AS', 'X', 'BO', 'H', 'FC'] ); + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'DREIDINGAtomTypes'); + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'SYBYLAtomTypes'); + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'SLogPAtomTypes'); + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'FunctionalClassAtomTypes', + 'FunctionalClassesToUse' => + ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] ); + + + $TopologicalAtomTorsionsFingerprints->GenerateFingerprints(); + print "$TopologicalAtomTorsionsFingerprints\n"; + + GetDescription + $Description = $TopologicalAtomTorsionsFingerprints->GetDescription(); + + Returns a string containing description of topological atom torsions + fingerprints. + + GenerateFingerprints + $TopologicalAtomTorsionsFingerprints->GenerateFingerprints(); + + Generates topological atom torsions fingerprints and returns + *TopologicalAtomTorsionsFingerprints*. + + GetAtomTorsionsIDs + $AtomPairIDsRef = $TopologicalAtomTorsionsFingerprints->GetAtomTorsionsIDs(); + @AtomPairIDs = $TopologicalAtomTorsionsFingerprints->GetAtomTorsionsIDs(); + + Returns atom torsion IDs corresponding to atom torsion count values + in topological atom torsions fingerprints vector as an array or + reference to an array. + + SetAtomIdentifierType + $TopologicalAtomTorsionsFingerprints->SetAtomIdentifierType($IdentifierType); + + Sets atom *IdentifierType* to use during atom torsions fingerprints + generation and returns *TopologicalAtomTorsionsFingerprints*. + + Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, + EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, + SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. + + SetAtomicInvariantsToUse + $TopologicalAtomTorsionsFingerprints->SetAtomicInvariantsToUse($ValuesRef); + $TopologicalAtomTorsionsFingerprints->SetAtomicInvariantsToUse(@Values); + + Sets atomic invariants to use during *AtomicInvariantsAtomTypes* + value of *AtomIdentifierType* for topological atom torsions + fingerprints generation and returns + *TopologicalAtomTorsionsFingerprints*. + + 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 + $TopologicalTorsionsFingerprints->SetFunctionalClassesToUse($ValuesRef); + $TopologicalTorsionsFingerprints->SetFunctionalClassesToUse(@Values); + + Sets functional classes invariants to use during + *FunctionalClassAtomTypes* value of *AtomIdentifierType* for + topological atom torsions fingerprints generation and returns + *TopologicalAtomTorsionsFingerprints*. + + 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 + + StringifyTopologicalAtomTorsionsFingerprints + $String = $TopologicalAtomTorsionsFingerprints-> + StringifyTopologicalAtomTorsionsFingerprints(); + + Returns a string containing information about + *TopologicalAtomTorsionsFingerprints* 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, + TopologicalAtomTripletsFingerprints.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. +