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diff docs/modules/txt/ExtendedConnectivityFingerprints.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/ExtendedConnectivityFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,419 @@ +NAME + ExtendedConnectivityFingerprints + +SYNOPSIS + use Fingerprints::ExtendedConnectivityFingerprints; + + use Fingerprints::ExtendedConnectivityFingerprints qw(:all); + +DESCRIPTION + ExtendedConnectivityFingerprints [ Ref 48, Ref 52 ] class provides the + following methods: + + new, GenerateFingerprints, GetDescription, SetAtomIdentifierType, + SetAtomicInvariantsToUse, SetFunctionalClassesToUse, + SetNeighborhoodRadius, StringifyExtendedConnectivityFingerprints + + ExtendedConnectivityFingerprints is derived from Fingerprints class + which in turn is derived from ObjectProperty base class that provides + methods not explicitly defined in ExtendedConnectivityFingerprints, + 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 + ExtendedConnectivityFingerprints corresponding to following + AtomtomIdentifierTypes: + + AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes + + Based on the values specified for AtomIdentifierType, + AtomicInvariantsToUse and FunctionalClassesToUse, initial atom types are + assigned to all non-hydrogen atoms in a molecule and these atom types + strings are converted into initial atom identifier integers using + TextUtil::HashCode function. The duplicate atom identifiers are removed. + + For NeighborhoodRadius value of *0*, the initial set of unique atom + identifiers comprises the molecule fingerprints. Otherwise, atom + neighborhoods are generated for each non-hydrogen atom up-to specified + NeighborhoodRadius value. For each non-hydrogen central atom at a + specific radius, its neighbors at next radius level along with their + bond orders and previously calculated atom identifiers are collected + which in turn are used to generate a new integer atom identifier; the + bond orders and atom identifier pairs list is first sorted by bond order + followed by atom identifiers to make these values graph invariant. + + After integer atom identifiers have been generated for all non-hydrogen + atoms at all specified neighborhood radii, the duplicate integer atom + identifiers corresponding to same hash code value generated using + TextUtil::HashCode are tracked by keeping the atom identifiers at lower + radius. Additionally, all structurally duplicate integer atom + identifiers at each specified radius are also tracked by identifying + equivalent atom and bonds corresponding to substructures used for + generating atom identifier and keeping integer atom identifier with + lowest value. + + For *ExtendedConnnectivity* value of fingerprints Type, the duplicate + identifiers are removed from the list and the unique atom identifiers + constitute the extended connectivity fingerprints of a molecule. + + For *ExtendedConnnectivityCount* value of fingerprints Type, the + occurrence of each unique atom identifiers appears is counted and the + unique atom identifiers along with their count constitute the extended + connectivity fingerprints of a molecule. + + For *ExtendedConnectivityBits* value of fingerprints -m, --mode, the + unique atom identifiers are used as a random number seed to generate a + random integer value between 0 and --Size which in turn is used to set + corresponding bits in the fingerprint bit-vector string. + + The current release of MayaChemTools generates the following types of + extended connectivity fingerprints vector strings: + + FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi + us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 + 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414 + 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103 + 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338 + 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303... + + FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes + :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524 + 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 + 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...; + 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2 + 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1 + + FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp + es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100 + 0000000001010000000110000011000000000000100000000000000000000000100001 + 1000000110000000000000000000000000010011000000000000000000000000010000 + 0000000000000000000000000010000000000000000001000000000000000000000000 + 0000000000010000100001000000000000101000000000000000100000000000000... + + FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp + es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803 + 0300000091000004000000020000100000000124008200020000000040020000000000 + 2080000000820040010020000000008040000000000080001000000000400000000000 + 4040000090000061010000000800200000000000001400000000020080000000000020 + 00008020200000408000 + + FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu + s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8 + 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567 + 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012 + 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455 + 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404... + + FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes: + Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039 + 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32 + 9205671 571109041 639579325 683993318 723853089 810600886 885767127...; + 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2 + 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1 + + FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType + s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000 + 0000000001000100000000001000000000000000000000000000000000101000000010 + 0000001000000000010000000000000000000000000000000000000000000000000100 + 0000000000001000000000000001000000000001001000000000000000000000000000 + 0000000000000000100000000000001000000000000000000000000000000000000... + + FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A + lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822 + 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094 + 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076 + 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070 + 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ... + + FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp + haNumericalValues;ValuesString;25189973 528584866 662581668 671034184 + 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450 + 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430 + 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134 + 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566... + + FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp + haNumericalValues;ValuesString;224051550 746527773 998750766 103704190 + 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20 + 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344 + 041929 581773587 638555787 692022098 811840536 929651561 936421792 988 + 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271... + + FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph + aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1 + 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654 + 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981 + 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6 + 41915747 679881756 721736571 794256218 908276640 992898760 10987549... + + FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph + aNumericalValues;ValuesString;199957044 313356892 455463968 465982819 + 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153 + 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906 + 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138 + 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ... + + FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha + NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1 + 700688206 265614156 363161397 681332588 810600886 885767127 950172500 + 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189 + 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327 + 654 256360355 279492740 291251259 317592700 333763396 972105960 101... + + FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN + umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1 + 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813 + 335715751 534801009 684609658 829361048 972945982 999881534 1007655741 + 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162 + 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344... + + METHODS + new + $NewExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + %NamesAndValues); + + Using specified *ExtendedConnectivityFingerprints* property names + and values hash, new method creates a new object and returns a + reference to newly created ExtendedConnectivityFingerprints object. + By default, the following properties are initialized: + + Molecule = '' + Type = 'ExtendedConnectivity' + NeighborhoodRadius = 2 + AtomIdentifierType = '' + AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN'] + FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] + + Examples: + + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes'); + + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivityCount', + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes'); + + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivityBits', + 'Molecule' => $Molecule, + 'Size' => 1024, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes'); + + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivity', + 'Molecule' => $Molecule, + 'NeighborhoodRadius' => 2, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes', + 'AtomicInvariantsToUse' => + ['AS', 'X', 'BO', 'H', 'FC', 'MN'] ); + + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivity', + 'Molecule' => $Molecule, + 'NeighborhoodRadius' => 2, + 'AtomIdentifierType' => + 'FunctionalClassAtomTypes', + 'FunctionalClassesToUse' => + ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] ); + + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivity', + 'Molecule' => $Molecule,; + 'AtomIdentifierType' => + 'MMFF94AtomTypes'); + + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivityCount', + 'Molecule' => $Molecule,; + 'AtomIdentifierType' => + 'MMFF94AtomTypes'); + + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivityCount', + 'Molecule' => $Molecule,; + 'AtomIdentifierType' => + 'SLogPAtomTypes'); + + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivity', + 'Molecule' => $Molecule,; + 'AtomIdentifierType' => + 'SLogPAtomTypes'); + + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivity', + 'Molecule' => $Molecule,; + 'AtomIdentifierType' => + 'SYBYLAtomTypes'); + + $ExtendedConnectivityFingerprints->GenerateFingerprints(); + print "$ExtendedConnectivityFingerprints\n"; + + GenerateFingerprints + $ExtendedConnectivityFingerprints->GenerateFingerprints(); + + Generates extended connectivity fingerprints and returns + *ExtendedConnectivityFingerprints*. + + GetDescription + $Description = $ExtendedConnectivityFingerprints->GetDescription(); + + Returns a string containing description of extended connectivity + fingerprints fingerprints. + + SetAtomIdentifierType + $ExtendedConnectivityFingerprints->SetAtomIdentifierType($IdentifierType); + + Sets atom *IdentifierType* to use during extended connectivity + fingerprints generation and returns + *ExtendedConnectivityFingerprints*. + + Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, + EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, + SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. + + SetAtomicInvariantsToUse + $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse($ValuesRef); + $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse(@Values); + + Sets atomic invariants to use during *AtomicInvariantsAtomTypes* + value of *AtomIdentifierType* for extended connectivity fingerprints + generation and returns *ExtendedConnectivityFingerprints*. + + Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB, + TB, H, Ar, RA, FC, MN, SM*. Default value [ Ref 24 ]: + *AS,X,BO,H,FC,MN*. + + 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 + $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse($ValuesRef); + $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse(@Values); + + Sets functional classes invariants to use during + *FunctionalClassAtomTypes* value of *AtomIdentifierType* for + extended connectivity fingerprints generation and returns + *ExtendedConnectivityFingerprints*. + + 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 + + SetNeighborhoodRadius + $ExtendedConnectivityFingerprints->SetNeighborhoodRadius($Radius); + + Sets neighborhood radius to use during extended connectivity + fingerprints generation and returns + *ExtendedConnectivityFingerprints*. + + StringifyExtendedConnectivityFingerprints + $String = $Fingerprints->StringifyExtendedConnectivityFingerprints(); + + Returns a string containing information about + *ExtendedConnectivityFingerprints* object. + +AUTHOR + Manish Sud <msud@san.rr.com> + +SEE ALSO + Fingerprints.pm, FingerprintsStringUtil.pm, + AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm, + EStateIndiciesFingerprints.pm, MACCSKeys.pm, PathLengthFingerprints.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. +