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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/man3/TopologicalAtomPairsFingerprints.3 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,503 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +TopologicalAtomPairsFingerprints +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use Fingerprints::TopologicalAtomPairsFingerprints; +.PP +use Fingerprints::TopologicalAtomPairsFingerprints qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBTopologicalAtomPairsFingerprints\fR [ Ref 57, Ref 59, Ref 72 ] class provides the following methods: +.PP +new, GenerateFingerprints, GetAtomPairIDs, GetDescription, SetAtomIdentifierType, +SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetMaxDistance, +SetMinDistance, StringifyTopologicalAtomPairsFingerprints +.PP +\&\fBTopologicalAtomPairsFingerprints\fR is derived from \fBFingerprints\fR class which in turn +is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined +in \fBTopologicalAtomPairsFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR classes using Perl's +\&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property: +.PP +.Vb 3 +\& Set<PropertyName>(<PropertyValue>); +\& $PropertyValue = Get<PropertyName>(); +\& Delete<PropertyName>(); +.Ve +.PP +The current release of MayaChemTools supports generation of \fBAtomTypesFingerpritns\fR +corresponding to following \fBAtomtomIdentifierTypes\fR: +.PP +.Vb 3 +\& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +\& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, +\& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes +.Ve +.PP +Based on the values specified for \fBAtomIdentifierType\fR along with other specified +parameters such as \fBAtomicInvariantsToUse\fR and \fBFunctionalClassesToUse\fR, 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 \fBMinDistance\fR and \fBMaxDistance\fR are identified and counted. An atom pair +identifier is generated for each unique atom pair; the format of atom pair identifier is: +.PP +.Vb 1 +\& <AtomType1>\-D<n>\-<AtomType2> +\& +\& AtomType1, AtomType2: Atom types assigned to atom1 and atom2 +\& D: Distance between atom1 and atom2 +\& +\& where AtomType1 <= AtomType2 +.Ve +.PP +The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute +topological atom pairs fingerprints of the molecule. +.PP +The current release of MayaChemTools generates the following types of topological atom pairs +fingerprints vector strings: +.PP +.Vb 6 +\& 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\-... +.Ve +.SS "\s-1METHODS\s0" +.IX Subsection "METHODS" +.IP "\fBnew\fR" 4 +.IX Item "new" +.Vb 2 +\& $NewTopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( +\& %NamesAndValues); +.Ve +.Sp +Using specified \fITopologicalAtomPairsFingerprints\fR property names and values hash, \fBnew\fR +method creates a new object and returns a reference to newly created \fBTopologicalAtomPairsFingerprints\fR +object. By default, the following properties are initialized: +.Sp +.Vb 7 +\& Molecule = \*(Aq\*(Aq +\& Type = \*(AqTopologicalAtomPairs\*(Aq +\& MinDistance = 1 +\& MaxDistance = 10 +\& AtomIdentifierType = \*(Aq\*(Aq +\& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] +\& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq] +.Ve +.Sp +Examples: +.Sp +.Vb 4 +\& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqAtomicInvariantsAtomTypes\*(Aq); +\& +\& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqMinDistance\*(Aq => 1, +\& \*(AqMaxDistance\*(Aq => 10, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqAtomicInvariantsAtomTypes\*(Aq, +\& \*(AqAtomicInvariantsToUse\*(Aq => +\& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] ); +\& +\& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqEStateAtomTypes\*(Aq); +\& +\& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqSLogPAtomTypes\*(Aq); +\& +\& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqMinDistance\*(Aq => 1, +\& \*(AqMaxDistance\*(Aq => 10, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqFunctionalClassAtomTypes\*(Aq, +\& \*(AqFunctionalClassesToUse\*(Aq => +\& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]); +\& +\& +\& $TopologicalAtomPairsFingerprints\->GenerateFingerprints(); +\& print "$TopologicalAtomPairsFingerprints\en"; +.Ve +.IP "\fBGetDescription\fR" 4 +.IX Item "GetDescription" +.Vb 1 +\& $Description = $TopologicalAtomPairsFingerprints\->GetDescription(); +.Ve +.Sp +Returns a string containing description of topological atom pairs fingerprints fingerprints. +.IP "\fBGenerateFingerprints\fR" 4 +.IX Item "GenerateFingerprints" +.Vb 1 +\& $TopologicalAtomPairsFingerprints\->GenerateFingerprints(); +.Ve +.Sp +Generates topological atom pairs fingerprints and returns \fITopologicalAtomPairsFingerprints\fR. +.IP "\fBGetAtomPairIDs\fR" 4 +.IX Item "GetAtomPairIDs" +.Vb 2 +\& $AtomPairIDsRef = $TopologicalAtomPairsFingerprints\->GetAtomPairIDs(); +\& @AtomPairIDs = $TopologicalAtomPairsFingerprints\->GetAtomPairIDs(); +.Ve +.Sp +Returns atom pair IDs corresponding to atom pairs count values in topological atom pairs +fingerprints vector as an array or reference to an array. +.IP "\fBSetAtomIdentifierType\fR" 4 +.IX Item "SetAtomIdentifierType" +.Vb 1 +\& $TopologicalAtomPairsFingerprints\->SetAtomIdentifierType($IdentifierType); +.Ve +.Sp +Sets atom \fIIdentifierType\fR to use during atom pairs fingerprints generation and +returns \fITopologicalAtomPairsFingerprints\fR. +.Sp +Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes\fR. +.IP "\fBSetAtomicInvariantsToUse\fR" 4 +.IX Item "SetAtomicInvariantsToUse" +.Vb 2 +\& $TopologicalAtomPairsFingerprints\->SetAtomicInvariantsToUse($ValuesRef); +\& $TopologicalAtomPairsFingerprints\->SetAtomicInvariantsToUse(@Values); +.Ve +.Sp +Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR +for topological atom pairs fingerprints generation and returns \fITopologicalAtomPairsFingerprints\fR. +.Sp +Possible values for atomic invariants are: \fI\s-1AS\s0, X, \s-1BO\s0, \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0, +H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value: \fI\s-1AS\s0,X,BO,H,FC\fR. +.Sp +The atomic invariants abbreviations correspond to: +.Sp +.Vb 1 +\& 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) +.Ve +.Sp +Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to: +.Sp +.Vb 1 +\& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n> +.Ve +.Sp +Except for \s-1AS\s0 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. +.Sp +In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words +are also allowed: +.Sp +.Vb 12 +\& 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 +.Ve +.Sp +\&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant +atom types. +.IP "\fBSetFunctionalClassesToUse\fR" 4 +.IX Item "SetFunctionalClassesToUse" +.Vb 2 +\& $TopologicalAtomPairsFingerprints\->SetFunctionalClassesToUse($ValuesRef); +\& $TopologicalAtomPairsFingerprints\->SetFunctionalClassesToUse(@Values); +.Ve +.Sp +Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR +for topological atom pairs fingerprints generation and returns \fITopologicalAtomPairsFingerprints\fR. +.Sp +Possible values for atom functional classes are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR. +Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR. +.Sp +The functional class abbreviations correspond to: +.Sp +.Vb 9 +\& 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 +.Ve +.Sp +\&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom +types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]: +.Sp +.Vb 4 +\& HydrogenBondDonor: NH, NH2, OH +\& HydrogenBondAcceptor: N[!H], O +\& PositivelyIonizable: +, NH2 +\& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH +.Ve +.IP "\fBSetMaxDistance\fR" 4 +.IX Item "SetMaxDistance" +.Vb 1 +\& $TopologicalAtomPairsFingerprints\->SetMaxDistance($Distance); +.Ve +.Sp +Sets maximum distance to use during topological atom pairs fingerprints generation and +returns \fITopologicalAtomPairsFingerprints\fR. +.IP "\fBSetMinDistance\fR" 4 +.IX Item "SetMinDistance" +.Vb 1 +\& $TopologicalAtomPairsFingerprints\->SetMinDistance($Distance); +.Ve +.Sp +Sets minimum distance to use during topological atom pairs fingerprints generation and +returns \fITopologicalAtomPairsFingerprints\fR. +.IP "\fBStringifyTopologicalAtomPairsFingerprints\fR" 4 +.IX Item "StringifyTopologicalAtomPairsFingerprints" +.Vb 2 +\& $String = $TopologicalAtomPairsFingerprints\-> +\& StringifyTopologicalAtomPairsFingerprints(); +.Ve +.Sp +Returns a string containing information about \fITopologicalAtomPairsFingerprints\fR object. +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "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 +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.