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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/man3/ExtendedConnectivityFingerprints.3 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,559 @@ +.\" 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" +ExtendedConnectivityFingerprints +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use Fingerprints::ExtendedConnectivityFingerprints; +.PP +use Fingerprints::ExtendedConnectivityFingerprints qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +ExtendedConnectivityFingerprints [ Ref 48, Ref 52 ] class provides the following methods: +.PP +new, GenerateFingerprints, GetDescription, SetAtomIdentifierType, +SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetNeighborhoodRadius, +StringifyExtendedConnectivityFingerprints +.PP +\&\fBExtendedConnectivityFingerprints\fR is derived from \fBFingerprints\fR class which in turn +is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined +in \fBExtendedConnectivityFingerprints\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 \fBExtendedConnectivityFingerprints\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, \fBAtomicInvariantsToUse\fR +and \fBFunctionalClassesToUse\fR, 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 +\&\fBTextUtil::HashCode\fR function. The duplicate atom identifiers are removed. +.PP +For \fBNeighborhoodRadius\fR value of \fI0\fR, the initial set of unique atom identifiers comprises +the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen +atom up-to specified \fBNeighborhoodRadius\fR 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. +.PP +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 \fBTextUtil::HashCode\fR 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. +.PP +For \fIExtendedConnnectivity\fR value of fingerprints \fBType\fR, the duplicate identifiers are +removed from the list and the unique atom identifiers constitute the extended connectivity +fingerprints of a molecule. +.PP +For \fIExtendedConnnectivityCount\fR value of fingerprints \fBType\fR, 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. +.PP +For \fIExtendedConnectivityBits\fR value of fingerprints \fB\-m, \-\-mode\fR, the unique atom identifiers +are used as a random number seed to generate a random integer value between 0 and \fB\-\-Size\fR which +in turn is used to set corresponding bits in the fingerprint bit-vector string. +.PP +The current release of MayaChemTools generates the following types of extended connectivity +fingerprints vector strings: +.PP +.Vb 6 +\& 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... +.Ve +.SS "\s-1METHODS\s0" +.IX Subsection "METHODS" +.IP "\fBnew\fR" 4 +.IX Item "new" +.Vb 2 +\& $NewExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( +\& %NamesAndValues); +.Ve +.Sp +Using specified \fIExtendedConnectivityFingerprints\fR property names and values hash, \fBnew\fR +method creates a new object and returns a reference to newly created \fBExtendedConnectivityFingerprints\fR +object. By default, the following properties are initialized: +.Sp +.Vb 6 +\& Molecule = \*(Aq\*(Aq +\& Type = \*(AqExtendedConnectivity\*(Aq +\& NeighborhoodRadius = 2 +\& AtomIdentifierType = \*(Aq\*(Aq +\& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq, \*(AqMN\*(Aq] +\& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq] +.Ve +.Sp +Examples: +.Sp +.Vb 4 +\& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqAtomicInvariantsAtomTypes\*(Aq); +\& +\& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( +\& \*(AqType\*(Aq => \*(AqExtendedConnectivityCount\*(Aq, +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqAtomicInvariantsAtomTypes\*(Aq); +\& +\& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( +\& \*(AqType\*(Aq => \*(AqExtendedConnectivityBits\*(Aq, +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqSize\*(Aq => 1024, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqAtomicInvariantsAtomTypes\*(Aq); +\& +\& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( +\& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq, +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqNeighborhoodRadius\*(Aq => 2, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqAtomicInvariantsAtomTypes\*(Aq, +\& \*(AqAtomicInvariantsToUse\*(Aq => +\& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq, \*(AqMN\*(Aq] ); +\& +\& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( +\& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq, +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqNeighborhoodRadius\*(Aq => 2, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqFunctionalClassAtomTypes\*(Aq, +\& \*(AqFunctionalClassesToUse\*(Aq => +\& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq] ); +\& +\& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( +\& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq, +\& \*(AqMolecule\*(Aq => $Molecule,; +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqMMFF94AtomTypes\*(Aq); +\& +\& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( +\& \*(AqType\*(Aq => \*(AqExtendedConnectivityCount\*(Aq, +\& \*(AqMolecule\*(Aq => $Molecule,; +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqMMFF94AtomTypes\*(Aq); +\& +\& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( +\& \*(AqType\*(Aq => \*(AqExtendedConnectivityCount\*(Aq, +\& \*(AqMolecule\*(Aq => $Molecule,; +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqSLogPAtomTypes\*(Aq); +\& +\& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( +\& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq, +\& \*(AqMolecule\*(Aq => $Molecule,; +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqSLogPAtomTypes\*(Aq); +\& +\& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( +\& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq, +\& \*(AqMolecule\*(Aq => $Molecule,; +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqSYBYLAtomTypes\*(Aq); +\& +\& $ExtendedConnectivityFingerprints\->GenerateFingerprints(); +\& print "$ExtendedConnectivityFingerprints\en"; +.Ve +.IP "\fBGenerateFingerprints\fR" 4 +.IX Item "GenerateFingerprints" +.Vb 1 +\& $ExtendedConnectivityFingerprints\->GenerateFingerprints(); +.Ve +.Sp +Generates extended connectivity fingerprints and returns \fIExtendedConnectivityFingerprints\fR. +.IP "\fBGetDescription\fR" 4 +.IX Item "GetDescription" +.Vb 1 +\& $Description = $ExtendedConnectivityFingerprints\->GetDescription(); +.Ve +.Sp +Returns a string containing description of extended connectivity fingerprints +fingerprints. +.IP "\fBSetAtomIdentifierType\fR" 4 +.IX Item "SetAtomIdentifierType" +.Vb 1 +\& $ExtendedConnectivityFingerprints\->SetAtomIdentifierType($IdentifierType); +.Ve +.Sp +Sets atom \fIIdentifierType\fR to use during extended connectivity fingerprints generation and +returns \fIExtendedConnectivityFingerprints\fR. +.Sp +Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes\fR. +.IP "\fBSetAtomicInvariantsToUse\fR" 4 +.IX Item "SetAtomicInvariantsToUse" +.Vb 2 +\& $ExtendedConnectivityFingerprints\->SetAtomicInvariantsToUse($ValuesRef); +\& $ExtendedConnectivityFingerprints\->SetAtomicInvariantsToUse(@Values); +.Ve +.Sp +Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR +for extended connectivity fingerprints generation and returns \fIExtendedConnectivityFingerprints\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 [ Ref 24 ]: \fI\s-1AS\s0,X,BO,H,FC,MN\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 +\& $ExtendedConnectivityFingerprints\->SetFunctionalClassesToUse($ValuesRef); +\& $ExtendedConnectivityFingerprints\->SetFunctionalClassesToUse(@Values); +.Ve +.Sp +Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR +for extended connectivity fingerprints generation and returns \fIExtendedConnectivityFingerprints\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 "\fBSetNeighborhoodRadius\fR" 4 +.IX Item "SetNeighborhoodRadius" +.Vb 1 +\& $ExtendedConnectivityFingerprints\->SetNeighborhoodRadius($Radius); +.Ve +.Sp +Sets neighborhood radius to use during extended connectivity fingerprints generation and +returns \fIExtendedConnectivityFingerprints\fR. +.IP "\fBStringifyExtendedConnectivityFingerprints\fR" 4 +.IX Item "StringifyExtendedConnectivityFingerprints" +.Vb 1 +\& $String = $Fingerprints\->StringifyExtendedConnectivityFingerprints(); +.Ve +.Sp +Returns a string containing information about \fIExtendedConnectivityFingerprints\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, MACCSKeys.pm, +PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.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.