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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/scripts/txt/ExtendedConnectivityFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,850 @@ +NAME + ExtendedConnectivityFingerprints.pl - Generate extended connectivity + fingerprints for SD files + +SYNOPSIS + ExtendedConnectivityFingerprints.pl SDFile(s)... + + ExtendedConnectivityFingerprints.pl [--AromaticityModel + *AromaticityModelType*] [-a, --AtomIdentifierType + *AtomicInvariantsAtomTypes*] [--AtomicInvariantsToUse + *"AtomicInvariant,AtomicInvariant..."*] [--FunctionalClassesToUse + *"FunctionalClass1,FunctionalClass2..."*] [--BitsOrder *Ascending | + Descending*] [-b, --BitStringFormat *BinaryString | HexadecimalString*] + [--CompoundID *DataFieldName or LabelPrefixString*] [--CompoundIDLabel + *text*] [--CompoundIDMode] [--DataFields + *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode *All | Common | + Specify | CompoundID*] [-f, --Filter *Yes | No*] [--FingerprintsLabel + *text*] [-h, --help] [-k, --KeepLargestComponent *Yes | No*] [-m, --mode + *ExtendedConnectivity | ExtendedConnecticityCount | + ExtendedConnecticityBits*] [-n, --NeighborhoodRadius *number*] + [--OutDelim *comma | tab | semicolon*] [--output *SD | FP | text | all*] + [-o, --overwrite] [-q, --quote *Yes | No*] [-r, --root *RootName*] [-s, + --size *number*] [--UsePerlCoreRandom *Yes | No*] [-v, + --VectorStringFormat *IDsAndValuesString | IDsAndValuesPairsString | + ValuesAndIDsString | ValuesAndIDsPairsString*] [-w, --WorkingDir + dirname] SDFile(s)... + +DESCRIPTION + Generate extended connectivity fingerprints [ Ref 48, Ref 52 ] for + *SDFile(s)* and create appropriate SD, FP or CSV/TSV text file(s) + containing fingerprints vector strings corresponding to molecular + fingerprints. + + Multiple SDFile names are separated by spaces. The valid file extensions + are *.sdf* and *.sd*. All other file names are ignored. All the SD files + in a current directory can be specified either by **.sdf* or the current + directory name. + + The current release of MayaChemTools supports generation of extended + connectivity fingerprints corresponding to following -a, + --AtomIdentifierTypes: + + AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes + + Based on values specified for -a, --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 -n, --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 + -n, --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 atoms and bonds corresponding to substructures used for + generating atom identifier and keeping integer atom identifier with + lowest value. + + For *ExtendedConnnectivity* value of fingerprints -m, --mode, 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 -m, --mode, 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. + + Example of *SD* file containing extended connectivity fingerprints + string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <ExtendedConnectivityFingerprints> + FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radiu + s2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 66 + 6191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414087 + 99 49532520 64643108 79385615 96062769 273726379 564565671 855141035 90 + 6706094 988546669 1018231313 1032696425 1197507444 1331250018 133853... + + $$$$ + ... ... + ... ... + + Example of *FP* file containing extended connectivity fingerprints + string data: + + # + # Package = MayaChemTools 7.4 + # Release Date = Oct 21, 2010 + # + # TimeStamp = Fri Mar 11 14:43:57 2011 + # + # FingerprintsStringType = FingerprintsVector + # + # Description = ExtendedConnectivity:AtomicInvariantsAtomTypes:Radius2 + # VectorStringFormat = ValuesString + # VectorValuesType = AlphaNumericalValues + # + Cmpd1 60;73555770 333564680 352413391 666191900 1001270906 137167432... + Cmpd2 41;73555770 333564680 666191900 1142173602 1363635752 14814699... + ... ... + ... .. + + Example of CSV *Text* file containing extended connectivity fingerprints + string data: + + "CompoundID","ExtendedConnectivityFingerprints" + "Cmpd1","FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTy + pes:Radius2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352 + 413391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 + 2141408799 49532520 64643108 79385615 96062769 273726379 564565671 8551 + 41035 906706094 988546669 1018231313 1032696425 1197507444 13312500..." + ... ... + ... ... + + 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... + +OPTIONS + --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel | + MMFFAromaticityModel | ChemAxonBasicAromaticityModel | + ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | + MayaChemToolsAromaticityModel* + Specify aromaticity model to use during detection of aromaticity. + Possible values in the current release are: *MDLAromaticityModel, + TriposAromaticityModel, MMFFAromaticityModel, + ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, + DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default + value: *MayaChemToolsAromaticityModel*. + + The supported aromaticity model names along with model specific + control parameters are defined in AromaticityModelsData.csv, which + is distributed with the current release and is available under + lib/data directory. Molecule.pm module retrieves data from this file + during class instantiation and makes it available to method + DetectAromaticity for detecting aromaticity corresponding to a + specific model. + + -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | + FunctionalClassAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | + MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | + UFFAtomTypes* + Specify atom identifier type to use for assignment of initial atom + identifier to non-hydrogen atoms during calculation of extended + connectivity fingerprints [ Ref 48, Ref 52]. Possible values in the + current release are: *AtomicInvariantsAtomTypes, + FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, + UFFAtomTypes*. Default value: *AtomicInvariantsAtomTypes*. + + --AtomicInvariantsToUse *"AtomicInvariant,AtomicInvariant..."* + This value is used during *AtomicInvariantsAtomTypes* value of a, + --AtomIdentifierType option. It's a list of comma separated valid + atomic invariant atom types. + + Possible values for atomic invarians 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. + + --BitsOrder *Ascending | Descending* + Bits order to use during generation of fingerprints bit-vector + string for *ExtendedConnectivityBits* value of -m, --mode option. + Possible values: *Ascending, Descending*. Default: *Ascending*. + + *Ascending* bit order which corresponds to first bit in each byte as + the lowest bit as opposed to the highest bit. + + Internally, bits are stored in *Ascending* order using Perl vec + function. Regardless of machine order, big-endian or little-endian, + vec function always considers first string byte as the lowest byte + and first bit within each byte as the lowest bit. + + -b, --BitStringFormat *BinaryString | HexadecimalString* + Format of fingerprints bit-vector string data in output SD, FP or + CSV/TSV text file(s) specified by --output used during + *ExtendedConnectivityBits* value of -m, --mode option. Possible + values: *BinaryString, HexadecimalString*. Default value: + *BinaryString*. + + *BinaryString* corresponds to an ASCII string containing 1s and 0s. + *HexadecimalString* contains bit values in ASCII hexadecimal format. + + Examples: + + FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp + es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100 + 0000000001010000000110000011000000000000100000000000000000000000100001 + 1000000110000000000000000000000000010011000000000000000000000000010000 + 0000000000000000000000000010000000000000000001000000000000000000000000 + 0000000000010000100001000000000000101000000000000000100000000000000... + + FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType + s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000 + 0000000001000100000000001000000000000000000000000000000000101000000010 + 0000001000000000010000000000000000000000000000000000000000000000000100 + 0000000000001000000000000001000000000001001000000000000000000000000000 + 0000000000000000100000000000001000000000000000000000000000000000000... + + --FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."* + This value is used during *FunctionalClassAtomTypes* value of a, + --AtomIdentifierType option. It's a list of comma separated valid + functional classes. + + 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 + + *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 + + --CompoundID *DataFieldName or LabelPrefixString* + This value is --CompoundIDMode specific and indicates how compound + ID is generated. + + For *DataField* value of --CompoundIDMode option, it corresponds to + datafield label name whose value is used as compound ID; otherwise, + it's a prefix string used for generating compound IDs like + LabelPrefixString<Number>. Default value, *Cmpd*, generates compound + IDs which look like Cmpd<Number>. + + Examples for *DataField* value of --CompoundIDMode: + + MolID + ExtReg + + Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of + --CompoundIDMode: + + Compound + + The value specified above generates compound IDs which correspond to + Compound<Number> instead of default value of Cmpd<Number>. + + --CompoundIDLabel *text* + Specify compound ID column label for FP or CSV/TSV text file(s) used + during *CompoundID* value of --DataFieldsMode option. Default: + *CompoundID*. + + --CompoundIDMode *DataField | MolName | LabelPrefix | + MolNameOrLabelPrefix* + Specify how to generate compound IDs and write to FP or CSV/TSV text + file(s) along with generated fingerprints for *FP | text | all* + values of --output option: use a *SDFile(s)* datafield value; use + molname line from *SDFile(s)*; generate a sequential ID with + specific prefix; use combination of both MolName and LabelPrefix + with usage of LabelPrefix values for empty molname lines. + + Possible values: *DataField | MolName | LabelPrefix | + MolNameOrLabelPrefix*. Default: *LabelPrefix*. + + For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line + in *SDFile(s)* takes precedence over sequential compound IDs + generated using *LabelPrefix* and only empty molname values are + replaced with sequential compound IDs. + + This is only used for *CompoundID* value of --DataFieldsMode option. + + --DataFields *"FieldLabel1,FieldLabel2,..."* + Comma delimited list of *SDFiles(s)* data fields to extract and + write to CSV/TSV text file(s) along with generated fingerprints for + *text | all* values of --output option. + + This is only used for *Specify* value of --DataFieldsMode option. + + Examples: + + Extreg + MolID,CompoundName + + -d, --DataFieldsMode *All | Common | Specify | CompoundID* + Specify how data fields in *SDFile(s)* are transferred to output + CSV/TSV text file(s) along with generated fingerprints for *text | + all* values of --output option: transfer all SD data field; transfer + SD data files common to all compounds; extract specified data + fields; generate a compound ID using molname line, a compound + prefix, or a combination of both. Possible values: *All | Common | + specify | CompoundID*. Default value: *CompoundID*. + + -f, --Filter *Yes | No* + Specify whether to check and filter compound data in SDFile(s). + Possible values: *Yes or No*. Default value: *Yes*. + + By default, compound data is checked before calculating fingerprints + and compounds containing atom data corresponding to non-element + symbols or no atom data are ignored. + + --FingerprintsLabel *text* + SD data label or text file column label to use for fingerprints + string in output SD or CSV/TSV text file(s) specified by --output. + Default value: *ExtendedConnectivityFingerprints*. + + -h, --help + Print this help message. + + -k, --KeepLargestComponent *Yes | No* + Generate fingerprints for only the largest component in molecule. + Possible values: *Yes or No*. Default value: *Yes*. + + For molecules containing multiple connected components, fingerprints + can be generated in two different ways: use all connected components + or just the largest connected component. By default, all atoms + except for the largest connected component are deleted before + generation of fingerprints. + + -m, --mode *ExtendedConnectivity | ExtendedConnectivityCount | + ExtendedConnectivityBits* + Specify type of extended connectivity fingerprints to generate for + molecules in *SDFile(s)*. Possible values: *ExtendedConnectivity, + ExtendedConnecticityCount or ExtendedConnectivityBits*. Default + value: *ExtendedConnectivity*. + + For *ExtendedConnnectivity* value of fingerprints -m, --mode, a + fingerprint vector containing unique atom identifiers constitute the + extended connectivity fingerprints of a molecule. + + For *ExtendedConnnectivityCount* value of fingerprints -m, --mode, a + fingerprint vector containing unique atom identifiers along with + their count constitute the extended connectivity fingerprints of a + molecule. + + For *ExtendedConnnectivityBits* value of fingerprints -m, --mode, a + fingerprint bit vector indicating presence/absence of structurally + unique atom identifiers constitute the extended connectivity + fingerprints of a molecule. + + -n, --NeighborhoodRadius *number* + Atomic neighborhood radius for generating extended connectivity + neighborhoods. Default value: *2*. Valid values: >= 0. Neighborhood + radius of zero correspond to just the list of non-hydrogen atoms. + + Default value of *2* for atomic neighborhood radius generates + extended connectivity fingerprints corresponding to path length or + diameter value of *4* [ Ref 52b ]. + + --OutDelim *comma | tab | semicolon* + Delimiter for output CSV/TSV text file(s). Possible values: *comma, + tab, or semicolon* Default value: *comma*. + + --output *SD | FP | text | all* + Type of output files to generate. Possible values: *SD, FP, text, or + all*. Default value: *text*. + + -o, --overwrite + Overwrite existing files. + + -q, --quote *Yes | No* + Put quote around column values in output CSV/TSV text file(s). + Possible values: *Yes or No*. Default value: *Yes*. + + -r, --root *RootName* + New file name is generated using the root: <Root>.<Ext>. Default for + new file names: <SDFileName><ExtendedConnectivityFP>.<Ext>. The file + type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values + are used for SD, FP, comma/semicolon, and tab delimited text files, + respectively.This option is ignored for multiple input files. + + -s, --size *number* + Size of bit-vector to use during generation of fingerprints + bit-vector string for *ExtendedConnectivityBits* value of -m, + --mode. Default value: *1024*. Valid values correspond to any + positive integer which satisfies the following criteria: power of 2, + >= 32 and <= 2 ** 32. + + Examples: + + 512 + 1024 + 2048 + + --UsePerlCoreRandom *Yes | No* + Specify whether to use Perl CORE::rand or MayaChemTools + MathUtil::random function during random number generation for + setting bits in fingerprints bit-vector strings. Possible values: + *Yes or No*. Default value: *Yes*. + + *No* value option for --UsePerlCoreRandom allows the generation of + fingerprints bit-vector strings which are same across different + platforms. + + The random number generator implemented in MayaChemTools is a + variant of linear congruential generator (LCG) as described by + Miller et al. [ Ref 120 ]. It is also referred to as Lehmer random + number generator or Park-Miller random number generator. + + Unlike Perl's core random number generator function rand, the random + number generator implemented in MayaChemTools, MathUtil::random, + generates consistent random values across different platforms for a + specific random seed and leads to generation of portable + fingerprints bit-vector strings. + + -v, --VectorStringFormat *ValuesString | IDsAndValuesString | + IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString* + Format of fingerprints vector string data in output SD, FP or + CSV/TSV text file(s) specified by --output used during + <ExtendedConnectivityCount> value of -m, --mode option. Possible + values: *ValuesString, IDsAndValuesString | IDsAndValuesPairsString + | ValuesAndIDsString | ValuesAndIDsPairsString*. + + Default value during <ExtendedConnectivityCount> value of -m, --mode + option: *IDsAndValuesString*. + + Default value during <ExtendedConnectivity> value of -m, --mode + option: *ValuesString*. + + Examples: + + 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 + + -w, --WorkingDir *DirName* + Location of working directory. Default: current directory. + +EXAMPLES + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using atomic invariants atom types in vector + string format and create a SampleECAIFP.csv file containing sequential + compound IDs along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -r SampleECAIFP -o Sample.sdf + + To generate extended connectivity count fingerprints corresponding to + neighborhood radius up to 2 using atomic invariants atom types in vector + string format and create a SampleECAIFP.csv file containing sequential + compound IDs along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount + -r SampleECAIFP -o Sample.sdf + + To generate extended connectivity bits fingerprints as hexadecimal + bit-string corresponding to neighborhood radius up to 2 using atomic + invariants atom types in vector string format and create a + SampleECAIFP.csv file containing sequential compound IDs along with + fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits + -r SampleECAIFP -o Sample.sdf + + To generate extended connectivity bits fingerprints as binary bit-string + corresponding to neighborhood radius up to 2 using atomic invariants + atom types in vector string format and create a SampleECAIFP.csv file + containing sequential compound IDs along with fingerprints vector + strings data, type: + + % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits + --BitStringFormat BinaryString -r SampleECAIFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using atomic invariants atom types in vector + string format and create SampleECAIFP.sdf, SampleECAIFP.fpf and + SampleECAIFP.csv files containing sequential compound IDs in CSV file + along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl --output all -r SampleECAIFP + -o Sample.sdf + + To generate extended connectivity count fingerprints corresponding to + neighborhood radius up to 2 using atomic invariants atom types in vector + string format and create SampleECAIFP.sdf, SampleECAIFP.fpf and + SampleECAIFP.csv files containing sequential compound IDs in CSV file + along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount + --output all -r SampleECAIFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using functional class atom types in vector + string format and create a SampleECFCFP.csv file containing sequential + compound IDs along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes + -r SampleECFCFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using DREIDING atom types in vector string + format and create a SampleECFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a DREIDINGAtomTypes + -r SampleECFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using E-state atom types in vector string + format and create a SampleECFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a EStateAtomTypes + -r SampleECFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using MMFF94 atom types in vector string + format and create a SampleECFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a MMFF94AtomTypes + -r SampleECFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using SLogP atom types in vector string + format and create a SampleECFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a SLogPAtomTypes + -r SampleECFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using SYBYL atom types in vector string + format and create a SampleECFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a SYBYLAtomTypes + -r SampleECFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using TPSA atom types in vector string + format and create a SampleECFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a TPSAAtomTypes + -r SampleECFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using UFF atom types in vector string format + and create a SampleECFP.csv file containing sequential compound IDs + along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a UFFAtomTypes + -r SampleECFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 3 using atomic invariants atom types in vector + string format and create a SampleECAIFP.csv file containing sequential + compound IDs along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes -n 3 + -r SampleECAIFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 3 using functional class atom types in vector + string format and create a SampleECFCFP.csv file containing sequential + compound IDs along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes -n 3 + -r SampleECFCFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using only AS,X atomic invariants atom types + in vector string format and create a SampleECAIFP.csv file containing + sequential compound IDs along with fingerprints vector strings data, + type: + + % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes + --AtomicInvariantsToUse "AS,X" -r SampleECAIFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using only HBD,HBA functional class atom + types in vector string format and create a SampleECFCFP.csv file + containing sequential compound IDs along with fingerprints vector + strings data, type: + + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes + --FunctionalClassesToUse "HBD,HBA" -r SampleECFCFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using atomic invariants atom types in vector + string format and create a SampleECAIFP.csv file containing compound ID + from molecule name line along with fingerprints vector strings data, + type: + + % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolName + -r SampleECAIFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using functional class atom types in vector + string format and create a SampleECFCFP.csv file containing compound IDs + using specified data field along with fingerprints vector strings data, + type: + + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID Mol_ID + -r SampleECFCFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using atomic invariants atom types in vector + string format and create a SampleECAIFP.tsv file containing compound ID + using combination of molecule name line and an explicit compound prefix + along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleECAIFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using functional class atom types in vector + string format and create a SampleECFCFP.csv file containing specific + data fields columns along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes + --DataFieldsMode Specify --DataFields Mol_ID -r SampleECFCFP + -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using atomic invariants atom types in vector + string format and create a SampleECAIFP.tsv file containing common data + fields columns along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Common -r SampleECAIFP -o Sample.sdf + + To generate extended connectivity fingerprints corresponding to + neighborhood radius up to 2 using functional class atom types in vector + string format and create SampleECFCFP.sdf, SampleECFCFP.fpf and + SampleECFCFP.csv files containing all data fields columns in CSV file + along with fingerprints vector strings data, type: + + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes + --DataFieldsMode All --output all -r SampleECFCFP + -o Sample.sdf + +AUTHOR + Manish Sud <msud@san.rr.com> + +SEE ALSO + InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, + AtomNeighborhoodsFingerprints.pl, MACCSKeysFingerprints.pl, + PathLengthFingerprints.pl, TopologicalAtomPairsFingerprints.pl, + TopologicalAtomTorsionsFingerprints.pl, + TopologicalPharmacophoreAtomPairsFingerprints.pl, + TopologicalPharmacophoreAtomTripletsFingerprints.pl + +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. +