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## 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

## 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.

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