comparison mayachemtools/docs/scripts/man1/ExtendedConnectivityFingerprints.1 @ 0:73ae111cf86f draft

Uploaded

0:73ae111cf86f

.\" 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++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is turned on, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.ie \nF \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    nr % 0
.    rr F
.\}
.el \{\
.    de IX
..
.\}
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
.IX Title "EXTENDEDCONNECTIVITYFINGERPRINTS 1"
.TH EXTENDEDCONNECTIVITYFINGERPRINTS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
ExtendedConnectivityFingerprints.pl \- Generate extended connectivity fingerprints for SD files
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
ExtendedConnectivityFingerprints.pl SDFile(s)...
.PP
ExtendedConnectivityFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR]
[\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes\fR]
[\fB\-\-AtomicInvariantsToUse\fR \fI\*(L"AtomicInvariant,AtomicInvariant...\*(R"\fR]
[\fB\-\-FunctionalClassesToUse\fR \fI\*(L"FunctionalClass1,FunctionalClass2...\*(R"\fR]
[\fB\-\-BitsOrder\fR \fIAscending | Descending\fR] [\fB\-b, \-\-BitStringFormat\fR \fIBinaryString | HexadecimalString\fR]
[\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR] [\fB\-\-CompoundIDLabel\fR \fItext\fR]
[\fB\-\-CompoundIDMode\fR] [\fB\-\-DataFields\fR \fI\*(L"FieldLabel1,FieldLabel2,...\*(R"\fR]
[\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR]  [\fB\-f, \-\-Filter\fR \fIYes | No\fR]
[\fB\-\-FingerprintsLabel\fR \fItext\fR] [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR]
[\fB\-m, \-\-mode\fR \fIExtendedConnectivity | ExtendedConnecticityCount | ExtendedConnecticityBits\fR]
[\fB\-n, \-\-NeighborhoodRadius\fR \fInumber\fR] [\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] [\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR]
[\fB\-o, \-\-overwrite\fR] [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-s, \-\-size\fR \fInumber\fR]
[\fB\-\-UsePerlCoreRandom\fR \fIYes | No\fR]
[\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR]
[\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)...
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Generate extended connectivity fingerprints [ Ref 48, Ref 52 ] for \fISDFile(s)\fR and create appropriate
\&\s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) containing fingerprints vector strings corresponding to molecular fingerprints.
.PP
Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR
and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory
can be specified either by \fI*.sdf\fR or the current directory name.
.PP
The current release of MayaChemTools supports generation of extended connectivity fingerprints
corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR:
.PP
.Vb 3
\&    AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
\&    FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
\&    SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
.Ve
.PP
Based on values specified for \fB\-a, \-\-AtomIdentifierType\fR, \fB\-\-AtomicInvariantsToUse\fR
and \fB\-\-FunctionalClassesToUse\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 \fB\-n, \-\-NeighborhoodRadius\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 \fB\-n, \-\-NeighborhoodRadius\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 atoms 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 \fB\-m, \-\-mode\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 \fB\-m, \-\-mode\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
Example of \fI\s-1SD\s0\fR file containing extended connectivity fingerprints string data:
.PP
.Vb 10
\&    ... ...
\&    ... ...
\&    $$$$
\&    ... ...
\&    ... ...
\&    ... ...
\&    41 44  0  0  0  0  0  0  0  0999 V2000
\&     \-3.3652    1.4499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
\&    ... ...
\&    2  3  1  0  0  0  0
\&    ... ...
\&    M  END
\&    >  <CmpdID>
\&    Cmpd1
\&
\&    >  <ExtendedConnectivityFingerprints>
\&    FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radiu
\&    s2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 66
\&    6191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414087
\&    99 49532520 64643108 79385615 96062769 273726379 564565671 855141035 90
\&    6706094 988546669 1018231313 1032696425 1197507444 1331250018 133853...
\&
\&    $$$$
\&    ... ...
\&    ... ...
.Ve
.PP
Example of \fI\s-1FP\s0\fR file containing extended connectivity fingerprints string data:
.PP
.Vb 10
\&    #
\&    # 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...
\&    ... ...
\&    ... ..
.Ve
.PP
Example of \s-1CSV\s0 \fIText\fR file containing extended connectivity fingerprints string data:
.PP
.Vb 8
\&    "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..."
\&    ... ...
\&    ... ...
.Ve
.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
.SH "OPTIONS"
.IX Header "OPTIONS"
.IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
.IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
Specify aromaticity model to use during detection of aromaticity. Possible values in the current
release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
.Sp
The supported aromaticity model names along with model specific control parameters
are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
for detecting aromaticity corresponding to a specific model.
.IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | FunctionalClassAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4
.IX Item "-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: \fIAtomicInvariantsAtomTypes, FunctionalClassAtomTypes,
DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR.
.ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant,AtomicInvariant...""\fR" 4
.el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant,AtomicInvariant...''\fR" 4
.IX Item "--AtomicInvariantsToUse AtomicInvariant,AtomicInvariant..."
This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
option. It's a list of comma separated valid atomic invariant atom types.
.Sp
Possible values for atomic invarians 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 "\fB\-\-BitsOrder\fR \fIAscending | Descending\fR" 4
.IX Item "--BitsOrder Ascending | Descending"
Bits order to use during generation of fingerprints bit-vector string for \fIExtendedConnectivityBits\fR
value of \fB\-m, \-\-mode\fR option. Possible values: \fIAscending, Descending\fR. Default: \fIAscending\fR.
.Sp
\&\fIAscending\fR bit order which corresponds to first bit in each byte as the lowest bit as
opposed to the highest bit.
.Sp
Internally, bits are stored in \fIAscending\fR 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.
.IP "\fB\-b, \-\-BitStringFormat\fR \fIBinaryString | HexadecimalString\fR" 4
.IX Item "-b, --BitStringFormat BinaryString | HexadecimalString"
Format of fingerprints bit-vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
\&\fB\-\-output\fR used during \fIExtendedConnectivityBits\fR value of \fB\-m, \-\-mode\fR option. Possible
values: \fIBinaryString, HexadecimalString\fR. Default value: \fIBinaryString\fR.
.Sp
\&\fIBinaryString\fR corresponds to an \s-1ASCII\s0 string containing 1s and 0s. \fIHexadecimalString\fR
contains bit values in \s-1ASCII\s0 hexadecimal format.
.Sp
Examples:
.Sp
.Vb 6
\&    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...
.Ve
.ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4
.el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4
.IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..."
This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
option. It's a list of comma separated valid functional classes.
.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
.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 "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
.IX Item "--CompoundID DataFieldName or LabelPrefixString"
This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
.Sp
For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
look like Cmpd<Number>.
.Sp
Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
.Sp
.Vb 2
\&    MolID
\&    ExtReg
.Ve
.Sp
Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
.Sp
.Vb 1
\&    Compound
.Ve
.Sp
The value specified above generates compound IDs which correspond to Compound<Number>
instead of default value of Cmpd<Number>.
.IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
.IX Item "--CompoundIDLabel text"
Specify compound \s-1ID\s0 column label for \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
of \fB\-\-DataFieldsMode\fR option. Default: \fICompoundID\fR.
.IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
.IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value;
use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
.Sp
Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
Default: \fILabelPrefix\fR.
.Sp
For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
values are replaced with sequential compound IDs.
.Sp
This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
.ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
.el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
.IX Item "--DataFields FieldLabel1,FieldLabel2,..."
Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option.
.Sp
This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
.Sp
Examples:
.Sp
.Vb 2
\&    Extreg
\&    MolID,CompoundName
.Ve
.IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
.IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
.IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
.IX Item "-f, --Filter Yes | No"
Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
Default value: \fIYes\fR.
.Sp
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.
.IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
.IX Item "--FingerprintsLabel text"
\&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
\&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fIExtendedConnectivityFingerprints\fR.
.IP "\fB\-h, \-\-help\fR" 4
.IX Item "-h, --help"
Print this help message.
.IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
.IX Item "-k, --KeepLargestComponent Yes | No"
Generate fingerprints for only the largest component in molecule. Possible values:
\&\fIYes or No\fR. Default value: \fIYes\fR.
.Sp
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.
.IP "\fB\-m, \-\-mode\fR \fIExtendedConnectivity | ExtendedConnectivityCount | ExtendedConnectivityBits\fR" 4
.IX Item "-m, --mode ExtendedConnectivity | ExtendedConnectivityCount | ExtendedConnectivityBits"
Specify type of extended connectivity fingerprints to generate for molecules in \fISDFile(s)\fR.
Possible values: \fIExtendedConnectivity, ExtendedConnecticityCount or
ExtendedConnectivityBits\fR. Default value: \fIExtendedConnectivity\fR.
.Sp
For \fIExtendedConnnectivity\fR value of fingerprints \fB\-m, \-\-mode\fR, a fingerprint vector
containing unique atom identifiers constitute the extended connectivity fingerprints
of a molecule.
.Sp
For \fIExtendedConnnectivityCount\fR value of fingerprints \fB\-m, \-\-mode\fR, a fingerprint vector
containing unique atom identifiers along with their count constitute the extended connectivity
fingerprints of a molecule.
.Sp
For \fIExtendedConnnectivityBits\fR value of fingerprints \fB\-m, \-\-mode\fR, a fingerprint bit vector
indicating presence/absence of structurally unique atom identifiers constitute the extended
connectivity fingerprints of a molecule.
.IP "\fB\-n, \-\-NeighborhoodRadius\fR \fInumber\fR" 4
.IX Item "-n, --NeighborhoodRadius number"
Atomic neighborhood radius for generating extended connectivity neighborhoods. Default
value: \fI2\fR.  Valid values: >= 0. Neighborhood radius of zero correspond to just the list
of non-hydrogen atoms.
.Sp
Default value of \fI2\fR for atomic neighborhood radius generates extended connectivity
fingerprints corresponding to path length or diameter value of \fI4\fR [ Ref 52b ].
.IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
.IX Item "--OutDelim comma | tab | semicolon"
Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
Default value: \fIcomma\fR.
.IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
.IX Item "--output SD | FP | text | all"
Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
.IP "\fB\-o, \-\-overwrite\fR" 4
.IX Item "-o, --overwrite"
Overwrite existing files.
.IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
.IX Item "-q, --quote Yes | No"
Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
\&\fIYes or No\fR. Default value: \fIYes\fR.
.IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
.IX Item "-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 \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
delimited text files, respectively.This option is ignored for multiple input files.
.IP "\fB\-s, \-\-size\fR \fInumber\fR" 4
.IX Item "-s, --size number"
Size of bit-vector to use during generation of fingerprints bit-vector string for
\&\fIExtendedConnectivityBits\fR value of \fB\-m, \-\-mode\fR. Default value: \fI1024\fR.
Valid values correspond to any positive integer which satisfies the following criteria:
power of 2, >= 32 and <= 2 ** 32.
.Sp
Examples:
.Sp
.Vb 3
\&   512
\&   1024
\&   2048
.Ve
.IP "\fB\-\-UsePerlCoreRandom\fR \fIYes | No\fR" 4
.IX Item "--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: \fIYes or No\fR. Default value: \fIYes\fR.
.Sp
\&\fINo\fR value option for \fB\-\-UsePerlCoreRandom\fR allows the generation of fingerprints
bit-vector strings which are same across different platforms.
.Sp
The random number generator implemented in MayaChemTools is a variant of
linear congruential generator (\s-1LCG\s0) as described by Miller et al. [ Ref 120 ].
It is also referred to as Lehmer random number generator or Park-Miller
random number generator.
.Sp
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.
.IP "\fB\-v, \-\-VectorStringFormat\fR \fIValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
.IX Item "-v, --VectorStringFormat ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
\&\fB\-\-output\fR used during <ExtendedConnectivityCount> value of \fB\-m, \-\-mode\fR option. Possible
values: \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
ValuesAndIDsPairsString\fR.
.Sp
Default value during <ExtendedConnectivityCount> value of \fB\-m, \-\-mode\fR option:
\&\fIIDsAndValuesString\fR.
.Sp
Default value during <ExtendedConnectivity> value of \fB\-m, \-\-mode\fR option: \fIValuesString\fR.
.Sp
Examples:
.Sp
.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
.Ve
.IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
.IX Item "-w, --WorkingDir DirName"
Location of working directory. Default: current directory.
.SH "EXAMPLES"
.IX Header "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:
.PP
.Vb 1
\&    % ExtendedConnectivityFingerprints.pl \-r SampleECAIFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityCount
\&      \-r SampleECAIFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityBits
\&      \-r SampleECAIFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityBits
\&      \-\-BitStringFormat BinaryString \-r SampleECAIFP \-o Sample.sdf
.Ve
.PP
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 \s-1CSV\s0 file along with fingerprints
vector strings data, type:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-\-output all \-r SampleECAIFP
\&      \-o Sample.sdf
.Ve
.PP
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 \s-1CSV\s0 file along with fingerprints
vector strings data, type:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityCount
\&      \-\-output all \-r SampleECAIFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes
\&      \-r SampleECFCFP \-o Sample.sdf
.Ve
.PP
To generate extended connectivity fingerprints corresponding to neighborhood radius up to
2 using \s-1DREIDING\s0 atom types in vector string format and create a SampleECFP.csv file
containing sequential compound IDs along with fingerprints vector strings data, type:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a DREIDINGAtomTypes
\&      \-r SampleECFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a EStateAtomTypes
\&      \-r SampleECFP \-o Sample.sdf
.Ve
.PP
To generate extended connectivity fingerprints corresponding to neighborhood radius up to
2 using \s-1MMFF94\s0 atom types in vector string format and create a SampleECFP.csv file
containing sequential compound IDs along with fingerprints vector strings data, type:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a MMFF94AtomTypes
\&      \-r SampleECFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a SLogPAtomTypes
\&      \-r SampleECFP \-o Sample.sdf
.Ve
.PP
To generate extended connectivity fingerprints corresponding to neighborhood radius up to
2 using \s-1SYBYL\s0 atom types in vector string format and create a SampleECFP.csv file
containing sequential compound IDs along with fingerprints vector strings data, type:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a SYBYLAtomTypes
\&      \-r SampleECFP \-o Sample.sdf
.Ve
.PP
To generate extended connectivity fingerprints corresponding to neighborhood radius up to
2 using \s-1TPSA\s0 atom types in vector string format and create a SampleECFP.csv file
containing sequential compound IDs along with fingerprints vector strings data, type:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a TPSAAtomTypes
\&      \-r SampleECFP \-o Sample.sdf
.Ve
.PP
To generate extended connectivity fingerprints corresponding to neighborhood radius up to
2 using \s-1UFF\s0 atom types in vector string format and create a SampleECFP.csv file
containing sequential compound IDs along with fingerprints vector strings data, type:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a UFFAtomTypes
\&      \-r SampleECFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes \-n 3
\&      \-r SampleECAIFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes \-n 3
\&      \-r SampleECFCFP \-o Sample.sdf
.Ve
.PP
To generate extended connectivity fingerprints corresponding to neighborhood radius up to
2 using only \s-1AS\s0,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:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes
\&      \-\-AtomicInvariantsToUse "AS,X" \-r SampleECAIFP \-o Sample.sdf
.Ve
.PP
To generate extended connectivity fingerprints corresponding to neighborhood radius up to
2 using only \s-1HBD\s0,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:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes
\&      \-\-FunctionalClassesToUse "HBD,HBA" \-r SampleECFCFP \-o Sample.sdf
.Ve
.PP
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 \s-1ID\s0 from molecule name line along with fingerprints vector strings
data, type:
.PP
.Vb 3
\&    % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes
\&      \-\-DataFieldsMode CompoundID \-CompoundIDMode MolName
\&      \-r SampleECAIFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 3
\&    % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes
\&      \-\-DataFieldsMode CompoundID \-CompoundIDMode DataField \-\-CompoundID Mol_ID
\&      \-r SampleECFCFP \-o Sample.sdf
.Ve
.PP
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 \s-1ID\s0 using combination of molecule name line and an explicit compound
prefix along with fingerprints vector strings data, type:
.PP
.Vb 3
\&    % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes
\&      \-\-DataFieldsMode CompoundID \-CompoundIDMode MolnameOrLabelPrefix
\&      \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleECAIFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 3
\&    % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes
\&      \-\-DataFieldsMode  Specify \-\-DataFields Mol_ID \-r SampleECFCFP
\&      \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes
\&      \-\-DataFieldsMode Common \-r SampleECAIFP \-o Sample.sdf
.Ve
.PP
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 \s-1CSV\s0 file along with fingerprints
vector strings data, type:
.PP
.Vb 3
\&    % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes
\&      \-\-DataFieldsMode All  \-\-output all \-r SampleECFCFP
\&      \-o Sample.sdf
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
.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.