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## NAME

MACCSKeysFingerprints.pl - Generate MACCS key fingerprints for SD files

## SYNOPSIS

MACCSKeysFingerprints.pl SDFile(s)...

MACCSKeysFingerprints.pl [--AromaticityModel AromaticityModelType] [--BitsOrder Ascending | Descending] [-b, --BitStringFormat BinaryString | HexadecimalString] [--CompoundID DataFieldName or LabelPrefixString] [--CompoundIDLabel text] [--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix] [--DataFields "FieldLabel1,FieldLabel2,..."] [-d, --DataFieldsMode All | Common | Specify | CompoundID] [-f, --Filter Yes | No] [--FingerprintsLabel text] [-h, --help] [-k, --KeepLargestComponent Yes | No] [-m, --mode MACCSKeyBits | MACCSKeyCount] [--OutDelim comma | tab | semicolon] [--output SD | FP | text | all] [-o, --overwrite] [-q, --quote Yes | No] [-r, --root RootName] [-s, --size number] [-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString] [-w, --WorkingDir DirName]

## DESCRIPTION

Generate MACCS (Molecular ACCess System) keys fingerprints [ Ref 45-47 ] for SDFile(s) and create appropriate SD, FP or CSV/TSV text file(s) containing fingerprints bit-vector or 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.

For each MACCS keys definition, atoms are processed to determine their membership to the key and the appropriate molecular fingerprints strings are generated. An atom can belong to multiple MACCS keys.

For MACCSKeyBits value of -m, --mode option, a fingerprint bit-vector string containing zeros and ones is generated and for MACCSKeyCount value, a fingerprint vector string corresponding to number of MACCS keys [ Ref 45-47 ] is generated.

MACCSKeyBits | MACCSKeyCount values for -m, --mode option along with two possible 166 | 322 values of -s, --size supports generation of four different types of MACCS keys fingerprint: MACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount.

Example of SD file containing MAACS keys fingerprints string data:

... ...
... ...
$$$$
... ...
... ...
... ...
41 44 0 0 0 0 0 0 0 0999 V2000 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
... ...
2 3 1 0 0 0 0
... ...
M END
> <CmpdID>
Cmpd1
> <MACCSKeysFingerprints>
FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;000000000
00000000000000000000000000000000100100001001000000001001000000001110001
00101010111100011011000100110110000011011110100110111111111111011111111
11111111110111000
$$$$
... ...
... ...

Example of FP file containing MAACS keys fingerprints string data:

#
# Package = MayaChemTools 7.4
# Release Date = Oct 21, 2010
#
# TimeStamp = Fri Mar 11 14:57:24 2011
#
# FingerprintsStringType = FingerprintsBitVector
#
# Description = MACCSKeyBits
# Size = 166
# BitStringFormat = BinaryString
# BitsOrder = Ascending
#
Cmpd1 00000000000000000000000000000000000000000100100001001000000001...
Cmpd2 00000000000000000000000010000000001000000010000000001000000000...
... ...
... ..

Example of CSV Text file containing MAACS keys fingerprints string data:

"CompoundID","MACCSKeysFingerprints"
"Cmpd1","FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;
00000000000000000000000000000000000000000100100001001000000001001000000
00111000100101010111100011011000100110110000011011110100110111111111111
01111111111111111110111000"
... ...
... ...

The current release of MayaChemTools generates the following types of MACCS keys fingerprints bit-vector and vector strings:

FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
0000000000000000000000000000000001001000010010000000010010000000011100
0100101010111100011011000100110110000011011110100110111111111111011111
11111111111110111000
FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000
000000021210210e845f8d8c60b79dffbffffd1
FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
1110011111100101111111000111101100110000000000000011100010000000000000
0000000000000000000000000000000000000000000000101000000000000000000000
0000000000000000000000000000000000000000000000000000000000000000000000
0000000000000000000000000000000000000011000000000000000000000000000000
0000000000000000000000000000000000000000
FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7
e7af3edc000c1100000000000000500000000000000000000000000000000300000000
000000000
FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0
0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0
5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1
3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1
FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0
0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...

## 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.

--BitsOrder Ascending | Descending

  Bits order to use during generation of fingerprints bit-vector string for MACCSKeyBits 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 MACCSKeyBits 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;MACCSKeyBits;166;BinaryString;Ascending;00000000
  0000000000000000000000000000000001001000010010000000010010000000011100
  0100101010111100011011000100110110000011011110100110111111111111011111
  11111111111110111000
  FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000
  000000021210210e845f8d8c60b79dffbffffd1
  FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
  1110011111100101111111000111101100110000000000000011100010000000000000
  0000000000000000000000000000000000000000000000101000000000000000000000
  0000000000000000000000000000000000000000000000000000000000000000000000
  0000000000000000000000000000000000000011000000000000000000000000000000
  0000000000000000000000000000000000000000
  FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7
  e7af3edc000c1100000000000000500000000000000000000000000000000300000000
  000000000
--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: MACCSKeyFingerprints.

-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 MACCSKeyBits | MACCSKeyCount

  Specify type of MACCS keys [ Ref 45-47 ] fingerprints to generate for molecules in SDFile(s). Possible values: MACCSKeyBits, MACCSKeyCount. Default value: MACCSKeyBits.

  For MACCSKeyBits value of -m, --mode option, a fingerprint bit-vector string containing zeros and ones is generated and for MACCSKeyCount value, a fingerprint vector string corresponding to number of MACCS keys is generated.

  MACCSKeyBits | MACCSKeyCount values for -m, --mode option along with two possible 166 | 322 values of -s, --size supports generation of four different types of MACCS keys fingerprint: MACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount.

  Definition of MACCS keys uses the following atom and bond symbols to define atom and bond environments:

  Atom symbols for 166 keys [ Ref 47 ]:
  A : Any valid periodic table element symbol
  Q : Hetro atoms; any non-C or non-H atom
  X : Halogens; F, Cl, Br, I
  Z : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I
  Atom symbols for 322 keys [ Ref 46 ]:
  A : Any valid periodic table element symbol
  Q : Hetro atoms; any non-C or non-H atom
  X : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I
  Z is neither defined nor used
  Bond types:
  - : Single
  = : Double
  T : Triple
  # : Triple
  ~ : Single or double query bond
  % : An aromatic query bond
  None : Any bond type; no explicit bond specified
  $ : Ring bond; $ before a bond type specifies ring bond
  ! : Chain or non-ring bond; ! before a bond type specifies chain bond
  @ : A ring linkage and the number following it specifies the atoms position in the line, thus @1 means linked back to the first atom in the list.
  Aromatic: Kekule or Arom5
  Kekule: Bonds in 6-membered rings with alternate single/double bonds or perimeter bonds
  Arom5: Bonds in 5-membered rings with two double bonds and a hetro atom at the apex of the ring.

  MACCS 166 keys [ Ref 45-47 ] are defined as follows:

  Key Description
  1 ISOTOPE
  2 103 < ATOMIC NO. < 256
  3 GROUP IVA,VA,VIA PERIODS 4-6 (Ge...)
  4 ACTINIDE
  5 GROUP IIIB,IVB (Sc...)
  6 LANTHANIDE
  7 GROUP VB,VIB,VIIB (V...)
  8 QAAA@1
  9 GROUP VIII (Fe...)
  10 GROUP IIA (ALKALINE EARTH)
  11 4M RING
  12 GROUP IB,IIB (Cu...)
  13 ON(C)C
  14 S-S
  15 OC(O)O
  16 QAA@1
  17 CTC
  18 GROUP IIIA (B...)
  19 7M RING
  20 SI
  21 C=C(Q)Q
  22 3M RING
  23 NC(O)O
  24 N-O
  25 NC(N)N
  26 C$=C($A)$A
  27 I
  28 QCH2Q
  29 P
  30 CQ(C)(C)A
  31 QX
  32 CSN
  33 NS
  34 CH2=A
  35 GROUP IA (ALKALI METAL)
  36 S HETEROCYCLE
  37 NC(O)N
  38 NC(C)N
  39 OS(O)O
  40 S-O
  41 CTN
  42 F
  43 QHAQH
  44 OTHER
  45 C=CN
  46 BR
  47 SAN
  48 OQ(O)O
  49 CHARGE
  50 C=C(C)C
  51 CSO
  52 NN
  53 QHAAAQH
  54 QHAAQH
  55 OSO
  56 ON(O)C
  57 O HETEROCYCLE
  58 QSQ
  59 Snot%A%A
  60 S=O
  61 AS(A)A
  62 A$A!A$A
  63 N=O
  64 A$A!S
  65 C%N
  66 CC(C)(C)A
  67 QS
  68 QHQH (&...)
  69 QQH
  70 QNQ
  71 NO
  72 OAAO
  73 S=A
  74 CH3ACH3
  75 A!N$A
  76 C=C(A)A
  77 NAN
  78 C=N
  79 NAAN
  80 NAAAN
  81 SA(A)A
  82 ACH2QH
  83 QAAAA@1
  84 NH2
  85 CN(C)C
  86 CH2QCH2
  87 X!A$A
  88 S
  89 OAAAO
  90 QHAACH2A
  91 QHAAACH2A
  92 OC(N)C
  93 QCH3
  94 QN
  95 NAAO
  96 5M RING
  97 NAAAO
  98 QAAAAA@1
  99 C=C
  100 ACH2N
  101 8M RING
  102 QO
  103 CL
  104 QHACH2A
  105 A$A($A)$A
  106 QA(Q)Q
  107 XA(A)A
  108 CH3AAACH2A
  109 ACH2O
  110 NCO
  111 NACH2A
  112 AA(A)(A)A
  113 Onot%A%A
  114 CH3CH2A
  115 CH3ACH2A
  116 CH3AACH2A
  117 NAO
  118 ACH2CH2A > 1
  119 N=A
  120 HETEROCYCLIC ATOM > 1 (&...)
  121 N HETEROCYCLE
  122 AN(A)A
  123 OCO
  124 QQ
  125 AROMATIC RING > 1
  126 A!O!A
  127 A$A!O > 1 (&...)
  128 ACH2AAACH2A
  129 ACH2AACH2A
  130 QQ > 1 (&...)
  131 QH > 1
  132 OACH2A
  133 A$A!N
  134 X (HALOGEN)
  135 Nnot%A%A
  136 O=A > 1
  137 HETEROCYCLE
  138 QCH2A > 1 (&...)
  139 OH
  140 O > 3 (&...)
  141 CH3 > 2 (&...)
  142 N > 1
  143 A$A!O
  144 Anot%A%Anot%A
  145 6M RING > 1
  146 O > 2
  147 ACH2CH2A
  148 AQ(A)A
  149 CH3 > 1
  150 A!A$A!A
  151 NH
  152 OC(C)C
  153 QCH2A
  154 C=O
  155 A!CH2!A
  156 NA(A)A
  157 C-O
  158 C-N
  159 O > 1
  160 CH3
  161 N
  162 AROMATIC
  163 6M RING
  164 O
  165 RING
  166 FRAGMENTS

  MACCS 322 keys set as defined in tables 1, 2 and 3 [ Ref 46 ] include:

  . 26 atom properties of type P, as listed in Table 1
  . 32 one-atom environments, as listed in Table 3
  . 264 atom-bond-atom combinations listed in Table 4

  Total number of keys in three tables is : 322

  Atom symbol, X, used for 322 keys [ Ref 46 ] doesn't refer to Halogens as it does for 166 keys. In order to keep the definition of 322 keys consistent with the published definitions, the symbol X is used to imply "others" atoms, but it's internally mapped to symbol X as defined for 166 keys during the generation of key values.

  Atom properties-based keys (26):

  Key Description
  1 A(AAA) or AA(A)A - atom with at least three neighbors
  2 Q - heteroatom
  3 Anot%not-A - atom involved in one or more multiple bonds, not aromatic
  4 A(AAAA) or AA(A)(A)A - atom with at least four neighbors
  5 A(QQ) or QA(Q) - atom with at least two heteroatom neighbors
  6 A(QQQ) or QA(Q)Q - atom with at least three heteroatom neighbors
  7 QH - heteroatom with at least one hydrogen attached
  8 CH2(AA) or ACH2A - carbon with at least two single bonds and at least two hydrogens attached
  9 CH3(A) or ACH3 - carbon with at least one single bond and at least three hydrogens attached
  10 Halogen
  11 A(-A-A-A) or A-A(-A)-A - atom has at least three single bonds
  12 AAAAAA@1 > 2 - atom is in at least two different six-membered rings
  13 A($A$A$A) or A$A($A)$A - atom has more than two ring bonds
  14 A$A!A$A - atom is at a ring/chain boundary. When a comparison is done with another atom the path passes through the chain bond.
  15 Anot%A%Anot%A - atom is at an aromatic/nonaromatic boundary. When a comparison is done with another atom the path passes through the aromatic bond.
  16 A!A!A - atom with more than one chain bond
  17 A!A$A!A - atom is at a ring/chain boundary. When a comparison is done with another atom the path passes through the ring bond.
  18 A%Anot%A%A - atom is at an aromatic/nonaromatic boundary. When a comparison is done with another atom the path passes through the nonaromatic bond.
  19 HETEROCYCLE - atom is a heteroatom in a ring.
  20 rare properties: atom with five or more neighbors, atom in four or more rings, or atom types other than H, C, N, O, S, F, Cl, Br, or I
  21 rare properties: atom has a charge, is an isotope, has two or more multiple bonds, or has a triple bond.
  22 N - nitrogen
  23 S - sulfur
  24 O - oxygen
  25 A(AA)A(A)A(AA) - atom has two neighbors, each with three or more neighbors (including the central atom).
  26 CHACH2 - atom has two hydrocarbon (CH2) neighbors

  Atomic environments properties-based keys (32):

  Key Description
  27 C(CC)
  28 C(CCC)
  29 C(CN)
  30 C(CCN)
  31 C(NN)
  32 C(NNC)
  33 C(NNN)
  34 C(CO)
  35 C(CCO)
  36 C(NO)
  37 C(NCO)
  38 C(NNO)
  39 C(OO)
  40 C(COO)
  41 C(NOO)
  42 C(OOO)
  43 Q(CC)
  44 Q(CCC)
  45 Q(CN)
  46 Q(CCN)
  47 Q(NN)
  48 Q(CNN)
  49 Q(NNN)
  50 Q(CO)
  51 Q(CCO)
  52 Q(NO)
  53 Q(CNO)
  54 Q(NNO)
  55 Q(OO)
  56 Q(COO)
  57 Q(NOO)
  58 Q(OOO)

  Note: The first symbol is the central atom, with atoms bonded to the central atom listed in parentheses. Q is any non-C, non-H atom. If only two atoms are in parentheses, there is no implication concerning the other atoms bonded to the central atom.

  Atom-Bond-Atom properties-based keys: (264)

  Key Description
  59 C-C
  60 C-N
  61 C-O
  62 C-S
  63 C-Cl
  64 C-P
  65 C-F
  66 C-Br
  67 C-Si
  68 C-I
  69 C-X
  70 N-N
  71 N-O
  72 N-S
  73 N-Cl
  74 N-P
  75 N-F
  76 N-Br
  77 N-Si
  78 N-I
  79 N-X
  80 O-O
  81 O-S
  82 O-Cl
  83 O-P
  84 O-F
  85 O-Br
  86 O-Si
  87 O-I
  88 O-X
  89 S-S
  90 S-Cl
  91 S-P
  92 S-F
  93 S-Br
  94 S-Si
  95 S-I
  96 S-X
  97 Cl-Cl
  98 Cl-P
  99 Cl-F
  100 Cl-Br
  101 Cl-Si
  102 Cl-I
  103 Cl-X
  104 P-P
  105 P-F
  106 P-Br
  107 P-Si
  108 P-I
  109 P-X
  110 F-F
  111 F-Br
  112 F-Si
  113 F-I
  114 F-X
  115 Br-Br
  116 Br-Si
  117 Br-I
  118 Br-X
  119 Si-Si
  120 Si-I
  121 Si-X
  122 I-I
  123 I-X
  124 X-X
  125 C=C
  126 C=N
  127 C=O
  128 C=S
  129 C=Cl
  130 C=P
  131 C=F
  132 C=Br
  133 C=Si
  134 C=I
  135 C=X
  136 N=N
  137 N=O
  138 N=S
  139 N=Cl
  140 N=P
  141 N=F
  142 N=Br
  143 N=Si
  144 N=I
  145 N=X
  146 O=O
  147 O=S
  148 O=Cl
  149 O=P
  150 O=F
  151 O=Br
  152 O=Si
  153 O=I
  154 O=X
  155 S=S
  156 S=Cl
  157 S=P
  158 S=F
  159 S=Br
  160 S=Si
  161 S=I
  162 S=X
  163 Cl=Cl
  164 Cl=P
  165 Cl=F
  166 Cl=Br
  167 Cl=Si
  168 Cl=I
  169 Cl=X
  170 P=P
  171 P=F
  172 P=Br
  173 P=Si
  174 P=I
  175 P=X
  176 F=F
  177 F=Br
  178 F=Si
  179 F=I
  180 F=X
  181 Br=Br
  182 Br=Si
  183 Br=I
  184 Br=X
  185 Si=Si
  186 Si=I
  187 Si=X
  188 I=I
  189 I=X
  190 X=X
  191 C#C
  192 C#N
  193 C#O
  194 C#S
  195 C#Cl
  196 C#P
  197 C#F
  198 C#Br
  199 C#Si
  200 C#I
  201 C#X
  202 N#N
  203 N#O
  204 N#S
  205 N#Cl
  206 N#P
  207 N#F
  208 N#Br
  209 N#Si
  210 N#I
  211 N#X
  212 O#O
  213 O#S
  214 O#Cl
  215 O#P
  216 O#F
  217 O#Br
  218 O#Si
  219 O#I
  220 O#X
  221 S#S
  222 S#Cl
  223 S#P
  224 S#F
  225 S#Br
  226 S#Si
  227 S#I
  228 S#X
  229 Cl#Cl
  230 Cl#P
  231 Cl#F
  232 Cl#Br
  233 Cl#Si
  234 Cl#I
  235 Cl#X
  236 P#P
  237 P#F
  238 P#Br
  239 P#Si
  240 P#I
  241 P#X
  242 F#F
  243 F#Br
  244 F#Si
  245 F#I
  246 F#X
  247 Br#Br
  248 Br#Si
  249 Br#I
  250 Br#X
  251 Si#Si
  252 Si#I
  253 Si#X
  254 I#I
  255 I#X
  256 X#X
  257 C$C
  258 C$N
  259 C$O
  260 C$S
  261 C$Cl
  262 C$P
  263 C$F
  264 C$Br
  265 C$Si
  266 C$I
  267 C$X
  268 N$N
  269 N$O
  270 N$S
  271 N$Cl
  272 N$P
  273 N$F
  274 N$Br
  275 N$Si
  276 N$I
  277 N$X
  278 O$O
  279 O$S
  280 O$Cl
  281 O$P
  282 O$F
  283 O$Br
  284 O$Si
  285 O$I
  286 O$X
  287 S$S
  288 S$Cl
  289 S$P
  290 S$F
  291 S$Br
  292 S$Si
  293 S$I
  294 S$X
  295 Cl$Cl
  296 Cl$P
  297 Cl$F
  298 Cl$Br
  299 Cl$Si
  300 Cl$I
  301 Cl$X
  302 P$P
  303 P$F
  304 P$Br
  305 P$Si
  306 P$I
  307 P$X
  308 F$F
  309 F$Br
  310 F$Si
  311 F$I
  312 F$X
  313 Br$Br
  314 Br$Si
  315 Br$I
  316 Br$X
  317 Si$Si
  318 Si$I
  319 Si$X
  320 I$I
  321 I$X
  322 X$X
--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><MACCSKeysFP>.<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 MACCS keys [ Ref 45-47 ] set to use during fingerprints generation. Possible values: 166 or 322. Default value: 166.

-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 MACCSKeyCount value of -m, --mode option. Possible values: ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString. Defaultvalue: ValuesString.

  Examples:

  FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
  ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
  0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0
  0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0
  5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1
  3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1
  FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
  ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0
  0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0
  0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
  0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
  0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...
-w, --WorkingDir DirName

  Location of working directory. Default: current directory.

## EXAMPLES

To generate MACCS keys fingerprints of size 166 in binary bit-vector string format and create a SampleMACCS166FPBin.csv file containing sequential compound IDs along with fingerprints bit-vector strings data, type:

% MACCSKeysFingerprints.pl -r SampleMACCS166FPBin -o Sample.sdf

To generate MACCS keys fingerprints of size 166 in binary bit-vector string format and create SampleMACCS166FPBin.sdf, SampleMACCS166FPBin.csv and SampleMACCS166FPBin.csv files containing sequential compound IDs in CSV file along with fingerprints bit-vector strings data, type:

% MACCSKeysFingerprints.pl --output all -r SampleMACCS166FPBin -o Sample.sdf

To generate MACCS keys fingerprints of size 322 in binary bit-vector string format and create a SampleMACCS322FPBin.csv file containing sequential compound IDs along with fingerprints bit-vector strings data, type:

% MACCSKeysFingerprints.pl -size 322 -r SampleMACCS322FPBin -o Sample.sdf

To generate MACCS keys fingerprints of size 166 corresponding to count of keys in ValuesString format and create a SampleMACCS166FPCount.csv file containing sequential compound IDs along with fingerprints vector strings data, type:

% MACCSKeysFingerprints.pl -m MACCSKeyCount -r SampleMACCS166FPCount -o Sample.sdf

To generate MACCS keys fingerprints of size 322 corresponding to count of keys in ValuesString format and create a SampleMACCS322FPCount.csv file containing sequential compound IDs along with fingerprints vector strings data, type:

% MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322 -r SampleMACCS322FPCount -o Sample.sdf

To generate MACCS keys fingerprints of size 166 in hexadecimal bit-vector string format with ascending bits order and create a SampleMACCS166FPHex.csv file containing compound IDs from MolName along with fingerprints bit-vector strings data, type:

% MACCSKeysFingerprints.pl -m MACCSKeyBits --size 166 --BitStringFormat HexadecimalString --BitsOrder Ascending --DataFieldsMode CompoundID --CompoundIDMode MolName -r SampleMACCS166FPBin -o Sample.sdf

To generate MACCS keys fingerprints of size 166 corresponding to count of keys in IDsAndValuesString format and create a SampleMACCS166FPCount.csv file containing compound IDs from MolName line along with fingerprints vector strings data, type:

% MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 --VectorStringFormat IDsAndValuesString --DataFieldsMode CompoundID --CompoundIDMode MolName -r SampleMACCS166FPCount -o Sample.sdf

To generate MACCS keys fingerprints of size 166 corresponding to count of keys in IDsAndValuesString format and create a SampleMACCS166FPCount.csv file containing compound IDs using specified data field along with fingerprints vector strings data, type:

% MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 --VectorStringFormat IDsAndValuesString --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID Mol_ID -r SampleMACCS166FPCount -o Sample.sdf

To generate MACCS keys fingerprints of size 322 corresponding to count of keys in ValuesString format and create a SampleMACCS322FPCount.tsv file containing compound IDs derived from combination of molecule name line and an explicit compound prefix along with fingerprints vector strings data in a column labels MACCSKeyCountFP, type:

% MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix --CompoundID Cmpd --CompoundIDLabel MolID --FingerprintsLabel MACCSKeyCountFP --OutDelim Tab -r SampleMACCS322FPCount -o Sample.sdf

To generate MACCS keys fingerprints of size 166 corresponding to count of keys in ValuesString format and create a SampleMACCS166FPCount.csv file containing specific data fields columns along with fingerprints vector strings data, type:

% MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 --VectorStringFormat ValuesString --DataFieldsMode Specify --DataFields Mol_ID -r SampleMACCS166FPCount -o Sample.sdf

To generate MACCS keys fingerprints of size 322 corresponding to count of keys in ValuesString format and create a SampleMACCS322FPCount.csv file containing common data fields columns along with fingerprints vector strings data, type:

% MACCSKeysFingerprints.pl -m MACCSKeyCount --size 322 --VectorStringFormat ValuesString --DataFieldsMode Common -r SampleMACCS322FPCount -o Sample.sdf

To generate MACCS keys fingerprints of size 166 corresponding to count of keys in ValuesString format and create SampleMACCS166FPCount.sdf, SampleMACCS166FPCount.fpf and SampleMACCS166FPCount.csv files containing all data fields columns in CSV file along with fingerprints vector strings data, type:

% MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 --output all --VectorStringFormat ValuesString --DataFieldsMode All -r SampleMACCS166FPCount -o Sample.sdf

## AUTHOR

Manish Sud

## SEE ALSO

InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.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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