Mercurial > repos > deepakjadmin > mayatool3_test2
view docs/scripts/txt/MACCSKeysFingerprints.txt @ 0:4816e4a8ae95 draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
| parents | |
| children |
line wrap: on
line source
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 <msud@san.rr.com> 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.