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1 <html>
2 <head>
3 <title>MayaChemTools:Documentation:FileIO::FingerprintsSDFileIO.pm</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FingerprintsFPFileIO.html" title="FingerprintsFPFileIO.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./FingerprintsTextFileIO.html" title="FingerprintsTextFileIO.html">Next</a></td><td width="34%" align="middle"><strong>FileIO::FingerprintsSDFileIO.pm</strong></td><td width="33%" align="right"><a href="././code/FingerprintsSDFileIO.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/FingerprintsSDFileIO.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/FingerprintsSDFileIO.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/FingerprintsSDFileIO.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/FingerprintsSDFileIO.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
16 </table>
17 </div>
18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>FingerprintsSDFileIO</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use FileIO::FingerprintsSDFileIO;</p>
26 <p>use FileIO::FingerprintsSDFileIO qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>FingerprintsSDFileIO</strong> class provides the following methods:</p>
31 <p> <a href="#new">new</a>, <a href="#getcompoundstring">GetCompoundString</a>, <a href="#getfingerprints">GetFingerprints</a>, <a href="#getfingerprintsstring">GetFingerprintsString</a>
32 , <a href="#isfingerprintsdatavalid">IsFingerprintsDataValid</a>, <a href="#isfingerprintsfiledatavalid">IsFingerprintsFileDataValid</a>, <a href="#isfingerprintssdfile">IsFingerprintsSDFile</a>, <a href="#next">Next</a>
33 , <a href="#read">Read</a>, <a href="#setbitstringformat">SetBitStringFormat</a>, <a href="#setbitsorder">SetBitsOrder</a>, <a href="#setcompoundidmode">SetCompoundIDMode</a>, <a href="#setcompoundstring">SetCompoundString</a>
34 , <a href="#setdetaillevel">SetDetailLevel</a>, <a href="#setfingerprints">SetFingerprints</a>, <a href="#setfingerprintsstring">SetFingerprintsString</a>, <a href="#setfingerprintsstringmode">SetFingerprintsStringMode</a>
35 , <a href="#setvectorstringformat">SetVectorStringFormat</a>, <a href="#writefingerprints">WriteFingerprints</a>, <a href="#writefingerprintsstring">WriteFingerprintsString</a>
36 </p><p>The following methods can also be used as functions:</p>
37 <p>IsFingerprintsSDFile</p>
38 <p><strong>FingerprintsSDFileIO</strong> class is derived from <em>FileIO</em> class and uses its methods to support
39 generic file related functionality.</p>
40 <p>The fingerprints SD file format with <strong>.sdf</strong> or <strong>.sd</strong> file extensions supports two types of
41 fingerprints string data: fingerprints bit-vectors and fingerprints vector strings. The fingerprints
42 string data is treated as value of a fingerprints data field label in a SD file.</p>
43 <p>Example of SD file format containing fingerprints string data:</p>
44 <div class="OptionsBox">
45 ... ...
46 <br/> ... ...
47 <br/> $$$$
48 <br/> ... ...
49 <br/> ... ...
50 <br/> ... ...
51 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
52 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
53 <br/> ... ...
54 <br/> 2 3 1 0 0 0 0
55 <br/> ... ...
56 <br/> M END
57 <br/> &gt; &lt;CmpdID&gt;
58 <br/> Test</div>
59 <div class="OptionsBox">
60 &gt; &lt;PathLengthFingerprints&gt;
61 <br/> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
62 <br/> h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
63 <br/> 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
64 <br/> 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
65 <br/> 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
66 <br/> aa0660a11014a011d46</div>
67 <div class="OptionsBox">
68 $$$$
69 <br/> ... ...
70 <br/> ... ...</div>
71 <p>The current release of MayaChemTools supports the following types of fingerprint
72 bit-vector and vector strings:</p>
73 <div class="OptionsBox">
74 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
75 <br/> us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
76 <br/> C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
77 <br/> 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
78 <br/> TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
79 <br/> -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...</div>
80 <div class="OptionsBox">
81 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
82 <br/> ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
83 <br/> .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
84 <br/> O.X1.BO2;2 4 14 3 10 1 1 1 3 2</div>
85 <div class="OptionsBox">
86 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
87 <br/> ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
88 <br/> N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1</div>
89 <div class="OptionsBox">
90 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
91 <br/> umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
92 <br/> 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
93 <br/> 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
94 <br/> O9 O10 O11 O12 OS F Cl Br I Hal P S1 S2 S3 Me1 Me2;5 0 0 0 2 0 0 0 0 1
95 <br/> 1 0 0 1 0 0 0 14 0 4 2 1 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0...</div>
96 <div class="OptionsBox">
97 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
98 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
99 <br/> H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
100 <br/> .024 -2.270</div>
101 <div class="OptionsBox">
102 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
103 <br/> ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
104 <br/> 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
105 <br/> 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
106 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div>
107 <div class="OptionsBox">
108 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
109 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
110 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
111 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
112 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
113 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
114 <div class="OptionsBox">
115 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
116 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
117 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
118 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
119 <br/> 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
120 <br/> 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</div>
121 <div class="OptionsBox">
122 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
123 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
124 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
125 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
126 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
127 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
128 <div class="OptionsBox">
129 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
130 <br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
131 <br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
132 <br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
133 <br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
134 <br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div>
135 <div class="OptionsBox">
136 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
137 <br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
138 <br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
139 <br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
140 <br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
141 <br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div>
142 <div class="OptionsBox">
143 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
144 <br/> 0000000000000000000000000000000001001000010010000000010010000000011100
145 <br/> 0100101010111100011011000100110110000011011110100110111111111111011111
146 <br/> 11111111111110111000</div>
147 <div class="OptionsBox">
148 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
149 <br/> 1110011111100101111111000111101100110000000000000011100010000000000000
150 <br/> 0000000000000000000000000000000000000000000000101000000000000000000000
151 <br/> 0000000000000000000000000000000000000000000000000000000000000000000000
152 <br/> 0000000000000000000000000000000000000011000000000000000000000000000000
153 <br/> 0000000000000000000000000000000000000000</div>
154 <div class="OptionsBox">
155 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
156 <br/> 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
157 <br/> 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
158 <br/> 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
159 <br/> 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
160 <br/> 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</div>
161 <div class="OptionsBox">
162 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
163 <br/> 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
164 <br/> 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
165 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
166 <br/> 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
167 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...</div>
168 <div class="OptionsBox">
169 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
170 <br/> th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
171 <br/> 0100010101011000101001011100110001000010001001101000001001001001001000
172 <br/> 0010110100000111001001000001001010100100100000000011000000101001011100
173 <br/> 0010000001000101010100000100111100110111011011011000000010110111001101
174 <br/> 0101100011000000010001000011000010100011101100001000001000100000000...</div>
175 <div class="OptionsBox">
176 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
177 <br/> 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
178 <br/> C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
179 <br/> 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
180 <br/> 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
181 <br/> 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....</div>
182 <div class="OptionsBox">
183 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
184 <br/> h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
185 <br/> 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N
186 <br/> 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
187 <br/> CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
188 <br/> OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...</div>
189 <div class="OptionsBox">
190 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
191 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
192 <br/> .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
193 <br/> H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
194 <br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
195 <br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...</div>
196 <div class="OptionsBox">
197 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
198 <br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
199 <br/> Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
200 <br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
201 <br/> 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
202 <br/> 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...</div>
203 <div class="OptionsBox">
204 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
205 <br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
206 <br/> C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
207 <br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
208 <br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div>
209 <div class="OptionsBox">
210 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
211 <br/> lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
212 <br/> H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
213 <br/> ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
214 <br/> 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2</div>
215 <div class="OptionsBox">
216 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
217 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
218 <br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
219 <br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
220 <br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
221 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
222 <br/> 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...</div>
223 <div class="OptionsBox">
224 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
225 <br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
226 <br/> .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
227 <br/> D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
228 <br/> -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
229 <br/> 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...</div>
230 <div class="OptionsBox">
231 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
232 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
233 <br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
234 <br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
235 <br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
236 <br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
237 <br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div>
238 <div class="OptionsBox">
239 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
240 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
241 <br/> 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
242 <br/> 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
243 <br/> 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
244 <br/> 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...</div>
245 <div class="OptionsBox">
246 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
247 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
248 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
249 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
250 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
251 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
252 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
253 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
254 <div class="OptionsBox">
255 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
256 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
257 <br/> 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
258 <br/> 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
259 <br/> 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
260 <br/> 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...</div>
261 <p>
262 </p>
263 <h2>METHODS</h2>
264 <dl>
265 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
266 <dd>
267 <div class="OptionsBox">
268 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(%IOParameters);</div>
269 <p>Using specified <em>IOParameters</em> names and values hash, <strong>new</strong> method creates a new
270 object and returns a reference to a newly created <strong>FingerprintsSDFileIO</strong> object. By default,
271 the following properties are initialized during <em>Read</em> mode:</p>
272 <div class="OptionsBox">
273 Name = '';
274 <br/> Mode = 'Read';
275 <br/> Status = 0;
276 <br/> FingerprintsStringMode = 'AutoDetect';
277 <br/> FingerprintsFieldLabel = 'AutoDetect';
278 <br/> CompoundIDMode = 'LabelPrefix';
279 <br/> CompoundIDFieldLabel = undef;
280 <br/> CompoundIDPrefix = 'Cmpd';
281 <br/> ValidateData = 1;
282 <br/> DetailLevel = 1;</div>
283 <p>During <em>Write</em> mode, the following properties get initialize by default:</p>
284 <div class="OptionsBox">
285 FingerprintsStringMode = undef;</div>
286 <div class="OptionsBox">
287 BitStringFormat = HexadecimalString;
288 <br/> BitsOrder = Ascending;</div>
289 <div class="OptionsBox">
290 VectorStringFormat = NumericalValuesString or ValuesString;</div>
291 <p>Examples:</p>
292 <div class="OptionsBox">
293 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
294 'Name' =&gt; 'Sample.sdf',
295 'Mode' =&gt; 'Read');</div>
296 <div class="OptionsBox">
297 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
298 'Name' =&gt; 'Sample.sdf',
299 'Mode' =&gt; 'Read',;
300 'FingerprintsStringMode' =&gt;
301 'AutoDetect',
302 'FingerprintsFieldLabel' =&gt;
303 'Fingerprints',
304 'CompoundIDMode' =&gt;
305 'DataField',
306 'CompoundIDFieldLabel' =&gt;
307 'CompoundID');</div>
308 <div class="OptionsBox">
309 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
310 'Name' =&gt; 'Sample.sdf',
311 'Mode' =&gt; 'Write',
312 'FingerprintsStringMode' =&gt;
313 'FingerprintsBitVectorString',
314 'Overwrite' =&gt; 1,
315 'BitStringFormat' =&gt; 'HexadecimalString',
316 'BitsOrder' =&gt; 'Ascending');</div>
317 <div class="OptionsBox">
318 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
319 'Name' =&gt; 'Sample.sd',
320 'Mode' =&gt; 'Write',
321 'FingerprintsStringMode' =&gt;
322 'FingerprintsVectorString',
323 'Overwrite' =&gt; 1,
324 'VectorStringFormat' =&gt; 'IDsAndValuesString',
325 'FingerprintsLabel' =&gt; 'Fingerprints');</div>
326 </dd>
327 <dt><strong><a name="getcompoundstring" class="item"><strong>GetCompoundString</strong></a></strong></dt>
328 <dd>
329 <div class="OptionsBox">
330 $CompoundString = $FingerprintsSDFileIO-&gt;GetCompoundString();</div>
331 <p>Returns <strong>CompoundString</strong> for current compound.</p>
332 </dd>
333 <dt><strong><a name="getfingerprints" class="item"><strong>GetFingerprints</strong></a></strong></dt>
334 <dd>
335 <div class="OptionsBox">
336 $FingerprintsObject = $FingerprintsSDFileIO-&gt;GetFingerprints();</div>
337 <p>Returns <strong>FingerprintsObject</strong> generated for current compound using fingerprints bit-vector
338 or vector string data. The fingerprints object corresponds to any of the supported fingerprints
339 such as PathLengthFingerprints, ExtendedConnectivity, and so on.</p>
340 </dd>
341 <dt><strong><a name="getfingerprintsstring" class="item"><strong>GetFingerprintsString</strong></a></strong></dt>
342 <dd>
343 <div class="OptionsBox">
344 $FingerprintsString = $FingerprintsSDFileIO-&gt;GetFingerprintsString();</div>
345 <p>Returns <strong>FingerprintsString</strong> for current compound.</p>
346 </dd>
347 <dt><strong><a name="isfingerprintsdatavalid" class="item"><strong>IsFingerprintsDataValid</strong></a></strong></dt>
348 <dd>
349 <div class="OptionsBox">
350 $Status = $FingerprintsSDFileIO-&gt;IsFingerprintsDataValid();</div>
351 <p>Returns 1 or 0 based on whether <strong>FingerprintsObject</strong> is valid.</p>
352 </dd>
353 <dt><strong><a name="isfingerprintsfiledatavalid" class="item"><strong>IsFingerprintsFileDataValid</strong></a></strong></dt>
354 <dd>
355 <div class="OptionsBox">
356 $Status = $FingerprintsSDFileIO-&gt;IsFingerprintsFileDataValid();</div>
357 <p>Returns 1 or 0 based on whether fingerprints file contains valid fingerprints data.</p>
358 </dd>
359 <dt><strong><a name="isfingerprintssdfile" class="item"><strong>IsFingerprintsSDFile</strong></a></strong></dt>
360 <dd>
361 <div class="OptionsBox">
362 $Status = $FingerprintsSDFileIO-&gt;IsFingerprintsSDFile($FileName);
363 <br/> $Status = FileIO::FingerprintsSDFileIO::IsFingerprintsSDFile($FileName);</div>
364 <p>Returns 1 or 0 based on whether <em>FileName</em> is a SD file.</p>
365 </dd>
366 <dt><strong><a name="next_or_read" class="item"><strong>Next or Read</strong></a></strong></dt>
367 <dd>
368 <div class="OptionsBox">
369 $FingerprintsSDFileIO = $FingerprintsSDFileIO-&gt;Next();
370 <br/> $FingerprintsSDFileIO = $FingerprintsSDFileIO-&gt;Read();</div>
371 <p>Reads next available compound fingerprints in SD file, processes the data, generates appropriate
372 fingerprints object, and returns <strong>FingerprintsSDFileIO</strong>. The generated fingerprints object is available
373 using method <strong>GetFingerprints</strong>.</p>
374 </dd>
375 <dt><strong><a name="setbitstringformat" class="item"><strong>SetBitStringFormat</strong></a></strong></dt>
376 <dd>
377 <div class="OptionsBox">
378 $FingerprintsSDFileIO-&gt;SetBitStringFormat($Format);</div>
379 <p>Sets bit string <em>Format</em> for fingerprints bit-vector string data in a SD file and returns <strong>FingerprintsSDFileIO</strong>.
380 Possible values for <strong>BitStringFormat</strong>: <em>BinaryString or HexadecimalString</em>.</p>
381 </dd>
382 <dt><strong><a name="setbitsorder" class="item"><strong>SetBitsOrder</strong></a></strong></dt>
383 <dd>
384 <div class="OptionsBox">
385 $FingerprintsSDFileIO-&gt;SetBitsOrder($BitsOrder);</div>
386 <p>Sets <em>BitsOrder</em> for fingerprints bit-vector string data in SD file and returns <strong>FingerprintsSDFileIO</strong>.
387 Possible values for <strong>BitsOrder</strong>: <em>Ascending or Descending</em>.</p>
388 </dd>
389 <dt><strong><a name="setcompoundidmode" class="item"><strong>SetCompoundIDMode</strong></a></strong></dt>
390 <dd>
391 <div class="OptionsBox">
392 $FingerprintsSDFileIO-&gt;SetCompoundIDMode($Mode);</div>
393 <p>Sets compound ID <em>Mode</em> for fingerprints bit-vector string data in a SD file and returns <strong>FingerprintsSDFileIO</strong>.
394 Possible values for <strong>CompoundIDMode</strong>: <em>DataField, MolName, LabelPrefix, or MolNameOrLabelPrefix</em>.</p>
395 </dd>
396 <dt><strong><a name="setcompoundstring" class="item"><strong>SetCompoundString</strong></a></strong></dt>
397 <dd>
398 <div class="OptionsBox">
399 $FingerprintsSDFileIO-&gt;SetCompoundString($CompoundString);</div>
400 <p>Sets <em>CompoundString</em> and returns <strong>FingerprintsSDFileIO</strong>.</p>
401 </dd>
402 <dt><strong><a name="setdetaillevel" class="item"><strong>SetDetailLevel</strong></a></strong></dt>
403 <dd>
404 <div class="OptionsBox">
405 $FingerprintsSDFileIO-&gt;SetDetailLevel($Level);</div>
406 <p>Sets details <em>Level</em> for generating diagnostics messages during SD file processing and returns
407 <strong>FingerprintsSDFileIO</strong>. Possible values: <em>Positive integers</em>.</p>
408 </dd>
409 <dt><strong><a name="setfingerprints" class="item"><strong>SetFingerprints</strong></a></strong></dt>
410 <dd>
411 <div class="OptionsBox">
412 $FingerprintsSDFileIO-&gt;SetFingerprints($FingerprintsObject);</div>
413 <p>Sets <em>FingerprintsObject</em> for current data line and returns <strong>FingerprintsSDFileIO</strong>.</p>
414 </dd>
415 <dt><strong><a name="setfingerprintsstring" class="item"><strong>SetFingerprintsString</strong></a></strong></dt>
416 <dd>
417 <div class="OptionsBox">
418 $FingerprintsSDFileIO-&gt;SetFingerprintsString($FingerprintsString);</div>
419 <p>Sets <em>FingerprintsString</em> for current data line and returns <strong>FingerprintsSDFileIO</strong>.</p>
420 </dd>
421 <dt><strong><a name="setfingerprintsstringmode" class="item"><strong>SetFingerprintsStringMode</strong></a></strong></dt>
422 <dd>
423 <div class="OptionsBox">
424 $FingerprintsSDFileIO-&gt;SetFingerprintsStringMode($Mode);</div>
425 <p>Sets <em>FingerprintsStringMode</em> for SD file and returns <strong>FingerprintsFPFileIO</strong>.
426 Possible values: <em>AutoDetect, FingerprintsBitVectorString, or FingerprintsVectorString</em></p>
427 </dd>
428 <dt><strong><a name="setvectorstringformat" class="item"><strong>SetVectorStringFormat</strong></a></strong></dt>
429 <dd>
430 <div class="OptionsBox">
431 $FingerprintsSDFileIO-&gt;SetVectorStringFormat($Format);</div>
432 <p>Sets <em>VectorStringFormat</em> for SD file and returns <strong>FingerprintsFPFileIO</strong>. Possible values:
433 <em>IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString</em>.</p>
434 </dd>
435 <dt><strong><a name="writefingerprints" class="item"><strong>WriteFingerprints</strong></a></strong></dt>
436 <dd>
437 <div class="OptionsBox">
438 $FingerprintsFPFileIO-&gt;WriteFingerprints($FingerprintsObject,
439 $CompoundID);</div>
440 <p>Writes fingerprints string generated from <em>FingerprintsObject</em> object and other data including
441 <em>CompoundID</em> to SD file and returns <strong>FingerprintsSDFileIO</strong>.</p>
442 </dd>
443 <dt><strong><a name="writefingerprintsstring" class="item"><strong>WriteFingerprintsString</strong></a></strong></dt>
444 <dd>
445 <div class="OptionsBox">
446 $FingerprintsSDFileIO-&gt;WriteFingerprints($FingerprintsString,
447 $CompoundID);</div>
448 <p>Writes <em>FingerprintsString</em> and other data including <em>CompoundID</em> to SD file and returns
449 <strong>FingerprintsSDFileIO</strong>.</p>
450 <p>Caveats:</p>
451 <div class="OptionsBox">
452 o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat
453 values are ignored during writing of fingerprints and it's written to the file
454 as it is.
455 <br/> o CompoundString is not checked to remove any existing fingerprints data</div>
456 </dd>
457 </dl>
458 <p>
459 </p>
460 <h2>AUTHOR</h2>
461 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
462 <p>
463 </p>
464 <h2>SEE ALSO</h2>
465 <p><a href="./FingerprintsTextFileIO.html">FingerprintsTextFileIO.pm</a>,&nbsp<a href="./FingerprintsFPFileIO.html">FingerprintsFPFileIO.pm</a>,&nbsp<a href="./SDFileIO.html">SDFileIO.pm</a>
466 </p>
467 <p>
468 </p>
469 <h2>COPYRIGHT</h2>
470 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
471 <p>This file is part of MayaChemTools.</p>
472 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
473 the terms of the GNU Lesser General Public License as published by the Free
474 Software Foundation; either version 3 of the License, or (at your option)
475 any later version.</p>
476 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
477 <table width="100%" border=0 cellpadding=0 cellspacing=2>
478 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FingerprintsFPFileIO.html" title="FingerprintsFPFileIO.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./FingerprintsTextFileIO.html" title="FingerprintsTextFileIO.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>FileIO::FingerprintsSDFileIO.pm</strong></td></tr>
479 </table>
480 </div>
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483 <img src="../../images/h2o2.png">
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