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diff --git a/java/docs/feature/SSKey3DS.html b/java/docs/feature/SSKey3DS.html new file mode 100644 index 0000000..fad741d --- /dev/null +++ b/java/docs/feature/SSKey3DS.html @@ -0,0 +1,779 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.SSKEY3DS" +></A +>Pharmacophore fingerprint</H2 +><P +>Pharmacophore fingerprint [<A +HREF="bibliography.html#GXSB00" +>gxsb00</A +>]. +<DIV +CLASS="TABLE" +><A +NAME="AEN8" +></A +><P +><B +>Table 1. Pharmacophore fingerprint definition</B +></P +><TABLE +BORDER="1" +CLASS="CALSTABLE" +><THEAD +><TR +><TH +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Bit position</TH +><TH +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Set when</TH +></TR +></THEAD +><TBODY +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>1</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Fraction of rotatable bonds > 0.0</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>2</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Fraction of rotatable bonds > 0.1</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>3</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Fraction of rotatable bonds > 0.2</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>4</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Fraction of rotatable bonds > 0.3</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>5</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Fraction of rotatable bonds > 0.4</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>6</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 2</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>7</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 8</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>8</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 16</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>9</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 20</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>10</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 26</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>11</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 32</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>12</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 38</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>13</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a heterocycle</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>14</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains an aromatic hydroxy group</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>15</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains an aliphatic hydroxy group</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>16</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains an aliphatic secondary amine</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>17</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains an aliphatic tertiary amine</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>18</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a phenyl ring</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>19</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a ring containing nitrogen</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>20</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a -SO<SUB +>2</SUB +> group</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>21</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a -SO</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>22</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains an ester </TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>23</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains an amide </TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>24</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a 5-membered non-aromatic ring</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>25</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a 5-membered aromatic ring</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>26</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a 9-membered or larger (fused) ring</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>27</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a fused ring system</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>28</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a fused aromatic ring system</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>29</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a -OSO group</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>30</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a halogen atom</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>31</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a nitrogen atom attached to alpha-carbon of aromatic system</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>32</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a -NO<SUB +>2</SUB +> group</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>33</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains rings separated by 2-3 non-ring atoms</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>34</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains rings separated by 4-5 non-ring atoms</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>35</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a NN group</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>36</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a carbon atom attached to 3 carbons and a hetero atom</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>37</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains an oxygen atom separated by 2 atoms</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>38</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a methyl group attached to hetero atom</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>39</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a double bond</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>40</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a non-H atom linked to 3 heteroatoms</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>41</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a quaternary atom</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>42</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains 2 methylenes separated by 2 atoms</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>43</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains a non-ring oxygen atom attached to aromatic system</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>44</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Molecule contains 2 non-C,H atoms separated by 2 atoms</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>45</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Number of hydrogen bond acceptors >= 1</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>46</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Number of hydrogen bond acceptors >= 2</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>47</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Number of hydrogen bond acceptors >= 3</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>48</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Number of hydrogen bond acceptors >= 4</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>49</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Number of hydrogen bond acceptors >= 5</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>50</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Number of hydrogen bond acceptors >= 6</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>51</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Number of hydrogen bond acceptors >= 7</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>52</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Number of hydrogen bond acceptors >= 8</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>53</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Number of hydrogen bond acceptors >= 9</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>54</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Number of hydrogen bond acceptors >= 10</TD +></TR +></TBODY +></TABLE +></DIV +></P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +><A +HREF="bibliography.html" +ACCESSKEY="N" +>Next</A +></TD +></TR +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
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