\renewcommand{\sectitle}{The acidobasic.xml File} \section*{\sectitle} \addcontentsline{toc}{section}{\numberline{}\sectitle} \begin{verbatim} <?xml version="1.0" encoding="UTF-8" standalone="yes"?> <!-- DTD for polymer elements' pka data, used by the 'GNU polyxmass' suite of mass spectrometry applications. Copyright 2003, 2004 Filippo Rusconi - Licensed under the GNU GPL --> <!DOCTYPE acidobasicdata [ <!ELEMENT acidobasicdata (monomers*,modifs*)> <!ELEMENT monomers (mnm*)> <!ELEMENT modifs (mdf*)> <!ELEMENT mnm (code,chemgroup*)> <!ELEMENT mdf (name,chemgroup*)> <!ELEMENT chemgroup (name,(pka,acidcharged)?,polrule*,chemgrouprule*)> <!ELEMENT chemgrouprule (entity,name,outcome)> <!ELEMENT pka (#PCDATA)> <!ELEMENT value (#PCDATA)> <!ELEMENT code (#PCDATA)> <!ELEMENT outcome (#PCDATA)> <!ELEMENT name (#PCDATA)> <!ELEMENT entity (#PCDATA)> <!ELEMENT acidcharged (#PCDATA)> <!ELEMENT polrule (#PCDATA)> ]> <acidobasicdata> <monomers> <mnm> <code>A</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> </mnm> <mnm> <code>C</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> <chemgroup> <name>Lateral SH2</name> <pka>8.3</pka> <acidcharged>FALSE</acidcharged> <polrule>never_trapped</polrule> </chemgroup> </mnm> <mnm> <code>D</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.36</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> <chemgroup> <name>Lateral COOH</name> <pka>3.65</pka> <acidcharged>FALSE</acidcharged> <polrule>never_trapped</polrule> <chemgrouprule> <entity>MNM_MODIF</entity> <name>AmidationAsp</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> </mnm> <mnm> <code>E</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.36</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> <chemgroup> <name>Lateral COOH</name> <pka>4.25</pka> <acidcharged>FALSE</acidcharged> <polrule>never_trapped</polrule> <chemgrouprule> <entity>MNM_MODIF</entity> <name>AmidationGlu</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> </mnm> <mnm> <code>F</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> </mnm> <mnm> <code>G</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> </mnm> <mnm> <code>H</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.36</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> <chemgroup> <name>In-ring NH+</name> <pka>6</pka> <acidcharged>TRUE</acidcharged> <polrule>never_trapped</polrule> </chemgroup> </mnm> <mnm> <code>I</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> </mnm> <mnm> <code>K</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.36</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> <chemgroup> <name>Lateral NH2</name> <pka>10.53</pka> <acidcharged>TRUE</acidcharged> <polrule>never_trapped</polrule> <chemgrouprule> <entity>MNM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> </mnm> <mnm> <code>L</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> </mnm> <mnm> <code>M</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> </mnm> <mnm> <code>N</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> </mnm> <mnm> <code>P</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> </mnm> <mnm> <code>Q</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> </mnm> <mnm> <code>R</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.36</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> <chemgroup> <name>Lateral guanidinium</name> <pka>12.48</pka> <acidcharged>TRUE</acidcharged> <polrule>never_trapped</polrule> </chemgroup> </mnm> <mnm> <code>S</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> <chemgroup> <name>Lateral alcohol</name> <pka>13</pka> <acidcharged>FALSE</acidcharged> <polrule>never_trapped</polrule> <chemgrouprule> <entity>MNM_MODIF</entity> <name>Phosphorylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> </mnm> <mnm> <code>T</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> <chemgroup> <name>Lateral alcohol</name> <pka>13</pka> <acidcharged>FALSE</acidcharged> <polrule>never_trapped</polrule> <chemgrouprule> <entity>MNM_MODIF</entity> <name>Phosphorylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> </mnm> <mnm> <code>V</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> </mnm> <mnm> <code>W</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.35</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> </mnm> <mnm> <code>Y</code> <chemgroup> <name>N-term NH2</name> <pka>9.6</pka> <acidcharged>TRUE</acidcharged> <polrule>left_trapped</polrule> <chemgrouprule> <entity>LE_PLM_MODIF</entity> <name>Acetylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> <chemgroup> <name>C-term COOH</name> <pka>2.36</pka> <acidcharged>FALSE</acidcharged> <polrule>right_trapped</polrule> </chemgroup> <chemgroup> <name>Lateral phenol</name> <pka>10.1</pka> <acidcharged>FALSE</acidcharged> <polrule>never_trapped</polrule> <chemgrouprule> <entity>MNM_MODIF</entity> <name>Phosphorylation</name> <outcome>LOST</outcome> </chemgrouprule> </chemgroup> </mnm> </monomers> <modifs> <mdf> <name>Phosphorylation</name> <chemgroup> <name>none_set</name> <pka>12</pka> <acidcharged>FALSE</acidcharged> </chemgroup> <chemgroup> <name>none_set</name> <pka>7</pka> <acidcharged>FALSE</acidcharged> </chemgroup> </mdf> </modifs> </acidobasicdata> \end{verbatim} %%% Local Variables: %%% mode: latex %%% TeX-master: "polyxmass" %%% End: