Michael Johnston | 27 Jun 17:29 2008
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Added HSE and HSD - Charmm histidines. [...]

Commit from mjohnston 2008-06-27 17:29 CEST
Added HSE and HSD - Charmm histidines. However this map is not required when using PDB v 3.0 Module File name Revision
Adun UL/ULFramework/Resources/iupacPdbMap.plist 1.1 >>> 1.2


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2008-06-27 17:29 CEST</td>
      </tr></table>Added HSE and HSD - Charmm histidines.
However this map is not required when using PDB v 3.0

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">UL/ULFramework/Resources/iupacPdbMap.plist</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/iupacPdbMap.plist?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/iupacPdbMap.plist?r1=1.1&amp;r2=1.2">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/iupacPdbMap.plist?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
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Michael Johnston | 27 Jun 17:31 2008
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Formalised ULPasteboardDataSource protocol

Commit from mjohnston 2008-06-27 17:31 CEST
Formalised ULPasteboardDataSource protocol Module File name Revision
Adun UL/ULPasteboard.m 1.2 >>> 1.3
Adun UL/ULPasteboard.h 1.2 >>> 1.3


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2008-06-27 17:31 CEST</td>
      </tr></table>Formalised ULPasteboardDataSource protocol

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">UL/ULPasteboard.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULPasteboard.m?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULPasteboard.m?r1=1.2&amp;r2=1.3">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULPasteboard.m?rev=1.3&amp;content-type=text/vnd.viewcvs-markup">1.3</a></td>
      </tr>
<tr class="itemM1">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">UL/ULPasteboard.h</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULPasteboard.h?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULPasteboard.h?r1=1.2&amp;r2=1.3">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULPasteboard.h?rev=1.3&amp;content-type=text/vnd.viewcvs-markup">1.3</a></td>
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Michael Johnston | 27 Jun 17:44 2008
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Added unarchiveFromFile: method. [...]

Commit from mjohnston 2008-06-27 17:44 CEST
Added unarchiveFromFile: method. There is a problem unarchive the date field from a gnustep object on cocoa. The problem seems to only exist with specific gnustep version but I'm not sure which yet. Unfortunately the problem is fatal - it automatically causes the program to crash. Since the archives with the problem can't be identified a priori yet I've had to remove decoding of the date field under Cocoa. Module File name Revision
Adun UL/ViewController.m 1.46 >>> 1.47
Adun Kernel/AdunKernel/Framework/AdunModelObject.m 1.21 >>> 1.22
Adun Kernel/AdunKernel/Headers/AdunKernel/AdunModelObject.h 1.18 >>> 1.19


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2008-06-27 17:44 CEST</td>
      </tr></table>Added unarchiveFromFile: method.
There is a problem unarchive the date field from a gnustep object on cocoa. The problem seems to only exist with specific gnustep version but I'm not sure which yet.
Unfortunately the problem is fatal - it automatically causes the program to crash.
Since the archives with the problem can't be identified a priori yet I've had to remove decoding of the date field under Cocoa.

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">UL/ViewController.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ViewController.m?rev=1.46&amp;content-type=text/vnd.viewcvs-markup">1.46</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ViewController.m?r1=1.46&amp;r2=1.47">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ViewController.m?rev=1.47&amp;content-type=text/vnd.viewcvs-markup">1.47</a></td>
      </tr>
<tr class="itemM1">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Framework/AdunModelObject.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunModelObject.m?rev=1.21&amp;content-type=text/vnd.viewcvs-markup">1.21</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunModelObject.m?r1=1.21&amp;r2=1.22">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunModelObject.m?rev=1.22&amp;content-type=text/vnd.viewcvs-markup">1.22</a></td>
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Headers/AdunKernel/AdunModelObject.h</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunModelObject.h?rev=1.18&amp;content-type=text/vnd.viewcvs-markup">1.18</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunModelObject.h?r1=1.18&amp;r2=1.19">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunModelObject.h?rev=1.19&amp;content-type=text/vnd.viewcvs-markup">1.19</a></td>
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Michael Johnston | 27 Jun 17:46 2008
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Added gslVectorRepresentation method to NSArray.

Commit from mjohnston 2008-06-27 17:46 CEST
Added gslVectorRepresentation method to NSArray. Module File name Revision
Adun Kernel/AdunKernel/Framework/AdunDataMatrix.m 1.38 >>> 1.39
Adun Kernel/AdunKernel/Headers/AdunKernel/AdunDataMatrix.h 1.22 >>> 1.23


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2008-06-27 17:46 CEST</td>
      </tr></table>Added gslVectorRepresentation method to NSArray.

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Framework/AdunDataMatrix.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunDataMatrix.m?rev=1.38&amp;content-type=text/vnd.viewcvs-markup">1.38</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunDataMatrix.m?r1=1.38&amp;r2=1.39">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunDataMatrix.m?rev=1.39&amp;content-type=text/vnd.viewcvs-markup">1.39</a></td>
      </tr>
<tr class="itemM1">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Headers/AdunKernel/AdunDataMatrix.h</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunDataMatrix.h?rev=1.22&amp;content-type=text/vnd.viewcvs-markup">1.22</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunDataMatrix.h?r1=1.22&amp;r2=1.23">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunDataMatrix.h?rev=1.23&amp;content-type=text/vnd.viewcvs-markup">1.23</a></td>
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Michael Johnston | 27 Jun 17:45 2008
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Added convenience methods [...]

Commit from mjohnston 2008-06-27 17:45 CEST
Added convenience methods initWithDataSource: and systemWithDataSource: Module File name Revision
Adun Kernel/AdunKernel/Framework/AdunSystem.m 1.18 >>> 1.19
Adun Kernel/AdunKernel/Headers/AdunKernel/AdunSystem.h 1.10 >>> 1.11


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2008-06-27 17:45 CEST</td>
      </tr></table>Added convenience methods
initWithDataSource: and systemWithDataSource:

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Framework/AdunSystem.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunSystem.m?rev=1.18&amp;content-type=text/vnd.viewcvs-markup">1.18</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunSystem.m?r1=1.18&amp;r2=1.19">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunSystem.m?rev=1.19&amp;content-type=text/vnd.viewcvs-markup">1.19</a></td>
      </tr>
<tr class="itemM1">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Headers/AdunKernel/AdunSystem.h</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunSystem.h?rev=1.10&amp;content-type=text/vnd.viewcvs-markup">1.10</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunSystem.h?r1=1.10&amp;r2=1.11">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunSystem.h?rev=1.11&amp;content-type=text/vnd.viewcvs-markup">1.11</a></td>
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Michael Johnston | 27 Jun 17:33 2008
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Enable dragging of analysis table contents.

Commit from mjohnston 2008-06-27 17:33 CEST
Enable dragging of analysis table contents. Module File name Revision
Adun UL/ULAnalyserDataSetView.m 1.17 >>> 1.18


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2008-06-27 17:33 CEST</td>
      </tr></table>Enable dragging of analysis table contents.

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">UL/ULAnalyserDataSetView.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULAnalyserDataSetView.m?rev=1.17&amp;content-type=text/vnd.viewcvs-markup">1.17</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULAnalyserDataSetView.m?r1=1.17&amp;r2=1.18">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULAnalyserDataSetView.m?rev=1.18&amp;content-type=text/vnd.viewcvs-markup">1.18</a></td>
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Michael Johnston | 27 Jun 17:32 2008
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Fixed hydrogen naming in Histidines (HSE and HSD).

Commit from mjohnston 2008-06-27 17:32 CEST
Fixed hydrogen naming in Histidines (HSE and HSD). Module File name Revision
Adun UL/ULFramework/Resources/ForceFields/Charmm27/Charmm27Topology.ffml 1.2 >>> 1.3


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2008-06-27 17:32 CEST</td>
      </tr></table>Fixed hydrogen naming in Histidines (HSE and HSD).

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">UL/ULFramework/Resources/ForceFields/Charmm27/Charmm27Topology.ffml</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/ForceFields/Charmm27/Charmm27Topology.ffml?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/ForceFields/Charmm27/Charmm27Topology.ffml?r1=1.2&amp;r2=1.3">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/ForceFields/Charmm27/Charmm27Topology.ffml?rev=1.3&amp;content-type=text/vnd.viewcvs-markup">1.3</a></td>
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Michael Johnston | 27 Jun 17:31 2008
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Updated todos.

Commit from mjohnston 2008-06-27 17:31 CEST
Updated todos. Module File name Revision
Adun UL/ULFramework/ULURLDownload.h 1.4 >>> 1.5


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2008-06-27 17:31 CEST</td>
      </tr></table>Updated todos.

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">UL/ULFramework/ULURLDownload.h</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/ULURLDownload.h?rev=1.4&amp;content-type=text/vnd.viewcvs-markup">1.4</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/ULURLDownload.h?r1=1.4&amp;r2=1.5">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/ULURLDownload.h?rev=1.5&amp;content-type=text/vnd.viewcvs-markup">1.5</a></td>
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Michael Johnston | 27 Jun 17:49 2008
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Added forceFieldForSystem: method. [...]

Commit from mjohnston 2008-06-27 17:49 CEST
Added forceFieldForSystem: method. Detects the force-field the system was built using and creates and returns an instance of the corresponding force-field class. Module File name Revision
Adun Kernel/AdunKernel/Framework/AdunMolecularMechanicsForceField.m 1.15 >>> 1.16
Adun Kernel/AdunKernel/Headers/AdunKernel/AdunMolecularMechanicsForceField.h 1.4 >>> 1.5


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2008-06-27 17:49 CEST</td>
      </tr></table>Added forceFieldForSystem: method.
Detects the force-field the system was built using and creates and returns an instance of the corresponding force-field class.

    <table cellspacing="0" cellpadding="3" class="history">
<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Framework/AdunMolecularMechanicsForceField.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunMolecularMechanicsForceField.m?rev=1.15&amp;content-type=text/vnd.viewcvs-markup">1.15</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunMolecularMechanicsForceField.m?r1=1.15&amp;r2=1.16">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunMolecularMechanicsForceField.m?rev=1.16&amp;content-type=text/vnd.viewcvs-markup">1.16</a></td>
      </tr>
<tr class="itemM1">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Headers/AdunKernel/AdunMolecularMechanicsForceField.h</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunMolecularMechanicsForceField.h?rev=1.4&amp;content-type=text/vnd.viewcvs-markup">1.4</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunMolecularMechanicsForceField.h?r1=1.4&amp;r2=1.5">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunMolecularMechanicsForceField.h?rev=1.5&amp;content-type=text/vnd.viewcvs-markup">1.5</a></td>
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Michael Johnston | 27 Jun 17:50 2008
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BugFix: Not passing system parameter in initWithSystem: method.

Commit from mjohnston 2008-06-27 17:50 CEST
BugFix: Not passing system parameter in initWithSystem: method. Module File name Revision
Adun Kernel/AdunKernel/Framework/AdunGRFNonbondedTerm.m 1.16 >>> 1.17
Adun Kernel/AdunKernel/Framework/AdunPureNonbondedTerm.m 1.18 >>> 1.19
Adun Kernel/AdunKernel/Framework/AdunShiftedNonbondedTerm.m 1.19 >>> 1.20


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2008-06-27 17:50 CEST</td>
      </tr></table>BugFix: Not passing system parameter in initWithSystem: method.

    <table cellspacing="0" cellpadding="3" class="history">
<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Framework/AdunGRFNonbondedTerm.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunGRFNonbondedTerm.m?rev=1.16&amp;content-type=text/vnd.viewcvs-markup">1.16</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunGRFNonbondedTerm.m?r1=1.16&amp;r2=1.17">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunGRFNonbondedTerm.m?rev=1.17&amp;content-type=text/vnd.viewcvs-markup">1.17</a></td>
      </tr>
<tr class="itemM1">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Framework/AdunPureNonbondedTerm.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunPureNonbondedTerm.m?rev=1.18&amp;content-type=text/vnd.viewcvs-markup">1.18</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunPureNonbondedTerm.m?r1=1.18&amp;r2=1.19">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunPureNonbondedTerm.m?rev=1.19&amp;content-type=text/vnd.viewcvs-markup">1.19</a></td>
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Framework/AdunShiftedNonbondedTerm.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunShiftedNonbondedTerm.m?rev=1.19&amp;content-type=text/vnd.viewcvs-markup">1.19</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunShiftedNonbondedTerm.m?r1=1.19&amp;r2=1.20">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunShiftedNonbondedTerm.m?rev=1.20&amp;content-type=text/vnd.viewcvs-markup">1.20</a></td>
      </tr>
</table>
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