CVS commit messages for the Adun project

Michael Johnston | 3 May 2012 18:57

Some scripts to help with testing

Commit from mjohnston

2012-05-03 18:57 CEST

Some scripts to help with testing Module File name Revision

+	Adun	Tests/PrintConfiguration.sh	1.1
+	Adun	Tests/SetLocalTestEnvironment.sh	1.1
+	Adun	Tests/UnsetLocalTestEnvironment.sh	1.1

<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2012-05-03 18:57 CEST</td>
      </tr></table>Some scripts to help with testing

    <table cellspacing="0" cellpadding="3" class="history">
<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemA0">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Tests/PrintConfiguration.sh</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tests/PrintConfiguration.sh?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
<tr class="itemA1">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Tests/SetLocalTestEnvironment.sh</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tests/SetLocalTestEnvironment.sh?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
<tr class="itemA0">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Tests/UnsetLocalTestEnvironment.sh</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tests/UnsetLocalTestEnvironment.sh?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
</table>
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Michael Johnston | 4 May 2012 14:43

Turn off verbose output by default

Commit from mjohnston

2012-05-04 14:43 CEST

Turn off verbose output by default Module File name Revision

Adun

Tools/AdunShell/AdunShellTool.m

1.23

>>>

1.24

<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2012-05-04 14:43 CEST</td>
      </tr></table>Turn off verbose output by default

    <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">Tools/AdunShell/AdunShellTool.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tools/AdunShell/AdunShellTool.m?rev=1.23&amp;content-type=text/vnd.viewcvs-markup">1.23</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tools/AdunShell/AdunShellTool.m?r1=1.23&amp;r2=1.24">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tools/AdunShell/AdunShellTool.m?rev=1.24&amp;content-type=text/vnd.viewcvs-markup">1.24</a></td>
      </tr>
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Cesar Avila | 9 May 2012 14:18

Some accesory awk scripts that I use for testing the effect of mutation [...]

Commit from clavila

2012-05-09 14:18 CEST

Some accesory awk scripts that I use for testing the effect of mutation on free energy of binding for two proteins. Module File name Revision

+	Adun	Scripts/aa2Ambercg.awk	1.1
+	Adun	Scripts/unfold.awk	1.1
+	Adun	Scripts/extractChain.awk	1.1

<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from clavila</td>
        <td align="right">2012-05-09 14:18 CEST</td>
      </tr></table>Some accesory awk scripts that I use for testing the effect of mutation
on free energy of binding for two proteins.

    <table cellspacing="0" cellpadding="3" class="history">
<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemA0">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Scripts/aa2Ambercg.awk</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/aa2Ambercg.awk?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
<tr class="itemA1">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Scripts/unfold.awk</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/unfold.awk?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
<tr class="itemA0">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Scripts/extractChain.awk</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/extractChain.awk?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
</table>
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Cesar Avila | 9 May 2012 14:35

Fixed for (commented out) a method that is no longer available.

Commit from clavila

2012-05-09 14:35 CEST

Fixed for (commented out) a method that is no longer available. Module File name Revision

Adun

Scripts/RMSDtraj.st

1.2

>>>

1.3

<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from clavila</td>
        <td align="right">2012-05-09 14:35 CEST</td>
      </tr></table>Fixed for (commented out) a method that is no longer available.

    <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">Scripts/RMSDtraj.st</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/RMSDtraj.st?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/Scripts/RMSDtraj.st?r1=1.2&amp;r2=1.3">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/RMSDtraj.st?rev=1.3&amp;content-type=text/vnd.viewcvs-markup">1.3</a></td>
      </tr>
</table>
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Cesar Avila | 9 May 2012 14:39

Added flag for GSL libs in strange locations

Commit from clavila

2012-05-09 14:39 CEST

Added flag for GSL libs in strange locations Module File name Revision

Adun

Plugins/Results/RMSD/GNUmakefile.preamble

1.1

>>>

1.2

<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from clavila</td>
        <td align="right">2012-05-09 14:39 CEST</td>
      </tr></table>Added flag for GSL libs in strange locations

    <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">Plugins/Results/RMSD/GNUmakefile.preamble</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Plugins/Results/RMSD/GNUmakefile.preamble?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/Plugins/Results/RMSD/GNUmakefile.preamble?r1=1.1&amp;r2=1.2">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Plugins/Results/RMSD/GNUmakefile.preamble?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
      </tr>
</table>
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Cesar Avila | 9 May 2012 14:41

Added HIE residue (needed for multiscale simulations)

Commit from clavila

2012-05-09 14:41 CEST

Added HIE residue (needed for multiscale simulations) Module File name Revision

Adun

UL/ULFramework/Resources/ForceFields/CG/CGTopology.ffml

1.1

>>>

1.2

<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from clavila</td>
        <td align="right">2012-05-09 14:41 CEST</td>
      </tr></table>Added HIE residue (needed for multiscale simulations)

    <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">UL/ULFramework/Resources/ForceFields/CG/CGTopology.ffml</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/ForceFields/CG/CGTopology.ffml?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/ForceFields/CG/CGTopology.ffml?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/ForceFields/CG/CGTopology.ffml?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
      </tr>
</table>
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Cesar Avila | 9 May 2012 14:48

Deleted a line that was no longer needed

Commit from clavila

2012-05-09 14:48 CEST

Deleted a line that was no longer needed Module File name Revision

Adun

Plugins/Controllers/Freeze/Freeze.m

1.6

>>>

1.7

<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from clavila</td>
        <td align="right">2012-05-09 14:48 CEST</td>
      </tr></table>Deleted a line that was no longer needed

    <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">Plugins/Controllers/Freeze/Freeze.m</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Plugins/Controllers/Freeze/Freeze.m?rev=1.6&amp;content-type=text/vnd.viewcvs-markup">1.6</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Plugins/Controllers/Freeze/Freeze.m?r1=1.6&amp;r2=1.7">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Plugins/Controllers/Freeze/Freeze.m?rev=1.7&amp;content-type=text/vnd.viewcvs-markup">1.7</a></td>
      </tr>
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Michael Johnston | 9 May 2012 15:32

Bash script which lists, in the sense of ls -lh, the files in the working copy which have been modified [...]

Commit from mjohnston

2012-05-09 15:32 CEST

Bash script which lists, in the sense of ls -lh, the files in the working copy which have been modified or will be changed with a 'cvs update'. The main purpose is to be able to determine when working copy changes were made Module File name Revision

+

Adun

DistributionTools/ModifiedFiles.sh

1.1

<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2012-05-09 15:32 CEST</td>
      </tr></table>Bash script which lists, in the sense of ls -lh, the files in the working copy which have been modified
or will be changed with a 'cvs update'.
The main purpose is to be able to determine when working copy changes were made

    <table cellspacing="0" cellpadding="3" class="history">
<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemA0">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">DistributionTools/ModifiedFiles.sh</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/DistributionTools/ModifiedFiles.sh?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
</table>
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Michael Johnston | 9 May 2012 16:00

Modify so directory to check under is supplied as arg

Commit from mjohnston

2012-05-09 16:00 CEST

Modify so directory to check under is supplied as arg Module File name Revision

Adun

DistributionTools/ModifiedFiles.sh

1.1

>>>

1.2

<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2012-05-09 16:00 CEST</td>
      </tr></table>Modify so directory to check under is supplied as arg

    <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">DistributionTools/ModifiedFiles.sh</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/DistributionTools/ModifiedFiles.sh?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/DistributionTools/ModifiedFiles.sh?r1=1.1&amp;r2=1.2">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/DistributionTools/ModifiedFiles.sh?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
      </tr>
</table>
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Michael Johnston | 9 May 2012 17:42

Moved and improved scripts and files [...]

Commit from mjohnston

2012-05-09 17:42 CEST

Moved and improved scripts and files Now can create a sandbox install of Adun for tests (under gnustep) This (should) bypass any installed Adun libs/executable/plugins, user-settings and user modified PATH and LD_LIBRARY_PATH Also the PrintConfiguration.sh script dumps information about the environment Adun is running under - this includes most relevant debug information. Module File name Revision

-	Adun	Tests/PrintConfiguration.sh	1.1
-	Adun	Tests/SetLocalTestEnvironment.sh	1.1
-	Adun	Tests/UnsetLocalTestEnvironment.sh	1.1
+	Adun	Tests/Environment/PrintConfiguration.sh		1.1
+	Adun	Tests/Environment/README.Environment		1.1
+	Adun	Tests/Environment/Sandbox.conf		1.1
+	Adun	Tests/Environment/SetLocalTestEnvironment.sh		1.1
+	Adun	Tests/Environment/UnsetLocalTestEnvironment.sh		1.1

<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2012-05-09 17:42 CEST</td>
      </tr></table>Moved and improved scripts and files
Now can create a sandbox install of Adun for tests (under gnustep)
This (should) bypass any installed Adun libs/executable/plugins, user-settings and user modified PATH and LD_LIBRARY_PATH
Also the PrintConfiguration.sh script dumps information about the environment Adun is running under - this includes most relevant debug information.

    <table cellspacing="0" cellpadding="3" class="history">
<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemR0">
<td class="itemact">-</td>
        <td class="item">Adun</td>
        <td class="item">Tests/PrintConfiguration.sh</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tests/Attic/PrintConfiguration.sh?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
      </tr>
<tr class="itemR1">
<td class="itemact">-</td>
        <td class="item">Adun</td>
        <td class="item">Tests/SetLocalTestEnvironment.sh</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tests/Attic/SetLocalTestEnvironment.sh?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
      </tr>
<tr class="itemR0">
<td class="itemact">-</td>
        <td class="item">Adun</td>
        <td class="item">Tests/UnsetLocalTestEnvironment.sh</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tests/Attic/UnsetLocalTestEnvironment.sh?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
      </tr>
<tr class="itemA1">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Tests/Environment/PrintConfiguration.sh</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tests/Environment/PrintConfiguration.sh?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
<tr class="itemA0">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Tests/Environment/README.Environment</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tests/Environment/README.Environment?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
<tr class="itemA1">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Tests/Environment/Sandbox.conf</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tests/Environment/Sandbox.conf?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
<tr class="itemA0">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Tests/Environment/SetLocalTestEnvironment.sh</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tests/Environment/SetLocalTestEnvironment.sh?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
<tr class="itemA1">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Tests/Environment/UnsetLocalTestEnvironment.sh</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Tests/Environment/UnsetLocalTestEnvironment.sh?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
</table>
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