Commit 0d3736e3 authored by Jacob Durrant's avatar Jacob Durrant

Deleting files from master branch to move development branch into master.

parent 76f6a3d7
Changes
=======
2.0.3
-----
1. Updated citation.
2. Convex hull now calculated based on locations of all heavy atoms. In 2.0.1,
it was all alpha carbons. Take care when comparing POVME 2.0.1 and POVME
2.0.2/2.0.3 output.
3. Fixed NumPy warning.
4. Spelling error ("Angstroms").
\ No newline at end of file
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python POVME2_GUI.py
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>AMIsApplet</key>
<true/>
<key>AMStayOpen</key>
<false/>
<key>BuildMachineOSBuild</key>
<string>13A563a</string>
<key>CFBundleDevelopmentRegion</key>
<string>English</string>
<key>CFBundleDocumentTypes</key>
<array>
<dict>
<key>CFBundleTypeExtensions</key>
<array>
<string>*</string>
</array>
<key>CFBundleTypeName</key>
<string>Automator workflow file</string>
<key>CFBundleTypeOSTypes</key>
<array>
<string>****</string>
</array>
<key>CFBundleTypeRole</key>
<string>Viewer</string>
</dict>
</array>
<key>CFBundleExecutable</key>
<string>Application Stub</string>
<key>CFBundleIconFile</key>
<string>AutomatorApplet</string>
<key>CFBundleIdentifier</key>
<string>com.apple.automator.POVME.MacOSX</string>
<key>CFBundleInfoDictionaryVersion</key>
<string>6.0</string>
<key>CFBundleName</key>
<string>POVME.MacOSX</string>
<key>CFBundlePackageType</key>
<string>APPL</string>
<key>CFBundleShortVersionString</key>
<string>1.2</string>
<key>CFBundleSignature</key>
<string>????</string>
<key>CFBundleURLTypes</key>
<array/>
<key>CFBundleVersion</key>
<string>381</string>
<key>DTCompiler</key>
<string>com.apple.compilers.llvm.clang.1_0</string>
<key>DTPlatformBuild</key>
<string>5A11344p</string>
<key>DTPlatformVersion</key>
<string>GM</string>
<key>DTSDKBuild</key>
<string>13A563a</string>
<key>DTSDKName</key>
<string></string>
<key>DTXcode</key>
<string>0500</string>
<key>DTXcodeBuild</key>
<string>5A11344p</string>
<key>LSMinimumSystemVersion</key>
<string>10.5</string>
<key>LSMinimumSystemVersionByArchitecture</key>
<dict>
<key>x86_64</key>
<string>10.6</string>
</dict>
<key>LSUIElement</key>
<true/>
<key>NSAppleScriptEnabled</key>
<string>YES</string>
<key>NSMainNibFile</key>
<string>ApplicationStub</string>
<key>NSPrincipalClass</key>
<string>NSApplication</string>
<key>NSServices</key>
<array/>
<key>UTExportedTypeDeclarations</key>
<array/>
<key>UTImportedTypeDeclarations</key>
<array/>
</dict>
</plist>
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>AMApplicationBuild</key>
<string>381</string>
<key>AMApplicationVersion</key>
<string>2.4</string>
<key>AMDocumentVersion</key>
<string>2</string>
<key>actions</key>
<array>
<dict>
<key>action</key>
<dict>
<key>AMAccepts</key>
<dict>
<key>Container</key>
<string>List</string>
<key>Optional</key>
<true/>
<key>Types</key>
<array>
<string>com.apple.applescript.object</string>
</array>
</dict>
<key>AMActionVersion</key>
<string>1.0.2</string>
<key>AMApplication</key>
<array>
<string>Automator</string>
</array>
<key>AMParameterProperties</key>
<dict>
<key>source</key>
<dict/>
</dict>
<key>AMProvides</key>
<dict>
<key>Container</key>
<string>List</string>
<key>Types</key>
<array>
<string>com.apple.applescript.object</string>
</array>
</dict>
<key>ActionBundlePath</key>
<string>/System/Library/Automator/Run AppleScript.action</string>
<key>ActionName</key>
<string>Run AppleScript</string>
<key>ActionParameters</key>
<dict>
<key>source</key>
<string>on run {input, parameters} set p to POSIX path of (path to me) return {p} end run</string>
</dict>
<key>BundleIdentifier</key>
<string>com.apple.Automator.RunScript</string>
<key>CFBundleVersion</key>
<string>1.0.2</string>
<key>CanShowSelectedItemsWhenRun</key>
<false/>
<key>CanShowWhenRun</key>
<true/>
<key>Category</key>
<array>
<string>AMCategoryUtilities</string>
</array>
<key>Class Name</key>
<string>RunScriptAction</string>
<key>InputUUID</key>
<string>FEE013EE-B901-460C-883A-F7AC8B5EDE7E</string>
<key>Keywords</key>
<array>
<string>Run</string>
</array>
<key>OutputUUID</key>
<string>494828F9-1CE2-4F19-AC89-D7134816A7F0</string>
<key>UUID</key>
<string>F68E1868-F5E5-49C1-AABC-A8E03A2F1C13</string>
<key>UnlocalizedApplications</key>
<array>
<string>Automator</string>
</array>
<key>arguments</key>
<dict>
<key>0</key>
<dict>
<key>default value</key>
<string>on run {input, parameters}
(* Your script goes here *)
return input
end run</string>
<key>name</key>
<string>source</string>
<key>required</key>
<string>0</string>
<key>type</key>
<string>0</string>
<key>uuid</key>
<string>0</string>
</dict>
</dict>
<key>isViewVisible</key>
<false/>
<key>location</key>
<string>309.500000:444.000000</string>
<key>nibPath</key>
<string>/System/Library/Automator/Run AppleScript.action/Contents/Resources/English.lproj/main.nib</string>
</dict>
<key>isViewVisible</key>
<false/>
</dict>
<dict>
<key>action</key>
<dict>
<key>AMAccepts</key>
<dict>
<key>Container</key>
<string>List</string>
<key>Optional</key>
<true/>
<key>Types</key>
<array>
<string>com.apple.cocoa.string</string>
</array>
</dict>
<key>AMActionVersion</key>
<string>2.0.3</string>
<key>AMApplication</key>
<array>
<string>Automator</string>
</array>
<key>AMParameterProperties</key>
<dict>
<key>COMMAND_STRING</key>
<dict/>
<key>CheckedForUserDefaultShell</key>
<dict/>
<key>inputMethod</key>
<dict/>
<key>shell</key>
<dict/>
<key>source</key>
<dict/>
</dict>
<key>AMProvides</key>
<dict>
<key>Container</key>
<string>List</string>
<key>Types</key>
<array>
<string>com.apple.cocoa.string</string>
</array>
</dict>
<key>ActionBundlePath</key>
<string>/System/Library/Automator/Run Shell Script.action</string>
<key>ActionName</key>
<string>Run Shell Script</string>
<key>ActionParameters</key>
<dict>
<key>COMMAND_STRING</key>
<string>cd ${1}
cd ../
if [ -f /usr/bin/python ];
then
/usr/bin/python POVME2_GUI.py &gt;/dev/null 2&gt;&amp;1&amp;
else
if [ -f /usr/local/bin/python ];
then
/usr/local/bin/python POVME2_GUI.py &gt;/dev/null 2&gt;&amp;1&amp;
else
if [ -f /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python/python ];
then
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python/python POVME2_GUI.py
else
python POVME2_GUI.py &gt;/dev/null 2&gt;&amp;1&amp;
fi
fi
fi
sleep 5
# set focus
if [ -f /usr/bin/osascript ];
then
/usr/bin/osascript -e 'tell app "Finder" to set frontmost of process "Python" to true'
fi</string>
<key>CheckedForUserDefaultShell</key>
<true/>
<key>inputMethod</key>
<integer>1</integer>
<key>shell</key>
<string>/bin/bash</string>
<key>source</key>
<string></string>
</dict>
<key>BundleIdentifier</key>
<string>com.apple.RunShellScript</string>
<key>CFBundleVersion</key>
<string>2.0.3</string>
<key>CanShowSelectedItemsWhenRun</key>
<false/>
<key>CanShowWhenRun</key>
<true/>
<key>Category</key>
<array>
<string>AMCategoryUtilities</string>
</array>
<key>Class Name</key>
<string>RunShellScriptAction</string>
<key>InputUUID</key>
<string>DCCAA7DF-D67B-4573-BFA2-C1EDA5C04F3E</string>
<key>Keywords</key>
<array>
<string>Shell</string>
<string>Script</string>
<string>Command</string>
<string>Run</string>
<string>Unix</string>
</array>
<key>OutputUUID</key>
<string>89BC9F1F-15F2-4E6A-9BEA-D11BEE95F481</string>
<key>UUID</key>
<string>537481C5-6175-4A2B-80F7-E50360DF2909</string>
<key>UnlocalizedApplications</key>
<array>
<string>Automator</string>
</array>
<key>arguments</key>
<dict>
<key>0</key>
<dict>
<key>default value</key>
<integer>0</integer>
<key>name</key>
<string>inputMethod</string>
<key>required</key>
<string>0</string>
<key>type</key>
<string>0</string>
<key>uuid</key>
<string>0</string>
</dict>
<key>1</key>
<dict>
<key>default value</key>
<string></string>
<key>name</key>
<string>source</string>
<key>required</key>
<string>0</string>
<key>type</key>
<string>0</string>
<key>uuid</key>
<string>1</string>
</dict>
<key>2</key>
<dict>
<key>default value</key>
<false/>
<key>name</key>
<string>CheckedForUserDefaultShell</string>
<key>required</key>
<string>0</string>
<key>type</key>
<string>0</string>
<key>uuid</key>
<string>2</string>
</dict>
<key>3</key>
<dict>
<key>default value</key>
<string></string>
<key>name</key>
<string>COMMAND_STRING</string>
<key>required</key>
<string>0</string>
<key>type</key>
<string>0</string>
<key>uuid</key>
<string>3</string>
</dict>
<key>4</key>
<dict>
<key>default value</key>
<string>/bin/sh</string>
<key>name</key>
<string>shell</string>
<key>required</key>
<string>0</string>
<key>type</key>
<string>0</string>
<key>uuid</key>
<string>4</string>
</dict>
</dict>
<key>isViewVisible</key>
<true/>
<key>location</key>
<string>309.500000:402.000000</string>
<key>nibPath</key>
<string>/System/Library/Automator/Run Shell Script.action/Contents/Resources/English.lproj/main.nib</string>
</dict>
<key>isViewVisible</key>
<true/>
</dict>
</array>
<key>connectors</key>
<dict>
<key>04317E67-C6FA-428A-83E0-5CF21C60218D</key>
<dict>
<key>from</key>
<string>F68E1868-F5E5-49C1-AABC-A8E03A2F1C13 - F68E1868-F5E5-49C1-AABC-A8E03A2F1C13</string>
<key>to</key>
<string>537481C5-6175-4A2B-80F7-E50360DF2909 - 537481C5-6175-4A2B-80F7-E50360DF2909</string>
</dict>
</dict>
<key>workflowMetaData</key>
<dict>
<key>workflowTypeIdentifier</key>
<string>com.apple.Automator.application</string>
</dict>
</dict>
</plist>
python POVME2_GUI.py
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# To run the POVME Pocket ID example, type the following into
# the unix command line from the current directory:
python ../../POVME_pocket_id.py --filename rel1_example.pdb --pocket_detection_resolution 4.0 --pocket_measuring_resolution 1.0 --clashing_cutoff 3.0 --number_of_neighbors 4 --processors 4 --number_of_spheres 5 --sphere_padding 5.0
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