Python3 and some other changes.

CHANGES.md

 Changes
 =======
 
+2.1
+---
+
+1. Now Python 3 compatible.
+2. Fixed minor bug that assigned atoms with names like "HG21" to element "HG"
+   rather than "H". No longer supporting element "HG".
+3. Improved formatting (black) and docstrings.
+4. Moved GUI wrapper to new `depreciated/` folder. This feature is no longer
+   supported.
+
 2.0.3
 -----
 
@@ -9,4 +19,4 @@ Changes
    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
+4. Spelling error ("Angstroms").

POVME2.LINUX

-python POVME2_GUI.py

POVME2.MacOSX.app/Contents/Info.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>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>

POVME2.MacOSX.app/Contents/document.wflow

-<?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>

POVME2.Windows.bat

-python POVME2_GUI.py

tools/For_Durrant/Corrective_Formatting_for_MDA.py

@@ -3,7 +3,7 @@ from sys import argv
 #Get VMD-annotated PDB from user through sys.argv
 script, pdb_file = argv
 
-print "This script will create a PDB /n with the correct formatting for MDA"
+print("This script will create a PDB /n with the correct formatting for MDA")
 #Creates a new Universe with user input
 u = MDAnalysis.Universe(pdb_file, topology_format = 'PDB')
 #Writes a new trajectory in the format MDAnalysis can work with

tools/For_Durrant/P_Vol_Over_Time.py

@@ -19,9 +19,9 @@ for line in volumes:
 	vol_dic[a] = float(b)
 
 #Creates a list of the volumes from vol_dic
-vol_list = vol_dic.values()  
+vol_list = list(vol_dic.values())  
 #Creates a list of the frames from vol_dic
-frame_num = vol_dic.keys()   
+frame_num = list(vol_dic.keys())   
 #Creates scatterplot, x = frames, y = volumes
 plt.scatter(frame_num, vol_list, marker = '.', s = 50, c = 'orange')
 # X axis label
@@ -31,7 +31,7 @@ plt.ylabel('Binding Pocket Volume')
 # Plot Title
 plt.title('Binding Pocket Volume Over Time')
 #Sets parameters of X axis for viewing
-plt.xticks(range(-1, len(frame_num), (len(frame_num)/10)))
+plt.xticks(list(range(-1, len(frame_num), (len(frame_num)/10))))
 plt.xlim([- 1, len(frame_num)])
 # Shows plot
 plt.savefig('Scatterplot.png')
\ No newline at end of file

tools/For_Durrant/Return_Largest_Smallest.py

@@ -18,12 +18,12 @@ for line in volumes:
 
 #Finds maximum value in volumes and stores as max_val
 max_val = 0
-for val in vol_dic.values():
+for val in list(vol_dic.values()):
 	if val > max_val:
 		max_val = val
 
 #Finds the frame of the maximum value and stores as max_val_frame
-for frame, volume in vol_dic.items():
+for frame, volume in list(vol_dic.items()):
 	if volume == max_val:
 		max_val_frame = frame
 
@@ -32,15 +32,15 @@ min_val = min(vol_dic.values())
 
 #Finds frame of minimum volume and stores as min_val_frame
 
-for frame, volume in vol_dic.items():
+for frame, volume in list(vol_dic.items()):
 	if volume == min_val:
 		min_val_frame = frame
 		
 
-print """
+print("""
 The maximum pocket volume of this data set is %r, at frame %r,
 while the minimum pocket volume of this data set is %r, at frame %r.
- 		""" % (max_val, max_val_frame, min_val, min_val_frame)
+ 		""" % (max_val, max_val_frame, min_val, min_val_frame))
 	
 
 

tools/For_Durrant/Return_MDframe_POVMEframe.py

@@ -5,7 +5,7 @@ from sys import argv
 script, pdb_file = argv
 
 #Get number of the POVME frame from User
-frame_num = raw_input("What is the frame number you want? ")
+frame_num = input("What is the frame number you want? ")
 frame_num_int = int(frame_num)
 frame_num_str = str(frame_num)
 
@@ -20,5 +20,5 @@ with mda.Writer("MD_frame_" + frame_num_str + ".pdb",
 				start = frame_num_int,
 				multiframe = False) as pdb:
 						pdb.write(u)
-print "Created new PDB file for specified frame, titled 'MD_frame_%r.pdb'" %frame_num
-print "Your POVME frame is titled 'POVME_frame_%r.pdb' " % frame_num
\ No newline at end of file
+print("Created new PDB file for specified frame, titled 'MD_frame_%r.pdb'" %frame_num)
+print("Your POVME frame is titled 'POVME_frame_%r.pdb' " % frame_num)
\ No newline at end of file

tools/For_Durrant/Volumes_Histogram.py

@@ -21,7 +21,7 @@ for line in volumes:
 
 
 #Create a list of volume values, store in vol_list
-vol_list = vol_dic.values()
+vol_list = list(vol_dic.values())
 #Sets bin parameters for the histogram
 #bins = np.array([n for n in range(0, len(vol_list)#, 5)])