v1.2.10

build/lib/packman/__init__.py

@@ -14,5 +14,5 @@
 from .utilities import *
 
 
-#VERSION CHANGE HERE CHANGES IT IN docs AND setup.py; STILL NEED TO CHANGE IT IN requirement.txt
-__version__='1.2.9'
+#VERSION CHANGE HERE CHANGES IT IN docs AND setup.py
+__version__='1.2.10'

build/lib/packman/anm/anm.py

@@ -2,12 +2,11 @@
 """The 'ANM' object host file.
 
 This is file information, not the class information. This information is only for the API developers.
-Please read the 'ANM' object documentation for details. [ help(packman.anm.ANM) ]
+Please read the 'ANM' object documentation for details.
 
-Example:
-
-    >>>from packman.anm import ANM
-    >>>help( ANM )
+Example::
+    from packman.anm import ANM
+    help( ANM )
 
 Notes:
     * Tutorial: https://jerniganlab.github.io/Software/PACKMAN/Tutorials/compliance
@@ -278,14 +277,13 @@ def calculate_stiffness_compliance(self):
         self.compliance_profile = [numpy.nanmean(i) for i in compliance_map]
         return True
 
-    def calculate_movie(self,mode_number,scale=1.5,n=10, direction="both"):
-        """Get the movie of the obtained LINEAR modes.
+    def calculate_movie(self,mode_number,scale=1.5,n=20):
+        """Get the movie of the obtained LINEAR modes. The first frame is the original structure and the projection progresses in positive (+) direction, returning to original structure and then in negative direction (-) again returning to the original structure.
 
         Args:
             mode_number (int)                   : Mode number. (first non-rigid mode is 6th)
-            scale (float)                       : Multiplier; extent to which mode will be extrapolated. Defaults to 1.5.
-            n (int)                             : Number of frames in output                             Defaults to 10
-            direction (both/+/-)                : Explore specific direcrion of the motion.              Defaults to "both"
+            scale (float)                       : Multiplier; extent to which mode will be extrapolated.                 Defaults to 1.5
+            n (int)                             : Number of frames in output (should be =>8 and ideally multiple of 4)   Defaults to 20
 
         Note:
             - Scale and n parameters should be redesigned.
@@ -297,12 +295,7 @@ def calculate_movie(self,mode_number,scale=1.5,n=10, direction="both"):
         x0=self.coords
         new_coords=[]
         with open('ANM_'+str(mode_number)+'.pdb','w') as fh:
-            if(direction=="both"):
-                movement = [k for k in range(-n,n)]+[k for k in range(-n,n)[::-1]]
-            elif(direction=="+"):
-                movement = [k for k in range(n)]+[k for k in range(n)[::-1]]
-            elif(direction=="-"):
-                movement = [k for k in range(-n,1)]+[k for k in range(-n,1)[::-1]]
+            movement = [ numpy.sin(k*(1.0/float(n))*2*numpy.pi) for k in range(0,n+1,1) ]
             for j in movement:
                 for numi,i in enumerate(x0):
                     new_x=i[0]+scale*j*self.eigen_vectors[:,mode_number][(numi*3)+0]

build/lib/packman/anm/hd_anm.py

@@ -2,7 +2,7 @@
 """The 'hdANM' object host file.
 
 This is file information, not the class information. This information is only for the API developers.
-Please read the 'hdANM' object documentation for details. [ help(packman.anm.hdANM) ]
+Please read the 'hdANM' object documentation for details.
 
 About .hng File:
 - hdANM requires the information about hinges and domains in the .hng format.
@@ -11,20 +11,20 @@
 
 Filename_ChainID    Domain/HingeId   ResidueStartPosition:ResidueEndPosition
 
-Example of .hng file for PDBID 1EXR
+Example of .hng file for PDBID 1EXR::
 
-1EXR_A  D1  1:70
-1EXR_A  H1  70:90
-1EXR_A  D2  90:148
+    1EXR_A  D1  1:70
+    1EXR_A  H1  70:90
+    1EXR_A  D2  90:148
 
 Above format means that there are two domains (D1 and D2) separated by a hinge (H1). D1 stretches from residue 1 to 70; D2 stretches from 90 to 148 and hinge H1 is in the middle.
 
 
 
-Example:
+Example::
 
-    >>>from packman.anm import hdANM
-    >>>help( hdANM )
+    from packman.anm import hdANM
+    help( hdANM )
 
 Notes:
     * Tutorial:
@@ -552,15 +552,14 @@ def calculate_cross_correlation( self, n_modes = "all" ):
 
                 self.crosscorrelation_matrix[i][j] = trace_H_inv_ij / numpy.sqrt( trace_H_inv_ii*trace_H_inv_jj )
 
-    def calculate_movie(self,mode_number,scale=1.5,n=10, extrapolation="curvilinear", direction="both", ftype='cif'):
-        """This function generates the dynamic 3D projection of the normal modes obtained using hd-ANM. The 3D projection can be linearly extrapolated or curvilinearly extrapolated depending on the choices.
+    def calculate_movie(self, mode_number, scale=1.5, n=20, extrapolation="curvilinear", ftype='cif'):
+        """This function generates the dynamic 3D projection of the normal modes obtained using hd-ANM. The 3D projection can be linearly extrapolated or curvilinearly extrapolated depending on the choices. The first frame is the original structure and the projection progresses in positive (+) direction, returning to original structure and then in negative direction (-) again returning to the original structure.
 
         Args:
             mode_number (int)                   : Mode number. (first non-rigid mode is 6th)
-            scale (float)                       : Multiplier; extent to which mode will be extrapolated. Defaults to 1.5.
-            n (int)                             : Number of frames in output                             Defaults to 10
-            extrapolation (linear/curvilinear)  : Extrapolation method                                   Defaults to "curvilinear"
-            direction (both/+/-)                : Explore specific direcrion of the motion.              Defaults to "both"
+            scale (float)                       : Multiplier; extent to which mode will be extrapolated.                 Defaults to 1.5
+            n (int)                             : Number of frames in output (should be =>8 and ideally multiple of 4)   Defaults to 20
+            extrapolation (linear/curvilinear)  : Extrapolation method                                                   Defaults to "curvilinear"
             ftype (string)                      : Extension of the output file (.cif / .pdb)
 
         Note:
@@ -576,13 +575,7 @@ def calculate_movie(self,mode_number,scale=1.5,n=10, extrapolation="curvilinear"
         new_coords=[]
 
         if(extrapolation=="linear"):
-
-            if(direction=="both"):
-                movement = [k for k in range(-n,n)]+[k for k in range(-n,n)[::-1]]
-            elif(direction=="+"):
-                movement = [k for k in range(n)]+[k for k in range(n)[::-1]]
-            elif(direction=="-"):
-                movement = [k for k in range(-n,1)]+[k for k in range(-n,1)[::-1]]
+            movement = [ numpy.sin(k*(1.0/float(n))*2*numpy.pi) for k in range(0,n+1,1) ]
             ModelsOfTheProtein = []
             for j in movement:
                 HingeResidue=0
@@ -614,13 +607,7 @@ def calculate_movie(self,mode_number,scale=1.5,n=10, extrapolation="curvilinear"
 
 
         elif(extrapolation=="curvilinear"):
-
-            if(direction=="both"):
-                movement = [k for k in range(-n,n)]+[k for k in range(-n,n)[::-1]]
-            elif(direction=="+"):
-                movement = [k for k in range(n)]+[k for k in range(n)[::-1]]
-            elif(direction=="-"):
-                movement = [k for k in range(-n,1)]+[k for k in range(-n,1)[::-1]]
+            movement = [ numpy.sin(k*(1.0/float(n))*2*numpy.pi) for k in range(0,n+1,1) ]
             ModelsOfTheProtein = []
             for j in movement:
                 HingeResidue=0
@@ -660,11 +647,11 @@ def calculate_movie(self,mode_number,scale=1.5,n=10, extrapolation="curvilinear"
                     currentatm = Atom(self.atoms[numi].get_id() , self.atoms[numi].get_name(), numpy.array([new_x,new_y,new_z]), self.atoms[numi].get_occupancy(), self.atoms[numi].get_bfactor(), self.atoms[numi].get_element(),self.atoms[numi].get_charge(), self.atoms[numi].get_parent() )
                     AtomsOfTheFrame[numi] = currentatm
 
-                ModelsOfTheProtein.append( Model(j, AtomsOfTheFrame, None, None, None, None) )    
+                ModelsOfTheProtein.append( Model(j, AtomsOfTheFrame, None, None, None, None) )
 
             Annotations = self.atoms[0].get_parent().get_parent().get_parent().get_parent().get_data()
             prot = Protein(str(mode_number), ModelsOfTheProtein)
             prot.set_data(Annotations)
-            prot.write_structure( str(mode_number)+'.'+ftype ) 
+            prot.write_structure( str(mode_number)+'.'+ftype )
 
         return True

build/lib/packman/apps/__init__.py

@@ -7,7 +7,7 @@
 Notes:
     * Current apps list: - predict_hinge : A program to predict the hinge on the molecule given the atoms and relevent parameters
 
-Example:
+Example::
     * Review the packman.bin.PACKMAN.py file for the app use.
 
 Todo:

build/lib/packman/apps/predict_hinge.py

@@ -2,12 +2,12 @@
 """The 'predict_hinge' object host file.
 
 This is file information, not the class information. This information is only for the API developers.
-Please read the 'predict_hinge' object documentation for details. [ help(packman.apps.predict_hinge) ]
+Please read the 'predict_hinge' object documentation for details.
 
-Example:
+Example::
 
-    >>>from packman import apps
-    >>>help( apps.predict_hinge )
+    from packman.apps import predict_hinge
+    help( predict_hinge )
 
 Todo:
     * Finish writing up the documentation.

build/lib/packman/bin/PACKMAN.py

@@ -228,10 +228,17 @@ def show_frame(self,frame_name):
 
 class top_menu(tk.Frame):
     def __init__(self,parent):
-        tk.Frame.__init__(self)
-        tk.Button(parent, text = 'Home',             command = lambda: parent.show_frame('HomePage')        ).grid(row=0,column=0,sticky=E+W)
-        tk.Button(parent, text = 'Hinge Prediction', command = lambda: parent.show_frame('HingePrediction') ).grid(row=0,column=1,sticky=E+W)
-        tk.Button(parent, text = 'hdANM',            command = lambda: parent.show_frame('hdANM_GUI')       ).grid(row=0,column=2,sticky=E+W)
+        number_of_buttons = 3
+        Canvas_top_menu = tk.Canvas(parent)
+        Canvas_top_menu.grid(row=0,column=0,columnspan=3, sticky=E+W )
+
+        for i in range(0,number_of_buttons):
+            Grid.columnconfigure(Canvas_top_menu, i, weight=1)
+
+        #tk.Frame.__init__(self)
+        tk.Button(Canvas_top_menu, text = 'Home',             command = lambda: parent.show_frame('HomePage')        ).grid( row=0,column=0,sticky=E+W )
+        tk.Button(Canvas_top_menu, text = 'Hinge Prediction', command = lambda: parent.show_frame('HingePrediction') ).grid( row=0,column=1,sticky=E+W )
+        tk.Button(Canvas_top_menu, text = 'hdANM',            command = lambda: parent.show_frame('hdANM_GUI')       ).grid( row=0,column=2,sticky=E+W )
 
 
 
@@ -257,9 +264,9 @@ def __init__(self,parent):
         self.all_objects = self.__dict__
 
     def show(self):
-        self.Label1.grid(row=1,columnspan=3)
-        self.Label2.grid(row=2,columnspan=3)
-        self.Text1.grid(row=3,columnspan=3)
+        self.Label1.grid(row=1,columnspan=3, sticky=E+W, padx=10, pady=10 )
+        self.Label2.grid(row=2,columnspan=3, sticky=E+W, padx=10, pady=10 )
+        self.Text1.grid(row=3,columnspan=3, sticky=E+W, padx=10, pady=10 )
 
     def hide(self):
         for i in self.all_objects:
@@ -381,11 +388,10 @@ def run_PACKMAN(self):
         #At this point, everything is okay
 
 
-        #Results
+        #Hinge Prediction Results
         pop_up1 = tk.Toplevel()
         pop_up1.title('PACKMAN Results')
 
-        #Canvas
         Canvas1 = tk.Canvas(pop_up1)
         Canvas1.grid(row=0,column=0,columnspan=6,sticky=N+S+E+W, padx=10, pady=10 )
 
@@ -503,7 +509,6 @@ def show_details(content):
         #on_click() Ends here
         return True
 
-
 
 
 '''

build/lib/packman/molecule/annotations.py

@@ -4,10 +4,10 @@
 This is file information, not the class information. This information is only for the API developers.
 Please read the corrosponding object documentation for details.
 
-Example:
+Example::
 
-    >>>from packman import molecule
-    >>>help( molecule.Hinge )
+    from packman.molecule import Hinge
+    help( Hinge )
 
 Todo:
     * Finish writing up the documentation.

build/lib/packman/molecule/atom.py

@@ -2,15 +2,13 @@
 """The 'Atom' object host file.
 
 This is file information, not the class information. This information is only for the API developers.
-Please read the 'Atom' object documentation for details. [ help(packman.molecule.atoms.Atom) ]
+Please read the 'Atom' object documentation for details.
 
-Example:
-    >>>from packman.molecule import atom.Atom
-    >>>help( Atom )
-    OR
+Example::
+
+    from packman.molecule import Atom
+    help( Atom )
 
-    >>>from packman import molecule
-    >>>help( molecule.Atom )
 
 Todo:
     * Finish writing up the documentation.

build/lib/packman/molecule/chain.py

@@ -2,15 +2,12 @@
 """The 'Chain' object host file.
 
 This is file information, not the class information. This information is only for the API developers.
-Please read the 'Chain' object documentation for details. [ help(packman.molecule.chain.Chain) ]
+Please read the 'Chain' object documentation for details.
 
-Example:
-    >>>from packman.molecule import chain.Chain
-    >>>help( Chain )
-    OR
+Example::
 
-    >>>from packman import molecule
-    >>>help( molecule.Chain )
+    from packman.molecule import Chain
+    help( Chain )
 
 Note:
     * Iterating over chain only fetches the residues not the hetero atoms

build/lib/packman/molecule/hetmol.py

@@ -2,15 +2,12 @@
 """The 'HetMol' object host file.
 
 This is file information, not the class information. This information is only for the API developers.
-Please read the 'HetMol' object documentation for details. [ help(packman.molecule.residue.Residue) ]
+Please read the 'HetMol' object documentation for details.
 
-Example:
-    >>>from packman.molecule import residue.HetMol
-    >>>help( HetMol )
-    OR
+Example::
 
-    >>>from packman import HetMol
-    >>>help( molecule.HetMol )
+    from packman.molecule import HetMol
+    help( HetMol )
 
 Todo:
     * Finish writing up the documentation.

build/lib/packman/molecule/model.py

@@ -2,15 +2,12 @@
 """The 'Model' object host file.
 
 This is file information, not the class information. This information is only for the API developers.
-Please read the 'Model' object documentation for details. [ help(packman.molecule.model.Model) ]
+Please read the 'Model' object documentation for details.
 
-Example:
-    >>>from packman.molecule import model.Model
-    >>>help( Model )
-    OR
+Example::
 
-    >>>from packman import molecule
-    >>>help( molecule.Model )
+    from packman.molecule import Model
+    help( Model )
 
 Note:
     * The models are nothing but frames of the PDB file.
@@ -26,6 +23,7 @@
 
 
 import numpy
+import logging
 
 
 class Model():
@@ -81,9 +79,16 @@ def get_residues(self):
         """Get the generator of corresponding 'Residue' objects of the 'Model'
 
         Returns:
-            generator of 'Residue' objects if successful, None otherwise.
+            array of 'Residue' objects if successful, None otherwise.
         """
-        return [j for i in self.__AllChains.keys() for j in self.__AllChains[i].get_residues()]
+        #return [j for i in self.__AllChains.keys() for j in self.__AllChains[i].get_residues()]
+        residues = []
+        for i in self.__AllChains.keys():
+            try:
+                residues.extend( self.__AllChains[i].get_residues() )
+            except:
+                logging.warning("Chain "+str(i)+" either doesn't have residues or an error occurred; Model.get_residues() may have loaded other chains.")
+        return residues
 
     def get_atoms(self):
         """Get the generator of corresponding 'Atom' objects of the 'Model'