Minor updates

- added comments
- removed "run log.py" text following recent changes
- minor changes to optimisation.py

Author: ABrethome

wsterimol/filter_gen.py

@@ -14,7 +14,7 @@
 # Filter impossible structures after being generated via Pymol.
 # Plausible structures can be visualized from visualize.py
 # Use in Pymol command prompt:
-# run log.py
+# run wSterimol.py
 # run sterimoltools.py
 # run setup.py
 # run filter_gen.py

wsterimol/filter_opt.py

@@ -13,13 +13,11 @@
 
 # Filter optimised structures generated from Mopac or Gaussian
 # Use in Pymol command prompt:
-# run log.py
+# run wSterimol.py
 # run sterimoltools.py
 # run setup.py
 # run filter_opt.py
 # filter_opt (directory, verbose, setup_path)
-# example:
-
 
 def filter_opt(directory = "temp", setup_path = "default", verbose = "False"):
     # If the directory exists

wsterimol/generate.py

@@ -11,7 +11,7 @@
 
 # Generate possible conformer structures via Pymol
 # Use in Pymol command prompt:
-# run log.py
+# run wSterimol.py
 # run setup.py
 # run generate.py
 # generate [dihedral 1, .. ], (directory, setup_path, verbose, force)

wsterimol/optimisation.py

@@ -14,14 +14,14 @@
 
 # Optimisation of the structures via Pymol with MOPAC
 # Use in Pymol command prompt:
-# run log.py
+# run wSterimol.py
 # run sterimoltools.py
 # run setup.py
 # run optimisation.py
 # optimisation (directory, walltime, verbose, setup_path)
 # example: optimisation conformers
 
-def optimisation(directory = "temp", walltime = 300, verbose = "False", setup_path = "default"):
+def optimisation(directory = "temp", walltime = 300, verbose = "False", setup_path = "default", silentmode = "True"):
     # If the directory exists
     if os.path.exists(directory):
         # Log generation
@@ -33,6 +33,9 @@ def optimisation(directory = "temp", walltime = 300, verbose = "False", setup_pa
         #verbose
         if verbose.lower() in ['true', '1', 't', 'y', 'yes']: verbose = True
         else: verbose = False
+        #silentmode
+        if silentmode.lower() in ['true', '1', 't', 'y', 'yes']: silentmode = True
+        else: silentmode = False
         # Retrieve all the files in the directory
         files = [f for f in listdir(directory) if isfile(join(directory, f))]
         if len(files) > 0:
@@ -56,7 +59,7 @@ def optimisation(directory = "temp", walltime = 300, verbose = "False", setup_pa
                                     log.write("\n-------------------------\nJob starts [%s]" % join(directory, filename), verbose)
                                     # calculate the energy
                                     startupinfo = None
-                                    if platform.system() == "Windows":
+                                    if platform.system() == "Windows" and silentmode == True:
                                         # Prevent .exe window from popping up in Windows
                                         startupinfo = subprocess.STARTUPINFO()
                                         startupinfo.dwFlags |= subprocess.STARTF_USESTDHANDLES | subprocess.STARTF_USESHOWWINDOW
@@ -93,7 +96,7 @@ def optimisation(directory = "temp", walltime = 300, verbose = "False", setup_pa
                                     log.write("\n-------------------------\nJob starts [%s]" % join(directory, filename), verbose)
                                     # calculate the energy
                                     startupinfo = None
-                                    if platform.system() == "Windows":
+                                    if platform.system() == "Windows" and silentmode == True:
                                         # Prevent .exe window from popping up in Windows
                                         startupinfo = subprocess.STARTUPINFO()
                                         startupinfo.dwFlags |= subprocess.STARTF_USESTDHANDLES | subprocess.STARTF_USESHOWWINDOW

wsterimol/prepare_file.py

@@ -13,7 +13,7 @@
 
 # Prepare structures via Pymol for Mopac or Gaussian
 # Use in Pymol command prompt:
-# run log.py
+# run wSterimol.py
 # run sterimoltools.py
 # run setup.py
 # run prepare_file.py

wsterimol/setup.py

@@ -7,20 +7,20 @@ class Setup:
     def __init__(self, log, path = "default", exe = "default"):
         #default values
         self.software = "MOPAC" # Mopac by default
-        self.loaded = True # good by default
-        self.exe = "C:\PROGRA~1\MOPAC\MOPAC2016.exe" #default install for Mopac in Windows
+        self.loaded = True # good by default, then might get wrong
+        self.exe = "C:\PROGRA~1\MOPAC\MOPAC2016.exe" #default install for MOPAC in Windows
         self.SE = "PM6-DH2" # default force field
         self.charge = "0" # uncharged
         self.scf = "" # optimisation
         self.rmsd_cutoff = 0.1 # Angstroms
-        self.memories = "8"
-        self.procsshared = "8"
+        self.memories = "8" 
+        self.procsshared = "8" 
         self.leveloftheory = "wb97xd/6-31g(d)"
         self.spin = "1"
         self.RJCT = 0.50
-        self.singlepointcalculation = ""
+        self.singlepointcalculation = "" #none
         self.Temperature = 298
-        self.energywindow_cutoff = []
+        self.energywindow_cutoff = [] # none
         self.print_cutoff = 5.0
         self.angle_count = 5
         self.radii = "cpk"
@@ -61,7 +61,7 @@ def __init__(self, log, path = "default", exe = "default"):
                                 log.write("Warning: Specified path to executable doesn't exist. Use setup.ini value.")
                         if not os.path.exists(config[1]):
                             self.loaded = False
-                            log.write("Error: Specified path to executable in self.ini doesn't exist. [%s]" % config[1])
+                            log.write("Error: Specified path to executable in setup.ini doesn't exist. [%s]" % config[1])
                             return
                         self.exe = config[1]
                     elif config[0] == "SEMI_EMPIRICAL":

wsterimol/sterimol.py

@@ -16,8 +16,7 @@
 
 # Generate the Sterimol parameters from the optimised structures
 # Use in Pymol command prompt:
-# run log.py
-# run sterimoltools.py
+# run wSterimol.py
 # run setup.py
 # run sterimoltools.py
 # run sterimol.py

wsterimol/weight.py

@@ -106,9 +106,9 @@ def weight(setup_path = "default", verbose = "False"):
                     output.write("** For non-commercial use only                                  Version %.2f **\n" % version)
                     output.write("*******************************************************************************\n")
                     output.write("** Developed by:                                                             **\n")
-                    output.write("** Alex Brethome - University of Oxford                                      **\n")
+                    output.write("** Alexandre Brethome - University of Oxford                                 **\n")
                     output.write("** Robert Paton - Colorado State University (patonlab.com)                   **\n")
-                    output.write("** If you use wSterimol, please acknowledge: Brethome, A.; Fletcher, S. P.;  **\n")
+                    output.write("** If you use wSterimol, please acknowledge:Brethome, A. V.; Fletcher, S. P.;**\n")
                     output.write("** Paton, R. S. submitted 2018                                               **\n")
                     output.write("*******************************************************************************\n")
                     output.write("**                   ____ ______ ____ ___   ____ __  ___ ____   __           **\n")
@@ -166,6 +166,9 @@ def weight(setup_path = "default", verbose = "False"):
                     output.write("**                       %7.2f   %7.2f   %7.2f                         **\n" % (L1_weighted,B1_weighted,B5_weighted))
                     output.write("**                                                                           **\n")
                     output.write("*******************************************************************************\n")
+                    # log update showing results
+                    log.write(" wL (A)   wB1 (A)   wB5 (A) \n")
+                    log.write(" %7.2f   %7.2f   %7.2f \n" % (L1_weighted,B1_weighted,B5_weighted))
                     # calculate min max for each different energy windows
                     for k in range(len(setup.energywindow_cutoff)):
                         output.write("\n\n*******************************************************************************\n")