Merge pull request #46 from rsdefever/futurize-scripts

Add python2/python3 support to scripts with futurize

Author: rsdefever

Documentation/Tex/utilities.tex

@@ -1,5 +1,12 @@
 \chapter{Utilities}
 
+All Python utility scripts require the \texttt{future} package
+and \texttt{numpy} package, as listed in \texttt{requirements-py.txt}.
+Both packages are available via \texttt{pip} or \texttt{conda}.
+
+Please note that \texttt{python2} support is deprecated and may be removed
+in a future release.
+
 %\section{Input File GUI} 
 %\label{sec:GUI}
 %This script provides a graphical user interface (GUI) with which the user 
@@ -52,7 +59,7 @@ \chapter{Utilities}
 \section{Generate a Molecular Connectivity File}
 \label{sec:mcfgen}
 
-The script \texttt{mcf\_gen.py} is a tool that aims to ease the setup of molecular connectivity files from scratch (see section \ref{sec:MCF_File} to learn more
+The script \texttt{mcfgen.py} is a tool that aims to ease the setup of molecular connectivity files from scratch (see section \ref{sec:MCF_File} to learn more
 about MCFs), as the generation of these files by hand can be error prone. 
 In this section, a pentane MCF will be generated to demonstrate the use of this tool.
 The Transferable Potentials for Phase Equilibria (TraPPE) force field will be used to represent the pentane molecular interactions. 

Scripts/Frag_Library_Setup/library_setup.py

@@ -45,7 +45,12 @@
 #*******************************************************************************
 # IMPORT MODULES
 #*******************************************************************************
+from __future__ import print_function
+from builtins import input
+from builtins import str
+from builtins import range
 import sys, math, subprocess, os, linecache, argparse, re
+import warnings
 
 #*******************************************************************************
 # ARGUMENT PARSE
@@ -131,10 +136,10 @@ def cml_to_pdb(infilename):
 		if '</atomArray>' in line:
 			cml_end_atom = line_nbr + 1
 
-	for i in xrange(cml_start_atom+1, cml_end_atom):
+	for i in range(cml_start_atom+1, cml_end_atom):
 		cml_atom_info.append(re.findall('"([^"]*)"',linecache.getline(infilename, i)))
 
-	for i in xrange(cml_start_bonds+1, cml_end_bonds):
+	for i in range(cml_start_bonds+1, cml_end_bonds):
 		cml_bond_info.append(re.findall('"([^"]*)"',linecache.getline(infilename, i))[0].split())
 
 	temp=[]
@@ -254,9 +259,9 @@ def read_pdb(pdb_file):
 normal = '\033[0m'
 gcmc_flag = 0
 
-print bold+"\n********************** Cassandra Setup *********************\n"+normal
-print bold+"Cassandra location: "+normal+cassandra_path
-print bold+"Scanning input file"+normal
+print(bold+"\n********************** Cassandra Setup *********************\n"+normal)
+print(bold+"Cassandra location: "+normal+cassandra_path)
+print(bold+"Scanning input file"+normal)
 
 #Locate line number for the following keywords:
 # Nbr_Species
@@ -314,23 +319,23 @@ def read_pdb(pdb_file):
 else:
 	vdw_style = []
 	charge_style = []
-	for i in xrange(1,nbr_boxes+1):
+	for i in range(1,nbr_boxes+1):
 		vdw_style.append(linecache.getline(input_file, vdw_style_line+i).split()[0])
 		if charge_style_line:
 			charge_style.append(linecache.getline(input_file, charge_style_line+i).split()[0])
 	if vdw_style[1] != vdw_style[0]:
-		vdw_style = raw_input("VDW_Style for boxes don't match. " +
+		vdw_style = input("VDW_Style for boxes don't match. " +
 		                      "Enter the VDW_Style to use (" + vdw_style[0] + "/" + 
 		                      vdw_style[i-1] + "):")
 	else:
 		vdw_style = vdw_style[0]
 	if vdw_style != 'LJ' and vdw_style != 'lj' and \
 	   vdw_style != 'Mie' and vdw_style != 'mie':
-		print "Only 'LJ' and 'Mie' VDW_Styles are supported"
+		print("Only 'LJ' and 'Mie' VDW_Styles are supported")
 		quit()
 	if charge_style_line:
 		if charge_style[1] != charge_style[0]:
-			charge_style = raw_input("Charge_Style for boxes don't match. " +
+			charge_style = input("Charge_Style for boxes don't match. " +
 										 "Enter the Charge_Style to use (" + charge_style[0] + "/" + 
 										 charge_style[i-1] + "):")
 		else:
@@ -341,12 +346,12 @@ def read_pdb(pdb_file):
 
 #Obtain number of species
 nbr_species = int(linecache.getline(input_file,nbr_species_line+1))
-print bold+"  Number of species found: " + normal + str(nbr_species)
+print(bold+"  Number of species found: " + normal + str(nbr_species))
 
 #Intra_Scaling
 vdw_scaling = []
 charge_scaling = []
-for i in xrange(1,nbr_species+1):
+for i in range(1,nbr_species+1):
 	if intra_scaling_line:
 		if charge_style_line and charge_style == 'coul':
 			vdw_scaling.append(linecache.getline(input_file,intra_scaling_line+2*i-1))
@@ -384,15 +389,15 @@ def read_pdb(pdb_file):
 
 #Look for MCF files
 mcf_files = []
-for i in xrange(0,nbr_species):
+for i in range(0,nbr_species):
 	mcf_files.append(linecache.getline(input_file,molec_files_line+i+1).split()[0])
-	print bold+"  The MCF file number " + str(i+1) + " is: " + normal + mcf_files[i]
+	print(bold+"  The MCF file number " + str(i+1) + " is: " + normal + mcf_files[i])
 
 #Open the MCF files to record where atom, bond and fragment info is
 line_where_atom_info = []
 line_where_bond_info = []
 line_where_fragment_info = []
-for i in xrange(0,len(mcf_files)):
+for i in range(0,len(mcf_files)):
 	current_mcf = open(mcf_files[i],'r')
 	for line_number_mcf, line_mcf in enumerate(current_mcf):
 		if not line_mcf.strip():
@@ -411,11 +416,11 @@ def read_pdb(pdb_file):
 which_atoms_are_ring = []
 temp_list = []
 nbr_atoms = []
-for i in xrange(0, nbr_species):
+for i in range(0, nbr_species):
 	nbr_atoms.append(int(linecache.getline(mcf_files[i],
 	                     line_where_atom_info[i]+1).split()[0]))
 	atom_type_list[i] = [0]*nbr_atoms[i]
-	for j in xrange(0,nbr_atoms[i]):
+	for j in range(0,nbr_atoms[i]):
 		atom_type = linecache.getline(mcf_files[i],
 		                              line_where_atom_info[i]+2+j).split()[1]
 		#remove old '_s?' flags if present
@@ -435,12 +440,12 @@ def read_pdb(pdb_file):
 #Find how many fragments there are and get a list of them.
 nbr_fragments = []
 fragment_list = []
-for i in xrange(0, nbr_species):
+for i in range(0, nbr_species):
 	nbr_fragments.append(int(linecache.getline(mcf_files[i],
 	                            line_where_fragment_info[i]+1).split()[0]))
-	print bold+"    Species "+str(i+1)+" has "+str(nbr_fragments[i])+ " fragments" + normal
+	print(bold+"    Species "+str(i+1)+" has "+str(nbr_fragments[i])+ " fragments" + normal)
 	temp_list=[]
-	for j in xrange(0,nbr_fragments[i]):
+	for j in range(0,nbr_fragments[i]):
 		temp_list.append(linecache.getline(mcf_files[i],
 		                 line_where_fragment_info[i]+2+j).split()[2:])
 	fragment_list.append(temp_list)
@@ -466,9 +471,9 @@ def read_pdb(pdb_file):
 	temp_exoring = []
 
 if any([any(has_ring) for has_ring in fragment_has_ring]):
-	print bold+"Molecules with rings found. These are:" + normal
+	print(bold+"Molecules with rings found. These are:" + normal)
 	for i,species in enumerate(fragment_has_ring):
-		print bold+"Species "+str(i+1)+" has "+str(sum(species))+ " rings."+normal
+		print(bold+"Species "+str(i+1)+" has "+str(sum(species))+ " rings."+normal)
 
 #We know what fragments are ring for each species. Copy only those config_files 
 #for the species that have rings
@@ -489,16 +494,16 @@ def read_pdb(pdb_file):
 temperature = float(linecache.getline(input_file,temp_line+1).split()[0])
 
 #Rewrite the MCF files to append an '_s1' to the atom type
-for i in xrange(0,len(mcf_files)):
+for i in range(0,len(mcf_files)):
 	current_mcf = open(mcf_files[i],'r')
 	new_mcf_file = open(mcf_files[i]+"temp",'w')
 	total_lines = len(current_mcf.readlines())
 	current_mcf.close()
 	stride = 0
-	for line_number in xrange(1,total_lines+1):
+	for line_number in range(1,total_lines+1):
 		if line_number + stride > line_where_atom_info[i]+1 and \
 		   line_number + stride <= line_where_atom_info[i]+1 + nbr_atoms[i]:
-			for j in xrange(0,nbr_atoms[i]):
+			for j in range(0,nbr_atoms[i]):
 				this_line = linecache.getline(mcf_files[i],line_number+j+stride).split()
 				this_line[1] = atom_type_list[i][j]
 				new_mcf_file.write('    '.join(this_line)+'\n')
@@ -522,31 +527,31 @@ def read_pdb(pdb_file):
 #/species?/fragments
 #/species?/frag?
 
-for i in xrange(0, nbr_species):
+for i in range(0, nbr_species):
 
-	for j in xrange(0,nbr_fragments[i]):
+	for j in range(0,nbr_fragments[i]):
 		os.system("mkdir -p species"+str(i+1)+"/frag"+str(j+1))
 
 	if i not in pdb_without_conect: 
 		os.system("mkdir -p species"+str(i+1)+"/fragments/")
 
 #Now, create input files for fragment MCF generation
-for i in xrange(0, nbr_species):
+for i in range(0, nbr_species):
 
 	if i in pdb_without_conect:
-		print "\n\n" + bold + "MCF generation file not created for species "+str(i+1)+normal
+		print("\n\n" + bold + "MCF generation file not created for species "+str(i+1)+normal)
 		if nbr_fragments[i] == 0:
-			print bold+"No fragment configuration needed."+normal
+			print(bold+"No fragment configuration needed."+normal)
 		else:
-			print bold+"Fragment configuration will be taken from PDB file."+normal
+			print(bold+"Fragment configuration will be taken from PDB file."+normal)
 		continue
 
 	if nbr_atoms[i] >= 3:
 		for element in files_ring_to_copy:
 			if str(i) in element[0]:
 				os.system("cp "+element[1]+" species"+str(i+1)+"/fragments/molecule.pdb")
 
-		print "\n\n"+bold+"Creating input MCF generation file for species "+str(i+1)+" "+normal
+		print("\n\n"+bold+"Creating input MCF generation file for species "+str(i+1)+" "+normal)
 		input_mcf_gen = open("species"+str(i+1)+"/fragments/species"+str(i+1)+"_mcf_gen.inp",'w')
 		input_mcf_gen.write("# Run_Name\nspecies"+str(i+1)+"_mcf_gen")
 		input_mcf_gen.write("\n\n")
@@ -570,7 +575,7 @@ def read_pdb(pdb_file):
 		input_mcf_gen.write("# Box_Info\n1\nCUBIC\n30.0 30.0 30.0\n\nEND")
 		input_mcf_gen.close()
 
-		print bold+"Running Cassandra to generate MCF files"+normal
+		print(bold+"Running Cassandra to generate MCF files"+normal)
 		sys.stdout.flush()
 		os.chdir('./species'+str(i+1)+'/fragments/')
 		subprocess.call([cassandra_path,'species'+str(i+1)+'_mcf_gen.inp'])
@@ -580,7 +585,7 @@ def read_pdb(pdb_file):
 #Test if fragment and/or ring is rigid
 fragment_is_rigid = [] # Boolean entry for each i,j
 ring_is_rigid = [] # frag_id's for each frag that has a rigid ring
-for i in xrange(0, nbr_species):
+for i in range(0, nbr_species):
 
 	if nbr_atoms[i] < 3:
 
@@ -595,7 +600,7 @@ def read_pdb(pdb_file):
 	else:
 		temp_rigid = []
 		temp_ring_rigid = []
-		for j in xrange(0,nbr_fragments[i]):
+		for j in range(0,nbr_fragments[i]):
 			#Read mcf to see how many angles are fixed
 			frag_atoms_are_ring = []
 			angle_parms = {}
@@ -606,14 +611,14 @@ def read_pdb(pdb_file):
 			while line:
 				if "# Atom_Info" in line:
 					nbr_frag_atoms = int(frag_mcf.readline().split()[0])
-					for k in xrange(0,nbr_frag_atoms):
+					for k in range(0,nbr_frag_atoms):
 						line = frag_mcf.readline()
 						atom_ID = int(line.split()[0])
 						if line.split()[-1] == 'ring':
 							frag_atoms_are_ring.append(atom_ID)
 				elif "# Angle_Info" in line:
 					nbr_angles = int(frag_mcf.readline().split()[0])
-					for k in xrange(0,nbr_angles):
+					for k in range(0,nbr_angles):
 						line = frag_mcf.readline()
 						angle_ID = tuple([int(x) for x in line.split()[1:4]])
 						angle_type = line.split()[4]
@@ -629,7 +634,7 @@ def read_pdb(pdb_file):
 				if temp_rigid[j]:
 					#If the whole frag is rigid, the ring must be rigid
 					temp_ring_rigid.append(j)
-				elif any([angle_type == 'fixed' for angle_type in angle_parms.values()]):
+				elif any([angle_type == 'fixed' for angle_type in list(angle_parms.values())]):
 					#Must have some 'fixed' angles to have a rigid ring
 					nbr_ring_angles_fixed = 0
 					for angle_ID in angle_parms:
@@ -644,8 +649,8 @@ def read_pdb(pdb_file):
 
 #Create input file for each fragment of each species
 
-for i in xrange(0, nbr_species):
-	for j in xrange(0,nbr_fragments[i]):
+for i in range(0, nbr_species):
+	for j in range(0,nbr_fragments[i]):
 		if fragment_is_rigid[i][j]:
 			#Read PDB
 			atom_coords = read_pdb(pdb_files[i])
@@ -661,8 +666,8 @@ def read_pdb(pdb_file):
 			output_frag.close()
 		else:
 			if fragment_has_ring[i][j]:
-				print bold+"Generating RING FRAGMENT library species "+str(i+1)+\
-									 " fragment "+str(j+1)+normal
+				print(bold+"Generating RING FRAGMENT library species "+str(i+1)+\
+									 " fragment "+str(j+1)+normal)
 				input_frag = open("species"+str(i+1)+"/frag"+str(j+1)+"/frag"+str(j+1)+
 													".inp",'w')
 				input_frag.write("# Run_Name\nfrag"+str(j+1)+"\n\n")
@@ -714,8 +719,8 @@ def read_pdb(pdb_file):
 				subprocess.call([cassandra_path,'frag'+str(j+1)+'.inp'])
 				os.chdir('../../')
 			else:
-				print bold+"Generating fragment library species "+str(i+1)+\
-					         " fragment " + str(j+1)+normal
+				print(bold+"Generating fragment library species "+str(i+1)+\
+					         " fragment " + str(j+1)+normal)
 				input_frag = open("species"+str(i+1)+"/frag"+str(j+1)+"/frag"+str(j+1)+
 					                ".inp",'w')
 				input_frag.write("# Run_Name\nfrag"+str(j+1)+"\n\n")
@@ -764,13 +769,13 @@ def read_pdb(pdb_file):
 total_lines = len(in_file.readlines())
 in_file.close()
 omit = False
-for line_number in xrange(1,total_lines+1):
+for line_number in range(1,total_lines+1):
 
 	if line_number == frag_files_line:
 		new_file.write("# Fragment_Files\n")
 		total_frag_counter = 0
-		for i in xrange(0, nbr_species):
-			for j in xrange(0,nbr_fragments[i]):
+		for i in range(0, nbr_species):
+			for j in range(0,nbr_fragments[i]):
 				total_frag_counter += 1
 				new_file.write("species"+str(i+1)+"/frag"+str(j+1)+"/frag"+str(j+1)+
 				               ".dat  " + str(total_frag_counter)+"\n")
@@ -788,6 +793,13 @@ def read_pdb(pdb_file):
 in_file.close()
 new_file.close()
 
-print bold+"Removing temporary input file"+normal
+print(bold+"Removing temporary input file"+normal)
 os.system("rm "+ input_file+"; mv "+input_file+"temp "+input_file)
-print bold+"Finished"+normal
+print(bold+"Finished"+normal)
+
+# Python 2.x deprecation warning
+if (sys.version_info < (3,0)):
+    warnings.showwarning("\n\nSupport for Python2 is deprecated in "
+        "Cassandra and will be removed in a future release. Please "
+        "consider switching to Python3.\n\n", DeprecationWarning,
+        'library_setup.py', 801)