Merge pull request #5 from mdpoleto/1.4.0_branch

1.4.0 branch

TUPA.py

@@ -18,7 +18,7 @@
 # Parse user input and options
 ap = argparse.ArgumentParser(description=tupa_help.header,
                              formatter_class=argparse.RawDescriptionHelpFormatter,
-                             usage="python tupa.py [options]",
+                             usage="",
                              add_help=False)
 ap._optionals.title = 'Options'
 ap.add_argument('-h', '--help', action="store_true", help='Show this message and exit')
@@ -30,18 +30,18 @@
                 help='Output folder in which results will be written (default: Tupã_results/)')
 ap.add_argument('-config', type=str, default=None, required=False, metavar='',
                 help='Input configuration file (default: config.dat)')
-ap.add_argument('-template', type=str, default=None, required=False, metavar='',
-                help='Create a template for input configuration file (default: config_sample.dat)')
+ap.add_argument('-template', type=str, default=None, required=False, nargs="?", metavar='',
+                help='Create a template for input configuration file (default: config_template.dat)')
 ap.add_argument('-dumptime', type=int, default=None, required=False, metavar='', nargs='+',
                 help='Choose times (in ps) to dump the coordinates from.')
 
 cmd = ap.parse_args()
 start = timeit.default_timer()
-print(tupa_help.header)
+#print(tupa_help.header)
 
 
 if cmd.help is True:
-	#ap.print_help()
+	ap.print_help()
 	print(tupa_help.help)
 	sys.exit()
 else:
@@ -51,7 +51,10 @@
 traj_file     = cmd.traj
 outdir        = cmd.outdir
 configinput   = cmd.config
-template      = cmd.template
+if cmd.template == None:
+	template = "config_template.dat"
+else:
+	template      = cmd.template
 if cmd.dumptime == None:
 	dumptime = []
 else:
@@ -338,7 +341,7 @@ def pack_around(atom_group, center, boxinfo):
 	try:
 		u = mda.Universe(top_file, traj_file)
 	except Exception as e:
-		sys.exit("""\n>>> ERROR: Topology or Trajectory not found. Aren't you forgetting something?!\n""")
+		sys.exit("""\n>>> ERROR: Topology or Trajectory could not be loaded. Check your inputs!\n""")
 
 else:
 	sys.exit("""\n>>> ERROR: Topology or Trajectory not found. Aren't you forgetting something?!\n""")

tupa_help.py

@@ -23,16 +23,16 @@
 
 template_content = """[Environment Selection]
 # The atoms from which we calculate the electric field
-sele_environment    = segid PROA
+sele_environment    = resid 1-200
 
 
 [Probe Selection]
 # Provide the probe selection for the MODE of you choice
 # e.g. if bond is used, then selbond1 and selbond2 must be defined.
 mode                = ATOM    # ATOM or BOND or COORDINATE or LIST
-selatom             = segid PROA and (resid 160 and name OG)
-selbond1            = segid PROA and (resid 160 and name OG)
-selbond2            = segid LIG and name C1
+selatom             = resname LIG and name C5
+selbond1            = resname LIG and name C5
+selbond2            = resname LIG and name C1
 probecoordinate     = [0,0,0]
 file_of_coordinates = /path/to/file/of/list/of/probe/coordinates
 
@@ -43,8 +43,8 @@
 
 [Solvent]
 include_solvent     = True    # or False
-solvent_cutoff      = 10      # in Angstrom
-solvent_selection   = segid TIP3
+solvent_cutoff      = 15      # in Angstrom
+solvent_selection   = resname TIP3 or resname CL
 
 [Time]
 dt                  = 10      # Frequency of frames written in your trajectory (in picosecond)