Commit ab212cd8 authored by Jacob Durrant's avatar Jacob Durrant

Updates.

parent b17aa132
......@@ -22,8 +22,9 @@ this program. If not, see
----------------------
Begin by downloading POVME 2.1. An example input file is included with the
download (in the 'examples' directory). This input file is heavily commented
and may be even more useful that the information provided on this website.
download (in the 'povme/examples/' directory). This input file is heavily
commented and may be even more useful that the information provided on this
website.
POVME is released under the GNU General Public License. If you have any
questions, comments, or suggestions, please don't hesitate to contact me,
......
......@@ -1370,7 +1370,7 @@ def run_pocket_id(parameters):
if params["filename"] == "":
print("ERROR: Must specify the --filename parameter!")
print()
print("")
sys.exit(0)
for key in ["number_of_neighbors", "processors", "number_of_spheres"]:
......@@ -1384,10 +1384,10 @@ def run_pocket_id(parameters):
params[key] = float(params[key])
print("Specified command-line arguments:")
print()
print("")
for key in params:
print(" --" + key + ": " + str(params[key]))
print()
print("")
# Step 1: Load in the protein
......@@ -1562,16 +1562,16 @@ def run_pocket_id(parameters):
cluster_pts, let_ids[cluster_num]
)
except:
print()
print("")
printit(
"There was an error, but I don't think it was catastrophic. Could be that one of the pocket clusters was empty."
)
print()
print("")
f.write(pts_string)
f.close()
print()
print("")
printit(
"Done. See the pocket{n}.pdb files. Using a visualization program like VMD, identify which of these files includes the pocket you wish to measure. POVME Pocket ID has divided each pocket volume into "
+ str(params["number_of_spheres"])
......@@ -1580,7 +1580,7 @@ def run_pocket_id(parameters):
printit(
"The POVME PointsInclusionSphere commands are located in the header of each pocket{n}.pdb file. A text editor can be used to copy and paste these commands into a POVME input file."
)
print()
print("")
if __name__ == "__main__":
......
......@@ -1252,16 +1252,16 @@ class ConfigFile:
entities = []
def __init__(self, FileName):
def __init__(self, filename):
"""Generates a point field by filling the region with equally spaced
points.
Arguments:
FileName -- A string, the filename of the configuration file.
filename -- A string, the filename of the configuration file.
"""
f = open(FileName, "r")
f = open(filename, "r")
lines = f.readlines()
f.close()
......@@ -1396,6 +1396,10 @@ class RunPOVME:
start_time = time.time()
# First, check if running in test mode.
if "--test" in sys.argv:
print("Hi")
# Load the configuration file
if len(argv) == 1:
print("\nPOVME " + __version__)
......@@ -1403,7 +1407,7 @@ class RunPOVME:
"\nPlease specify the input file from the command line!\n\nExample: python POVME.py input_file.ini"
)
self.reference({})
print()
print("")
sys.exit()
config = ConfigFile(argv[1])
......
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