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Make compatible with Python 3 #35

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8 changes: 4 additions & 4 deletions POVME/POVME2_GUI.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/usr/bin/python

from Tkinter import *
from tkinter import *
#------------------------------------------------------------------------------#
# #
# POVME2_GUI #
Expand All @@ -12,7 +12,7 @@ def __init__(self,Master=None,**kw):
#Your code here
#

apply(Frame.__init__,(self,Master),kw)
Frame.__init__(*(self,Master), **kw)
self.__Frame2 = Frame(self)
self.__Frame2.pack(side='top')
self.__Label1 = Label(self.__Frame2,background='#000000'
Expand Down Expand Up @@ -828,8 +828,8 @@ def is_int(self, str):
except ValueError:
return False

import tkMessageBox
import tkFileDialog
import tkinter.messagebox
import tkinter.filedialog
import os
#import shutil
import sys
Expand Down
106 changes: 54 additions & 52 deletions POVME/POVME3.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,13 +21,14 @@
import POVME.packages.binana.peel as peel
import multiprocessing
import platform
from functools import reduce

#from guppy import hpy

#hp=hpy()

try: from cStringIO import StringIO
except: from StringIO import StringIO
try: from io import StringIO
except: from io import StringIO

from scipy.spatial.distance import cdist
from scipy.spatial.distance import pdist
Expand Down Expand Up @@ -89,7 +90,7 @@ def log(astr, parameters):
'''

# Print the output to the screen.
print astr
print(astr)

# Save it to the output file as well.
try:
Expand Down Expand Up @@ -135,7 +136,7 @@ def __init__(self, inputs, num_processors, task_class):
self.results = []

if num_processors != 1 and (platform.system().upper()[:3] == "WIN" or "NT" in platform.system().upper()): # If it's windows, you can only use one processor.
print "WARNING: Use of multiple processors is not supported in Windows. Proceeding with one processor..."
print("WARNING: Use of multiple processors is not supported in Windows. Proceeding with one processor...")
num_processors = 1

if num_processors == 1: # so just running on 1 processor, perhaps under windows
Expand All @@ -157,7 +158,7 @@ def __init__(self, inputs, num_processors, task_class):

# reduce the number of processors if too many have been specified
if len(inputs) < num_processors:
print 'Too many processors requested (%i requested, vs %i frames to analyze). Lowering number requested.' %(num_processors, len(inputs))
print('Too many processors requested (%i requested, vs %i frames to analyze). Lowering number requested.' %(num_processors, len(inputs)))
num_processors = len(inputs)

if len(inputs) == 0: # if there are no inputs, there's nothing to do.
Expand Down Expand Up @@ -849,6 +850,7 @@ def determineFirstConvexHull(index_and_pdbs,parameters):
hydros = this_pdb.selections.select_atoms({'element_stripped':['H']})
not_hydros = this_pdb.selections.invert_selection(hydros)
not_hydros_coors = this_pdb.information.get_coordinates()[not_hydros]
break


akl_toussaint_pts = convex_hull_3d.akl_toussaint(not_hydros_coors) # quickly reduces input size
Expand Down Expand Up @@ -878,9 +880,9 @@ def value_func(self, item, results_queue, color = False):
results_queue -- A multiprocessing.Queue() object for storing the calculation output

"""
print '---------------------------------'
print 'STARTING CALC VOLUME'#,hp.heap()
print '---------------------------------'
print('---------------------------------')
print('STARTING CALC VOLUME')#,hp.heap()
print('---------------------------------')


frame_indx = item[0]
Expand Down Expand Up @@ -1140,7 +1142,7 @@ def value_func(self, item, results_queue, color = False):
extra_data_to_add['CalculateSurfaceArea'] = surfA
#print "Surface Area for frame %r: %r" %(frame_indx, len(surfacePointsSet.intersection(adjacentPointsSet)))
#if parameters[SaveIndividualPocketVolumes] == True:
for color in coloredMaps.keys():
for color in list(coloredMaps.keys()):
#First make a copy of coloredMaps[color] that only contains the points over the intensity threshold
#print color, coloredMaps[color]
#log('AAAAA' + color + str(frame_indx), parameters)
Expand Down Expand Up @@ -1188,9 +1190,9 @@ def value_func(self, item, results_queue, color = False):
#else:
# log("\tFrame " + str(frame_indx) + ": " + repr(volume) + " A^3", parameters)
self.results.append((frame_indx, volume, extra_data_to_add))
print '---------------------------------'
print 'FINISHING CALC VOLUME'#,hp.heap()
print '---------------------------------'
print('---------------------------------')
print('FINISHING CALC VOLUME')#,hp.heap()
print('---------------------------------')

#if len(extra_data_to_add.keys()) != 0:
#else: self.results.append((frame_indx, volume))
Expand Down Expand Up @@ -1219,8 +1221,8 @@ def value_func(self, item, results_queue):
pdb.fileio.load_pym_into(pym_filename)

ligand_atoms = pdb.select_atoms({'resname_stripped':parameters[DefinePocketByLigand]})
print parameters[DefinePocketByLigand]
print ligand_atoms
print(parameters[DefinePocketByLigand])
print(ligand_atoms)
ligand_coords = pdb.get_coordinates()[ligand_atoms].round()
ligand_coords_set = set([tuple(row) for row in ligand_coords])
self.results.append(ligand_coords_set)
Expand Down Expand Up @@ -1597,7 +1599,7 @@ def __init__ (self, FileName):
# has more than 2 members, python will crash. However, each entity in self.entities should have only 2 members
# due to the processing code above.
for parameter,values in self.entities:
print parameter, values
print(parameter, values)
#if unexpected config keyword in config file, throw this exception
if parameter not in all_parameters:
raise Exception('%s is not a valid parameter. Valid parameters are: %r' %(parameter,all_parameters))
Expand Down Expand Up @@ -1683,13 +1685,13 @@ def load_multi_frame_pdb(self, filename, parameters):
log("", parameters)
log("Reading frames from " + filename, parameters)

f = open(filename, 'rb')
f = open(filename, 'r')
while True:

if parameters[NumFrames] != -1:
if len(pdb_strings) >= parameters[NumFrames]: break

line = f.readline()
line = str(f.readline())

if len(line) == 0:
pdb_strings.append(growing_string)
Expand Down Expand Up @@ -1717,18 +1719,18 @@ def __init__(self, argv):
argv -- A list of the command-line arguments.

'''
print '---------------------------------'
print 'START'#,hp.heap()
print '---------------------------------'
print('---------------------------------')
print('START')#,hp.heap()
print('---------------------------------')

start_time = time.time()

# Load the configuration file
if len(argv) == 1:
print "\nPOVME " + version
print "\nPlease specify the input file from the command line!\n\nExample: python POVME.py input_file.ini"
print("\nPOVME " + version)
print("\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])
Expand Down Expand Up @@ -1768,7 +1770,7 @@ def __init__(self, argv):
# print out parameters
#consider this section for deletion
log("Parameters:", parameters)
for i in parameters.keys():
for i in list(parameters.keys()):

if i == 'NumFrames' and parameters[NumFrames] == -1: continue # So only show this parameter if it's value is not the default.

Expand All @@ -1779,24 +1781,24 @@ def __init__(self, argv):
if parameters[i] != "": log("\t" + str(i) + ": " + str(parameters[i]), parameters)
#this section ^ total garbage

print '---------------------------------'
print 'PARAMETERS DEFINED'#,hp.heap()
print '---------------------------------'
print('---------------------------------')
print('PARAMETERS DEFINED')#,hp.heap()
print('---------------------------------')

pts = None

if parameters[PDBFileName] != '': # so there's a PDB point specified for calculating the volume.

# load the points in they aren't already present

print '---------------------------------'
print 'ABOUT TO LOAD RECEPTORS'#,hp.heap()
print '---------------------------------'
print('---------------------------------')
print('ABOUT TO LOAD RECEPTORS')#,hp.heap()
print('---------------------------------')
# load the PDB frames
index_and_pdbs = self.load_multi_frame_pdb(parameters[PDBFileName], parameters)
print '---------------------------------'
print 'RECEPTORS LOADED'#,hp.heap()
print '---------------------------------'
print('---------------------------------')
print('RECEPTORS LOADED')#,hp.heap()
print('---------------------------------')

# calculate all the volumes
log("", parameters)
Expand Down Expand Up @@ -1968,9 +1970,9 @@ def __init__(self, argv):

log("Calculating the pocket volume of each frame", parameters)
tmp = Multithreading([(index, pdb_object, parameters) for index, pdb_object in index_and_pdbs], parameters[NumProcessors], MultithreadingCalcVolumeTask)
print '---------------------------------'
print 'VOLUMES CALCULATED'#,hp.heap()
print '---------------------------------'
print('---------------------------------')
print('VOLUMES CALCULATED')#,hp.heap()
print('---------------------------------')

# delete the temp swap directory if necessary

Expand Down Expand Up @@ -2015,7 +2017,7 @@ def __init__(self, argv):
if parameters[CompressOutput] == True: traj_file = gzip.open(parameters[OutputFilenamePrefix] + "volume_trajectory.pdb.gz", 'wb')
else: traj_file = open(parameters[OutputFilenamePrefix] + "volume_trajectory.pdb", 'w')

for frame_index in range(1,len(volume_dic.keys())+1):
for frame_index in range(1,len(list(volume_dic.keys()))+1):
if parameters[CompressOutput] == True: frame_file = gzip.open(parameters[OutputFrameFilenamePrefix] + "frame_" + str(frame_index) + ".pdb.gz", 'rb')
else: frame_file = open(parameters[OutputFrameFilenamePrefix] + "frame_" + str(frame_index) + ".pdb", 'r')

Expand All @@ -2028,12 +2030,12 @@ def __init__(self, argv):
traj_file.close()

#if parameters[SaveColoredMap] == True:
colors = tmp.results[0][2]['SaveColoredMap'].keys()
colors = list(tmp.results[0][2]['SaveColoredMap'].keys())
for color in colors:
if parameters[CompressOutput] == True: traj_file = gzip.open(parameters[OutputFilenamePrefix] + color + "_trajectory.pdb.gz", 'wb')
else: traj_file = open(parameters[OutputFilenamePrefix] + color + "_volume_trajectory.pdb", 'w')

for frame_index in range(1,len(volume_dic.keys())+1):
for frame_index in range(1,len(list(volume_dic.keys()))+1):
if parameters[CompressOutput] == True: frame_file = gzip.open(parameters[OutputFrameFilenamePrefix] + "frame_" + str(frame_index) + "_" + color + ".pdb.gz", 'rb')
else: frame_file = open(parameters[OutputFrameFilenamePrefix] + "frame_" + str(frame_index) + "_" + color + ".pdb", 'r')

Expand Down Expand Up @@ -2067,9 +2069,9 @@ def __init__(self, argv):



print '---------------------------------'
print 'ABOUT TO CALCULATE OCCUPANCY AVERAGE'#,hp.heap()
print '---------------------------------'
print('---------------------------------')
print('ABOUT TO CALCULATE OCCUPANCY AVERAGE')#,hp.heap()
print('---------------------------------')
# Generate the frame-averages volumetric density map
#if parameters[SaveVolumetricDensityDX] == True or parameters[SaveVolumetricDensityNpy] == True:
unique_points = {}
Expand Down Expand Up @@ -2127,22 +2129,22 @@ def __init__(self, argv):



print '---------------------------------'
print 'CALCULATED OCCUPANCY AVERAGE'#,hp.heap()
print '---------------------------------'
print('---------------------------------')
print('CALCULATED OCCUPANCY AVERAGE')#,hp.heap()
print('---------------------------------')


#if parameters[SaveColoredMap] == True:

print '---------------------------------'
print 'ABOUT TO CALCULATE COLOR MAPS'#,hp.heap()
print '---------------------------------'
print('---------------------------------')
print('ABOUT TO CALCULATE COLOR MAPS')#,hp.heap()
print('---------------------------------')

#print 'Saving Colored Maps!'
#start = time.time()


colors = tmp.results[0][2]['SaveColoredMap'].keys()
colors = list(tmp.results[0][2]['SaveColoredMap'].keys())
for color in colors:
overall_min = numpy.ones(3) * 1e100
overall_max = numpy.ones(3) * -1e100
Expand Down Expand Up @@ -2197,9 +2199,9 @@ def __init__(self, argv):
#if parameters[SaveVolumetricDensityNpy] == True:
numpy.save(colorParams['OutputFrameFilenamePrefix']+'volumetric_density.npy', all_pts)
#print 'time to save map for %s: %s' %(color, str(time.time()-start3))
print '---------------------------------'
print 'CALCULATED COLOR MAPS'#,hp.heap()
print '---------------------------------'
print('---------------------------------')
print('CALCULATED COLOR MAPS')#,hp.heap()
print('---------------------------------')


if __name__ == "__main__": dorun = runit(sys.argv)
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