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import argparse
parser = argparse.ArgumentParser(description='Translate a dx file to cube format')
parser.add_argument('dx_input',
help='Name of the dx_input file (required arguement)')
parser.add_argument('pqr_input',
help='Name of the pqr_input file (required arguement)')
parser.add_argument('output',
help='Name of the output file (required arguement)')
args = parser.parse_args()
counter = 0
#DX STUFF
if args.dx_input.endswith('.dx'):
print "Success"
else:
print "Error converting file"
try:
with open(args.dx_input, 'r') as in_f, open(args.output, 'w') as out_f, open(args.pqr_input, 'r') as in_pqr:
out_f.write("CPMD CUBE FILE.\n"
"OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n")
#Discard comments at top of file.
line = in_f.readline()
newline = in_pqr.readline()
while line.startswith('#'):
line = in_f.readline()
while newline.startswith('REMARK'):
newline = in_pqr.readline()
split_line = line.split()
grid_sizes = [int(x)*-1 for x in split_line[-3:]]
split_line = in_f.readline().split()
origin = [float(x) for x in split_line[-3:]]
parameter_fmt = "{:>4} {:>11.6f} {:>11.6f} {:>11.6f}\n"
try:
while newline.startswith('ATOM'):
pqr_line = in_pqr.readline()
new_split_line = pqr_line.split()
atom_num = new_split_line[1]
except IndexError:
pass
in_pqr.seek(0)
newline = in_pqr.readline()
while newline.startswith('REMARK'):
newline = in_pqr.readline()
origin_line = parameter_fmt.format(atom_num, *origin)
out_f.write(origin_line)
for x in xrange(3):
split_line = in_f.readline().split()
grid_dims = [float(item) for item in split_line[-3:]]
dim_lin = parameter_fmt.format(grid_sizes[x], *grid_dims)
out_f.write(dim_lin)
atoms_parameter_fmt = "{:>4} {:>11.6f} {:>11.6f} {:>11.6f} {:>11.6f}\n"
a = True
xreal_center = []
yreal_center = []
zreal_center = []
try:
while a == True:
if not newline.startswith('TER'):
new_split_line = newline.split()
radius = new_split_line[-1]
xyz = new_split_line[-5:-2]
line_atom_num = new_split_line[1]
atom_radius = new_split_line[-1]
pqr_lin = atoms_parameter_fmt.format(int(line_atom_num), float(new_split_line[-2]), float(xyz[0]), float(xyz[1]), float(xyz[2]))
out_f.write(pqr_lin)
newline = in_pqr.readline()
xreal_center.append(float(xyz[0]))
yreal_center.append(float(xyz[1]))
zreal_center.append(float(xyz[2]))
else:
a = False
except IndexError:
pass
x_avg = sum(xreal_center)/float(atom_num)
y_avg = sum(yreal_center)/float(atom_num)
z_avg = sum(zreal_center)/float(atom_num)
print x_avg, y_avg, z_avg
#print origin
#new_origin = []
#for item in origin:
# newitem = item/0.529177
#new_new = item/2 + newitem/2
# new_origin.append(newitem)
#print new_origin
#Consume unneeded object lines.
in_f.readline()
in_f.readline()
##TODO: put atoms here
value_format = ["{:< 13.5E}"]
value_format = ' '.join(value_format * 6) + '\n'
print value_format
group = []
line = in_f.readline()
while not line.startswith('attribute'):
values = [float(item) for item in line.split()]
group.extend(values)
if len(group) >= 6:
out_f.write(value_format.format(*group))
group = []
line = in_f.readline()
if group:
group_strs = ["{:< 13.5E}".format(item) for item in group]
out_f.write(' '.join(group_strs))
except IOError:
print "file doesn't exist"
'''
for line in dx_data:
dx_data_2 = dx_data
data_point = line.strip("\n")
dx_data_2.pop(0)
dx_data._2append(data_point)
for line in dx_data_2:
if line.startswith('#'):
dx_data_2.remove(line)
continue
elif "gridpositions" in line:
new_line = line.split()
grid_values = new_line[-3:]
#grid values for cube file, will need grid_valies[0]
break
elif line.startswith('delta'):
line.insert('0')
line.remove(delta)
#PQR STUFF
if args.pqr_input.endswith('.pqr'):
print "yay"
else:
print "nay"
try:
with open(args.pqr_input, 'r') as f:
pqr_data = f.readlines()
except IOError:
print "file doesn't exist"
for line in pqr_data:
data_point = line.strip("\n")
pqr_data.pop(0)
pqr_data.append(data_point)
for line in pqr_data:
if line.startswith('REMARK'):
pqr_data.remove(line)
continue
counter +=1
#the number next to the origin in cube format
'''
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