def returncenters(guvfilename, molar, grcutoff):
'''Given distribution, returns placed atoms
Input: guvfilename and molarity
Returns: Placed centers as Atom objects
'''
conc = molar * 6.0221415E-4
shellindices = grid.readshellindices()
if guvfilename[-3:] == ".dx":
(distribution, origin, delta, gridcount) = \
grid.readdx(guvfilename)
elif guvfilename[-3:] == ".h5":
grids = grid.h5ToGrids(guvfilename)
print "Warning, assuming target molecule is 'O', please contact the developer for more info."
if 'guv' not in grids['O'].keys():
exit("Error, guv distribution not found in file")
gGrid = grids['O']['guv']
distribution = gGrid.distribution
origin = gGrid.origin
delta = gGrid.deltas
gridcount = gGrid.gridcount
else:
exit("Error, incompatible file type! -> {0}".format(guvfilename))
(popzero, totalpop, gridvolume) = converttopop(distribution,
delta, conc)
return doplacement(popzero, conc, gridvolume, origin, delta, shellindices,
grcutoff)
def main():
parser = \
argparse.ArgumentParser(description=''+
'Converts volumetric data via grid.py.\n'+
'Currently available formats:\n\n'+
"Input:\n"+
'OpenDX (.dx)\n'+
'3D-RISM TINKER "xuv" style (.guv, .huv, etc)\n'+
'3D-RISM GAMESS "UxDATA" style (UVDATA, VVDATA, etc)\n'+
'MDF 3D-RISM HDF5 "H5" style\n\n'+
'Output:\n'+
'OpenDX (.dx)\n'+
'Accelrys DS grid file (.grd) NOT UHBD grid!!!\n'+
'Input filetypes are determined by file names.')
outtypes = ['dx', 'grd']
parser.add_argument('inputfile',
type=str,
help='Input volumetric data file')
parser.add_argument('outtype',
type=str,
help='Type of output file: %s' % outtypes)
args = parser.parse_args()
if args.outtype not in outtypes:
exit("Error! Output type not recognized. Choose from %s" % outtypes)
if not os.path.isfile(args.inputfile):
exit("Error! Input file not found.")
# Read
intypes = ['dx', 'uv', 'DATA']
if '.dx' in args.inputfile:
print "Reading OpenDX input"
#Contains only one distribution
mygrids = {'.': grid.dx2Grid(args.inputfile)}
elif args.inputfile[-2:] == 'uv':
print "Reading TINKER xuv input"
## Temporarily try 2.7+/3.0+
#my = {key: value for (key, value) in sequence}
# Using Python 2.6 compatible "dictionary comprehension"
mygrids = dict(('%d.' % (i+1), mygrid) for (i, mygrid) in \
enumerate(grid.TKRguv2Grids(args.inputfile)))
elif "DATA" in args.inputfile:
print "Reading UxDATA input"
mygrids = grid.data2Grids(args.inputfile) # Already a dictionary
for key in mygrids.keys():
# Modify keys to be used as output filenames
mygrids['%s.' % key] = mygrids.pop(key)
elif ".uv.h5" in args.inputfile:
print "Reading MDF .h5 input"
mygrids = {}
for speciesname, dictofgrids in grid.h5ToGrids(
args.inputfile).iteritems():
for disttype, mygrid in dictofgrids.iteritems():
mygrids["%s.%s." % (speciesname, disttype)] = mygrid
# Write
if args.outtype == 'dx':
print "Outputting .dx file(s)"
for key, mygrid in mygrids.iteritems():
mygrid.writedx('%sdx' % key)
elif args.outtype == 'grd':
print "Outputting Accelrys DS .grd file(s)"
for key, mygrid in mygrids.iteritems():
mygrid.writegrd('%sgrd' % key)
def main():
parser = \
argparse.ArgumentParser(description=''+
'Converts volumetric data via grid.py.\n'+
'Currently available formats:\n\n'+
"Input:\n"+
'OpenDX (.dx)\n'+
'3D-RISM TINKER "xuv" style (.guv, .huv, etc)\n'+
'3D-RISM GAMESS "UxDATA" style (UVDATA, VVDATA, etc)\n'+
'MDF 3D-RISM HDF5 "H5" style\n\n'+
'Output:\n'+
'OpenDX (.dx)\n'+
'Accelrys DS grid file (.grd) NOT UHBD grid!!!\n'+
'Input filetypes are determined by file names.')
outtypes = ['dx', 'grd']
parser.add_argument('inputfile', type=str, help='Input volumetric data file')
parser.add_argument('outtype', type=str, help='Type of output file: %s' % outtypes)
args = parser.parse_args()
if args.outtype not in outtypes:
exit("Error! Output type not recognized. Choose from %s" % outtypes)
if not os.path.isfile(args.inputfile):
exit("Error! Input file not found.")
# Read
intypes = ['dx', 'uv', 'DATA']
if '.dx' in args.inputfile:
print "Reading OpenDX input"
#Contains only one distribution
mygrids = {'.' : grid.dx2Grid(args.inputfile)}
elif args.inputfile[-2:] == 'uv':
print "Reading TINKER xuv input"
## Temporarily try 2.7+/3.0+
#my = {key: value for (key, value) in sequence}
# Using Python 2.6 compatible "dictionary comprehension"
mygrids = dict(('%d.' % (i+1), mygrid) for (i, mygrid) in \
enumerate(grid.TKRguv2Grids(args.inputfile)))
elif "DATA" in args.inputfile:
print "Reading UxDATA input"
mygrids = grid.data2Grids(args.inputfile) # Already a dictionary
for key in mygrids.keys():
# Modify keys to be used as output filenames
mygrids['%s.' % key] = mygrids.pop(key)
elif ".uv.h5" in args.inputfile:
print "Reading MDF .h5 input"
mygrids = {}
for speciesname, dictofgrids in grid.h5ToGrids(args.inputfile).iteritems():
for disttype, mygrid in dictofgrids.iteritems():
mygrids["%s.%s." % (speciesname, disttype)] = mygrid
# Write
if args.outtype == 'dx':
print "Outputting .dx file(s)"
for key, mygrid in mygrids.iteritems():
mygrid.writedx('%sdx' % key)
elif args.outtype == 'grd':
print "Outputting Accelrys DS .grd file(s)"
for key, mygrid in mygrids.iteritems():
mygrid.writegrd('%sgrd' % key)
