#!/Users/nosaka/Documents/UNCC/ITSC 3155/Twitter Visualizations/venv/bin/python import grid.grid as grid import numpy as np import os datadir = os.path.join(os.path.dirname(grid.__file__), "tests", "data") print "Testing reading TINKER guv files.." datafilename = os.path.join(datadir, 'TKRguv', 'h2o.guv.sample') dists = grid.TKRguv2Grids(datafilename) assert len(dists) == 2 assert 1.1 > dists[0].distribution[31, 31, 31] > 0.9 print "Testing reading UxDATA files.." uxdatafilename = os.path.join(datadir, 'UxDATAfiles', 'UVDATA.sample') uxdists = grid.data2Grids(uxdatafilename, disttypes=['g', 'c']) assert len(uxdists) == 4 assert 1.1 > uxdists['O.g'].distribution[31, 31, 31] > 0.9 dxfilename = os.path.join(datadir, "dxfiles", "AlaDP_3DRISM_smallbuffer.dx.gz") griddata = grid.dx2Grid(dxfilename) print "Testing Trilinear interpolation.." assert griddata.getvalue([9.0, 1.0, 1.0]) - 0.609013742553 < 1 * 10**(-10) # Test 3D->RDF function. print "Testing RDF interpolation..." rdfnearO = griddata.interpRDF([3.6, 6.653, 0.00], 0.1, 10.0) #Carbonyl O rdfnearH = griddata.interpRDF([6.737, 6.359, 0], 0.1, 10.0) #NH H rdfnearH2 = griddata.interpRDF([2.733, 4.556, 0], 0.1, 10.0) #another NH H #Debugging section
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)
import numpy as np
import os
datadir = os.path.join(os.path.dirname(grid.__file__),"tests","data")
print "Testing reading TINKER guv files.."
datafilename = os.path.join(datadir,'TKRguv','h2o.guv.sample')
dists = grid.TKRguv2Grids(datafilename)
assert len(dists) == 2
assert 1.1 > dists[0].distribution[31,31,31] > 0.9
print "Testing reading UxDATA files.."
uxdatafilename = os.path.join(datadir,'UxDATAfiles','UVDATA.sample')
uxdists = grid.data2Grids(uxdatafilename, disttypes=['g','c'])
assert len(uxdists) == 4
assert 1.1 > uxdists['O.g'].distribution[31,31,31] > 0.9
dxfilename = os.path.join(datadir, "dxfiles",
"AlaDP_3DRISM_smallbuffer.dx.gz")
griddata = grid.dx2Grid(dxfilename)
print "Testing Trilinear interpolation.."
assert griddata.getvalue([9.0,1.0,1.0]) - 0.609013742553 < 1 * 10**(-10)
# Test 3D->RDF function.
print "Testing RDF interpolation..."
rdfnearO = griddata.interpRDF([3.6, 6.653, 0.00], 0.1, 10.0) #Carbonyl O
rdfnearH = griddata.interpRDF([6.737, 6.359, 0], 0.1, 10.0) #NH H
rdfnearH2 = griddata.interpRDF([2.733, 4.556, 0], 0.1, 10.0) #another NH H