#!/usr/bin/env python
import grid.grid as grid
import sys
print "# Input format: RDFfromDX.py <dxfilename> <x> <y> <z> <delta> <max> (concentration)"
print "If you input a concentration (particles per unit volume), the coordination number will also be printed in the 3rd column"
if len(sys.argv) < 6:
quit("Error, insufficient arguments")
dxfilename, x, y, z, delta, maxval = sys.argv[1:7]
concentration = False
if len(sys.argv) > 7:
concentration = float(sys.argv[7])
griddata = grid.dx2Grid(dxfilename)
if not concentration:
rdf = griddata.interpRDF([float(x),float(y),float(z)], float(delta), float(maxval))
for i, value in enumerate(rdf):
print i*float(delta), value
else:
rdf, coordnums = griddata.interpRDF([float(x),float(y),float(z)], float(delta), float(maxval), concentration)
for i, value in enumerate(rdf):
print i*float(delta), value, coordnums[i]
import grid.grid as grid
import numpy as np
import os
testscriptdir = os.getcwd()
# Test reading/writing
print "Testing reading/writing dx files.."
dxfilename = os.path.join(testscriptdir, "data", "dxfiles",
"AlaDP_3DRISM_smallbuffer.dx.gz")
originalgrid = grid.dx2Grid(dxfilename)
maxvalue = originalgrid.distribution.max()
maxindices = tuple(np.argwhere(originalgrid.distribution == maxvalue)[0])
originalgrid.distribution[maxindices] = maxvalue * 2.0
originalgrid.writedx("modified.dx")
newgrid = grid.dx2Grid("modified.dx")
newmax = newgrid.distribution.max()
assert newmax == maxvalue * 2.0
#cleanup
os.remove("modified.dx")
# Test shells
print "Testing shell-related utilities.."
storedprecomputedshells = grid.readshellindices()
newshells = grid.precomputeshellindices(40)
for storedshell, newshell in zip(storedprecomputedshells, newshells):
for storedpoint, newpoint in zip(storedshell, newshell):
for storedindex, newindex in zip(storedpoint, newpoint):
assert storedindex == newindex
#!/Users/nosaka/Documents/UNCC/ITSC 3155/Twitter Visualizations/venv/bin/python
import grid.grid as grid
import sys
print "# Input format: RDFfromDX.py <dxfilename> <x> <y> <z> <delta> <max> (concentration)"
print "If you input a concentration (particles per unit volume), the coordination number will also be printed in the 3rd column"
if len(sys.argv) < 6:
quit("Error, insufficient arguments")
dxfilename, x, y, z, delta, maxval = sys.argv[1:7]
concentration = False
if len(sys.argv) > 7:
concentration = float(sys.argv[7])
griddata = grid.dx2Grid(dxfilename)
if not concentration:
rdf = griddata.interpRDF([float(x),float(y),float(z)], float(delta), float(maxval))
for i, value in enumerate(rdf):
print i*float(delta), value
else:
rdf, coordnums = griddata.interpRDF([float(x),float(y),float(z)], float(delta), float(maxval), concentration)
for i, value in enumerate(rdf):
print i*float(delta), value, coordnums[i]
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 #import matplotlib #import pylab #from numpy import arange #xset = arange(0, 10.0, 0.1)
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)