d = math.pow(xlist1[i] - xlist2[j], 2.0) + \
math.pow(ylist1[i] - ylist2[j], 2.0) + \
math.pow(zlist1[i] - zlist2[j], 2.0)
d = math.sqrt(d)
if (d != dists[i, j]):
return None
return d
###############################################################################
filename = ""
if (len(sys.argv)) == 2:
filename = sys.argv[1]
else:
print "usage :", sys.argv[0], " xyzfile"
exit(1)
xlist, ylist, zlist, atoms = xyznanop.read_ncxyz(filename, False)
d = mindist(xlist, ylist, zlist, atoms)
if d == None:
exit(1)
if d < 2.25:
print filename
def compare (filename1, filename2, verbose, dumpalsoobmol):
xlist1, ylist1, zlist1, atoms1 = xyznanop.read_ncxyz (filename1)
xlist2, ylist2, zlist2, atoms2 = xyznanop.read_ncxyz (filename2)
if len(atoms1) == len(atoms2):
mol1list = numpy.zeros((len(atoms1), 3))
mol2list = numpy.zeros((len(atoms2), 3))
for i in range(0, len(atoms1)):
mol1list[i, 0] = xlist1[i]
mol1list[i, 1] = ylist1[i]
mol1list[i, 2] = zlist1[i]
for i in range(0, len(atoms2)):
mol2list[i, 0] = xlist2[i]
mol2list[i, 1] = ylist2[i]
mol2list[i, 2] = zlist2[i]
if (verbose):
print "RMSD: ", kabsch_minima.rmsd(mol1list, mol2list)
rmatrix, translate2, translate1 = \
kabsch_minima.return_rotation_matrix(mol2list, mol1list, verbose)
if verbose:
print "Translate: ", filename1
for i in range(0, len(atoms1)):
xlist1[i] -= translate1[0]
ylist1[i] -= translate1[1]
zlist1[i] -= translate1[2]
if verbose:
print "Done"
if verbose:
xyznanop.write_ncxyz("out1.xyz", xlist1, ylist1, zlist1, atoms1)
if verbose:
print "Translate: ", filename2
for i in range(0, len(atoms1)):
xlist2[i] -= translate2[0]
ylist2[i] -= translate2[1]
zlist2[i] -= translate2[2]
d11 = rmatrix[0, 0]
d12 = rmatrix[0, 1]
d13 = rmatrix[0, 2]
d21 = rmatrix[1, 0]
d22 = rmatrix[1, 1]
d23 = rmatrix[1, 2]
d31 = rmatrix[2, 0]
d32 = rmatrix[2, 1]
d33 = rmatrix[2, 2]
qx = []
qy = []
qz = []
if verbose:
print "Rotate: ", filename2
for i in range(0,len(atoms2)):
qx.append(d11*xlist2[i] + d12*ylist2[i] + d13*zlist2[i])
qy.append(d21*xlist2[i] + d22*ylist2[i] + d23*zlist2[i])
qz.append(d31*xlist2[i] + d32*ylist2[i] + d33*zlist2[i])
if verbose:
print "Done"
if verbose:
xyznanop.write_ncxyz("out2.xyz", qx, qy, qz, atoms2)
for i in range(0, len(atoms1)):
mol1list[i, 0] = xlist1[i]
mol1list[i, 1] = ylist1[i]
mol1list[i, 2] = zlist1[i]
for i in range(0, len(atoms2)):
mol2list[i, 0] = qx[i]
mol2list[i, 1] = qy[i]
mol2list[i, 2] = qz[i]
rmsdfinal = kabsch_minima.rmsd(mol1list, mol2list)
if verbose:
print filename1, " ", filename2, " ", "RMSD: ", \
rmsdfinal
if dumpalsoobmol:
ormatrix = pybel.ob.matrix3x3()
for i in range(3):
for j in range(3):
ormatrix.Set(i, j, rmatrix[i,j])
myrm = pybel.ob.doubleArray(9)
ormatrix.GetArray(myrm)
print "Translate: ", filename1
mol1 = pybel.readfile("xyz", filename1).next()
print " read file"
mol1.OBMol.Translate(pybel.ob.vector3(-translate1[0], -translate1[1], -translate1[2]));
print " translate"
output = pybel.Outputfile("xyz", "pout1.xyz", overwrite=True)
output.write(mol1)
output.close()
print "Done"
print "Rotate and Translate: ", filename1
mol2 = pybel.readfile("xyz", filename2).next()
print " read file"
mol2.OBMol.Translate(pybel.ob.vector3(-translate2[0], -translate2[1], -translate2[2]));
print " translate"
mol2.OBMol.Rotate(myrm)
print " rotate"
output = pybel.Outputfile("xyz", "pout2.xyz", overwrite=True)
output.write(mol2)
output.close()
print "Done"
return rmsdfinal
else:
print "Wrong dim"
return None
import kabsch_minima
import xyznanop
filename1 = ""
filename2 = ""
verbose = False
dumpalsoobmol = False
if (len(sys.argv)) == 3:
filename1 = sys.argv[1]
filename2 = sys.argv[2]
else:
print "usage :", sys.argv[0], " target.xyz filename.xyz"
exit(1)
xlist1, ylist1, zlist1, atoms1 = xyznanop.read_ncxyz(filename1)
xlist2, ylist2, zlist2, atoms2 = xyznanop.read_ncxyz(filename2)
if len(atoms1) == len(atoms2):
mol1list = numpy.zeros((len(atoms1), 3))
mol2list = numpy.zeros((len(atoms2), 3))
for i in range(0, len(atoms1)):
mol1list[i, 0] = xlist1[i]
mol1list[i, 1] = ylist1[i]
mol1list[i, 2] = zlist1[i]
for i in range(0, len(atoms2)):
mol2list[i, 0] = xlist2[i]
mol2list[i, 1] = ylist2[i]
mol2list[i, 2] = zlist2[i]
sys.path.append("../modules")
import xyznanop
xyz1 = ""
xyz2 = ""
if (len(sys.argv)) == 3:
xyz1 = sys.argv[1]
xyz2 = sys.argv[2]
else:
print "usage: ", sys.argv[0], " file1.xyz file2.xyz"
exit(1)
x1, y1, z1, atoms1 = xyznanop.read_ncxyz(xyz1, trans=False)
x2, y2, z2, atoms2 = xyznanop.read_ncxyz(xyz2, trans=False)
if len(atoms1) != len(atoms2):
print "Error different number of atoms"
exit(1)
distances = []
for i in range(len(atoms1)):
if atoms1[i] != atoms2[i]:
print "Error different atom"
exit(1)
for j in range(len(atoms1)):
if (j != i):
botx, topx, boty, topy, botz, topz = \
nanoparticle.file_to_nanoparticle_list(filename, nanaparticles)
if (botx >= topx) or (boty >= topy) or \
(boty >= topy):
print "Error Invalid BOX"
exit()
minbox_x = 100000.0
maxbox_x = -100000.0
minbox_y = 100000.0
maxbox_y = -100000.0
minbox_z = 100000.0
maxbox_z = -100000.0
xlist, ylist, zlist, atoms = xyznanop.read_ncxyz(xyzfile, False)
xlist1 = xlist[:len(xlist) / 2]
ylist1 = ylist[:len(ylist) / 2]
zlist1 = zlist[:len(zlist) / 2]
atoms1 = atoms[:len(atoms) / 2]
xlist2 = xlist[len(xlist) / 2:]
ylist2 = ylist[len(ylist) / 2:]
zlist2 = zlist[len(zlist) / 2:]
atoms2 = atoms[len(atoms) / 2:]
if len(nanaparticles) != 2:
print "Only two nanoparticles can be used"
exit(1)
fp = open(filename)
for l in fp:
sl = l.split(",")
rootpath = "./"
#print sl[0]
#print find (sl[0], "./")
paths = [
line[2:] for line in subprocess.check_output(
"find " + rootpath + " -name " + sl[0], shell=True).splitlines()
]
if len(paths) == 0:
print "Error in ", sl[0]
else:
print "Found ", len(paths)
for i in range(1, len(paths)):
rmsd = compare("./" + paths[0], "./" + paths[i], False, False)
if rmsd > 1.0e-5:
print paths[0], " vs ", paths[i], " ", rmsd
xlist, ylist, zlist, atoms = xyznanop.read_ncxyz(paths[0], False)
d, dist = mindist(xlist, ylist, zlist, atoms)
print sl[0], " dist ", d, " (", dist, ") "
fp.close()
import xyznanop
import common
import sphere
import point
import util
import line
mypath = "./XYZ/"
onlyfiles = [f for f in listdir(mypath) if isfile(join(mypath, f))]
alldists = []
for file in onlyfiles:
if file.endswith('.xyz'):
print mypath + file
xlist, ylist, zlist, atoms = xyznanop.read_ncxyz(mypath + file)
xlist1 = xlist[0:(len(xlist) / 2) - 1]
ylist1 = ylist[0:(len(ylist) / 2) - 1]
zlist1 = zlist[0:(len(zlist) / 2) - 1]
xlist2 = xlist[len(xlist) / 2:len(xlist) - 1]
ylist2 = ylist[len(ylist) / 2:len(ylist) - 1]
zlist2 = zlist[len(zlist) / 2:len(zlist) - 1]
dists = []
for i in range(0, len(xlist1)):
dx = (xlist1[i] - xlist2[i])**2
dy = (ylist1[i] - ylist2[i])**2
dz = (zlist1[i] - zlist2[i])**2
parser.add_argument("-f", "--input-film", help="input the film file if needed", \
type=str, required=False, default="", dest="filmfile")
parser.add_argument("-v", "--verbose", help="increase output verbosity", \
default=False, action="store_true")
if len(sys.argv) == 1:
parser.print_help()
exit(1)
args = parser.parse_args()
verbose = args.verbose
xyzfname = args.xyzfile
xlist, ylist, zlist, atoms = xyznanop.read_ncxyz(xyzfname)
xlist = numpy.divide(xlist, CONVERTFCT)
ylist = numpy.divide(ylist, CONVERTFCT)
zlist = numpy.divide(zlist, CONVERTFCT)
alltraps = []
for pair in args.curvefiles.split(";"):
id, fname = pair.split(":")
print >> sys.stderr, id, fname
x, xval, sumx, \
y, yval, sumy, \
z, zval, sumz = read_filecurve (fname)
"Nanoparticle: ", n.get_volume(), " [", \
math.fabs(spheres[0].get_volume() - n.get_volume()), "] "
botx = min(scx)
boty = min(scy)
botz = min(scz)
topx = max(scx)
topy = max(scy)
topz = max(scz)
if (botx >= topx) or (boty >= topy) or \
(boty >= topy):
print "Error Invalid BOX"
exit()
xlistin, ylistin, zlistin, atoms = xyznanop.read_ncxyz(xyznc)
vdwradius = {'O': 0.60, 'Ti': 1.40}
sumofvdw = numpy.zeros((len(atoms), len(atoms)))
for i in range(0, len(atoms)):
for j in range(0, len(atoms)):
sumofvdw[i][j] = vdwradius[atoms[i]] + vdwradius[atoms[j]]
#print sumofvdw
xlistall = []
ylistall = []
zlistall = []
atomsall = []
lplacedcx = []
