dists = distance.cdist(coords1, coords2)
mindist = numpy.min(dists)
print "New mindist: ", mindist
return xlist, ylist, zlist, atoms
###############################################################################
filename = ""
step = 6.1
nstep = 1 # se nstep == 1 unico spostamento
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)
for i in range(nstep):
s = step / float(nstep)
xlist, ylist, zlist, atoms = \
move_mindist_vers (xlist, ylist, zlist, atoms, s)
xyznanop.write_ncxyz("out.xyz", xlist, ylist, zlist, atoms)
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
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]