def run(xds_inp):
xp = XPARM()
xp.set_info_from_xdsinp_or_inpstr(xdsinp=xds_inp)
xp.update_cell_based_on_axes()
print xp.xparm_str().rstrip()
def run(xds_inp):
xp = XPARM()
xp.set_info_from_xdsinp_or_inpstr(xdsinp=xds_inp)
d_map = numpy.zeros((xp.ny, xp.nx)) # resolution mapping
ed = numpy.zeros((3, 3))
ed[:, 0] = xp.X_axis
ed[:, 1] = xp.Y_axis
ed[:, 2] = numpy.cross(xp.X_axis, xp.Y_axis)
ed /= numpy.linalg.norm(ed, axis=0)
orgx, orgy = xp.origin
fs = xp.distance
qx, qy = xp.qx, xp.qy
org = -orgx * qx * ed[:, 0] - orgy * qy * ed[:, 1] + fs * ed[:, 2]
wavelen = xp.wavelength
s0 = xp.incident_beam / numpy.linalg.norm(xp.incident_beam) / wavelen
print "qx,qy=", qx, qy
print "s0=", s0
print "lambda=", wavelen
print "ORG=", org
print "ED="
print ed
ofs_pdb = open("detector_pos.pdb", "w")
ofs_pml = open("for_pymol.pml", "w")
for iseg, seg in enumerate(xp.segments):
print("Segment %d" % (iseg + 1))
eds = numpy.zeros((3, 3))
eds[:, 0] = seg.eds_x
eds[:, 1] = seg.eds_y
eds[:, 2] = numpy.cross(seg.eds_x, seg.eds_y)
eds /= numpy.linalg.norm(eds, axis=0)
edsl = numpy.dot(ed, eds)
ix, iy = numpy.meshgrid(range(seg.x1 - 1, seg.x2),
range(seg.y1 - 1, seg.y2))
tmp = numpy.zeros((ix.shape[0], ix.shape[1], 3))
for i in range(3):
tmp[:, :, i] = qx * (ix - seg.orgxs) * edsl[i, 0] + qy * (
iy - seg.orgys) * edsl[i, 1] + seg.fs * edsl[i, 2] + org[i]
write_atom(ofs_pdb, tmp, iseg)
ofs_pml.write("bond resi %d and name C1, resi %d and name C2\n" %
(iseg, iseg))
ofs_pml.write("bond resi %d and name C2, resi %d and name C4\n" %
(iseg, iseg))
ofs_pml.write("bond resi %d and name C3, resi %d and name C4\n" %
(iseg, iseg))
ofs_pml.write("bond resi %d and name C3, resi %d and name C1\n" %
(iseg, iseg))
tmpdenom = numpy.linalg.norm(tmp, axis=2) * wavelen
for i in range(3):
tmp[:, :, i] /= tmpdenom
s1 = tmp
s = s1 - s0
d_map[iy, ix] = 1. / numpy.linalg.norm(s, axis=2)
"""
for ix in range(seg.x1-1, seg.x2):
for iy in range(seg.y1-1, seg.y2):
tmp = (qx*(ix-seg.orgxs)*edsl[0,0]+qy*(iy-seg.orgys)*edsl[0,1]+seg.fs*edsl[0,2]+orgx,
qx*(ix-seg.orgxs)*edsl[1,0]+qy*(iy-seg.orgys)*edsl[1,1]+seg.fs*edsl[1,2]+orgy,
qx*(ix-seg.orgxs)*edsl[2,0]+qy*(iy-seg.orgys)*edsl[2,1]+seg.fs*edsl[2,2]+fs)
s1 = tmp/numpy.linalg.norm(tmp)/wavelen
s = s1-s0
d_map[iy,ix] = numpy.linalg.norm(s)
"""
ofs_pml.write("pseudoatom org, pos=(0,0,0)\n")
ofs_pml.write("pseudoatom s0, pos=(%f,%f,%f)\n" % tuple(s0 * 100))
ofs_pml.write("as spheres, org s0\n")
ofs_pml.write("color red, s0\n")
ofs_pml.write("distance selection1=org, selection2=s0\n")
ofs_pml.write("set sphere_scale, 10\n")
data = (d_map * 1000).astype(numpy.int32)
cbf.save_numpy_data_as_cbf(data.flatten(), data.shape[1], data.shape[0],
"d_map", "d_map_x1000.cbf")
