def raster3d_render_tls_graph_path(self, chain, cpartition):
"""Render TLS visualizations using Raster3D.
"""
basename = "%s_CHAIN%s_NTLS%d" % (self.struct_id, chain.chain_id,
cpartition.num_tls_segments())
png_path = "%s.png" % (basename)
console.stdoutln("Raster3D: rendering %s..." % (basename))
struct_id = self.struct_id
driver = R3DDriver.Raster3DDriver()
## XXX: Size hack: some structures have too many chains,
## or are just too large
show_chain = {}
for chx in self.struct.iter_chains():
if chx.chain_id == chain.chain_id:
show_chain[chx.chain_id] = True
continue
if chx.count_amino_acids() >= 100:
show_chain[chx.chain_id] = False
continue
show_chain[chx.chain_id] = True
## end size hack
## got target chain?
if self.tlsmd_analysis.target_chain != None:
for atm in self.tlsmd_analysis.target_chain.iter_all_atoms():
atm.orig_position = atm.position
atm.position = chain.target_chain_sresult.transform(
atm.position)
viewer = Viewer.GLViewer()
gl_struct = viewer.glv_add_struct(self.struct)
## orient the structure with the super-spiffy orientation algorithm
## which hilights the chain we are examining
ori = calc_orientation(self.struct, chain)
viewer.glo_update_properties(R=ori["R"],
cor=ori["centroid"],
zoom=ori["hzoom"],
near=ori["near"],
far=ori["far"],
width=ori["pwidth"],
height=ori["pheight"],
bg_color="White")
## turn off axes and unit cell visualization
gl_struct.glo_update_properties_path("gl_axes/visible", False)
gl_struct.glo_update_properties_path("gl_unit_cell/visible", False)
## setup base structural visualization
for gl_chain in gl_struct.glo_iter_children():
if not isinstance(gl_chain, Viewer.GLChain):
continue
## chain is hidden
if show_chain.get(gl_chain.chain.chain_id, False) == False:
gl_chain.properties.update(visible=False)
continue
if gl_chain.chain.chain_id == chain.chain_id:
if gl_chain.chain.has_amino_acids():
gl_chain.properties.update(lines=False,
trace=True,
trace_radius=0.25,
trace_color="0.80,0.80,0.80")
elif gl_chain.chain.has_nucleic_acids():
gl_chain.properties.update(lines=False,
ball_stick=True,
ball_stick_radius=0.25,
color="0.80,0.80,0.80")
else:
if gl_chain.chain.has_amino_acids():
gl_chain.properties.update(lines=False,
trace=True,
trace_radius=0.25,
trace_color="0.80,0.80,0.80")
elif gl_chain.chain.has_nucleic_acids():
gl_chain.properties.update(hetatm_visible=True,
trace=True,
trace_radius=0.35,
trace_color="0.80,0.80,0.80",
ball_stick=True,
ball_stick_radius=0.25,
color="0.60,0.60,0.70")
else:
gl_chain.properties.update(visible=True,
ball_stick=True,
ball_stick_radius=0.25,
cpk=False)
## add the TLS group visualizations
has_amino_acids = cpartition.chain.has_amino_acids()
has_nucleic_acids = cpartition.chain.has_nucleic_acids()
for tls in cpartition.iter_tls_segments():
if tls.method != "TLS":
continue
if self.tlsmd_analysis.target_chain is not None:
if tls.rmsd_pre_alignment <= 0.8:
continue
if (tls.rmsd_pre_alignment - tls.sresult.rmsd) < 0.5:
continue
tls_name = "TLS_%s" % (tls.filename_label())
gl_tls_group = TLS.GLTLSGroup(oatm_visible=False,
side_chain_visible=False,
hetatm_visible=True,
adp_prob=settings.ADP_PROB,
L_axis_scale=2.0,
L_axis_radius=0.20,
both_phases=True,
tls_group=tls.tls_group,
tls_info=tls.model_tls_info,
tls_name=tls_name,
tls_color=tls.color.name)
gl_struct.glo_add_child(gl_tls_group)
if tls.superposition_vscrew != None:
gl_tls_group.properties.update(
COR_vector=tls.superposition_vscrew)
## set width of trace according to the group's translationral tensor trace
mtls_info = tls.model_tls_info
tiso = (mtls_info["Tr1_eigen_val"] + mtls_info["Tr2_eigen_val"] +
mtls_info["Tr3_eigen_val"]) / 3.0
## too big usually for good visualization -- cheat and scale it down
radius = 0.30
if has_amino_acids:
gl_tls_group.gl_atom_list.properties.update(
trace_radius=radius)
elif has_nucleic_acids:
gl_tls_group.gl_atom_list.properties.update(
oatm_visible=True,
side_chain_visible=True,
trace=True,
trace_radius=0.25,
ball_stick=True,
ball_stick_radius=radius)
gl_tls_group.glo_update_properties(time=0.25)
## got target chain?
if self.tlsmd_analysis.target_chain is not None:
gl_chain = Viewer.GLChain(chain=self.tlsmd_analysis.target_chain)
gl_chain.properties.update(oatm_visible=False,
side_chain_visible=False,
hetatm_visible=True,
lines=False,
ball_stick=False,
trace=True,
trace_radius=0.25,
trace_color="0.40,0.40,0.40")
gl_struct.glo_add_child(gl_chain)
driver.glr_set_render_png_path(png_path)
viewer.glv_render_one(driver)
## got target chain?
if self.tlsmd_analysis.target_chain != None:
for atm in self.tlsmd_analysis.target_chain.iter_all_atoms():
atm.position = atm.orig_position
del atm.orig_position
return "", png_path
