def percent_vbur(
session,
selection,
radii="UMN",
radius=3.5,
scale=1.17,
method="Lebedev",
radialPoints=20,
angularPoints=1454,
minimumIterations=25,
onlyAtoms=None,
center=None,
useCentroid=True,
displaySphere=None,
pointSpacing=0.1,
intersectionScale=6,
palette="rainbow",
return_values=False,
steric_map=False,
useScene=False,
num_pts=100,
shape="circle",
labels="none",
reportComponent="total",
):
out = []
models = {
model: [
atom for atom in model.atoms
if onlyAtoms is not None and atom in onlyAtoms
]
for model in selection if isinstance(model, AtomicStructure)
}
s = "<pre>model\tcenter\t%Vbur\n"
for model in models:
if len(models[model]) == 0:
targets = None
else:
targets = [AtomSpec(atom.atomspec) for atom in models[model]]
if center is not None:
if isinstance(center, tuple):
mdl_center = np.array(center)
else:
mdl_center = [
AtomSpec(atom.atomspec) for atom in model.atoms
if atom in center
]
else:
mdl_center = []
rescol = ResidueCollection(model)
if useScene:
oop_vector = session.view.camera.get_position().axes()[2]
ip_vector = session.view.camera.get_position().axes()[1]
x_vec = session.view.camera.get_position().axes()[0]
basis = np.array([x_vec, ip_vector, oop_vector]).T
else:
oop_vector = None
ip_vector = None
basis = None
if len(mdl_center) == 0:
rescol.detect_components()
mdl_center = rescol.center
elif not isinstance(center, np.ndarray):
mdl_center = rescol.find([AtomSpec(c.atomspec) for c in center])
key_atoms = None
if not useCentroid and not isinstance(center, np.ndarray):
for c in mdl_center:
if targets is not None:
key_atoms = []
targets = rescol.find(targets)
for atom in targets:
if c in atom.connected or atom in c.connected:
key_atoms.append(atom)
else:
key_atoms = None
if (labels != "none"
or reportComponent != "total") and not useScene:
if not key_atoms:
session.logger.warning(
"bonds between center and coordinating atoms is required to"
" properly orient octants")
oop_vector = np.zeros(3)
for atom in key_atoms:
oop_vector += c.coords - atom.coords
if len(key_atoms) == 1:
ip_vector = perp_vector(oop_vector)
x_vec = np.cross(ip_vector, oop_vector)
else:
coords = [atom.coords for atom in key_atoms]
coords.append(c.coords)
coords = np.array(coords)
ip_vector = perp_vector(coords)
x_vec = np.cross(ip_vector, oop_vector)
x_vec /= np.linalg.norm(x_vec)
ip_vector = -np.cross(x_vec, oop_vector)
ip_vector /= np.linalg.norm(ip_vector)
basis = np.array([x_vec, ip_vector, oop_vector]).T
if steric_map:
x, y, z, min_alt, max_alt, basis, _ = rescol.steric_map(
center=c,
key_atoms=key_atoms,
radii=radii,
oop_vector=oop_vector,
ip_vector=ip_vector,
radius=radius,
return_basis=True,
num_pts=num_pts,
shape=shape,
)
vbur = rescol.percent_buried_volume(
targets=targets,
basis=basis,
center=c,
radius=radius,
radii=radii,
scale=scale,
method=method,
rpoints=int(radialPoints),
apoints=int(angularPoints),
min_iter=minimumIterations,
)
if steric_map:
out.append(
(model, c.atomspec, vbur, (x, y, z, min_alt, max_alt)))
else:
out.append((model, c.atomspec, vbur))
s += "%s\t%s\t" % (model.name, c.atomspec)
if hasattr(vbur, "__iter__"):
if reportComponent == "octants":
s += "%s\n" % ",".join(["%.1f%%" % v for v in vbur])
elif reportComponent == "quadrants":
s += "%s\n" % ",".join([
"%.1f%%" % v for v in [
vbur[0] + vbur[7],
vbur[1] + vbur[6],
vbur[2] + vbur[5],
vbur[3] + vbur[4],
]
])
else:
s += "%.1f%%\n" % sum(vbur)
else:
s += "%.1f%%\n" % vbur
if displaySphere is not None:
mdl = vbur_vis(
session,
rescol,
targets,
radii,
scale,
radius,
c,
pointSpacing,
intersectionScale,
displaySphere,
vbur,
labels,
basis=basis,
)
model.add(mdl)
atomspec = mdl[0].atomspec
center_coords = rescol.COM(c)
args = [
"color",
"radial",
atomspec,
"center",
",".join(["%.4f" % x for x in center_coords]),
"palette",
palette,
"range",
"0,%.2f" % radius,
"coordinateSystem",
model.atomspec,
";",
"transparency",
atomspec,
"30",
]
run(session, " ".join(args))
else:
if targets is not None:
key_atoms = []
targets = rescol.find(targets)
for atom in targets:
if any(c in atom.connected for c in mdl_center):
key_atoms.append(atom)
else:
key_atoms = None
if (labels != "none"
or reportComponent != "total") and not useScene:
if not key_atoms:
session.logger.warning(
"bonds between center and coordinating atoms is required to"
" properly orient octants")
oop_vector = np.zeros(3)
for atom in key_atoms:
if isinstance(mdl_center, np.ndarray):
oop_vector += mdl_center - atom.coords
else:
for c in mdl_center:
oop_vector += c.coords - atom.coords
if len(key_atoms) == 1:
ip_vector = perp_vector(oop_vector)
x_vec = np.cross(ip_vector, oop_vector)
else:
coords = [atom.coords for atom in key_atoms]
if isinstance(mdl_center, np.ndarray):
coords.append(mdl_center)
else:
coords.extend([c.coords for c in mdl_center])
coords = np.array(coords)
ip_vector = perp_vector(coords)
x_vec = np.cross(ip_vector, oop_vector)
x_vec /= np.linalg.norm(x_vec)
ip_vector = -np.cross(x_vec, oop_vector)
ip_vector /= np.linalg.norm(ip_vector)
basis = np.array([x_vec, ip_vector, oop_vector]).T
if steric_map:
x, y, z, min_alt, max_alt, basis, _ = rescol.steric_map(
center=mdl_center,
key_atoms=key_atoms,
radius=radius,
radii=radii,
oop_vector=oop_vector,
ip_vector=ip_vector,
return_basis=True,
num_pts=num_pts,
shape=shape,
)
vbur = rescol.percent_buried_volume(
targets=targets,
basis=basis,
center=mdl_center,
radius=radius,
radii=radii,
scale=scale,
method=method,
rpoints=int(radialPoints),
apoints=int(angularPoints),
min_iter=minimumIterations,
)
if steric_map:
if not isinstance(mdl_center, np.ndarray):
out.append(
(model, ",".join([c.atomspec for c in mdl_center]),
vbur, (x, y, z, min_alt, max_alt)))
else:
out.append(
(model, ",".join(["%.3f" % c for c in mdl_center]),
vbur, (x, y, z, min_alt, max_alt)))
else:
if not isinstance(mdl_center, np.ndarray):
s += "%s\t%s\t" % (model.name, ", ".join(
[c.atomspec for c in mdl_center]))
out.append(
(model, ", ".join([c.atomspec
for c in mdl_center]), vbur))
else:
s += "%s\t%s\t" % (model.name, ",".join(
["%.3f" % c for c in mdl_center]))
out.append(
(model, ",".join(["%.3f" % c
for c in mdl_center]), vbur))
if hasattr(vbur, "__iter__"):
if reportComponent == "octants":
s += "%s\n" % ",".join(["%.1f%%" % v for v in vbur])
elif reportComponent == "quadrants":
s += "%s\n" % ",".join([
"%.1f%%" % v for v in [
vbur[0] + vbur[7],
vbur[1] + vbur[6],
vbur[2] + vbur[5],
vbur[3] + vbur[4],
]
])
else:
s += "%.1f%%\n" % sum(vbur)
else:
s += "%.1f%%\n" % vbur
if displaySphere is not None:
mdl = vbur_vis(
session,
rescol,
targets,
radii,
scale,
radius,
mdl_center,
pointSpacing,
intersectionScale,
displaySphere,
vbur,
labels,
basis=basis,
)
model.add(mdl)
atomspec = mdl[0].atomspec
if not isinstance(mdl_center, np.ndarray):
center_coords = rescol.COM(mdl_center)
else:
center_coords = mdl_center
#XXX: the center will be wrong if the models are tiled
args = [
"color",
"radial",
atomspec,
"center",
",".join(["%.4f" % x for x in center_coords]),
"palette",
palette,
"range",
"0,%.2f" % radius,
"coordinateSystem",
model.atomspec,
";",
"transparency",
atomspec,
"30",
]
run(session, " ".join(args))
s = s.strip()
s += "</pre>"
if not return_values:
session.logger.info(s, is_html=True)
else:
return out
def percent_vbur(
session,
selection,
radii="UMN",
radius=3.5,
scale=1.17,
method="Lebedev",
radialPoints=20,
angularPoints=1454,
minimumIterations=25,
onlyAtoms=None,
center=None,
useCentroid=True,
displaySphere=None,
pointSpacing=0.075,
intersectionScale=2,
palette="rainbow",
return_values=False,
steric_map=False,
use_scene=False,
num_pts=100,
shape="circle",
):
out = []
models = {
model: [
atom for atom in model.atoms
if onlyAtoms is not None and atom in onlyAtoms
]
for model in selection if isinstance(model, AtomicStructure)
}
s = "<pre>model\tcenter\t%Vbur\n"
for model in models:
if len(models[model]) == 0:
targets = None
else:
targets = [AtomSpec(atom.atomspec) for atom in models[model]]
if center is not None:
if isinstance(center, tuple):
mdl_center = np.array(center)
else:
mdl_center = [
AtomSpec(atom.atomspec) for atom in model.atoms
if atom in center
]
else:
mdl_center = []
rescol = ResidueCollection(model)
if use_scene:
oop_vector = session.view.camera.get_position().axes()[2]
ip_vector = session.view.camera.get_position().axes()[1]
else:
oop_vector = None
ip_vector = None
if len(mdl_center) == 0:
rescol.detect_components()
mdl_center = rescol.center
elif not isinstance(center, np.ndarray):
mdl_center = rescol.find([AtomSpec(c.atomspec) for c in center])
if not useCentroid and not isinstance(center, np.ndarray):
for c in mdl_center:
if steric_map:
if targets is not None:
key_atoms = []
targets = rescol.find(targets)
for atom in targets:
if c in atom.connected or atom in c.connected:
key_atoms.append(atom)
else:
key_atoms = None
x, y, z, min_alt, max_alt, basis, targets = rescol.steric_map(
center=c,
key_atoms=key_atoms,
radii=radii,
oop_vector=oop_vector,
ip_vector=ip_vector,
radius=radius,
return_basis=True,
num_pts=num_pts,
shape=shape,
)
vbur = rescol.percent_buried_volume(
targets=targets,
basis=basis,
center=c,
radius=radius,
radii=radii,
scale=scale,
method=method,
rpoints=int(radialPoints),
apoints=int(angularPoints),
min_iter=minimumIterations,
)
out.append((model.name, c.atomspec, vbur,
(x, y, z, min_alt, max_alt)))
else:
vbur = rescol.percent_buried_volume(
targets=targets,
center=c,
radius=radius,
radii=radii,
scale=scale,
method=method,
rpoints=int(radialPoints),
apoints=int(angularPoints),
min_iter=minimumIterations,
)
s += "%s\t%s\t%4.1f%%\n" % (model.name, c.atomspec, vbur)
out.append((model.name, c.atomspec, vbur))
if displaySphere is not None:
mdl = vbur_vis(
session,
rescol,
targets,
radii,
scale,
radius,
c,
pointSpacing,
intersectionScale,
displaySphere,
)
model.add([mdl])
atomspec = mdl.atomspec
center_coords = rescol.COM(c)
#XXX: the center will be wrong if the models are tiled
args = [
"color",
"radial",
atomspec,
"center",
",".join(["%.4f" % x for x in center_coords]),
"palette",
palette,
";",
"transparency",
atomspec,
"30",
]
run(session, " ".join(args))
else:
if steric_map:
if targets is not None:
key_atoms = []
targets = rescol.find(targets)
for atom in targets:
if any(c in atom.connected for c in mdl_center):
key_atoms.append(atom)
else:
key_atoms = None
x, y, z, min_alt, max_alt, basis, targets = rescol.steric_map(
center=mdl_center,
key_atoms=key_atoms,
radius=radius,
radii=radii,
oop_vector=oop_vector,
ip_vector=ip_vector,
return_basis=True,
num_pts=num_pts,
shape=shape,
)
vbur = rescol.percent_buried_volume(
targets=targets,
basis=basis,
center=mdl_center,
radius=radius,
radii=radii,
scale=scale,
method=method,
rpoints=int(radialPoints),
apoints=int(angularPoints),
min_iter=minimumIterations,
)
if not isinstance(mdl_center, np.ndarray):
out.append(
(model.name, ",".join([c.atomspec
for c in mdl_center]), vbur,
(x, y, z, min_alt, max_alt)))
else:
out.append(
(model.name, ",".join(["%.3f" % c
for c in mdl_center]), vbur,
(x, y, z, min_alt, max_alt)))
else:
vbur = rescol.percent_buried_volume(
targets=targets,
center=mdl_center,
radius=radius,
radii=radii,
scale=scale,
method=method,
rpoints=int(radialPoints),
apoints=int(angularPoints),
min_iter=minimumIterations,
)
if not isinstance(mdl_center, np.ndarray):
s += "%s\t%s\t%4.1f%%\n" % (model.name, ", ".join(
[c.atomspec for c in mdl_center]), vbur)
out.append(
(model.name,
", ".join([c.atomspec for c in mdl_center]), vbur))
else:
s += "%s\t%s\t%4.1f%%\n" % (model.name, ",".join(
["%.3f" % c for c in mdl_center]), vbur)
out.append(
(model.name, ",".join(["%.3f" % c
for c in mdl_center]), vbur))
if displaySphere is not None:
mdl = vbur_vis(
session,
rescol,
targets,
radii,
scale,
radius,
mdl_center,
pointSpacing,
intersectionScale,
displaySphere,
)
model.add([mdl])
atomspec = mdl.atomspec
if not isinstance(mdl_center, np.ndarray):
center_coords = rescol.COM(mdl_center)
else:
center_coords = mdl_center
#XXX: the center will be wrong if the models are tiled
args = [
"color",
"radial",
atomspec,
"center",
",".join(["%.4f" % x for x in center_coords]),
"palette",
palette,
";",
"transparency",
atomspec,
"30",
]
run(session, " ".join(args))
s = s.strip()
s += "</pre>"
if not return_values:
session.logger.info(s, is_html=True)
else:
return out
