def parse_symmetry(session, group, center=None, axis=None, molecule=None):
# Handle products of symmetry groups.
groups = group.split('*')
from chimerax.geometry import Places
ops = Places()
for g in groups:
ops = ops * group_symmetries(session, g, molecule)
# Apply center and axis transformation.
if center is not None or axis is not None:
from chimerax.geometry import Place, vector_rotation, translation
tf = Place()
if center is not None and tuple(center) != (0, 0, 0):
tf = translation([-c for c in center])
if axis is not None and tuple(axis) != (0, 0, 1):
tf = vector_rotation(axis, (0, 0, 1)) * tf
if not tf.is_identity():
ops = ops.transform_coordinates(tf)
return ops
def group_symmetries(session, group, molecule):
from chimerax import geometry
from chimerax.core.errors import UserError
g0 = group[:1].lower()
gfields = group.split(',')
nf = len(gfields)
recenter = True
if g0 in ('c', 'd'):
# Cyclic or dihedral symmetry: C<n>, D<n>
try:
n = int(group[1:])
except ValueError:
raise UserError('Invalid symmetry group syntax "%s"' % group)
if n < 1:
raise UserError('Cn or Dn with n = %d < 1' % (n, ))
if g0 == 'c':
tflist = geometry.cyclic_symmetry_matrices(n)
else:
tflist = geometry.dihedral_symmetry_matrices(n)
elif g0 == 'i':
# Icosahedral symmetry: i[,<orientation>]
if nf == 1:
orientation = '222'
elif nf == 2:
orientation = gfields[1]
if not orientation in geometry.icosahedral_orientations:
raise UserError('Unknown icosahedron orientation "%s"' %
orientation)
else:
raise UserError('Invalid symmetry group syntax "%s"' % group)
tflist = geometry.icosahedral_symmetry_matrices(orientation)
elif g0 == 't' and nf <= 2:
# Tetrahedral symmetry t[,<orientation]
if nf == 1:
orientation = '222'
elif nf == 2:
orientation = gfields[1]
if not orientation in geometry.tetrahedral_orientations:
tos = ', '.join(geometry.tetrahedral_orientations)
raise UserError('Unknown tetrahedral symmetry orientation %s'
', must be one of %s' % (gfields[1], tos))
else:
raise UserError('Invalid symmetry group syntax "%s"' % group)
tflist = geometry.tetrahedral_symmetry_matrices(orientation)
elif g0 == 'o':
# Octahedral symmetry
if nf == 1:
tflist = geometry.octahedral_symmetry_matrices()
else:
raise UserError('Invalid symmetry group syntax "%s"' % group)
elif g0 == 'h':
# Helical symmetry: h,<rise>,<angle>,<n>[,<offset>]
if nf < 4 or nf > 5:
raise UserError('Invalid symmetry group syntax "%s"' % group)
try:
param = [float(f) for f in gfields[1:]]
except ValueError:
raise UserError('Invalid symmetry group syntax "%s"' % group)
if len(param) == 3:
param.append(0.0)
rise, angle, n, offset = param
n = int(n)
from chimerax.geometry import Places
tflist = Places([
geometry.helical_symmetry_matrix(rise, angle, n=i + offset)
for i in range(n)
])
elif gfields[0].lower() == 'shift' or (g0 == 't' and nf >= 3):
# Translation symmetry: t,<n>,<distance> or t,<n>,<dx>,<dy>,<dz>
if nf != 3 and nf != 5:
raise UserError('Invalid symmetry group syntax "%s"' % group)
try:
param = [float(f) for f in gfields[1:]]
except ValueError:
raise UserError('Invalid symmetry group syntax "%s"' % group)
n = param[0]
if n != int(n):
raise UserError('Invalid symmetry group syntax "%s"' % group)
n = int(n)
if nf == 3:
delta = (0, 0, param[1])
else:
delta = param[1:]
tflist = geometry.translation_symmetry_matrices(n, delta)
elif group.lower() == 'biomt':
# Biological unit
from . import biological_unit_matrices
tflist = biological_unit_matrices(molecule)
if len(tflist) == 0:
raise UserError('Molecule %s has no biological unit info' %
molecule.name)
if len(tflist) == 1 and tflist[0].is_identity():
log = session.logger
log.status('Molecule %s is the biological unit' % molecule.name)
tflist = tflist.transform_coordinates(molecule.position.inverse())
recenter = False
elif g0 == '#':
from chimerax.core.commands import ModelsArg
if nf == 1:
models = ModelsArg.parse(group, session)[0]
mslist = [model_symmetry(m) for m in models]
mslist = [ms for ms in mslist if ms is not None]
if len(mslist) == 0:
raise UserError('No symmetry for "%s"' % group)
elif len(mslist) > 1:
raise UserError('Multiple models "%s"' % group)
tflist = mslist[0]
recenter = False
elif nf == 2:
gf0, gf1 = gfields
models = ModelsArg.parse(gf0, session)[0]
mlist = [
m for m in models
if hasattr(m, 'placements') and callable(m.placements)
]
if len(mlist) == 0:
raise UserError('No placements for "%s"' % gf0)
elif len(mlist) > 1:
raise UserError('Multiple models with placements "%s"' % gf0)
m = mlist[0]
tflist = m.placements(gf1)
if len(tflist) == 0:
raise UserError('No placements "%s" for "%s"' % (gf1, gf0))
c = molecule.atoms.coords.mean(axis=0)
cg = molecule.position * c
cm = m.position.inverse() * cg
tflist = make_closest_placement_identity(tflist, cm)
recenter = False
else:
raise UserError('Unknown symmetry group "%s"' % group)
return tflist