def identity_matrix_index(matrices):
from Matrix import is_identity_matrix
for i in range(len(matrices)):
if is_identity_matrix(matrices[i]):
return i
return None
def identity_matrix_index(matrices):
from Matrix import is_identity_matrix
for i in range(len(matrices)):
if is_identity_matrix(matrices[i]):
return i
return None
def create_symmetry_copies(mol,
csys,
tflist,
cdist,
rdist,
exclude_identity=True):
if exclude_identity:
from Matrix import is_identity_matrix
tflist = [tf for tf in tflist if not is_identity_matrix(tf)]
close_contacts = not cdist is None
close_centers = not rdist is None
if not close_contacts and not close_centers:
transforms = tflist # Use all transforms
elif close_contacts and not close_centers:
transforms = contacting_transforms(mol, csys, tflist, cdist)
elif close_centers and not close_contacts:
transforms = close_center_transforms(mol, csys, tflist, rdist)
else:
transforms = unique(
contacting_transforms(mol, csys, tflist, cdist) +
close_center_transforms(mol, csys, tflist, rdist))
if hasattr(mol, 'symmetry_copies'):
remove_symmetry_copies(mol)
copies = []
from chimera import openModels, replyobj
from PDBmatrices import copy_molecule
from Matrix import chimera_xform
for tf in transforms:
copy = copy_molecule(mol)
copy.symmetry_xform = chimera_xform(tf)
copies.append(copy)
replyobj.status('Created symmetry copy %d of %d' %
(len(copies), len(transforms)))
if len(copies) == 0:
return copies
openModels.add(copies)
replyobj.status('')
mol.symmetry_copies = copies
mol.symmetry_reference_model = csys
# TODO: Set xform before opening so that code that detects open sees
# the correct position. Currently not possible. Bug 4486.
update_symmetry_positions(mol)
return copies
def check_orthogonality(matrices, name, tolerance):
from Matrix import transpose_matrix, multiply_matrices, is_identity_matrix
for mindex, m in enumerate(matrices):
mr = zero_translation(m)
mrt = transpose_matrix(mr)
p = multiply_matrices(mr, mrt)
if not is_identity_matrix(p, tolerance):
print ('%s matrix %d is not orthogonal, tolerance %.3g' %
(name, mindex, tolerance))
print_matrix(m, '%10.5f')
print ' matrix times transpose = '
print_matrix(p, '%10.5f')
def check_orthogonality(matrices, name, tolerance):
from Matrix import transpose_matrix, multiply_matrices, is_identity_matrix
for mindex, m in enumerate(matrices):
mr = zero_translation(m)
mrt = transpose_matrix(mr)
p = multiply_matrices(mr, mrt)
if not is_identity_matrix(p, tolerance):
print('%s matrix %d is not orthogonal, tolerance %.3g' %
(name, mindex, tolerance))
print_matrix(m, '%10.5f')
print ' matrix times transpose = '
print_matrix(p, '%10.5f')
def create_symmetry_copies(mol, csys, tflist, cdist, rdist,
exclude_identity = True):
if exclude_identity:
from Matrix import is_identity_matrix
tflist = [tf for tf in tflist if not is_identity_matrix(tf)]
close_contacts = not cdist is None
close_centers = not rdist is None
if not close_contacts and not close_centers:
transforms = tflist # Use all transforms
elif close_contacts and not close_centers:
transforms = contacting_transforms(mol, csys, tflist, cdist)
elif close_centers and not close_contacts:
transforms = close_center_transforms(mol, csys, tflist, rdist)
else:
transforms = unique(contacting_transforms(mol, csys, tflist, cdist) +
close_center_transforms(mol, csys, tflist, rdist))
if hasattr(mol, 'symmetry_copies'):
remove_symmetry_copies(mol)
copies = []
from chimera import openModels, replyobj
from PDBmatrices import copy_molecule
from Matrix import chimera_xform
for tf in transforms:
copy = copy_molecule(mol)
copy.symmetry_xform = chimera_xform(tf)
copies.append(copy)
replyobj.status('Created symmetry copy %d of %d'
% (len(copies), len(transforms)))
if len(copies) == 0:
return copies
openModels.add(copies)
replyobj.status('')
mol.symmetry_copies = copies
mol.symmetry_reference_model = csys
# TODO: Set xform before opening so that code that detects open sees
# the correct position. Currently not possible. Bug 4486.
update_symmetry_positions(mol)
return copies
def make_asu_copies(m, asu_list, crystal):
xflist = []
names = []
from Matrix import is_identity_matrix, chimera_xform
for asu in asu_list:
if is_identity_matrix(asu.transform):
continue
xflist.append(chimera_xform(asu.transform))
name = '%s %s' % (m.name, '%d %d %d' % asu.unit_cell_index)
if len(crystal.smtry_matrices) > 1:
name += ' sym %d' % asu.smtry_index
if len(crystal.ncs_matrices) > 1:
name += ' ncs %d' % asu.ncs_index
names.append(name)
cmodels = make_molecule_copies(m, xflist, names)
return cmodels
def make_asu_copies(m, asu_list, crystal):
xflist = []
names = []
from Matrix import is_identity_matrix, chimera_xform
for asu in asu_list:
if is_identity_matrix(asu.transform):
continue
xflist.append(chimera_xform(asu.transform))
name = '%s %s' % (m.name, '%d %d %d' % asu.unit_cell_index)
if len(crystal.smtry_matrices) > 1:
name += ' sym %d' % asu.smtry_index
if len(crystal.ncs_matrices) > 1:
name += ' ncs %d' % asu.ncs_index
names.append(name)
cmodels = make_molecule_copies(m, xflist, names)
return cmodels
def place_molecule_copies(m, tflist):
path, file_type, default_file_type, prefixable_type = m.openedAs
from Molecule import copy_molecule, transform_atom_positions
from Matrix import is_identity_matrix
for i,tf in enumerate(tflist):
if is_identity_matrix(tf):
continue
name = m.name + (' #%d' % (i+1))
c = find_model_by_name(name)
if c is None:
c = copy_molecule(m)
c.name = name
transform_atom_positions(c.atoms, tf)
chimera.openModels.add([c])
else:
transform_atom_positions(c.atoms, tf, m.atoms)
def place_molecule_copies(m, tflist):
path, file_type, default_file_type, prefixable_type = m.openedAs
from Molecule import copy_molecule, transform_atom_positions
from Matrix import is_identity_matrix
for i, tf in enumerate(tflist):
if is_identity_matrix(tf):
continue
name = m.name + (' #%d' % (i + 1))
c = find_model_by_name(name)
if c is None:
c = copy_molecule(m)
c.name = name
transform_atom_positions(c.atoms, tf)
chimera.openModels.add([c])
else:
transform_atom_positions(c.atoms, tf, m.atoms)
def surface_geometry(plist, tf, pad):
surfaces = []
for p in plist:
surfs = []
va, ta = p.maskedGeometry(p.Solid)
na = p.normals
if isinstance(pad, (float, int)) and pad != 0:
varray, tarray = offset_surface(va, ta, na, pad)
elif isinstance(pad, (list, tuple)) and len(pad) == 2:
varray, tarray = slab_surface(va, ta, na, pad)
else:
varray, tarray = va, ta
if not tf is None:
from Matrix import xform_matrix, multiply_matrices, is_identity_matrix
vtf = multiply_matrices(tf, xform_matrix(p.model.openState.xform))
if not is_identity_matrix(vtf):
apply_transform(vtf, varray)
surfaces.append((varray, tarray))
return surfaces
def surface_geometry(plist, tf, pad):
surfaces = []
for p in plist:
surfs = []
va, ta = p.maskedGeometry(p.Solid)
na = p.normals
if isinstance(pad, (float,int)) and pad != 0:
varray, tarray = offset_surface(va, ta, na, pad)
elif isinstance(pad, (list,tuple)) and len(pad) == 2:
varray, tarray = slab_surface(va, ta, na, pad)
else:
varray, tarray = va, ta
if not tf is None:
from Matrix import xform_matrix, multiply_matrices, is_identity_matrix
vtf = multiply_matrices(tf, xform_matrix(p.model.openState.xform))
if not is_identity_matrix(vtf):
apply_transform(vtf, varray)
surfaces.append((varray, tarray))
return surfaces
def group_symmetries(group, center, axis, mol):
from Commands import CommandError
g0 = group[:1].lower()
if g0 in ('c', 'd'):
# Cyclic or dihedral symmetry: C<n>, D<n>
try:
n = int(group[1:])
except ValueError:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
if n < 2:
raise CommandError, 'Cn or Dn with n = %d < 2' % (n,)
if g0 == 'c':
tflist = cyclic_symmetries(n)
else:
tflist = dihedral_symmetries(n)
elif g0 == 'i':
# Icosahedral symmetry: i[,<orientation>]
import Icosahedron as icos
gfields = group.split(',')
if len(gfields) == 1:
orientation = '222'
elif len(gfields) == 2:
orientation = gfields[1]
if not orientation in icos.coordinate_system_names:
raise CommandError, ('Unknown icosahedron orientation "%s"'
% orientation)
else:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
tflist = icos.icosahedral_symmetry_matrices(orientation)
elif g0 == 'h':
# Helical symmetry: h,<repeat>,<rise>[,<angle>[,<n>,<offet>]]
gfields = group.split(',')
nf = len(gfields)
if nf < 3 or nf > 6:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
try:
param = [float(f) for f in gfields[1:]]
except ValueError:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
if len(param) == 2:
param.append(360.0)
if len(param) == 3:
param.append(int(param[0]))
if len(param) == 4:
param.append(0)
repeat, rise, angle, n, offset = param
tflist = helical_symmetry(repeat, rise, angle, n, offset)
elif g0 == 't':
# Translation symmetry: t,<n>,<distance> or t,<n>,<dx>,<dy>,<dz>
gfields = group.split(',')
nf = len(gfields)
if nf != 3 and nf != 5:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
try:
param = [float(f) for f in gfields[1:]]
except ValueError:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
n = param[0]
if n != int(n):
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
if nf == 3:
delta = (0,0,param[1])
else:
delta = param[1:]
tflist = translation_symmetry(n, delta)
elif group.lower() == 'biomt':
# BIOMT biological unit matrices from PDB file header.
if not hasattr(mol, 'pdbHeaders'):
msg = 'Molecule %s has no BIOMT matrices or PDB headers' % mol.name
raise CommandError, msg
from PDBmatrices import pdb_biomt_matrices
tflist = pdb_biomt_matrices(mol.pdbHeaders)
if len(tflist) == 0:
msg = 'Molecule %s has no BIOMT matrices in PDB header' % mol.name
raise CommandError, msg
from Matrix import is_identity_matrix
if len(tflist) == 1 and is_identity_matrix(tflist[0]):
msg = 'Molecule %s has only identity BIOMT matrix in PDB header' % mol.name
raise CommandError, msg
else:
raise CommandError, 'Unknown symmetry group "%s"' % group
# Apply center and axis transformation.
if tuple(center) != (0,0,0) or tuple(axis) != (0,0,1):
import Matrix as m
tf = m.multiply_matrices(m.vector_rotation_transform(axis, (0,0,1)),
m.translation_matrix([-c for c in center]))
tfinv = m.invert_matrix(tf)
tflist = [m.multiply_matrices(tfinv, t, tf) for t in tflist]
return tflist
mc = molecule_center(molecule)
tflist = Crystal.pack_unit_cell(uc, gorigin, mc, tflist)
# Make multiple unit cells
#nc = self.number_of_cells()
nc = (3, 3, 3)
#if nc != (1,1,1) and uc:
# Compute origin.
oc_val = (1, 1, 1)
oc = tuple((((o + n - 1) % n) - (n - 1)) for o, n in zip(oc_val, nc))
tflist = Crystal.unit_cell_translations(uc, oc, nc, tflist)
from Molecule import copy_molecule, transform_atom_positions
from Matrix import is_identity_matrix
for i, tf in enumerate(tflist):
if is_identity_matrix(tf):
continue
name = m.name + (' #%d' % (i + 1))
c = copy_molecule(m)
c.name = name
c.unit_cell_copy = m
transform_atom_positions(c.atoms, tf)
chimera.openModels.add([c])
# else:
# transform_atom_positions(c.atoms, tf, m.atoms)
c.openState.xform = m.openState.xform
mlist.append(c)
# Write PDB file with transformed copies of molecule
import Midas
out_path = 'unitcell.pdb'
def group_symmetries(group, center, axis, mol):
from Commands import CommandError
g0 = group[:1].lower()
if g0 in ('c', 'd'):
# Cyclic or dihedral symmetry: C<n>, D<n>
try:
n = int(group[1:])
except ValueError:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
if n < 2:
raise CommandError, 'Cn or Dn with n = %d < 2' % (n, )
if g0 == 'c':
tflist = cyclic_symmetries(n)
else:
tflist = dihedral_symmetries(n)
elif g0 == 'i':
# Icosahedral symmetry: i[,<orientation>]
import Icosahedron as icos
gfields = group.split(',')
if len(gfields) == 1:
orientation = '222'
elif len(gfields) == 2:
orientation = gfields[1]
if not orientation in icos.coordinate_system_names:
raise CommandError, ('Unknown icosahedron orientation "%s"' %
orientation)
else:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
tflist = icos.icosahedral_symmetry_matrices(orientation)
elif g0 == 'h':
# Helical symmetry: h,<repeat>,<rise>[,<angle>[,<n>,<offet>]]
gfields = group.split(',')
nf = len(gfields)
if nf < 3 or nf > 6:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
try:
param = [float(f) for f in gfields[1:]]
except ValueError:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
if len(param) == 2:
param.append(360.0)
if len(param) == 3:
param.append(int(param[0]))
if len(param) == 4:
param.append(0)
repeat, rise, angle, n, offset = param
tflist = helical_symmetry(repeat, rise, angle, n, offset)
elif g0 == 't':
# Translation symmetry: t,<n>,<distance> or t,<n>,<dx>,<dy>,<dz>
gfields = group.split(',')
nf = len(gfields)
if nf != 3 and nf != 5:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
try:
param = [float(f) for f in gfields[1:]]
except ValueError:
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
n = param[0]
if n != int(n):
raise CommandError, 'Invalid symmetry group syntax "%s"' % group
if nf == 3:
delta = (0, 0, param[1])
else:
delta = param[1:]
tflist = translation_symmetry(n, delta)
elif group.lower() == 'biomt':
# BIOMT biological unit matrices from PDB file header.
if not hasattr(mol, 'pdbHeaders'):
msg = 'Molecule %s has no BIOMT matrices or PDB headers' % mol.name
raise CommandError, msg
from PDBmatrices import pdb_biomt_matrices
tflist = pdb_biomt_matrices(mol.pdbHeaders)
if len(tflist) == 0:
msg = 'Molecule %s has no BIOMT matrices in PDB header' % mol.name
raise CommandError, msg
from Matrix import is_identity_matrix
if len(tflist) == 1 and is_identity_matrix(tflist[0]):
msg = 'Molecule %s has only identity BIOMT matrix in PDB header' % mol.name
raise CommandError, msg
else:
raise CommandError, 'Unknown symmetry group "%s"' % group
# Apply center and axis transformation.
if tuple(center) != (0, 0, 0) or tuple(axis) != (0, 0, 1):
import Matrix as m
tf = m.multiply_matrices(m.vector_rotation_transform(axis, (0, 0, 1)),
m.translation_matrix([-c for c in center]))
tfinv = m.invert_matrix(tf)
tflist = [m.multiply_matrices(tfinv, t, tf) for t in tflist]
return tflist