def report_correlations_with_rotation(v1, v2, aboveThreshold, axis, center,
angleRange, plot):
from chimera import Vector, Point, replyobj
# Convert axis and center to v1 local coordinates so transformation
# is still valid if user rotates entire scene.
xf = v1.openState.xform.inverse()
axis = xf.apply(Vector(*axis)).data()
center = xf.apply(Point(*center)).data()
import FitMap, Matrix
replyobj.info('Correlation between %s and %s\n' % (v1.name, v2.name) +
'Rotation\tCorrelation\n')
a0, a1, astep = angleRange
angle = a0
clist = []
from Matrix import multiply_matrices, xform_matrix, rotation_transform, chimera_xform
while angle < a1:
tf = multiply_matrices(xform_matrix(v1.openState.xform),
rotation_transform(axis, angle, center),
xform_matrix(v1.openState.xform.inverse()))
xf = chimera_xform(tf)
olap, cor = FitMap.map_overlap_and_correlation(v1, v2, aboveThreshold,
xf)
replyobj.status('angle = %.4g, correlation = %.4g\n' % (angle, cor))
replyobj.info('%.4g\t%.4g\n' % (angle, cor))
clist.append((angle, cor))
angle += astep
if plot:
angles = [a for a, c in clist]
corr = [c for a, c in clist]
plot_correlation(angles, corr, v1, v2, axis, center)
def move_atoms_to_maximum(atoms, volume,
max_steps = 100, ijk_step_size_min = 0.01,
ijk_step_size_max = 0.5,
optimize_translation = True,
optimize_rotation = True,
move_whole_molecules = True,
request_stop_cb = None):
points = atom_coordinates(atoms)
point_weights = None # Each atom give equal weight in fit.
metric = 'sum product'
move_tf, stats = motion_to_maximum(points, point_weights, volume, max_steps,
ijk_step_size_min, ijk_step_size_max,
optimize_translation, optimize_rotation,
metric, request_stop_cb)
stats['data region'] = volume
stats['molecules'] = list(set([a.molecule for a in atoms]))
import move
move.move_models_and_atoms(move_tf, [], atoms, move_whole_molecules, volume)
from Matrix import chimera_xform
poc, clevel = points_outside_contour(points, chimera_xform(move_tf), volume)
stats['atoms outside contour'] = poc
stats['contour level'] = clevel
return stats
def report_correlations_with_rotation(v1, v2, aboveThreshold,
axis, center, angleRange, plot):
from chimera import Vector, Point, replyobj
# Convert axis and center to v1 local coordinates so transformation
# is still valid if user rotates entire scene.
xf = v1.openState.xform.inverse()
axis = xf.apply(Vector(*axis)).data()
center = xf.apply(Point(*center)).data()
import FitMap, Matrix
replyobj.info('Correlation between %s and %s\n' % (v1.name, v2.name) +
'Rotation\tCorrelation\n')
a0, a1, astep = angleRange
angle = a0
clist = []
from Matrix import multiply_matrices, xform_matrix, rotation_transform, chimera_xform
while angle < a1:
tf = multiply_matrices(xform_matrix(v1.openState.xform),
rotation_transform(axis, angle, center),
xform_matrix(v1.openState.xform.inverse()))
xf = chimera_xform(tf)
olap, cor = FitMap.map_overlap_and_correlation(v1, v2,
aboveThreshold, xf)
replyobj.status('angle = %.4g, correlation = %.4g\n' % (angle, cor))
replyobj.info('%.4g\t%.4g\n' % (angle, cor))
clist.append((angle,cor))
angle += astep
if plot:
angles = [a for a,c in clist]
corr = [c for a,c in clist]
plot_correlation(angles, corr, v1, v2, axis, center)
def align_best(reference,
probe,
transform=True,
sanitize=True,
ignore_warnings=False,
maxIters=50,
reflect=False,
**kwargs):
rdk_reference = _chimera_to_rdkit(reference, sanitize=sanitize)
rdk_probe = _chimera_to_rdkit(probe, sanitize=sanitize)
matches = rdk_reference.GetSubstructMatches(rdk_probe, uniquify=False)
if not matches:
raise chimera.UserError('Could not find any alignment.')
if not ignore_warnings and len(matches) > 1e6:
raise chimera.UserError(
"Too many possible alignments found! This can be "
"slow! Use `ignore_warnings true` to try.")
maps = [list(enumerate(match)) for match in matches]
best_rmsd, best_xform = 1000., None
for atom_map in maps:
rmsd, xform = GetAlignmentTransform(rdk_probe,
rdk_reference,
atomMap=atom_map,
maxIters=maxIters,
reflect=reflect)
if rmsd < best_rmsd:
best_rmsd = rmsd
best_xform = xform
if transform and best_xform is not None:
_transform_molecule(probe, chimera_xform(best_xform[:3]))
return best_rmsd
def shift_and_angle(tf, center):
from Matrix import chimera_xform, apply_matrix
moved_center = apply_matrix(tf, center)
shift_vector = map(lambda a, b: a - b, moved_center, center)
shift = norm(shift_vector)
axis, angle = chimera_xform(tf).getRotation()
return shift, angle
def fit_map_in_map(map1_path, map2_path, xformName,
initial_map1_transform = None,
map1_threshold = None,
ijk_step_size_min = 0.01, # Grid index units
ijk_step_size_max = 0.5, # Grid index units
max_steps = 5000,
optimize_translation = True,
optimize_rotation = True):
# Files have to have file suffix indicating volume format.
from VolumeViewer import open_volume_file
map1 = open_volume_file(map1_path)[0] # Assume files contain just one array
map2 = open_volume_file(map2_path)[0]
if initial_map1_transform:
from Matrix import chimera_xform
xf = chimera_xform(initial_map1_transform)
map1.surface_model().openState.globalXform(xf)
use_threshold = (map1_threshold != None)
from FitMap.fitmap import map_points_and_weights, motion_to_maximum
points, point_weights = map_points_and_weights(map1, use_threshold)
if len(points) == 0:
if use_threshold:
print 'No grid points above map threshold.'
else:
print 'Map has no non-zero values.'
return
move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps,
ijk_step_size_min, ijk_step_size_max,
optimize_translation, optimize_rotation)
import Matrix
if initial_map1_transform:
move_tf = Matrix.multiply_matrices(move_tf, initial_map1_transform)
header = ('\nFit map %s in map %s using %d points\n'
% (map1.name, map2.name, stats['points']) +
' correlation = %.4g, overlap = %.4g\n'
% (stats['correlation'], stats['overlap']) +
' steps = %d, shift = %.3g, angle = %.3g degrees\n'
% (stats['steps'], stats['shift'], stats['angle']))
print header
f = open(xformName,'w')
for i in range(4):
for j in range(3):
# print move_tf[j][i]
f.write('{:f}'.format(move_tf[j][i]))
f.write("\n")
f.close()
print move_tf
tfs = Matrix.transformation_description(move_tf)
print tfs
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 fit_map_in_map(
map1_path,
map2_path,
initial_map1_transform=None,
map1_threshold=None,
ijk_step_size_min=0.01, # Grid index units
ijk_step_size_max=0.5, # Grid index units
max_steps=2000,
optimize_translation=True,
optimize_rotation=True,
metric='sum product'
): # 'sum product' > overlap; other options are 'correlation' and 'correlation about mean'
# Files have to have file suffix indicating volume format.
map1 = open_volume_file(map1_path)[
0] # Assume files contain just one array
map2 = open_volume_file(map2_path)[0]
if initial_map1_transform:
from Matrix import chimera_xform
xf = chimera_xform(initial_map1_transform)
map1.surface_model().openState.globalXform(xf)
use_threshold = (map1_threshold != None)
points, point_weights = map_points_and_weights(map1, use_threshold)
if len(points) == 0:
if use_threshold:
print 'No grid points above map threshold.'
else:
print 'Map has no non-zero values.'
return
move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps,
ijk_step_size_min, ijk_step_size_max,
optimize_translation, optimize_rotation,
metric)
if initial_map1_transform:
move_tf = Matrix.multiply_matrices(move_tf, initial_map1_transform)
header = ('\nFit map %s in map %s using %d points\n' %
(map1.name, map2.name, stats['points']) +
' correlation = %.4g, overlap = %.4g\n' %
(stats['correlation'], stats['overlap']) +
' steps = %d, shift = %.3g, angle = %.3g degrees\n' %
(stats['steps'], stats['shift'], stats['angle']))
print header
tfs = Matrix.transformation_description(move_tf)
print tfs
def align(reference,
probe,
transform=True,
sanitize=True,
maxIters=50,
reflect=False,
**kwargs):
rdk_reference = _chimera_to_rdkit(reference, sanitize=sanitize)
rdk_probe = _chimera_to_rdkit(probe, sanitize=sanitize)
rmsd, xform = GetAlignmentTransform(rdk_probe,
rdk_reference,
maxIters=maxIters,
reflect=reflect)
if transform:
_transform_molecule(probe, chimera_xform(xform[:3]))
return rmsd
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 axis_center_angle_shift(tf):
from Matrix import chimera_xform
axis, angle = chimera_xform(tf).getRotation()
axis = axis.data()
t = map(lambda r: r[3], tf)
axt = cross_product(axis, t)
axaxt = cross_product(axis, axt)
from math import pi, cos, sin
a2 = 0.5 * angle * pi / 180 # Half angle in radians
try:
ct2 = cos(a2) / sin(a2)
except:
ct2 = None # Identity rotation
if ct2 == None:
axis_point = (0, 0, 0)
else:
axis_point = tuple(map(lambda a, b: .5 * ct2 * a - .5 * b, axt, axaxt))
from numpy import dot as inner_product
shift = inner_product(axis, t)
return axis, axis_point, angle, shift
def move_atom_to_maximum(a, max_steps = 100,
ijk_step_size_min = 0.001, ijk_step_size_max = 0.5):
from VolumeViewer import active_volume
dr = active_volume()
if dr == None or dr.model_transform() == None:
from chimera.replyobj import status
status('No data shown by volume viewer dialog')
return
points = atom_coordinates([a])
point_weights = None
move_tf, stats = motion_to_maximum(points, point_weights, dr, max_steps,
ijk_step_size_min, ijk_step_size_max,
optimize_translation = True,
optimize_rotation = False)
# Update atom position.
from Matrix import chimera_xform
xf = chimera_xform(move_tf)
mxf = a.molecule.openState.xform
p = mxf.inverse().apply(xf.apply(a.xformCoord()))
a.setCoord(p)
def align_o3a(reference,
probe,
transform=True,
sanitize=True,
maxIters=50,
reflect=False,
**kwargs):
rdk_reference = _chimera_to_rdkit(reference, sanitize=sanitize)
rdk_probe = _chimera_to_rdkit(probe, sanitize=sanitize)
FastFindRings(rdk_reference)
FastFindRings(rdk_probe)
reference_params = MMFFGetMoleculeProperties(rdk_reference)
probe_params = MMFFGetMoleculeProperties(rdk_probe)
o3a = GetO3A(rdk_probe,
rdk_reference,
prbPyMMFFMolProperties=probe_params,
refPyMMFFMolProperties=reference_params,
maxIters=maxIters,
reflect=reflect)
rmsd, xform = o3a.Trans()
if transform:
_transform_molecule(probe, chimera_xform(xform[:3]))
return rmsd