def unit_cell_box_drawing(unit_cell_corners,
corner_radius=1.0,
origin_radius=2.0,
cylinder_radius=0.2):
from chimerax.graphics import Drawing
md = Drawing('Unit cell box')
cd = Drawing('Corners')
ed = Drawing('Edges')
md.add_drawing(cd)
md.add_drawing(ed)
from chimerax.surface.shapes import sphere_geometry2, cylinder_geometry
cd.set_geometry(*sphere_geometry2(80))
ed.set_geometry(*cylinder_geometry())
from chimerax.geometry import Places, cylinder_rotations
import numpy
shift_and_scale = numpy.empty((8, 4), numpy.float32)
shift_and_scale[:, :3] = unit_cell_corners
shift_and_scale[1:, 3] = corner_radius
shift_and_scale[0, 3] = origin_radius
cd.positions = Places(shift_and_scale=shift_and_scale)
edges = [[0, 1], [0, 2], [0, 4], [1, 3], [1, 5], [2, 3], [2, 6], [3, 7],
[4, 5], [4, 6], [5, 7], [6, 7]]
xyz = [[], []]
for e in edges:
for i in range(2):
xyz[i].append(unit_cell_corners[e[i]])
xyz0, xyz1 = [numpy.array(x) for x in xyz]
rot44 = numpy.empty((12, 4, 4), numpy.float32)
cylinder_rotations(xyz0, xyz1,
numpy.ones(12, numpy.float32) * cylinder_radius, rot44)
rot44[:, 3, :3] = 0.5 * (xyz0 + xyz1)
ed.positions = Places(opengl_array=rot44)
return md
def _annotation_transforms(self):
n = len(self)
f = c_function(self._C_FUNCTION_PREFIX + '_annotation_transform',
args=(ctypes.c_void_p, ctypes.c_size_t, ctypes.c_void_p,
ctypes.c_void_p))
tf1 = numpy.empty((n, 4, 4), float32)
tf2 = numpy.empty((n, 4, 4), float32)
f(self._c_pointers, n, pointer(tf1), pointer(tf2))
from chimerax.geometry import Places
return (Places(opengl_array=tf1), Places(opengl_array=tf2))
def _chain_operators(self, chain_id):
cops = []
for chain_ids, operator_expr, ops in self.chain_ops:
if chain_id in chain_ids:
cops.extend(ops)
from chimerax.geometry import Places
return Places(cops)
def set_state_from_snapshot(self, session, data):
self.name = data['name']
self.id = data['id']
p = data['parent']
if p:
p.add([self])
pa = data['positions']
from numpy import float32, float64
if pa.dtype == float32:
# Fix old sessions that saved array as float32
pa = pa.astype(float64)
from chimerax.geometry import Places
self.positions = Places(place_array=pa)
self.display_positions = data['display_positions']
for d in self.all_drawings():
for attr in [
'allow_depth_cue', 'accept_shadow', 'accept_multishadow'
]:
if attr in data:
setattr(d, attr, data[attr])
if 'clip_cap' in data:
self.clip_cap = data['clip_cap']
if 'drawing state' in data:
from chimerax.graphics.gsession import DrawingState
DrawingState.set_state_from_snapshot(self, session,
data['drawing state'])
self.SESSION_SAVE_DRAWING = True
def parse_map_symmetry_file(filename):
import numpy
from collections import defaultdict
ncs_map = defaultdict(list)
with open(filename, 'rt') as infile:
data = infile.read().split('\n')
ncs_group_id = -1
i = 0
print(len(data))
while i < len(data):
line = data[i]
if line.startswith('new_ncs_group'):
ncs_group_id += 1
i += 1
continue
if line.startswith('new_operator'):
op, incr = _parse_operator(data[i + 1:])
ncs_map[ncs_group_id].append(op)
i += (incr + 1)
continue
else:
i += 1
continue
from chimerax.geometry import Places
ret = {}
for gid, ncslist in ncs_map.items():
ret[gid] = Places(place_array=numpy.array(ncslist))
return ret
def add_gaussians(grid,
xyz,
weights,
sdev,
cutoff_range,
transforms=None,
normalize=True):
from numpy import zeros, float32, empty
sdevs = zeros((len(xyz), 3), float32)
for a in (0, 1, 2):
sdevs[:, a] = sdev / grid.step[a]
if transforms is None:
from chimerax.geometry import Places
transforms = Places()
from ._map import sum_of_gaussians
ijk = empty(xyz.shape, float32)
matrix = grid.matrix()
for tf in transforms:
ijk[:] = xyz
(grid.xyz_to_ijk_transform * tf).transform_points(ijk, in_place=True)
sum_of_gaussians(ijk, weights, sdevs, cutoff_range, matrix)
if normalize:
from math import pow, pi
normalization = pow(2 * pi, -1.5) * pow(sdev, -3)
matrix *= normalization
def update_graphics(self, *_):
from chimerax.core.triggerset import DEREGISTER
ramas = self._visible_ramas
od = self._omega_drawing
rd = self._rama_drawing
if not len(ramas):
od.display = False
rd.display = False
return DEREGISTER
mgr = self._mgr
#mgr.color_cas_by_rama_score(ramas, self.hide_favored)
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas, self.hide_favored)
n = len(coords)
if n > 0:
xyzr = numpy.empty((n, 4), numpy.float32)
xyzr[:,:3] = coords
xyzr[:,3] = self.ca_radius
from chimerax.geometry import Places
rd.positions = Places(shift_and_scale = xyzr)
rd.colors = colors
rd.highlighted_positions = selecteds
rd.display = True
else:
rd.display = False
v, n, t, c = mgr._draw_cis_and_twisted_omegas(ramas)
if len(v):
od.set_geometry(v, n, t)
od.vertex_colors = c
od.display = True
else:
od.display = False
return DEREGISTER
def sym_axis_drawing_screw(fold_symmetry,
screw_component,
axyz0,
axyz1,
base_radius=0.3):
'''
Just draw as a dashed cylinder for now.
'''
import numpy
from chimerax.surface.shapes import dashed_cylinder_geometry
from chimerax.geometry import Places, cylinder_rotations, rotation
n = len(axyz0)
radius = base_radius * (1 + 0.1 * fold_symmetry)
radii = numpy.ones(n, numpy.float32) * radius
rot44 = numpy.empty([n, 4, 4], numpy.float32)
cylinder_rotations(axyz0, axyz1, radii, rot44)
rot44[:, 3, :3] = 0.5 * (axyz0 + axyz1)
from chimerax.graphics import Drawing
d = Drawing('{}-fold screw axis'.format(fold_symmetry))
d.set_geometry(*dashed_cylinder_geometry(segments=15))
d.color = _symmetry_colors[fold_symmetry][1]
d.positions = Places(opengl_array=rot44)
return d
def set_instance_positions_and_colors(drawings):
from chimerax.geometry import Places
for d in drawings:
if hasattr(d, 'position_list') and hasattr(d, 'color_list'):
clist = d.color_list
from numpy import array, uint8
d.colors = array(clist, uint8).reshape((len(clist), 4))
d.positions = Places(d.position_list)
def sym_clear(session, structures=None):
'''
Remove copies of structures that were made with sym command.
Parameters
----------
structures : list of AtomicStructure
List of structures to for which to remove copies.
'''
if structures is None:
from chimerax.atomic import all_structures
structures = all_structures(session)
for m in structures:
from chimerax.geometry import Places
m.positions = Places([m.position]) # Keep only first position.
for s in m.surfaces():
s.positions = Places([s.position])
def find_symmetries(self, group):
va = group._v_attrs
if 'symmetries' in va:
from chimerax.geometry import Places
sym = Places(place_array = va.symmetries)
else:
sym = None
return sym
def _target_transforms(self):
from chimerax.geometry import Places
f = c_function('distance_restraint_target_transform',
args=(ctypes.c_void_p, ctypes.c_size_t,
ctypes.POINTER(ctypes.c_float)))
n = len(self)
transforms = empty((n, 4, 4), float32)
f(self._c_pointers, n, pointer(transforms))
return Places(opengl_array=transforms)
def ijk_symmetry_matrices(data, symmetries):
if symmetries is None or len(symmetries) == 0:
from chimerax.geometry import Places
return Places()
isyms = symmetries.transform_coordinates(data.ijk_to_xyz_transform)
return isyms
def biological_unit_matrices(molecule):
if hasattr(molecule, 'metadata') and 'REMARK' in molecule.metadata:
s = pdb_biomt_matrices(molecule.metadata)
# elif hasattr(molecule, 'mmCIFHeaders'):
# s = PDBmatrices.mmcif_biounit_matrices(molecule.mmCIFHeaders)
else:
from chimerax.geometry import Places
s = Places([])
return s
def make_closest_placement_identity(tflist, center):
d = tflist.array()[:, :, 3] - center
d2 = (d * d).sum(axis=1)
i = d2.argmin()
tfinv = tflist[i].inverse()
rtflist = [tf * tfinv for tf in tflist]
from chimerax.geometry import Place, Places
rtflist[i] = Place()
return Places(rtflist)
def find_symmetries(self, group):
va = group._v_attrs
if 'symmetries' in va:
from chimerax.geometry import Places
from numpy import array, float64
sym = Places(place_array=array(va.symmetries, float64))
else:
sym = None
return sym
def _bond_cylinder_transforms(self):
'''Transforms mapping a unit cylinder onto the restraint bonds. Read only.'''
from chimerax.geometry import Places
f = c_function('distance_restraint_bond_transform',
args=(ctypes.c_void_p, ctypes.c_size_t,
ctypes.POINTER(ctypes.c_float)))
n = len(self)
transforms = empty((n, 4, 4), float32)
f(self._c_pointers, n, pointer(transforms))
return Places(opengl_array=transforms)
def placements(n, marker_set, each_edge=False):
plist = polygons(marker_set)
from chimerax.geometry import Places
tflist = Places([polygon_coordinate_frame(p) for p in plist if p.n == n])
if each_edge:
from chimerax import geometry
tflist = tflist * geometry.cyclic_symmetry_matrices(n)
return tflist
def __init__(self,
name,
hkls,
vals,
dim_scale=2.0,
highlight_negatives=True):
super().__init__(name)
from chimerax.surface.shapes import sphere_geometry2
self.set_geometry(*sphere_geometry2(80))
import numpy
from chimerax.geometry import Places, Place, identity
id_axes = identity().axes()
abs_vals = numpy.abs(vals)
import numpy
place_array = numpy.zeros((len(hkls), 3, 4))
place_array[:, :, 3] = hkls * dim_scale
place_array[:, :, :3] = id_axes
for i in range(3):
# Volume scales with value, so radius scales with cube root of value
place_array[:, i, i] *= abs_vals**(1 / 3)
# positions =[Place(origin=hkl*dim_scale, axes=id_axes*max(rval, 0))
# for (hkl, rval) in zip(hkls, vals)
# ]
if highlight_negatives:
import numpy
negatives = numpy.argwhere(vals < 0).flatten()
place_array[negatives, :, :3] = id_axes
# for ni in negatives:
# positions[ni] = Place(origin=positions[ni].origin(), axes=id_axes)
positions = Places(place_array=place_array)
self.set_positions(Places(positions))
from chimerax.core.colors import BuiltinColormaps
cmap = BuiltinColormaps['rdylbu'].linear_range(-1, 1)
colors = cmap.interpolated_rgba8(vals)
if highlight_negatives:
colors[vals < 0] = [255, 0, 0, 255]
self.set_colors(colors)
def _start_spotlight_mode(self):
zm = self._zone_mgr
zm.radius = zm.pad = self.spotlight_radius
zm.allow_remask_on_coord_updates()
# zm.coords = [self.spotlight_center]
self.triggers.activate_trigger('spotlight changed',
(self.spotlight_center, self.spotlight_radius)
)
if self._box_update_handler is None:
self._box_update_handler = self.crystal_mgr.triggers.add_handler(
'spotlight moved', self.update_spotlight)
self.update_spotlight(None, self.spotlight_center)
from chimerax.geometry import Places
self.positions = Places()
def add_balls(grid, xyz, radii, sdev, cutoff_range, transforms=None):
if transforms is None or len(transforms) == 0:
from chimerax.geometry import Places
transforms = Places()
from numpy import empty, float32
ijk = empty(xyz.shape, float32)
r = (radii - sdev) / grid.step[0]
matrix = grid.matrix()
from ._map import sum_of_balls
for tf in transforms:
ijk[:] = xyz
(grid.xyz_to_ijk_transform * tf).transform_points(ijk, in_place=True)
sum_of_balls(ijk, r, sdev, cutoff_range, matrix)
def _close_center_transforms(structures, transforms, distance):
from numpy import concatenate
points = concatenate([s.atoms.scene_coords for s in structures])
from chimerax.geometry import point_bounds, distance as point_distance, Places
box = point_bounds(points)
if box is None:
return []
center = box.center()
tfnear = Places([
tf for tf in transforms
if point_distance(center, tf * center) <= distance
])
return tfnear
def _contacting_transforms(structures, transforms, distance):
from numpy import concatenate, float32
points = concatenate([s.atoms.scene_coords
for s in structures]).astype(float32)
from chimerax.geometry import identity, find_close_points_sets, Places
ident = identity().matrix.astype(float32)
orig_points = [(points, ident)]
tfnear = Places([
tf for tf in transforms if len(
find_close_points_sets(orig_points, [(
points, tf.matrix.astype(float32))], distance)[0][0]) > 0
])
return tfnear
def pdb_mtrix_matrices(pdb_headers, add_identity=True, given=False):
h = pdb_headers
have_matrix = ('MTRIX1' in h and 'MTRIX2' in h and 'MTRIX3' in h)
if not have_matrix:
if add_identity:
from chimerax.geometry import identity
return [identity()]
else:
return []
row1_list = h['MTRIX1']
row2_list = h['MTRIX2']
row3_list = h['MTRIX3']
if len(row1_list) != len(row2_list) or len(row2_list) != len(row3_list):
if add_identity:
from chimerax.geometry import identity
return [identity()]
else:
return []
row_triples = zip(row1_list, row2_list, row3_list)
mlist = []
from chimerax.geometry import Place
for row_triple in row_triples:
matrix = []
for line in row_triple:
try:
mrow = [
float(f) for f in (line[10:20], line[20:30], line[30:40],
line[45:55])
]
except ValueError:
break
mgiven = (len(line) >= 60 and line[59] == '1')
if (mgiven and given) or (not mgiven and not given):
matrix.append(mrow)
if len(matrix) == 3:
mlist.append(Place(matrix))
if add_identity:
if len([m for m in mlist if m.is_identity()]) == 0:
# Often there is no MTRIX identity entry
from chimerax.geometry import identity
mlist.append(identity())
return Places(mlist)
def bond_cylinder_placements(bonds):
'''From chimerax.core.structure._bond_cylinder_placements.'''
n = len(bonds)
from numpy import empty, float32
p = empty((n, 4, 4), float32)
radii = numpy.ones(len(bonds))
from chimerax.geometry import cylinder_rotations, Places
axyz0, axyz1 = [a.coords for a in bonds.atoms]
cylinder_rotations(axyz0, axyz1, radii, p)
p[:, 3, :3] = 0.5 * (axyz0 + axyz1)
pl = Places(opengl_array=p)
return pl
def read_positions(session,
stream,
name,
models=None,
match_names=False,
child_models=False):
"""
Read position matrices and set positions of specified models.
"""
from chimerax.core.errors import UserError
if models is None or len(models) == 0:
raise UserError('Must specify models when opening positions file %s.' %
stream.name)
if not child_models:
models = _exclude_child_models(models)
lines = stream.readlines()
places = _parse_places(lines)
if len(places) == 0:
raise UserError('No positions specified in positions file %s.' %
stream.name)
if match_names:
n2p = dict(places)
mpos = [(m, n2p[m.name]) for m in models if m.name in n2p]
for m, position in mpos:
m.position = position
msg = (('Set position of model %s' % m.name) if len(mpos) == 1 else
('Set %d positions' % len(mpos)))
elif len(models) == 1:
m = models[0]
from chimerax.geometry import Places
m.positions = Places(p for name, p in places)
msg = (('Set position of model %s' % m.name) if len(places) == 1 else
('Set %d position for model %s' % (len(places), m.name)))
elif len(places) != len(models):
raise UserError(
'Number of models (%d) does not equal number of positions (%d) in position file %s'
% (len(models), len(places), stream.name))
else:
for m, (name, position) in zip(models, places):
m.position = position
msg = 'Set %d positions' % len(places)
return [], msg
def _bond_transforms(self):
'''
Transforms mapping a tripartite bond onto the restraint vectors. Read only.
'''
from chimerax.geometry import Places
f = c_function('adaptive_distance_restraint_bond_transforms',
args=(
ctypes.c_void_p,
ctypes.c_size_t,
ctypes.POINTER(ctypes.c_float),
ctypes.POINTER(ctypes.c_float),
))
n = len(self)
tf_ends = empty((n * 2, 4, 4), float32)
tf_m = empty((n, 4, 4), float32)
f(self._c_pointers, n, pointer(tf_ends), pointer(tf_m))
return tuple(Places(opengl_array=tf) for tf in (tf_ends, tf_m))
def symmetry_matrices(self):
h = self.header
for name in ('symop', 'xlen', 'ylen', 'zlen', 'alpha', 'beta',
'gamma'):
if not name in h:
return []
# Read space group symmetries in fractional coordinates
s = h['symop']
nsym = len(s) // 80
from chimerax.crystal import parse_symop
try:
usyms = [
parse_symop(s[80 * i:80 * (i + 1)].decode('utf-8').replace(
' ', '')) for i in range(nsym)
]
except Exception:
try:
msg = 'Unable to parse symmetry operators of %s\n%s\n' % (
self.name, s)
except Exception:
# Garbage in sym operator data can't be interpreted as text.
msg = 'Unable to parse symmetry operators of %s\n' % (
self.name, )
print(msg)
return []
a, b, c = float(h['xlen']), float(h['ylen']), float(h['zlen'])
if a == 0 or b == 0 or c == 0:
return []
from math import pi
alpha, beta, gamma = [d * pi / 180 for d in self.cell_angles]
# Convert symmetries to unit cell coordinates
from chimerax.crystal import unit_cell_to_xyz_matrix
u2r = unit_cell_to_xyz_matrix(a, b, c, alpha, beta, gamma)
r2u = u2r.inverse()
from chimerax.geometry import Places
syms = Places([u2r * u2u * r2u for u2u in usyms])
return syms
def update_graphics(self, *_, scale_by_scores = True):
from chimerax.core.triggerset import DEREGISTER
if not self.visible:
return DEREGISTER
rots, scales, colors = self._mgr.validate_scale_and_color_rotamers(
self._selected_rotamers, max_scale=self._MAX_SCALE,
non_favored_only = self._hide_favored)
d = self._drawing
if not len(rots):
d.display = False
return DEREGISTER
d.display = True
bonds = rots.ca_cb_bonds
transforms = bond_cylinder_placements(bonds)
if scale_by_scores:
transforms = Places(place_array=scale_transforms(scales, transforms.array()))
d.positions = transforms
d.colors = colors
return DEREGISTER
def make_unit_cell(model, xmap, draw = True):
from chimerax.geometry import Place, Places
cell = xmap.cell()
atoms = model.atoms
clipper_atoms = atom_list_from_sel(atoms)
coord = model.bounds().center()
from .clipper_python import Coord_orth
coord_orth = Coord_orth(coord)
coord_frac = coord_orth.coord_frac(cell)
sg = xmap.spacegroup()
unit_cell_frac_symops = xmap.unit_cell_symops(coord_frac, clipper_atoms)
if draw:
uc_places = []
for op in unit_cell_frac_symops.symops():
op_orth = op.rtop_orth(cell)
uc_places.append(Place(matrix=op_orth.matrix()[0:3,:]))
ucp = Places(uc_places)
model.positions = ucp
return unit_cell_frac_symops