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 extrusion_transforms(path, tangents, yaxis=None):
from chimerax.geometry import identity, vector_rotation, translation
tflist = []
if yaxis is None:
# Make xy planes for coordinate frames at each path point not rotate
# from one point to next.
tf = identity()
n0 = (0, 0, 1)
for p1, n1 in zip(path, tangents):
tf = vector_rotation(n0, n1) * tf
tflist.append(translation(p1) * tf)
n0 = n1
else:
# Make y-axis of coordinate frames at each point align with yaxis.
from chimerax.geometry import normalize_vector, cross_product, Place
for p, t in zip(path, tangents):
za = t
xa = normalize_vector(cross_product(yaxis, za))
ya = cross_product(za, xa)
tf = Place(
((xa[0], ya[0], za[0], p[0]), (xa[1], ya[1], za[1], p[1]),
(xa[2], ya[2], za[2], p[2])))
tflist.append(tf)
return tflist
def draw(self, renderer, draw_pass):
# TODO: Overlay drawing sets projection to identity which will defeat supersample
# image capture using pixel shifts that go into the projection matrix from the camera.
r = renderer
# Enable backface culling if discs have spaces between them so far side of
# globe is not visible.
r.enable_backface_culling(True)
# TODO: Enabling depth test causes globe to vanish if silhouette edges turned on. Why?
# TODO: Maybe overlay drawing should always use a cleared depth buffer, so
# overlay cannot be obscured by real models?
# Enable depth test so overlapped discs don't look like fish scales dependent
# on order of drawing of discs.
r.enable_depth_test(True)
ox, oy, oz = self.offset
w, h = r.render_size()
whmax = max(w,h)
sx, sy = h/whmax, w/whmax
r.set_projection_matrix(((sx, 0, 0, 0), (0, sy, 0, 0), (0, 0, 1, 0),
(ox, oy, oz, 1)))
rot = self.session.main_view.camera.position.zero_translation()
r.set_view_matrix(rot.inverse())
Drawing.draw(self, renderer, draw_pass)
# Restore drawing settings so other overlays get expected state.
from chimerax.geometry import identity
r.set_view_matrix(identity())
r.set_projection_matrix(((1, 0, 0, 0), (0, 1, 0, 0), (0, 0, 1, 0),
(0, 0, 0, 1)))
r.enable_depth_test(False)
r.enable_backface_culling(False)
def motion_to_maximum(points,
point_weights,
volume,
max_steps=2000,
ijk_step_size_min=0.01,
ijk_step_size_max=0.5,
optimize_translation=True,
optimize_rotation=True,
metric='sum product',
symmetries=[],
request_stop_cb=None):
'''
Use gradient ascent to rigidly rotate and shift a set of points within a
density map to maximize the average interpolated density value at the point
positions. Returns a Place object giving the motion of the points to the
local maximum. The point coordinates are not modified.
Optionally the correlation value or correlation about mean can
be optimized. Copies of the point set can be included in the optimization
by specifying a list of Place objects for the symmetries argument.
'''
from chimerax.geometry import identity
data_array, xyz_to_ijk_transform = \
volume.matrix_and_transform(identity(), subregion = None, step = 1)
move_tf, stats = \
locate_maximum(points, point_weights,
data_array, xyz_to_ijk_transform,
max_steps, ijk_step_size_min, ijk_step_size_max,
optimize_translation, optimize_rotation,
metric, None, symmetries, request_stop_cb)
return move_tf, stats
def atoms_outside_contour(atoms, volume=None):
if volume is None:
from chimerax.map import active_volume
volume = active_volume()
points = atom_coordinates(atoms)
from chimerax.geometry import identity
poc, clevel = points_outside_contour(points, identity(), volume)
return poc, clevel
def initial_camera_view(self, pad=0.05, set_pivot=True):
'''Set the camera position to show all displayed drawings,
looking down the z axis.'''
b = self.drawing_bounds()
if b is None:
return
c = self.camera
from chimerax.geometry import identity
c.position = identity()
c.view_all(b, window_size=self.window_size, pad=pad)
if set_pivot:
self._center_of_rotation = cr = b.center()
self._update_center_of_rotation = True
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 map_fitting_points(v, envelope, local_coords=False, include_zeros=False):
from chimerax.geometry import identity
point_to_scene_transform = None if local_coords else identity()
from . import fitmap as F
try:
points, point_weights = F.map_points_and_weights(
v, envelope, point_to_scene_transform, include_zeros=include_zeros)
except (MemoryError, ValueError) as e:
raise UserError('Out of memory, too many points in %s' % v.name)
if len(points) == 0:
msg = ('No grid points above map threshold.'
if envelope else 'Map has no non-zero values.')
raise UserError(msg)
return points, point_weights
def average_map_value_at_atom_positions(atoms, volume=None):
if volume is None:
from chimerax.map import active_volume
volume = active_volume()
points = atom_coordinates(atoms)
if volume is None or len(points) == 0:
return 0, len(points)
from chimerax.geometry import identity
data_array, xyz_to_ijk_transform = \
volume.matrix_and_transform(identity(), subregion = None, step = 1)
amv, npts = average_map_value(points, xyz_to_ijk_transform, data_array)
return amv, npts
def __init__(self, session, filename):
from chimerax.core import generic3d
self.model = generic3d.Generic3DModel(filename, session)
self.session = session
self.shapes = []
# parse input
self.warned = set()
self.lineno = 0
self.transforms = [identity()]
self.pure = [True] # True if corresponding transform has pure rotation
self.cur_color = [1.0, 1.0, 1.0, 1.0]
self.cur_transparency = 0
self.cur_pos = array([0.0, 0.0, 0.0])
self.cur_pos_is_move = True # set whenever cur_pos is set
self.cur_char_pos = array([0.0, 0.0, 0.0])
self.cur_font = ['SANS', 12, 'PLAIN']
self.cur_description = None
self.cur_atoms = None
self.num_objects = 0
self.LINE_RADIUS = 0.08
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 extend_crystal_map(volarray, ijk_cell_size, ijk_symmetries, out_array,
out_ijk_to_vol_ijk_transform):
ksz, jsz, isz = out_array.shape
otf = out_ijk_to_vol_ijk_transform
from chimerax.geometry import identity
itf = identity()
nsym = len(ijk_symmetries)
from numpy import empty, float32, delete as delete_array_elements
values = empty((nsym, ), float32)
nnc = 0 # Number of grid points not covered by symmetry
dmax = None # Maximum value discrepancy for multiple overlaps
from chimerax.map_data import interpolate_volume_data
for k in range(ksz):
for j in range(jsz):
for i in range(isz):
vijk = otf * (i, j, k)
vlist = []
for sym in ijk_symmetries:
svijk = sym * vijk
scijk = [p % s for p, s in zip(svijk, ijk_cell_size)
] # Wrap to unit cell.
vlist.append(scijk)
values[:] = 0
outside = interpolate_volume_data(vlist, itf, volarray,
'linear', values)[1]
n = len(values) - len(outside)
if n >= 1:
out_array[k, j, i] = float(values.sum()) / n
if n >= 2:
# Record maximum value discrepancy for multiple overlaps
vinside = delete_array_elements(values, outside)
d = vinside.max() - vinside.min()
if dmax is None or d > dmax:
dmax = d
else:
nnc += 1 # Count grid points not covered by symmetry.
return nnc, dmax
def fit_search(models, points, point_weights, volume, n,
rotations = True, shifts = True, radius = None,
angle_tolerance = 6, shift_tolerance = 3,
asymmetric_unit = True,
minimum_points_in_contour = 0.5,
metric = 'sum product',
optimize_translation = True, optimize_rotation = True,
max_steps = 2000,
ijk_step_size_min = 0.01, ijk_step_size_max = 0.5,
request_stop_cb = None):
bounds = volume.surface_bounds()
if bounds is None:
xyz_min, xyz_max = volume.xyz_bounds(step = 1)
from chimerax.geometry import Bounds
bounds = Bounds(xyz_min, xyz_max)
asym_center_f = (.75,.55,.55)
asym_center = tuple(x0 + (x1-x0)*f
for x0, x1, f in zip(bounds.xyz_min, bounds.xyz_max, asym_center_f))
from chimerax.geometry import translation, identity
center = points.mean(axis=0)
ctf = translation(-center)
ijk_to_xyz_tf = volume.matrix_indices_to_xyz_transform(step = 1)
xyz_to_ijk_tf = ijk_to_xyz_tf.inverse()
data_array = volume.matrix(step = 1)
vtfinv = volume.position.inverse()
mtv_list = [vtfinv * m.position for m in models]
flist = []
outside = 0
from math import pi
from chimerax.geometry import bins
b = bins.Binned_Transforms(angle_tolerance*pi/180, shift_tolerance, center)
fo = {}
from .fitmap import locate_maximum
for i in range(n):
if request_stop_cb and request_stop_cb('Fit %d of %d' % (i+1,n)):
break
shift = ((random_translation(bounds) if radius is None
else random_translation_step(center, radius)) if shifts
else translation(center))
rot = random_rotation() if rotations else identity()
tf = shift * rot * ctf
optimize = True
max_opt = 2
while optimize and max_opt > 0:
p_to_ijk_tf = xyz_to_ijk_tf * tf
move_tf, stats = \
locate_maximum(points, point_weights, data_array, p_to_ijk_tf,
max_steps, ijk_step_size_min, ijk_step_size_max,
optimize_translation, optimize_rotation,
metric, request_stop_cb = None)
ptf = tf * move_tf
optimize = False
max_opt -= 1
if asymmetric_unit:
atf = unique_symmetry_position(ptf, center, asym_center,
volume.data.symmetries)
if not atf is ptf:
ptf = tf = atf
optimize = not b.close_transforms(ptf)
close = b.close_transforms(ptf)
if len(close) == 0:
transforms = [ptf * mtv for mtv in mtv_list]
stats['hits'] = 1
f = Fit(models, transforms, volume, stats)
f.ptf = ptf
flist.append(f)
b.add_transform(ptf)
fo[id(ptf)] = f
else:
s = fo[id(close[0])].stats
s['hits'] += 1
# Filter out solutions with too many points outside volume contour.
fflist = [f for f in flist if (in_contour(f.ptf, points, volume, f.stats)
>= minimum_points_in_contour)]
fset = set(fflist)
outside = sum([f.stats['hits'] for f in flist if not f in fset])
# Sort fits by correlation, then average map value.
fflist.sort(key = fit_order)
fflist.reverse() # Best first
return fflist, outside
def write_mol2(session,
file_name,
*,
models=None,
atoms=None,
status=None,
anchor=None,
rel_model=None,
sybyl_hyd_naming=True,
combine_models=False,
skip_atoms=None,
res_num=False,
gaff_type=False,
gaff_fail_error=None):
"""Write a Mol2 file.
Parameters
----------
file_name : str, or file object open for writing
Output file.
models : a list/tuple/set of models (:py:class:`~chimerax.atomic.Structure`s)
or a single :py:class:`~chimerax.atomic.Structure`
The structure(s) to write out. If None (and 'atoms' is also None) then
write out all structures.
atoms : an :py:class:`~chimerax.atomic.Atoms` collection or None. If not None,
then 'models' must be None.
status : function or None
If not None, a function that takes a string -- used to report the progress of the write.
anchor : :py:class:`~chimerax.atomic.Atoms` collection
Atoms (and their implied internal bonds) that should be written out to the
@SET section of the file as the rigid framework for flexible ligand docking.
rel_model : Model whose coordinate system the coordinates should be written out reletive to,
i.e. take the output atoms' coordinates and apply the inverse of the rel_model's transform.
sybyl_hyd_naming : bool
Controls whether hydrogen names should be "Sybyl-like" or "PDB-like" -- e.g. HG21 vs. 1HG2.
combine_models : bool
Controls whether multiple structures will be combined into a single @MOLECULE
section (value: True) or each given its own section (value: False).
skip_atoms : list/set of :py:class:`~chimerax.atomic.Atom`s or an :py:class:`~chimerax.atomic.Atoms` collection or None
Atoms to not output
res_num : bool
Controls whether residue sequence numbers are included in the substructure name.
Since Sybyl Mol2 files include them, this defaults to True.
gaff_type : bool
If 'gaff_type' is True, outout GAFF atom types instead of Sybyl atom types.
`gaff_fail_error`, if specified, is the type of error to throw (e.g. UserError)
if there is no gaff_type attribute for an atom, otherwise throw the standard AttributeError.
"""
if status:
status("Writing Mol2 file %s" % file_name)
from chimerax import io
f = io.open_output(file_name, "utf-8")
sort_key_func = serial_sort_key = lambda a, ri={}: write_mol2_sort_key(
a, res_indices=ri)
from chimerax.atomic import Structure, Atoms, Residue
class JPBGroup:
def __init__(self, atoms):
atom_set = set(atoms)
pbs = []
for s in atoms.unique_structures:
pbg = s.pbg_map.get(s.PBG_METAL_COORDINATION, None)
if not pbg:
continue
for pb in pbg.pseudobonds:
if pb.atoms[0] in atom_set and pb.atoms[1] in atom_set:
pbs.append(pb)
self._pbs = pbs
@property
def pseudobonds(self):
return self._pbs
if models is None:
if atoms is None:
structures = session.models.list(type=Structure)
else:
structures = atoms
else:
if atoms is None:
if isinstance(models, Structure):
structures = [models]
else:
structures = [m for m in models if isinstance(m, Structure)]
else:
raise ValueError(
"Cannot specify both 'models' and 'atoms' keywords")
if isinstance(structures, Atoms):
class Jumbo:
def __init__(self, atoms):
self.atoms = atoms
self.residues = atoms.unique_residues
self.bonds = atoms.intra_bonds
self.name = "(selection)"
self.pbg_map = {
Structure.PBG_METAL_COORDINATION: JPBGroup(atoms)
}
structures = [Jumbo(structures)]
sort_key_func = lambda a: (a.structure.id, ) + serial_sort_key(a)
combine_models = False
# transform...
if rel_model is None:
from chimerax.geometry import identity
xform = identity()
else:
xform = rel_model.scene_position.inverse()
# need to find amide moieties since Sybyl has an explicit amide type
if status:
status("Finding amides")
from chimerax.chem_group import find_group
amides = find_group("amide", structures)
amide_Ns = set([amide[2] for amide in amides])
amide_CNs = set([amide[0] for amide in amides])
amide_CNs.update(amide_Ns)
amide_Os = set([amide[1] for amide in amides])
substructure_names = None
if combine_models and len(structures) > 1:
# create a fictitious jumbo model
class Jumbo:
def __init__(self, structures):
self.name = structures[0].name + " (combined)"
from chimerax.atomic import concatenate
self.atoms = concatenate([s.atoms for s in structures])
self.bonds = concatenate([s.bonds for s in structures])
self.residues = concatenate([s.residues for s in structures])
self.pbg_map = {
Structure.PBG_METAL_COORDINATION: JPBGroup(self.atoms)
}
# if combining single-residue structures,
# can be more informative to use model name
# instead of residue type for substructure
if len(structures) == len(self.residues):
rnames = self.residues.names
if len(set(rnames)) < len(rnames):
snames = [s.name for s in structures]
if len(set(snames)) == len(snames):
self.substructure_names = dict(
zip(self.residues, snames))
structures = [Jumbo(structures)]
if hasattr(structures[-1], 'substructure_names'):
substructure_names = structures[-1].substructure_names
delattr(structures[-1], 'substructure_names')
sort_key_func = lambda a: (a.structure.id, ) + serial_sort(a)
# write out structures
for struct in structures:
if hasattr(struct, 'mol2_comments'):
for m2c in struct.mol2_comments:
print(m2c, file=f)
if hasattr(struct, 'solvent_info'):
print(struct.solvent_info, file=f)
# molecule section header
print("%s" % MOLECULE_HEADER, file=f)
# molecule name
print("%s" % struct.name, file=f)
atoms = list(struct.atoms)
bonds = list(struct.bonds)
# add metal-coordination bonds
coord_grp = struct.pbg_map.get(Structure.PBG_METAL_COORDINATION, None)
if coord_grp:
bonds.extend(list(coord_grp.pseudobonds))
if skip_atoms:
skip_atoms = set(skip_atoms)
atoms = [a for a in atoms if a not in skip_atoms]
bonds = [
b for b in bonds if b.atoms[0] not in skip_atoms
and b.atoms[1] not in skip_atoms
]
residues = struct.residues
# Put the atoms in the order we want for output
if status:
status("Putting atoms in input order")
atoms.sort(key=sort_key_func)
# if anchor is not None, then there will be two entries in
# the @SET section of the file...
if anchor:
sets = 2
else:
sets = 0
# number of entries for various sections...
print("%d %d %d 0 %d" % (len(atoms), len(bonds), len(residues), sets),
file=f)
# type of molecule
if hasattr(struct, "mol2_type"):
mtype = struct.mol2_type
else:
mtype = "SMALL"
from chimerax.atomic import Sequence
for r in struct.residues:
if Sequence.protein3to1(r.name) != 'X':
mtype = "PROTEIN"
break
if Sequence.nucleic3to1(r.name) != 'X':
mtype = "NUCLEIC_ACID"
break
print(mtype, file=f)
# indicate type of charge information
if hasattr(struct, 'charge_model'):
print(struct.charge_model, file=f)
else:
print("NO_CHARGES", file=f)
if hasattr(struct, 'mol2_comment'):
print("\n%s" % struct.mol2_comment, file=f)
else:
print("\n", file=f)
if status:
status("writing atoms")
# atom section header
print("%s" % ATOM_HEADER, file=f)
# make a dictionary of residue indices so that we can do quick look ups
res_indices = {}
for i, r in enumerate(residues):
res_indices[r] = i + 1
for i, atom in enumerate(atoms):
# atom ID, starting from 1
print("%7d" % (i + 1), end=" ", file=f)
# atom name, possibly rearranged if it's a hydrogen
if sybyl_hyd_naming and not atom.name[0].isalpha():
atom_name = atom.name[1:] + atom.name[0]
else:
atom_name = atom.name
print("%-8s" % atom_name, end=" ", file=f)
# use correct relative coordinate position
coord = xform * atom.scene_coord
print("%9.4f %9.4f %9.4f" % tuple(coord), end=" ", file=f)
# atom type
if gaff_type:
try:
atom_type = atom.gaff_type
except AttributeError:
if not gaff_fail_error:
raise
raise gaff_fail_error(
"%s has no Amber/GAFF type assigned.\n"
"Use the AddCharge tool to assign Amber/GAFF types." %
atom)
elif hasattr(atom, 'mol2_type'):
atom_type = atom.mol2_type
elif atom in amide_Ns:
atom_type = "N.am"
elif atom.structure_category == "solvent" \
and atom.residue.name in Residue.water_res_names:
if atom.element.name == "O":
atom_type = "O.t3p"
else:
atom_type = "H.t3p"
elif atom.element.name == "N" and len(
[r for r in atom.rings() if r.aromatic]) > 0:
atom_type = "N.ar"
elif atom.idatm_type == "C2" and len(
[nb for nb in atom.neighbors if nb.idatm_type == "Ng+"]) > 2:
atom_type = "C.cat"
elif sulfur_oxygen(atom):
atom_type = "O.2"
else:
try:
atom_type = chimera_to_sybyl[atom.idatm_type]
except KeyError:
session.logger.warning(
"Atom whose IDATM type has no equivalent"
" Sybyl type: %s (type: %s)" % (atom, atom.idatm_type))
atom_type = str(atom.element)
print("%-5s" % atom_type, end=" ", file=f)
# residue-related info
res = atom.residue
# residue index
print("%5d" % res_indices[res], end=" ", file=f)
# substructure identifier and charge
if hasattr(atom, 'charge') and atom.charge is not None:
charge = atom.charge
else:
charge = 0.0
if substructure_names:
rname = substructure_names[res]
elif res_num:
rname = "%3s%-5d" % (res.name, res.number)
else:
rname = "%3s" % res.name
print("%s %9.4f" % (rname, charge), file=f)
if status:
status("writing bonds")
# bond section header
print("%s" % BOND_HEADER, file=f)
# make an atom-index dictionary to speed lookups
atom_indices = {}
for i, a in enumerate(atoms):
atom_indices[a] = i + 1
for i, bond in enumerate(bonds):
a1, a2 = bond.atoms
# ID
print("%6d" % (i + 1), end=" ", file=f)
# atom IDs
print("%4d %4d" % (atom_indices[a1], atom_indices[a2]),
end=" ",
file=f)
# bond order; give it our best shot...
if hasattr(bond, 'mol2_type'):
print(bond.mol2_type, file=f)
continue
amide_A1 = a1 in amide_CNs
amide_A2 = a2 in amide_CNs
if amide_A1 and amide_A2:
print("am", file=f)
continue
if amide_A1 or amide_A2:
if a1 in amide_Os or a2 in amide_Os:
print("2", file=f)
else:
print("1", file=f)
continue
aromatic = False
# 'bond' might be a metal-coordination bond so do a test for rings
if hasattr(bond, 'rings'):
for ring in bond.rings():
if ring.aromatic:
aromatic = True
break
if aromatic:
print("ar", file=f)
continue
try:
geom1 = idatm_info[a1.idatm_type].geometry
except KeyError:
print("1", file=f)
continue
try:
geom2 = idatm_info[a2.idatm_type].geometry
except KeyError:
print("1", file=f)
continue
# sulfone/sulfoxide is classically depicted as double-
# bonded despite the high dipolar character of the
# bond making it have single-bond character. For
# output, use the classical values.
if sulfur_oxygen(a1) or sulfur_oxygen(a2):
print("2", file=f)
continue
if geom1 not in [2, 3] or geom2 not in [2, 3]:
print("1", file=f)
continue
# if either endpoint atom is in an aromatic ring and
# the bond isn't, it's a single bond...
for endp in [a1, a2]:
aromatic = False
for ring in endp.rings():
if ring.aromatic:
aromatic = True
break
if aromatic:
break
else:
# neither endpoint in aromatic ring
if geom1 == 2 and geom2 == 2:
print("3", file=f)
else:
print("2", file=f)
continue
print("1", file=f)
if status:
status("writing residues")
# residue section header
print("%s" % SUBSTR_HEADER, file=f)
for i, res in enumerate(residues):
# residue id field
print("%6d" % (i + 1), end=" ", file=f)
# residue name field
if substructure_names:
rname = substructure_names[res]
elif res_num:
rname = "%3s%-4d" % (res.name, res.number)
else:
rname = "%3s" % res.name
print(rname, end=" ", file=f)
# ID of the root atom of the residue
chain_atom = res.principal_atom
if chain_atom is None:
# if writing out a selection, not all residue atoms
# might be in atom_indices...
for chain_atom in res.atoms:
if chain_atom in atom_indices:
break
print("%5d" % atom_indices[chain_atom], end=" ", file=f)
print("RESIDUE 4", end=" ", file=f)
# Sybyl seems to use chain 'A' when chain ID is blank,
# so run with that
chain_id = res.chain_id
if not chain_id.strip():
chain_id = 'A'
print("%-4s %3s" % (chain_id, res.name), end=" ", file=f)
# number of out-of-substructure bonds
cross_res_bonds = 0
for a in res.atoms:
for nb in a.neighbors:
if nb.residue != res:
cross_res_bonds += 1
print("%5d" % cross_res_bonds, end="", file=f)
# print "ROOT" if first or only residue of a chain
if not res.chain or res.chain.existing_residues[0] == res:
print(" ROOT", file=f)
else:
print(file=f)
# write flexible ligand docking info
if anchor:
if status:
status("writing anchor info")
print("%s" % SET_HEADER, file=f)
atom_indices = {}
for i, a in enumerate(atoms):
atom_indices[a] = i + 1
bond_indices = {}
for i, b in enumerate(bonds):
bond_indices[b] = i + 1
print(
"ANCHOR STATIC ATOMS <user> **** Anchor Atom Set",
file=f)
print(len(anchor), end=" ", file=f)
for a in anchor:
if a in atom_indices:
print(atom_indices[a], end=" ", file=f)
print(file=f)
print(
"RIGID STATIC BONDS <user> **** Rigid Bond Set",
file=f)
bonds = anchor.intra_bonds
print(len(bonds), end=" ", file=f)
for b in bonds:
if b in bond_indices:
print(bond_indices[b], end=" ", file=f)
print(file=f)
if file_name != f:
f.close()
if status:
status("Wrote Mol2 file %s" % file_name)
def coordinate_system_transform(from_cs, to_cs):
global cst
if cst:
return cst[(from_cs, to_cs)]
transform = cst
e = icosahedron_edge_length() # Triangle edge length of unit icosahedron.
from math import sqrt
s25 = e / 2 # Sin/Cos for angle between 2-fold and 5-fold axis
c25 = sqrt(1 - s25 * s25)
s35 = e / sqrt(3) # Sin/Cos for angle between 3-fold and 5-fold axis
c35 = sqrt(1 - s35 * s35)
from chimerax.geometry import Place
transform[('2n5', '222')] = Place(
((1, 0, 0, 0), (0, c25, -s25, 0), (0, s25, c25, 0)))
transform[('2n5', '2n3')] = Place(
((1, 0, 0, 0), (0, c35, s35, 0), (0, -s35, c35, 0)))
# Axes permutations.
# 90 degree rotation about z:
transform[('222', '222r')] = Place(
((0, 1, 0, 0), (-1, 0, 0, 0), (0, 0, 1, 0)))
# 180 degree rotation about y:
transform[('2n3', '2n3r')] = \
transform[('2n5', '2n5r')] = Place(((-1, 0, 0, 0),
(0, 1, 0, 0),
(0, 0, -1, 0)))
# 180 degree rotation about x:
transform[('n25', 'n25r')] = Place(
((1, 0, 0, 0), (0, -1, 0, 0), (0, 0, -1, 0)))
# x <-> y and z -> -z:
transform[('n25', '2n5')] = Place(
((0, 1, 0, 0), (1, 0, 0, 0), (0, 0, -1, 0)))
# Extend to all pairs of transforms.
tlist = []
while len(transform) > len(tlist):
tlist = transform.keys()
# Add inverse transforms
for f, t in tlist:
if not (t, f) in transform:
transform[(t, f)] = transform[(f, t)].inverse()
# Use transitivity
for f1, t1 in tlist:
for f2, t2 in tlist:
if f2 == t1 and f1 != t2 and not (f1, t2) in transform:
transform[(f1, t2)] = transform[(f2, t2)] \
* transform[(f1, t1)]
from chimerax.geometry import identity
i = identity()
for s in coordinate_system_names:
transform[(s, s)] = i
return transform[(from_cs, to_cs)]
def fit_sequence(models,
volume,
steps,
subtract_maps=[],
envelope=True,
include_zeros=False,
metric='overlap',
optimize_translation=True,
optimize_rotation=True,
max_steps=2000,
ijk_step_size_min=0.01,
ijk_step_size_max=0.5,
request_stop_cb=None,
log=None):
from chimerax.geometry import identity
data_array, xyz_to_ijk_transform = \
volume.matrix_and_transform(identity(), subregion = None, step = 1)
size = tuple(data_array.shape[::-1])
from numpy import float32, multiply, add, array
from chimerax.map_data import grid_indices
grid_points = grid_indices(size, float32)
xyz_to_ijk_transform.inverse().transform_points(grid_points, in_place=True)
grid_points_to_scene_transform = identity()
# Make float32 copy for subtracting interpolated molecule maps.
d = array(data_array, float32)
from chimerax.atomic import Atoms
from .move import position_history as h
h.record_position(models, Atoms(), volume)
fits = {}
from . import fitmap as F
from chimerax.map.volume import minimum_rms_scale
from .search import Fit
for s in range(steps):
mi = s % len(models)
v = models[mi]
if request_stop_cb and request_stop_cb('Fitting %s in %s, step %d' %
(v.name, volume.name, s + 1)):
return
# Subtract off other maps.
d[:] = data_array
for m in models + subtract_maps:
if not m is v:
values = m.interpolated_values(grid_points,
grid_points_to_scene_transform,
subregion=None,
step=None)
level = m.minimum_surface_level
scale = minimum_rms_scale(values, data_array.ravel(), level)
multiply(values, scale, values)
add(d, values.reshape(d.shape), d)
# Fit in difference map.
points, point_weights = F.map_points_and_weights(
v, envelope, include_zeros=include_zeros)
move_tf, stats = F.locate_maximum(points,
point_weights,
d,
xyz_to_ijk_transform,
max_steps,
ijk_step_size_min,
ijk_step_size_max,
optimize_translation,
optimize_rotation,
metric,
request_stop_cb=None)
v.position = move_tf * v.position
fits[v] = Fit([v], None, volume, stats)
if log:
log.info(F.map_fit_message(v, volume, stats))
h.record_position(models, Atoms(), volume)
flist = [fits[m] for m in models if m in fits]
return flist
def locate_maximum(points,
point_weights,
data_array,
xyz_to_ijk_transform,
max_steps=2000,
ijk_step_size_min=0.01,
ijk_step_size_max=0.5,
optimize_translation=True,
optimize_rotation=True,
metric='sum product',
rotation_center=None,
symmetries=[],
request_stop_cb=None):
segment_steps = 4
cut_step_size_threshold = .25
step_cut_factor = .5
step_grow_factor = 1.2
ijk_step_size = ijk_step_size_max
np = len(points)
from time import time
report_interval = 1.0 # seconds
next_report_time = time() + report_interval
if metric == 'correlation about mean':
from numpy import sum, float64
wm = sum(point_weights, dtype=float64) / len(point_weights)
point_wts = point_weights.copy()
point_wts -= wm
else:
point_wts = point_weights
from chimerax.geometry import identity
move_tf = identity()
if rotation_center is None:
from numpy import sum, float64
rotation_center = rc = sum(points, axis=0, dtype=float64) / np
syminv = [s.inverse() for s in symmetries]
# Use temporary value and gradient arrays instead of reallocating each step.
from numpy import empty, float32
values = empty((np, ), float32)
gradients = empty(points.shape, float32)
step = 0
while step < max_steps and ijk_step_size > ijk_step_size_min:
xyz_to_ijk_tf = xyz_to_ijk_transform * move_tf
rc = (rotation_center if len(symmetries) == 0 else move_tf.inverse() *
rotation_center)
seg_tf = step_to_maximum(points,
point_wts,
data_array,
xyz_to_ijk_tf,
segment_steps,
ijk_step_size,
optimize_translation,
optimize_rotation,
rc,
metric,
syminv=syminv,
values=values,
gradients=gradients)
step += segment_steps
mm = maximum_ijk_motion(points, xyz_to_ijk_tf, seg_tf)
mmcut = cut_step_size_threshold * segment_steps * ijk_step_size
if mm < mmcut:
ijk_step_size *= step_cut_factor
else:
ijk_step_size = min(ijk_step_size * step_grow_factor,
ijk_step_size_max)
move_tf = move_tf * seg_tf
if request_stop_cb and time() >= next_report_time:
next_report_time = time() + report_interval
shift, angle = move_tf.shift_and_angle(rc)
if request_stop_cb('%d steps, shift %.3g, rotation %.3g degrees' %
(step, shift, angle)):
break
# Record statistics of optimization.
shift, angle = move_tf.shift_and_angle(rc)
axis, axis_point, angle, axis_shift = move_tf.axis_center_angle_shift()
xyz_to_ijk_tf = xyz_to_ijk_transform * move_tf
stats = {
'shift': shift,
'axis': axis,
'axis point': axis_point,
'angle': angle,
'axis shift': axis_shift,
'steps': step,
'points': np,
'transform': move_tf
}
amv, npts = average_map_value(points,
xyz_to_ijk_tf,
data_array,
syminv=syminv,
values=values)
stats['average map value'] = amv
stats['points in map'] = npts # Excludes out-of-bounds points
stats['symmetries'] = len(symmetries)
if not point_weights is None:
map_values = volume_values(points,
xyz_to_ijk_tf,
data_array,
syminv=syminv,
values=values)
olap, cor, corm = overlap_and_correlation(point_weights, map_values)
stats['overlap'] = olap
stats['correlation'] = cor
stats['correlation about mean'] = corm
return move_tf, stats