def _straight_initial(self):
from numpy import mean, dot, newaxis
from numpy.linalg import norm
if len(self.coords) > len(self.IDEAL_COORDS):
# "Normal" helices can be approximated by using all
# coordinates on the assumption that the helix length
# is sufficiently larger than the helix radius that
# the biggest eigenvector will be the helical axis
from numpy.linalg import svd
from numpy import argmax
centroid = mean(self.coords, axis=0)
rel_coords = self.coords - centroid
ignore, vals, vecs = svd(rel_coords)
axis = vecs[argmax(vals)]
else:
from chimerax.geometry import align_points
num_pts = len(self.coords)
tf, rmsd = align_points(self.IDEAL_COORDS[:num_pts], self.coords)
centroid = tf * self.IDEAL_PARAMS[0]
axis = tf.transform_vector(self.IDEAL_PARAMS[1])
rel_coords = self.coords - centroid
axis_pos = dot(rel_coords, axis)[:, newaxis]
radial_vecs = rel_coords - axis * axis_pos
radius = mean(norm(radial_vecs, axis=1))
return centroid, axis, radius
def make_fmet_from_met(session, residue):
err_string = "make_fmet_from_met() is only applicable to N-terminal methionine residues!"
if residue.name != 'MET':
raise TypeError(err_string)
n = residue.find_atom('N')
if n is None:
raise TypeError('Missing N atom! Is your residue complete?')
for nb in n.neighbors:
if nb.residue != residue:
raise TypeError(err_string)
if nb.element.name == 'H':
nb.delete()
from chimerax.mmcif import find_template_residue
import numpy
fme = find_template_residue(session, 'FME')
ref_atoms = ('C', 'CA', 'N')
r_coords = numpy.array([residue.find_atom(a).coord for a in ref_atoms])
t_coords = numpy.array([fme.find_atom(a).coord for a in ref_atoms])
from chimerax.geometry import align_points
tf, rms = align_points(t_coords, r_coords)
from chimerax.atomic.struct_edit import add_atom
atom_pairs = (('N', 'H'), ('N', 'CN'), ('CN', 'O1'), ('CN', 'HCN'))
for (bname, aname) in atom_pairs:
ta = fme.find_atom(aname)
add_atom(aname,
ta.element,
residue,
tf * ta.coord,
bonded_to=residue.find_atom(bname))
residue.name = 'FME'
def align_and_prune(xyz, ref_xyz, cutoff_distance, indices=None):
import numpy
if indices is None:
indices = numpy.arange(len(xyz))
axyz, ref_axyz = xyz[indices], ref_xyz[indices]
from chimerax.geometry import align_points
p, rms = align_points(axyz, ref_axyz)
dxyz = p * axyz - ref_axyz
d2 = (dxyz * dxyz).sum(axis=1)
cutoff2 = cutoff_distance * cutoff_distance
i = d2.argsort()
if d2[i[-1]] <= cutoff2:
return p, rms, indices
# cull 10% or...
index1 = int(len(d2) * 0.9)
# cull half the long pairings
index2 = int(((d2 <= cutoff2).sum() + len(d2)) / 2)
# whichever is fewer
index = max(index1, index2)
survivors = indices[i[:index]]
if len(survivors) < 3:
raise IterationError(
"Alignment failed;"
" pruning distances > %g left less than 3 atom pairs" %
cutoff_distance)
return align_and_prune(xyz, ref_xyz, cutoff_distance, survivors)
def minimize_link_lengths(mols, pbonds, iterations, frames, session):
if len(mols) == 0:
from chimerax.core.errors import UserError
raise UserError('No structures specified for minimizing crosslinks.')
mol_links, mol_pbonds = links_by_molecule(pbonds, mols)
if len(mol_links) == 0:
from chimerax.core.errors import UserError
raise UserError('No pseudobonds between molecules.')
if len(mols) == 1:
iterations = min(1, iterations)
if not frames is None:
pos0 = dict((m, m.position) for m in mols)
from numpy import array, float64
from chimerax.geometry import align_points
for i in range(iterations):
for m in mols:
if m in mol_links:
atom_pairs = mol_links[m]
moving = array([a1.scene_coord for a1, a2 in atom_pairs],
float64)
fixed = array([a2.scene_coord for a1, a2 in atom_pairs],
float64)
tf, rms = align_points(moving, fixed)
m.position = tf * m.position
lengths = [pb.length for pb in mol_pbonds]
lengths.sort(reverse=True)
lentext = ', '.join('%.1f' % d for d in lengths)
session.logger.info('%d crosslinks, lengths: %s' %
(len(mol_pbonds), lentext))
if not frames is None:
for m in mols:
interpolate_position(m, pos0[m], m.position, frames,
session.triggers)
def align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance, atoms, to_atoms,
move, log, report_matrix):
xyz_from = patoms.scene_coords
if cutoff_distance is None:
from chimerax.geometry import align_points
tf, rmsd = align_points(xyz_from, xyz_to)
full_rmsd = rmsd
matched_patoms, matched_pto_atoms = patoms, pto_atoms
msg = 'RMSD between %d atom pairs is %.3f angstroms' % (len(patoms),
rmsd)
else:
if cutoff_distance <= 0.0:
raise UserError("Distance cutoff must be positive")
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)
np = len(indices)
dxyz = tf * xyz_from - xyz_to
d2 = (dxyz * dxyz).sum(axis=1)
import math
full_rmsd = math.sqrt(d2.sum() / len(d2))
matched_patoms, matched_pto_atoms = patoms[indices], pto_atoms[indices]
msg = 'RMSD between %d pruned atom pairs is %.3f angstroms;' \
' (across all %d pairs: %.3f)' % (np, rmsd, len(patoms), full_rmsd)
if report_matrix:
log.info(matrix_text(tf, atoms, to_atoms))
log.status(msg)
log.info(msg)
move_atoms(atoms, to_atoms, tf, move)
return matched_patoms, matched_pto_atoms, rmsd, full_rmsd, tf
def show_residue_fit(session, residues, map, range = 2, last_pos = None, motion_frames = 20):
'''Set camera to show first residue in list and display map in zone around given residues.'''
res = residues[0]
ratoms = res.atoms
anames = tuple(ratoms.names)
try:
i = [anames.index(aname) for aname in ('N', 'CA', 'C')]
except ValueError:
return None # Missing backbone atom
xyz = ratoms.filter(i).scene_coords
# Align backbone to template backbone coords
from chimerax.geometry import align_points, Place
from numpy import array
txyz = array([[ 12.83300018, 6.83900023, 6.73799992],
[ 12.80800056, 7.87400055, 5.70799971],
[ 11.91800022, 9.06700039, 5.9920001 ]])
p, rms = align_points(txyz, xyz)
# Set camera view relative to template.
c = session.main_view.camera
cp = c.position
if last_pos is None:
tc = Place(((-0.46696,0.38225,-0.79739,-3.9125),
(0.81905,-0.15294,-0.55296,-4.3407),
(-0.33332,-0.91132,-0.24166,-1.4889)))
if c.name == 'orthographic':
c.field_width = 12 # Set orthographic field of view, Angstroms
else:
# Maintain same relative camera position to backbone.
tc = last_pos.inverse() * cp
# Smooth interpolation
np = p*tc
if motion_frames > 1:
def interpolate_camera(session, f, cp=cp, np=np, center=np.inverse()*xyz[1], frames=motion_frames):
c = session.main_view.camera
p = np if f+1 == frames else cp.interpolate(np, center, frac = (f+1)/frames)
c.position = p
from chimerax.core.commands import motion
motion.CallForNFrames(interpolate_camera, motion_frames, session)
else:
c.position = np
from numpy import concatenate
zone_points = concatenate([r.atoms.scene_coords for r in residues])
from chimerax.surface import zone
for s in map.surfaces:
zone.surface_zone(s, zone_points, range, auto_update = True)
for r in residues:
r.atoms.displays = True
return p
def steady_transform(self, cset):
tfc = self._steady_transforms
if cset in tfc:
return tfc[cset]
atoms = self.steady_atoms
coords = coordset_coords(atoms, cset, self.structure)
if self._steady_coords is None:
self._steady_coords = coords
from chimerax.geometry import align_points
tf = align_points(coords, self._steady_coords)[0]
tfc[cset] = tf
return tf
def _orient(self):
gc = []
la = []
for g, (x, y) in zip(self.groups, self._layout_positions):
if g.shown():
gc.append(g.centroid())
la.append((x, y, 0))
if len(gc) < 2:
return
from chimerax.geometry import align_points, translation
from numpy import array, mean
p, rms = align_points(array(gc), array(la))
ra = p.zero_translation()
center = mean(gc, axis=0)
v = self._session().main_view
rc = v.camera.position.zero_translation()
rot = translation(center) * rc * ra * translation(-center)
v.move(rot)
def ncs_average_map(session, asu_map, full_map, reference_chain, ncs_chains):
from chimerax.match_maker.match import (
defaults, align
)
grid_points = asu_map.grid_points(asu_map.model_transform().inverse())
from chimerax.atomic import Residues, Atoms
interpolated_maps = []
interpolated_maps.append(asu_map.data.matrix())
original_map_position = full_map.position
dssp_cache={}
for ncs in ncs_chains:
score, s1, s2 = align(session, ncs, reference_chain, defaults['matrix'],
'nw', defaults['gap_open'], defaults['gap_extend'], dssp_cache)
ref_residues = []
ncs_residues = []
for i, (mr, rr) in enumerate(zip(s1, s2)):
if mr=='.' or rr=='.':
continue
ref_res = s1.residues[s1.gapped_to_ungapped(i)]
match_res = s2.residues[s2.gapped_to_ungapped(i)]
if not ref_res or not match_res:
continue
ref_residues.append(ref_res)
ncs_residues.append(match_res)
ref_residues = Residues(ref_residues)
ncs_residues = Residues(ncs_residues)
(ref_pa, ncs_pa) = paired_principal_atoms([ref_residues, ncs_residues])
from chimerax.geometry import align_points
tf, rms = align_points(ncs_pa.coords, ref_pa.coords)
#full_map.position = tf * full_map.position
from chimerax.core.commands import run
#run(session, "fitmap #{} in #{}".format(full_map.id_string, asu_map.id_string))
interpolated_maps.append(
full_map.interpolated_values(grid_points, point_xform=tf.inverse()).reshape(asu_map.data.size))
#full_map.position = original_map_position
asu_map.data.matrix()[:] = sum(interpolated_maps)/len(interpolated_maps)
asu_map.data.values_changed()
def build_next_atom_from_coords(residue, found_neighbors, template_new_atom):
# print('Building next atom {} from aligned coords of {}'.format(template_new_atom.name,
# ','.join([f[0].name for f in found_neighbors])))
bonded_to = [f[0] for f in found_neighbors]
m = residue.structure
n = len(found_neighbors)
found = set(f[0] for f in found_neighbors)
while len(found_neighbors) < 3:
for ra, ta in found_neighbors:
for tn in ta.neighbors:
rn = residue.find_atom(tn.name)
if rn and rn not in found:
found_neighbors.append((rn, tn))
found.add(rn)
if len(found_neighbors) <= n:
residue.session.logger.warning(
"Couldn't find more than two neighbor atoms. Falling back to simple geometry-based addition."
)
return build_next_atom_from_geometry(residue, *found_neighbors[0],
template_new_atom)
n = len(found_neighbors)
from chimerax.geometry import align_points
import numpy
ra_coords = numpy.array([f[0].coord for f in found_neighbors])
ta_coords = numpy.array([f[1].coord for f in found_neighbors])
bfactor = numpy.mean([f[0].bfactor for f in found_neighbors])
occupancy = numpy.mean([f[0].occupancy for f in found_neighbors])
tf, rms = align_points(ta_coords, ra_coords)
from chimerax.atomic.struct_edit import add_atom
ta = template_new_atom
a = add_atom(ta.name,
ta.element,
residue,
tf * ta.coord,
occupancy=occupancy,
bfactor=bfactor)
from chimerax.atomic.struct_edit import add_bond
for b in bonded_to:
add_bond(a, b)
def optimized_placement(polygon, vertex_degree):
lpairs = []
for l0 in polygon.edges:
l0j = joined_edge(l0)
if l0j:
lpairs.append((l0, l0j))
from chimerax.geometry import Place, align_points
if len(lpairs) == 0:
tf = Place()
elif len(lpairs) == 1:
l0, l1 = lpairs[0]
tf = edge_join_transform(l0, l1, vertex_degree)
else:
xyz0 = []
xyz1 = []
for l0, l1 in lpairs:
xyz0.extend(edge_alignment_points(l0))
xyz1.extend(reversed(edge_alignment_points(l1)))
from numpy import array
tf, rms = align_points(array(xyz0), array(xyz1))
return tf
def __init__(self, residue_groups, method, coordset0, coordset1):
# Get transform for each rigid segment
t0 = time()
calc_motion_parameters = segment_motion_methods[method]
self.motion_parameters = motion_params = []
self.motion_transforms = motion_transforms = []
from .util import segment_alignment_atoms
from chimerax.geometry import align_points
from chimerax.atomic import Atoms
for rList in residue_groups:
aatoms = Atoms(segment_alignment_atoms(rList))
raindices = aatoms.coord_indices
cList0 = coordset0[raindices]
c0 = cList0.mean(axis = 0)
cList1 = coordset1[raindices]
c1 = cList1.mean(axis = 0)
xform, rmsd = align_points(cList0, cList1)
atom_indices = rList.atoms.coord_indices
motion_transforms.append((atom_indices, xform))
axis, angle, center, shift = calc_motion_parameters(xform, c0, c1)
motion_params.append((atom_indices, axis, angle, center, shift))
t1 = time()
global stt
stt += t1-t0
def template_swap_res(res, res_type, *, preserve=False, bfactor=None):
"""change 'res' into type 'res_type'"""
fixed, buds, start, end = get_res_info(res)
if res_type == "HIS":
res_type = "HIP"
if res_type in ["A", "C", "G", "T"
] and res.name in ["DA", "DC", "DT", "DG"]:
res_type = "D" + res_type
from chimerax.atomic import TmplResidue, Atom
tmpl_res = TmplResidue.get_template(res_type, start=start, end=end)
if not tmpl_res:
raise TemplateError("No connectivity template for residue '%s'" %
res_type)
# sanity check: does the template have the bud atoms?
for bud in buds:
if tmpl_res.find_atom(bud) is None:
raise TemplateError("New residue type (%s) not compatible with"
" starting residue type (%s)" %
(res_type, res.name))
color_by_element = False
uniform_color = res.find_atom(buds[0]).color
het = res.find_atom("N") or res.find_atom("O4'")
if het:
carbon = res.find_atom("CA") or res.find_atom("C4'")
if carbon:
color_by_element = het.color != carbon.color
if color_by_element:
carbon_color = carbon.color
else:
uniform_color = het.color
bfactor = bfactor_for_res(res, bfactor)
if preserve:
if "CA" in fixed and res_type not in ['GLY', 'ALA']:
raise TemplateSwapError(
"'preserve' keyword not yet implemented for amino acids")
a1 = res.find_atom("O4'")
a2 = res.find_atom("C1'")
if not a1 or not a2:
preserve_pos = None
else:
dihed_names = {"N9": ["C4", "C8"], "N1": ["C2", "C6"]}
a3 = res.find_atom("N9") or res.find_atom("N1")
if a3:
if a2 not in a3.neighbors:
preserve_pos = None
else:
preserve_pos = a3.coord
else:
preserve_pos = None
if preserve_pos:
p1, p2, p3 = [a.coord for a in (a1, a2, a3)]
preserved_pos = False
prev_name, alt_name = dihed_names[a3.name]
a4 = res.find_atom(prev_name)
if a4 and a3 in a4.neighbors:
p4 = a4.coord
from chimerax.geometry import dihedral
preserve_dihed = dihedral(p1, p2, p3, p4)
else:
preserve_dihed = None
else:
preserve_dihed = None
# prune non-backbone atoms
for a in res.atoms:
if a.name not in fixed:
a.structure.delete_atom(a)
# add new sidechain
new_atoms = []
xf = None
from chimerax.atomic.struct_edit import add_bond
while len(buds) > 0:
bud = buds.pop()
tmpl_bud = tmpl_res.find_atom(bud)
res_bud = res.find_atom(bud)
try:
info = Atom.idatm_info_map[tmpl_bud.idatm_type]
geom = info.geometry
subs = info.substituents
except KeyError:
raise AssertionError(
"Can't determine atom type information for atom %s of residue %s"
% (bud, res))
# use .coord rather than .scene_coord: we want to set the new atom's coord,
# to which the proper xform will then be applied
for a, b in zip(tmpl_bud.neighbors, tmpl_bud.bonds):
if a.element.number == 1:
# don't add hydrogens
continue
if res.find_atom(a.name):
res_bonder = res.find_atom(a.name)
if res_bonder not in res_bud.neighbors:
add_bond(a, res_bonder)
continue
new_atom = None
num_bonded = len(res_bud.bonds)
if num_bonded >= subs:
raise AssertionError(
"Too many atoms bonded to %s of residue %s" % (bud, res))
if num_bonded == 0:
raise AssertionError(
"Atom %s of residue %s has no neighbors after pruning?!?" %
(bud, res))
# since fused ring systems may have distorted bond angles, always use dihedral placement
real1 = res_bud.neighbors[0]
kw = {}
if preserve:
if preserve_pos and not preserved_pos:
kw['pos'] = preserve_pos
preserved_pos = True
preserved_name = a.name
elif preserve_dihed is not None:
prev_name, alt_name = dihed_names[preserved_name]
if a.name == prev_name:
kw['dihed'] = preserve_dihed
elif a.name == alt_name:
kw['dihed'] = preserve_dihed + 180.0
if not kw and xf is not None:
kw['pos'] = xf * a.coord
new_atom = form_dihedral(res_bud, real1, tmpl_res, a, b, **kw)
new_atom.draw_mode = res_bud.draw_mode
new_atom.bfactor = bfactor
if color_by_element:
if new_atom.element.name == "C":
new_atom.color = carbon_color
else:
from chimerax.atomic.colors import element_color
new_atom.color = element_color(new_atom.element.number)
else:
new_atom.color = uniform_color
new_atoms.append(new_atom)
for bonded in a.neighbors:
bond_atom = res.find_atom(bonded.name)
if not bond_atom:
continue
add_bond(new_atom, bond_atom)
buds.append(new_atom.name)
# once we've placed 3 side chain atoms, we use superpositioning to
# place the remainder of the side chain, since dihedrals will
# likely distort ring closures if 'preserve' is true
if buds and not xf and len(new_atoms) >= 3:
placed_positions = []
tmpl_positions = []
for na in new_atoms:
placed_positions.append(na.coord)
tmpl_positions.append(tmpl_res.find_atom(na.name).coord)
import numpy
from chimerax.geometry import align_points
xf = align_points(numpy.array(tmpl_positions),
numpy.array(placed_positions))[0]
res.name = res_type
def get_rotamers(session,
res,
phi=None,
psi=None,
cis=False,
res_type=None,
rot_lib="Dunbrack",
log=False):
"""Takes a Residue instance and optionally phi/psi angles (if different from the Residue), residue
type (e.g. "TYR"), and/or rotamer library name. Returns a list of AtomicStructure instances (sublass of
AtomicStructure). The AtomicStructure are each a single residue (a rotamer) and are in descending
probability order. Each has an attribute "rotamer_prob" for the probability and "chis" for the
chi angles.
"""
res_type = res_type or res.name
if res_type == "ALA" or res_type == "GLY":
raise NoResidueRotamersError("No rotamers for %s" % res_type)
if not isinstance(rot_lib, RotamerLibrary):
rot_lib = session.rotamers.library(rot_lib)
# check that the residue has the n/c/ca atoms needed to position the rotamer
# and to ensure that it is an amino acid
from chimerax.atomic import Residue
match_atoms = {}
for bb_name in Residue.aa_min_backbone_names:
match_atoms[bb_name] = a = res.find_atom(bb_name)
if a is None:
raise LimitationError("%s missing from %s; needed to position CB" %
(bb_name, res))
match_atoms["CB"] = res.find_atom("CB")
if not phi and not psi:
phi, psi = res.phi, res.psi
omega = res.omega
cis = False if omega is None or abs(omega) > 90 else True
if log:
def _info(ang):
if ang is None:
return "none"
return "%.1f" % ang
if match_atoms["CA"].alt_locs:
al_info = " (alt loc %s)" % match_atoms["CA"].alt_loc
else:
al_info = ""
session.logger.info("%s%s: phi %s, psi %s %s" %
(res, al_info, _info(phi), _info(psi),
"cis" if cis else "trans"))
session.logger.status("Retrieving rotamers from %s library" %
rot_lib.display_name)
res_template_func = rot_lib.res_template_func
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
session.logger.status("Rotamers retrieved from %s library" %
rot_lib.display_name)
mapped_res_type = rot_lib.res_name_mapping.get(res_type, res_type)
template = rot_lib.res_template_func(mapped_res_type)
tmpl_N = template.find_atom("N")
tmpl_CA = template.find_atom("CA")
tmpl_C = template.find_atom("C")
tmpl_CB = template.find_atom("CB")
if match_atoms['CB']:
res_match_atoms, tmpl_match_atoms = [
match_atoms[x] for x in ("C", "CA", "CB")
], [tmpl_C, tmpl_CA, tmpl_CB]
else:
res_match_atoms, tmpl_match_atoms = [
match_atoms[x] for x in ("N", "CA", "C")
], [tmpl_N, tmpl_CA, tmpl_C]
from chimerax.geometry import align_points
from numpy import array
xform, rmsd = align_points(array([fa.coord for fa in tmpl_match_atoms]),
array([ta.coord for ta in res_match_atoms]))
n_coord = xform * tmpl_N.coord
ca_coord = xform * tmpl_CA.coord
cb_coord = xform * tmpl_CB.coord
info = Residue.chi_info[mapped_res_type]
bond_cache = {}
angle_cache = {}
from chimerax.atomic.struct_edit import add_atom, add_dihedral_atom, add_bond
structs = []
middles = {}
ends = {}
for i, rp in enumerate(params):
s = AtomicStructure(session, name="rotamer %d" % (i + 1))
structs.append(s)
r = s.new_residue(mapped_res_type, 'A', 1)
registerer = "swap_res get_rotamers"
AtomicStructure.register_attr(session,
"rotamer_prob",
registerer,
attr_type=float)
s.rotamer_prob = rp.p
AtomicStructure.register_attr(session, "chis", registerer)
s.chis = rp.chis
rot_N = add_atom("N", tmpl_N.element, r, n_coord)
rot_CA = add_atom("CA", tmpl_CA.element, r, ca_coord, bonded_to=rot_N)
rot_CB = add_atom("CB", tmpl_CB.element, r, cb_coord, bonded_to=rot_CA)
todo = []
for j, chi in enumerate(rp.chis):
n3, n2, n1, new = info[j]
b_len, angle = _len_angle(new, n1, n2, template, bond_cache,
angle_cache)
n3 = r.find_atom(n3)
n2 = r.find_atom(n2)
n1 = r.find_atom(n1)
new = template.find_atom(new)
a = add_dihedral_atom(new.name,
new.element,
n1,
n2,
n3,
b_len,
angle,
chi,
bonded=True)
todo.append(a)
middles[n1] = [a, n1, n2]
ends[a] = [a, n1, n2]
# if there are any heavy non-backbone atoms bonded to template
# N and they haven't been added by the above (which is the
# case for Richardson proline parameters) place them now
for tnnb in tmpl_N.neighbors:
if r.find_atom(tnnb.name) or tnnb.element.number == 1:
continue
tnnb_coord = xform * tnnb.coord
add_atom(tnnb.name, tnnb.element, r, tnnb_coord, bonded_to=rot_N)
# fill out bonds and remaining heavy atoms
from chimerax.geometry import distance, align_points
done = set([rot_N, rot_CA])
while todo:
a = todo.pop(0)
if a in done:
continue
tmpl_A = template.find_atom(a.name)
for bonded, bond in zip(tmpl_A.neighbors, tmpl_A.bonds):
if bonded.element.number == 1:
continue
rbonded = r.find_atom(bonded.name)
if rbonded is None:
# use middles if possible...
try:
p1, p2, p3 = middles[a]
conn = p3
except KeyError:
p1, p2, p3 = ends[a]
conn = p2
t1 = template.find_atom(p1.name)
t2 = template.find_atom(p2.name)
t3 = template.find_atom(p3.name)
xform = align_points(
array([t.coord for t in [t1, t2, t3]]),
array([p.coord for p in [p1, p2, p3]]))[0]
pos = xform * template.find_atom(bonded.name).coord
rbonded = add_atom(bonded.name,
bonded.element,
r,
pos,
bonded_to=a)
middles[a] = [rbonded, a, conn]
ends[rbonded] = [rbonded, a, conn]
if a not in rbonded.neighbors:
add_bond(a, rbonded)
if rbonded not in done:
todo.append(rbonded)
done.add(a)
return structs
def add_amino_acid_residue(model,
resname,
prev_res=None,
next_res=None,
chain_id=None,
number=None,
center=None,
insertion_code=' ',
add_b_factor=0,
occupancy=1,
phi=-135,
psi=135):
session = model.session
if (not chain_id or not number or center is None) and (not prev_res
and not next_res):
raise TypeError('If no anchor residues are specified, chain ID, '
'number and center must be provided!')
if prev_res and next_res:
raise TypeError('Cannot specify both previous and next residues!')
other_atom = None
insertion_point = None
import numpy
if prev_res:
ref_res = prev_res
b_factor = prev_res.atoms[numpy.in1d(
prev_res.atoms.names,
('N', 'CA', 'C', 'O', 'CB'))].bfactors.mean() + add_b_factor
pri = model.residues.index(prev_res)
if pri > 0 and pri < len(model.residues) - 1:
insertion_point = model.residues[pri + 1]
catom = prev_res.find_atom('C')
for n in catom.neighbors:
if n.residue != prev_res:
raise TypeError(
'This residue already has another bonded to its '
'C terminus!')
if chain_id is not None:
session.logger.warning(
'AddAA: chain_id argument is ignored when adding to an existing residue.'
)
chain_id = prev_res.chain_id
oxt = prev_res.find_atom('OXT')
if oxt is not None:
oxt.delete()
elif next_res:
ref_res = next_res
b_factor = next_res.atoms[numpy.in1d(
next_res.atoms.names,
('N', 'CA', 'C', 'O', 'CB'))].bfactors.mean() + add_b_factor
insertion_point = next_res
natom = next_res.find_atom('N')
for n in natom.neighbors:
if n.residue != next_res:
raise TypeError(
'This residue already has another bonded to its '
'N terminus!')
if chain_id is not None:
session.logger.warning(
'AddAA: chain_id argument is ignored when adding to an existing residue.'
)
chain_id = next_res.chain_id
for hname in ('H2', 'H3'):
h = next_res.find_atom(hname)
if h is not None:
h.delete()
h = next_res.find_atom('H1')
if h is not None:
h.name = 'H'
if next_res.name == 'PRO':
h = next_res.find_atom('H')
if h:
h.delete()
if number is None:
if prev_res:
number = prev_res.number + 1
elif next_res:
number = next_res.number - 1
from chimerax import mmcif
tmpl = mmcif.find_template_residue(session, resname)
from .place_ligand import new_residue_from_template
import numpy
# delete extraneous atoms
r = new_residue_from_template(model,
tmpl,
chain_id, [0, 0, 0],
number,
insert_code=insertion_code,
b_factor=b_factor,
precedes=insertion_point)
r.atoms[numpy.in1d(r.atoms.names,
['OXT', 'HXT', 'H2', 'H1', 'HN1', 'HN2'])].delete()
# Translate and rotate residue to (roughly) match the desired position
if not next_res and not prev_res:
r.atoms.coords += numpy.array(center) - r.atoms.coords.mean(axis=0)
b_factor = max(add_b_factor, 5)
else:
from chimerax.geometry import align_points
from chimerax.atomic.struct_edit import add_bond
if prev_res:
correct_o_position(prev_res, psi)
add_bond(r.find_atom('N'), prev_res.find_atom('C'))
n_pos = _find_next_N_position(prev_res)
ca_pos = _find_next_CA_position(n_pos, prev_res)
c_pos = _find_next_C_position(ca_pos, n_pos, prev_res, phi)
target_coords = numpy.array([n_pos, ca_pos, c_pos])
align_coords = numpy.array(
[r.find_atom(a).coord for a in ['N', 'CA', 'C']])
elif next_res:
add_bond(r.find_atom('C'), next_res.find_atom('N'))
c_pos = _find_prev_C_position(next_res, psi)
ca_pos = _find_prev_CA_position(c_pos, next_res)
#o_pos = _find_prev_O_position(c_pos, next_res)
n_pos = _find_prev_N_position(c_pos, ca_pos, next_res, psi)
target_coords = numpy.array([c_pos, ca_pos, n_pos])
align_coords = numpy.array(
[r.find_atom(a).coord for a in ['C', 'CA', 'N']])
tf = align_points(align_coords, target_coords)[0]
r.atoms.coords = tf * r.atoms.coords
correct_o_position(r, psi)
if r.name in ('GLU', 'ASP'):
fix_amino_acid_protonation_state(r)
if r.name == 'PRO':
r.atoms[r.atoms.names == 'H'].delete()
r.atoms.bfactors = b_factor
r.atoms.occupancies = occupancy
from . import copy_atom_style_from
copy_atom_style_from(session, r.atoms, ref_res)
model.atoms.selecteds = False
r.atoms.selecteds = True
return r
def _new_camera_position(self, residue, block_spotlight=True):
session = self.session
r = residue
from chimerax.atomic import Residue, Atoms
pt = residue.polymer_type
if pt == Residue.PT_NONE:
# No preferred orientation
ref_coords = None
target_coords = r.atoms.coords
centroid = target_coords.mean(axis=0)
elif pt == Residue.PT_AMINO:
ref_coords = self.peptide_ref_coords
try:
target_coords = Atoms(
[r.find_atom(name) for name in ('N', 'CA', 'C')]).coords
centroid = target_coords[1]
except ValueError:
# Either a key atom is missing, or this is a special residue
# e.g. NH2
ref_coords = None
target_coords = r.atoms.coords
centroid = target_coords.mean(axis=0)
elif pt == Residue.PT_NUCLEIC:
ref_coords = self.nucleic_ref_coords
try:
target_coords = Atoms([
r.find_atom(name) for name in ("C2'", "C1'", "O4'")
]).coords
centroid = target_coords[1]
except ValueError:
ref_coords = None
target_coords = r.atoms.coords
centroid = target_coords.mean(axis=0)
c = session.main_view.camera
cp = c.position
old_cofr = session.main_view.center_of_rotation
if ref_coords is not None:
from chimerax.geometry import align_points, Place
p, rms = align_points(ref_coords, target_coords)
else:
from chimerax.geometry import Place
p = Place(origin=centroid)
tc = self._camera_ref_pos(self.view_distance)
np = p * tc
new_cofr = centroid
if c.name == 'orthographic':
fw = c.field_width
new_fw = self._view_distance * 2
def interpolate_camera(session,
f,
cp=cp,
np=np,
oc=old_cofr,
nc=new_cofr,
fw=fw,
nfw=new_fw,
vr=self._view_distance,
center=np.inverse() * centroid,
frames=self._interpolate_frames):
frac = (f + 1) / frames
v = session.main_view
c = v.camera
p = np if f + 1 == frames else cp.interpolate(
np, center, frac=frac)
cofr = oc + frac * (nc - oc)
c.position = p
vd = c.view_direction()
cp = v.clip_planes
ncm, fcm = _get_clip_distances(session)
cp.set_clip_position('near', cofr - ncm * vr * vd, v)
cp.set_clip_position('far', cofr + fcm * vr * vd, v)
if c.name == 'orthographic':
c.field_width = fw + frac * (nfw - fw)
from chimerax.geometry import distance
if distance(new_cofr, old_cofr) < self._view_distance:
if block_spotlight:
self._block_clipper_spotlights()
from .delayed_reaction import call_after_n_events
call_after_n_events(self.session.triggers, 'frame drawn',
self._interpolate_frames,
self._release_clipper_spotlights, [])
from chimerax.core.commands import motion
motion.CallForNFrames(interpolate_camera, self._interpolate_frames,
session)
else:
interpolate_camera(session, 0, frames=1)
