def test_upsion_tau_acceptor(donor, donor_hyds, acceptor, r2, upsilon_low, upsilon_high,
theta, tau, tau_sym):
dc = donor._hb_coord
ac = acceptor._hb_coord
d2 = distance_squared(dc, ac)
if d2 > r2:
if hbond.verbose:
print("dist criteria failed (%g > %g)" % (sqrt(d2), sqrt(r2)))
return False
upsilon_high = 0 - upsilon_high
heavys = [a for a in donor.neighbors if a.element.number > 1]
if len(heavys) != 1:
raise AtomTypeError("upsilon tau donor (%s) not bonded to"
" exactly one heavy atom" % donor)
ang = angle(heavys[0]._hb_coord, dc, ac)
if ang < upsilon_low or ang > upsilon_high:
if hbond.verbose:
print("upsilon criteria failed (%g < %g or %g > %g)"
% (ang, upsilon_low, ang, upsilon_high))
return False
if hbond.verbose:
print("upsilon criteria OK (%g < %g < %g)" % (upsilon_low, ang, upsilon_high))
dp = dc
ap = ac
if not test_theta(dp, donor_hyds, ap, theta):
return False
return test_tau(tau, tau_sym, donor, dp, ap)
def build_next_atom_from_geometry(residue, residue_anchor, template_anchor,
template_new_atom):
from chimerax.atomic import struct_edit
from chimerax.geometry import distance, angle, dihedral
r = residue
m = r.structure
tnext = template_new_atom
if tnext is None:
raise TypeError('Template does not contain an atom with that name!')
tstub = template_anchor
rstub = residue_anchor
existing_rstub_neighbors = rstub.neighbors
n1 = rstub
n2 = n3 = None
t_direct_neighbors = []
r_direct_neighbors = []
for a2 in tstub.neighbors:
if a2.element.name != 'H':
n2 = r.find_atom(a2.name)
if n2:
t_direct_neighbors.append(a2)
r_direct_neighbors.append(n2)
if len(t_direct_neighbors) > 1:
a2, a3 = t_direct_neighbors[:2]
n2, n3 = r_direct_neighbors[:2]
else:
a2 = t_direct_neighbors[0]
n2 = r_direct_neighbors[0]
if not n2:
raise TypeError(
'No n2 found - Not enough connected atoms to form a dihedral!')
if not n3:
for a3 in a2.neighbors:
if a3 not in (a2, tstub) and a3.element.name != 'H':
n3 = r.find_atom(a3.name)
if n3:
break
if not n3:
raise TypeError(
'No n3 found - Not enough connected atoms to form a dihedral!')
# print('Building next atom {} from geometry of {}'.format(template_new_atom.name,
# ','.join([n.name for n in (n1, n2, n3)])))
dist = distance(tnext.coord, tstub.coord)
ang = angle(tnext.coord, tstub.coord, a2.coord)
dihe = dihedral(tnext.coord, tstub.coord, a2.coord, a3.coord)
# print('{}: {} {} {}'.format(next_atom_name, dist, ang, dihe))
a = struct_edit.add_dihedral_atom(tnext.name, tnext.element, n1, n2, n3,
dist, ang, dihe)
a.occupancy = rstub.occupancy
a.bfactor = rstub.bfactor
return a
def interpolate_dihedral(i0, i1, i2, i3, coords0, coords1, f, coord_set):
"""
Computer coordinate of atom a0 by interpolating dihedral angle
defined by atoms (a0, a1, a2, a3).
"""
t0 = time()
from chimerax.geometry import distance, angle, dihedral, dihedral_point
c00 = coords0[i0]
c01 = coords0[i1]
c02 = coords0[i2]
c03 = coords0[i3]
length0 = distance(c00, c01)
angle0 = angle(c00, c01, c02)
dihed0 = dihedral(c00, c01, c02, c03)
c10 = coords1[i0]
c11 = coords1[i1]
c12 = coords1[i2]
c13 = coords1[i3]
length1 = distance(c10, c11)
angle1 = angle(c10, c11, c12)
dihed1 = dihedral(c10, c11, c12, c13)
length = length0 + (length1 - length0) * f
angle = angle0 + (angle1 - angle0) * f
ddihed = dihed1 - dihed0
if ddihed > 180:
ddihed -= 360
elif ddihed < -180:
ddihed += 360
dihed = dihed0 + ddihed * f
c1 = coord_set[i1, :]
c2 = coord_set[i2, :]
c3 = coord_set[i3, :]
t2 = time()
c0 = dihedral_point(c1, c2, c3, length, angle, dihed)
t3 = time()
coord_set[i0:] = c0
t1 = time()
global iit, dpt
iit += t1 - t0
dpt += t3 - t2
def metal_clash(metal_pos, pos, parent_pos, parent_atom, parent_type_info):
if parent_atom.element.valence < 5 and parent_type_info.geometry != linear:
# non-sp1 carbons, et al, can't coordinate metals
return False
from chimerax.geometry import distance, angle
if distance(metal_pos, pos) > 2.7:
# "_metal_dist" is 2.7 + putative S-H bond length of 1.25;
# see nitrogen stripping in CYS 77 and 120 in 3r24
return False
# 135.0 is not strict enough (see :1004.a in 1nyr)
if angle(parent_pos, pos, metal_pos) > 120.0:
return True
return False
def _len_angle(new, n1, n2, template, bond_cache, angle_cache):
from chimerax.geometry import distance, angle
bond_key = (n1, new)
angle_key = (n2, n1, new)
try:
bl = bond_cache[bond_key]
ang = angle_cache[angle_key]
except KeyError:
n2pos = template.find_atom(n2).coord
n1pos = template.find_atom(n1).coord
newpos = template.find_atom(new).coord
bond_cache[bond_key] = bl = distance(newpos, n1pos)
angle_cache[angle_key] = ang = angle(newpos, n1pos, n2pos)
return bl, ang
def test_theta(dp, donor_hyds, ap, theta):
if len(donor_hyds) == 0:
if hbond.verbose:
print("no hydrogens for theta test; default accept")
return True
for hyd_pos in donor_hyds:
ang = angle(ap, hyd_pos, dp)
if ang >= theta:
if hbond.verbose:
print("theta okay (%g >= %g)" % (ang, theta))
return True
if hbond.verbose:
print("theta failure (%g < %g)" % (ang, theta))
return False
def _extend_ends(self, centers, frac):
n = len(centers)
if self.curved:
tc = self.center # Torus center
r0,r1 = centers[0] - tc, centers[-1] - tc # radial vectors from center of torus.
from chimerax.geometry import angle, rotation
a = frac * angle(r0,r1) / (n-1)
c0 = tc + rotation(self.axis, -a) * r0
c1 = tc + rotation(self.axis, a) * r1
else:
e = frac/(n-1) * (centers[-1] - centers[0])
c0 = centers[0] - e
c1 = centers[-1] + e
n = len(centers)
from numpy import concatenate
ecenters = concatenate((c0.reshape(1,3), centers, c1.reshape(1,3)))
return ecenters
def test_phi(dp, ap, bp, phi_plane, phi):
if phi_plane:
normal = normalize_vector(
cross_product(phi_plane[1] - phi_plane[0],
phi_plane[2] - phi_plane[1]))
D = dot(normal, phi_plane[1])
bproj = project(bp, normal, D)
aproj = project(ap, normal, D)
dproj = project(dp, normal, D)
ang = angle(bproj, aproj, dproj)
if ang < phi:
if hbond.verbose:
print("phi criteria failed (%g < %g)" % (ang, phi))
return False
if hbond.verbose:
print("phi criteria OK (%g >= %g)" % (ang, phi))
else:
if hbond.verbose:
print("phi criteria irrelevant")
return True
def form_dihedral(res_bud, real1, tmpl_res, a, b, pos=None, dihed=None):
from chimerax.atomic.struct_edit import add_atom, add_dihedral_atom
res = res_bud.residue
if pos:
return add_atom(a.name, a.element, res, pos, info_from=real1)
# use neighbors of res_bud rather than real1 to avoid clashes with
# other res_bud neighbors in case bond to real1 neighbor freely rotates
inres = [
nb for nb in res_bud.neighbors if nb != real1 and nb.residue == res
]
if len(inres) < 1:
inres = [x for x in res.atoms if x not in [res_bud, real1]]
if real1.residue != res or len(inres) < 1:
raise AssertionError(
"Can't form in-residue dihedral for %s of residue %s" %
(res_bud, res))
if dihed:
real1 = res.find_atom("C1'")
real2 = res.find_atom("O4'")
else:
real2 = inres[0]
xyz0, xyz1, xyz2 = [
tmpl_res.find_atom(a.name).coord for a in (res_bud, real1, real2)
]
xyz = a.coord
blen = b.length
from chimerax.geometry import angle, dihedral
ang = angle(xyz, xyz0, xyz1)
if dihed is None:
dihed = dihedral(xyz, xyz0, xyz1, xyz2)
return add_dihedral_atom(a.name,
a.element,
res_bud,
real1,
real2,
blen,
ang,
dihed,
info_from=real1)
def don_generic(donor, donor_hyds, acceptor, sp2_O_rp2, sp3_O_rp2, sp3_N_rp2,
sp2_O_r2, sp3_O_r2, sp3_N_r2, gen_rp2, gen_r2, min_hyd_angle, min_bonded_angle):
if hbond.verbose:
print("don_generic")
dc = donor._hb_coord
ac = acceptor._hb_coord
acc_type = acceptor.idatm_type
if acc_type not in type_info:
return False
geom = type_info[acc_type].geometry
element = acceptor.element.name
if element == 'O' and geom == planar:
if hbond.verbose:
print("planar O")
r2 = sp2_O_r2
rp2 = sp2_O_rp2
elif element == 'O' and geom == tetrahedral or element == 'N' and geom == planar:
if hbond.verbose:
print("planar N or tet O")
r2 = sp3_O_r2
rp2 = sp3_O_rp2
elif element == 'N' and geom == tetrahedral:
if hbond.verbose:
print("tet N")
r2 = sp3_N_r2
rp2 = sp3_N_rp2
else:
if hbond.verbose:
print("generic acceptor")
if acceptor.element.name == "S":
r2 = sulphur_compensate(gen_r2)
min_bonded_angle = min_bonded_angle - 9
r2 = gen_r2
rp2 = gen_rp2
ap = acceptor._hb_coord
dp = donor._hb_coord
if len(donor_hyds) == 0:
d2 = distance_squared(dc, ac)
if d2 > r2:
if hbond.verbose:
print("dist criteria failed (%g > %g)" % (sqrt(d2), sqrt(r2)))
return False
else:
for hyd_pos in donor_hyds:
if distance_squared(hyd_pos, ap) < rp2:
break
else:
if hbond.verbose:
print("hyd dist criteria failed (all >= %g)" % (sqrt(rp2)))
return False
if hbond.verbose:
print("dist criteria OK")
for bonded in donor.neighbors:
if bonded.element.number <= 1:
continue
bp = bonded._hb_coord
ang = angle(bp, dp, ap)
if ang < min_bonded_angle:
if hbond.verbose:
print("bonded angle too sharp (%g < %g)" % (ang, min_bonded_angle))
return False
if len(donor_hyds) == 0:
if hbond.verbose:
print("No specific hydrogen positions; default accept")
return True
for hyd_pos in donor_hyds:
ang = angle(dp, hyd_pos, ap)
if ang >= min_hyd_angle:
if hbond.verbose:
print("hydrogen angle okay (%g >= %g)" % (ang, min_hyd_angle))
return True
if hbond.verbose:
print("hydrogen angle(s) too sharp (< %g)" % min_hyd_angle)
return False
def don_theta_tau(donor, donor_hyds, acceptor, sp2_O_rp2, sp2_O_theta, sp3_O_rp2, sp3_O_theta,
sp3_O_phi, sp3_N_rp2, sp3_N_theta, sp3_N_upsilon, gen_rp2, gen_theta, is_water=False):
# 'is_water' only for hydrogenless water
if hbond.verbose:
print("don_theta_tau")
if len(donor_hyds) == 0 and not is_water:
if hbond.verbose:
print("No hydrogens; default failure")
return False
ap = acceptor._hb_coord
dp = donor._hb_coord
acc_type = acceptor.idatm_type
if acc_type not in type_info:
if hbond.verbose:
print("Unknown acceptor type failure")
return False
geom = type_info[acc_type].geometry
element = acceptor.element.name
if element == 'O' and geom == planar:
if hbond.verbose:
print("planar O")
for hyd_pos in donor_hyds:
if distance_squared(hyd_pos, ap) <= sp2_O_rp2:
break
else:
if not is_water:
if hbond.verbose:
print("dist criteria failed (all > %g)"% sqrt(sp2_O_rp2))
return False
theta = sp2_O_theta
elif element == 'O' and geom == tetrahedral or element == 'N' and geom == planar:
if hbond.verbose:
print("planar N or tet O")
for hyd_pos in donor_hyds:
if distance_squared(hyd_pos, ap) <= sp3_O_rp2:
break
else:
if not is_water:
if hbond.verbose:
print("dist criteria failed (all > %g)" % sqrt(sp3_O_rp2))
return False
theta = sp3_O_theta
# only test phi for acceptors with two bonded atoms
if acceptor.num_bonds == 2:
if hbond.verbose:
print("testing donor phi")
bonded = acceptor.neighbors
phi_plane, base_pos = get_phi_plane_params(acceptor, bonded[0], bonded[1])
if not test_phi(donor._hb_coord, ap, base_pos, phi_plane, sp3_O_phi):
return False
elif element == 'N' and geom == tetrahedral:
if hbond.verbose:
print("tet N")
for hyd_pos in donor_hyds:
if distance_squared(hyd_pos, ap) <= sp3_N_rp2:
break
else:
if not is_water:
if hbond.verbose:
print("dist criteria failed (all > %g)" % sqrt(sp3_N_rp2))
return False
theta = sp3_N_theta
# test upsilon against lone pair directions
bonded_pos = []
for bonded in acceptor.neighbors:
bonded_pos.append(bonded._hb_coord)
lp_pos = bond_positions(ap, geom, 1.0, bonded_pos)
if len(lp_pos) > 0:
# fixed lone pair positions
for lp in bond_positions(ap, geom, 1.0, bonded_pos):
# invert position so that we are measuring angles correctly
ang = angle(dp, ap, ap - (lp - ap))
if ang > sp3_N_upsilon:
if hbond.verbose:
print("acceptor upsilon okay (%g > %g)" % (ang, sp3_N_upsilon))
break
else:
if hbond.verbose:
print("all acceptor upsilons failed (< %g)" % sp3_N_upsilon)
return False
# else: indefinite lone pair positions; default okay
else:
if hbond.verbose:
print("generic acceptor")
if acceptor.element.name == "S":
gen_rp2 = sulphur_compensate(gen_rp2)
for hyd_pos in donor_hyds:
if distance_squared(hyd_pos, ap) <= gen_rp2:
break
else:
if hbond.verbose:
print("dist criteria failed (all > %g)" % sqrt(gen_rp2))
return False
theta = gen_theta
if hbond.verbose:
print("dist criteria OK")
return test_theta(dp, donor_hyds, ap, theta)
def don_upsilon_tau(donor, donor_hyds, acceptor,
sp2_O_r2, sp2_O_upsilon_low, sp2_O_upsilon_high, sp2_O_theta, sp2_O_tau,
sp3_O_r2, sp3_O_upsilon_low, sp3_O_upsilon_high, sp3_O_theta, sp3_O_tau, sp3_O_phi,
sp3_N_r2, sp3_N_upsilon_low, sp3_N_upsilon_high, sp3_N_theta, sp3_N_tau, sp3_N_upsilon_N,
gen_r2, gen_upsilon_low, gen_upsilon_high, gen_theta, tau_sym):
if hbond.verbose:
print("don_upsilon_tau")
acc_type = acceptor.idatm_type
if acc_type not in type_info:
return False
geom = type_info[acc_type].geometry
element = acceptor.element.name
if element == 'O' and geom == planar:
if hbond.verbose:
print("planar O")
return test_upsion_tau_acceptor(donor, donor_hyds, acceptor, sp2_O_r2,
sp2_O_upsilon_low, sp2_O_upsilon_high, sp2_O_theta, sp2_O_tau, tau_sym)
elif element == 'O' and geom == tetrahedral or element == 'N' and geom == planar:
if hbond.verbose:
print("planar N or tet O")
return test_upsion_tau_acceptor(donor, donor_hyds, acceptor, sp3_O_r2,
sp3_O_upsilon_low, sp3_O_upsilon_high, sp3_O_theta, sp3_O_tau, tau_sym)
elif element == 'N' and geom == tetrahedral:
if hbond.verbose:
print("tet N")
# test upsilon at the N
# see if lone pairs point at the donor
bonded_pos = []
for bonded in acceptor.neighbors:
bonded_pos.append(bonded._hb_coord)
if len(bonded_pos) > 1:
ap = acceptor._hb_coord
dp = donor._hb_coord
lone_pairs = bond_positions(ap, tetrahedral, 1.0, bonded_pos)
for lp in lone_pairs:
up_pos = ap - (lp - ap)
ang = angle(up_pos, ap, dp)
if ang >= sp3_N_upsilon_N:
if hbond.verbose:
print("upsilon(N) okay (%g >= %g)" % (ang, sp3_N_upsilon_N))
break
else:
if hbond.verbose:
print("all upsilon(N) failed (< %g)" % sp3_N_upsilon_N)
return False
elif hbond.verbose:
print("lone pair positions indeterminate at N; upsilon(N) default okay")
return test_upsion_tau_acceptor(donor, donor_hyds, acceptor, sp3_N_r2,
sp3_N_upsilon_low, sp3_N_upsilon_high, sp3_N_theta, sp3_N_tau, tau_sym)
else:
if hbond.verbose:
print("generic acceptor")
if acceptor.element.name == "S":
gen_r2 = sulphur_compensate(gen_r2)
return test_upsion_tau_acceptor(donor, donor_hyds, acceptor,
gen_r2, gen_upsilon_low, gen_upsilon_high, gen_theta, None, None)
if hbond.verbose:
print("failed criteria")
return False
def test_tau(tau, tau_sym, don_acc, dap, op):
if tau is None:
if hbond.verbose:
print("tau test irrelevant")
return True
# sulfonamides and phosphonamides can have bonded NH2 groups that are planar enough
# to be declared Npl, so use the hydrogen positions to determine planarity if possible
if tau_sym == 4:
bonded_pos = hyd_positions(don_acc)
else:
# since we expect tetrahedral hydrogens to be oppositely aligned from the attached
# tetrahedral center, we can't use their positions for tau testing
bonded_pos = []
heavys = [a for a in don_acc.neighbors if a.element.number > 1]
if 2 * len(bonded_pos) != tau_sym:
bonded_pos = hyd_positions(heavys[0], include_lone_pairs=True)
for b in heavys[0].neighbors:
if b == don_acc or b.element.number < 2:
continue
bonded_pos.append(b._hb_coord)
if not bonded_pos:
if hbond.verbose:
print("tau indeterminate; default okay")
return True
if 2 * len(bonded_pos) != tau_sym:
raise AtomTypeError(
"Unexpected tau symmetry (%d, should be %d) for donor/acceptor %s"
% (2 * len(bonded_pos), tau_sym, don_acc))
normal = normalize_vector(heavys[0]._hb_coord - dap)
if tau < 0.0:
test = lambda ang, t=tau: ang <= 0.0 - t
else:
test = lambda ang, t=tau: ang >= t
proj_other_pos = project(op, normal, 0.0)
proj_da_pos = project(dap, normal, 0.0)
for bpos in bonded_pos:
proj_bpos = project(bpos, normal, 0.0)
ang = angle(proj_other_pos, proj_da_pos, proj_bpos)
if test(ang):
if tau < 0.0:
if hbond.verbose:
print("tau okay (%g < %g)" % (ang, -tau))
return True
else:
if tau > 0.0:
if hbond.verbose:
print("tau too small (%g < %g)" % (ang, tau))
return False
if tau < 0.0:
if hbond.verbose:
print("all taus too big (> %g)" % -tau)
return False
if hbond.verbose:
print("all taus acceptable (> %g)" % tau)
return True
def find_hbonds(session,
structures,
*,
inter_model=True,
intra_model=True,
donors=None,
acceptors=None,
dist_slop=0.0,
angle_slop=0.0,
inter_submodel=False,
cache_da=False,
status=True):
"""Hydrogen bond detection based on criteria in "Three-dimensional
hydrogen-bond geometry and probability information from a
crystal survey", J. Computer-Aided Molecular Design, 10 (1996),
607-622
If donors and/or acceptors are specified (as :py:class:`~chimerax.atomic.Atoms` collections
or anything an Atoms collection can be constructued from), then H-bond donors/acceptors
are restricted to being from those atoms.
Dist/angle slop are the amount that distances/angles are allowed to exceed
the values given in the above reference and still be considered hydrogen bonds.
'cache_da' allows donors/acceptors in molecules to be cached if it is anticipated that
the same structures will be examined for H-bonds repeatedly (e.g. a dynamics trajectory).
If 'per_coordset' is True and 'structures' contains a single structure with multiple coordinate
sets, then hydrogen bonds will be computed for each coordset.
If 'status' is True, progress will be logged to the status line.
Returns a list of donor/acceptor pairs, unless the conditions for 'per_coordset' are
satisfied, in which case a list of such lists will be returned, one per coordset.
"""
# hack to speed up coordinate lookup...
from chimerax.atomic import Atoms, Atom
if len(structures) == 1 or not inter_model or (len(
set([
m if m.id is None else
(m.id[0] if len(m.id) == 1 else m.id[:-1]) for m in structures
])) == 1 and not inter_submodel):
Atom._hb_coord = Atom.coord
else:
Atom._hb_coord = Atom.scene_coord
try:
if donors and not isinstance(donors, Atoms):
limited_donors = Atoms(donors)
else:
limited_donors = donors
if acceptors and not isinstance(acceptors, Atoms):
limited_acceptors = Atoms(acceptors)
else:
limited_acceptors = acceptors
global _d_cache, _a_cache, _prev_limited
if cache_da:
if limited_donors:
dIDs = [id(d) for d in limited_donors]
dIDs.sort()
else:
dIDs = None
if limited_acceptors:
aIDs = [id(a) for a in limited_acceptors]
aIDs.sort()
else:
aIDs = None
key = (dIDs, aIDs)
if _prev_limited and _prev_limited != key:
flush_cache()
_prev_limited = key
from weakref import WeakKeyDictionary
if _d_cache is None:
_d_cache = WeakKeyDictionary()
_a_cache = WeakKeyDictionary()
else:
flush_cache()
global donor_params, acceptor_params
global processed_donor_params, processed_acceptor_params
global _compute_cache
global verbose
global _problem
_problem = None
global _truncated
_truncated = set()
bad_connectivities = 0
# Used (as necessary) to cache expensive calculations (by other functions also)
_compute_cache = {}
process_key = (dist_slop, angle_slop)
if process_key not in processed_acceptor_params:
# copy.deepcopy() refuses to copy functions (even as
# references), so do this instead...
a_params = []
for p in acceptor_params:
a_params.append(copy.copy(p))
for i in range(len(a_params)):
a_params[i][3] = _process_arg_tuple(a_params[i][3], dist_slop,
angle_slop)
processed_acceptor_params[process_key] = a_params
else:
a_params = processed_acceptor_params[process_key]
# compute some info for generic acceptors/donors
generic_acc_info = {}
# oxygens...
generic_O_acc_args = _process_arg_tuple([3.53, 90], dist_slop,
angle_slop)
generic_acc_info['misc_O'] = (acc_generic, generic_O_acc_args)
# dictionary based on bonded atom's geometry...
generic_acc_info['O2-'] = {
single: (acc_generic, generic_O_acc_args),
linear: (acc_generic, generic_O_acc_args),
planar: (acc_phi_psi,
_process_arg_tuple([3.53, 90, 130], dist_slop,
angle_slop)),
tetrahedral: (acc_generic, generic_O_acc_args)
}
generic_acc_info['O3-'] = generic_acc_info['O2-']
generic_acc_info['O2'] = {
single: (acc_generic, generic_O_acc_args),
linear: (acc_generic, generic_O_acc_args),
planar: (acc_phi_psi,
_process_arg_tuple([3.30, 110, 130], dist_slop,
angle_slop)),
tetrahedral: (acc_theta_tau,
_process_arg_tuple([3.03, 100, -180, 145], dist_slop,
angle_slop))
}
# list based on number of known bonded atoms...
generic_acc_info['O3'] = [(acc_generic, generic_O_acc_args),
(acc_theta_tau,
_process_arg_tuple([3.17, 100, -161, 145],
dist_slop, angle_slop)),
(acc_phi_psi,
_process_arg_tuple([3.42, 120, 135],
dist_slop, angle_slop))]
# nitrogens...
generic_N_acc_args = _process_arg_tuple([3.42, 90], dist_slop,
angle_slop)
generic_acc_info['misc_N'] = (acc_generic, generic_N_acc_args)
generic_acc_info['N2'] = (acc_phi_psi,
_process_arg_tuple([3.42, 140, 135],
dist_slop, angle_slop))
# tuple based on number of bonded heavy atoms...
generic_N3_mult_heavy_acc_args = _process_arg_tuple(
[3.30, 153, -180, 145], dist_slop, angle_slop)
generic_acc_info['N3'] = (
(acc_generic, generic_N_acc_args),
# only one example to draw from; weaken by .1A, 5 degrees
(acc_theta_tau,
_process_arg_tuple([3.13, 98, -180, 150], dist_slop, angle_slop)),
(acc_theta_tau, generic_N3_mult_heavy_acc_args),
(acc_theta_tau, generic_N3_mult_heavy_acc_args))
# one example only; weaken by .1A, 5 degrees
generic_acc_info['N1'] = (acc_theta_tau,
_process_arg_tuple([3.40, 136, -180, 145],
dist_slop, angle_slop))
# sulfurs...
# one example only; weaken by .1A, 5 degrees
generic_acc_info['S2'] = (acc_phi_psi,
_process_arg_tuple([3.83, 85, 140],
dist_slop, angle_slop))
generic_acc_info['Sar'] = generic_acc_info['S3-'] = (
acc_generic, _process_arg_tuple([3.83, 85], dist_slop, angle_slop))
# now the donors...
# planar nitrogens
gen_don_Npl_1h_params = (don_theta_tau,
_process_arg_tuple([
2.23, 136, 2.23, 141, 140, 2.46, 136, 140
], dist_slop, angle_slop))
gen_don_Npl_2h_params = (don_upsilon_tau,
_process_arg_tuple([
3.30, 90, -153, 135, -45, 3.30, 90, -146,
140, -37.5, 130, 3.40, 108, -166, 125,
-35, 140
], dist_slop, angle_slop))
gen_don_O_dists = [2.41, 2.28, 2.28, 3.27, 3.14, 3.14]
gen_don_O_params = (don_generic,
_process_arg_tuple(gen_don_O_dists, dist_slop,
angle_slop))
gen_don_N_dists = [2.36, 2.48, 2.48, 3.30, 3.42, 3.42]
gen_don_N_params = (don_generic,
_process_arg_tuple(gen_don_N_dists, dist_slop,
angle_slop))
gen_don_S_dists = [2.42, 2.42, 2.42, 3.65, 3.65, 3.65]
gen_don_S_params = (don_generic,
_process_arg_tuple(gen_don_S_dists, dist_slop,
angle_slop))
generic_don_info = {
'O': gen_don_O_params,
'N': gen_don_N_params,
'S': gen_don_S_params
}
from chimerax.atom_search import AtomSearchTree
metal_coord = {}
acc_trees = {}
hbonds = []
has_sulfur = {}
for structure in structures:
if status:
session.logger.status("Finding acceptors in model '%s'" %
structure.name,
blank_after=0)
if structure.PBG_METAL_COORDINATION in structure.pbg_map:
for pb in structure.pbg_map[
structure.PBG_METAL_COORDINATION].pseudobonds:
a1, a2 = pb.atoms
if a1.element.is_metal:
metal_coord.setdefault(a2, []).append(a1)
if a2.element.is_metal:
metal_coord.setdefault(a1, []).append(a2)
if cache_da and structure in _a_cache and (
dist_slop, angle_slop) in _a_cache[structure]:
acc_atoms = []
acc_data = []
for acc_atom, data in _a_cache[structure][(
dist_slop, angle_slop)].items():
if not acc_atom.deleted:
acc_atoms.append(acc_atom)
acc_data.append(data)
else:
acc_atoms, acc_data = _find_acceptors(structure, a_params,
limited_acceptors,
generic_acc_info)
if cache_da:
cache = WeakKeyDictionary()
for i in range(len(acc_atoms)):
cache[acc_atoms[i]] = acc_data[i]
if structure not in _a_cache:
_a_cache[structure] = {}
_a_cache[structure][(dist_slop, angle_slop)] = cache
#xyz = []
has_sulfur[structure] = False
for acc_atom in acc_atoms:
#c = acc_atom._hb_coord
#xyz.append([c[0], c[1], c[2]])
if acc_atom.element == Element.get_element('S'):
has_sulfur[structure] = True
if status:
session.logger.status("Building search tree of acceptor atoms",
blank_after=0)
acc_trees[structure] = AtomSearchTree(
acc_atoms,
data=acc_data,
sep_val=3.0,
scene_coords=(Atom._hb_coord == Atom.scene_coord))
if process_key not in processed_donor_params:
# find max donor distances before they get squared..
# copy.deepcopy() refuses to copy functions (even as
# references), so do this instead...
d_params = []
for p in donor_params:
d_params.append(copy.copy(p))
for di in range(len(d_params)):
geom_type = d_params[di][2]
arg_list = d_params[di][4]
don_rad = Element.bond_radius('N')
if geom_type == theta_tau:
max_dist = max((arg_list[0], arg_list[2], arg_list[5]))
elif geom_type == upsilon_tau:
max_dist = max((arg_list[0], arg_list[5], arg_list[11]))
elif geom_type == water:
max_dist = max((arg_list[1], arg_list[4], arg_list[8]))
else:
max_dist = max(gen_don_O_dists + gen_don_N_dists +
gen_don_S_dists)
don_rad = Element.bond_radius('S')
d_params[di].append(max_dist + dist_slop + don_rad +
Element.bond_radius('H'))
for i in range(len(d_params)):
d_params[i][4] = _process_arg_tuple(d_params[i][4], dist_slop,
angle_slop)
processed_donor_params[process_key] = d_params
else:
d_params = processed_donor_params[process_key]
generic_water_params = _process_arg_tuple(
[2.36, 2.36 + OH_bond_dist, 146], dist_slop, angle_slop)
generic_theta_tau_params = _process_arg_tuple([2.48, 132], dist_slop,
angle_slop)
generic_upsilon_tau_params = _process_arg_tuple([3.42, 90, -161, 125],
dist_slop, angle_slop)
generic_generic_params = _process_arg_tuple([2.48, 3.42, 130, 90],
dist_slop, angle_slop)
for dmi in range(len(structures)):
structure = structures[dmi]
if status:
session.logger.status("Finding donors in model '%s'" %
structure.name,
blank_after=0)
if cache_da and structure in _d_cache and (
dist_slop, angle_slop) in _d_cache[structure]:
don_atoms = []
don_data = []
for don_atom, data in _d_cache[structure][(
dist_slop, angle_slop)].items():
if not don_atom.deleted:
don_atoms.append(don_atom)
don_data.append(data)
else:
don_atoms, don_data = _find_donors(structure, d_params,
limited_donors,
generic_don_info)
if cache_da:
cache = WeakKeyDictionary()
for i in range(len(don_atoms)):
cache[don_atoms[i]] = don_data[i]
if structure not in _d_cache:
_d_cache[structure] = {}
_d_cache[structure][(dist_slop, angle_slop)] = cache
if status:
session.logger.status(
"Matching donors in model '%s' to acceptors" %
structure.name,
blank_after=0)
for i in range(len(don_atoms)):
donor_atom = don_atoms[i]
geom_type, tau_sym, arg_list, test_dist = don_data[i]
donor_hyds = hyd_positions(donor_atom)
coord = donor_atom._hb_coord
for acc_structure in structures:
if acc_structure == structure and not intra_model or acc_structure != structure and not inter_model:
continue
if not inter_submodel \
and acc_structure.id and structure.id \
and acc_structure.id[0] == structure.id[0] \
and acc_structure.id[:-1] == structure.id[:-1] \
and acc_structure.id[1:] != structure.id[1:]:
continue
if has_sulfur[acc_structure]:
from .common_geom import SULFUR_COMP
td = test_dist + SULFUR_COMP
else:
td = test_dist
accs = acc_trees[acc_structure].search(coord, td)
if verbose:
session.logger.info(
"Found %d possible acceptors for donor %s:" %
(len(accs), donor_atom))
for acc_data in accs:
session.logger.info("\t%s\n" % acc_data[0])
for acc_atom, geom_func, args in accs:
if acc_atom == donor_atom:
# e.g. hydroxyl
if verbose:
print("skipping: donor == acceptor")
continue
try:
if not geom_func(donor_atom, donor_hyds, *args):
continue
except ConnectivityError as e:
session.logger.info(
"Skipping possible acceptor with bad geometry: %s\n%s\n"
% (acc_atom, e))
bad_connectivities += 1
continue
except Exception:
print("donor:", donor_atom, " acceptor:", acc_atom)
raise
if verbose:
session.logger.info(
"\t%s satisfies acceptor criteria" % acc_atom)
if geom_type == upsilon_tau:
donor_func = don_upsilon_tau
add_args = generic_upsilon_tau_params + [tau_sym]
elif geom_type == theta_tau:
donor_func = don_theta_tau
add_args = generic_theta_tau_params
elif geom_type == water:
donor_func = don_water
add_args = generic_water_params
else:
if donor_atom.idatm_type in ["Npl", "N2+"]:
heavys = 0
for bonded in donor_atom.neighbors:
if bonded.element.number > 1:
heavys += 1
if heavys > 1:
info = gen_don_Npl_1h_params
else:
info = gen_don_Npl_2h_params
else:
info = generic_don_info[
donor_atom.element.name]
donor_func, arg_list = info
add_args = generic_generic_params
if donor_func == don_upsilon_tau:
# tack on generic
# tau symmetry
add_args = generic_upsilon_tau_params + [4]
elif donor_func == don_theta_tau:
add_args = generic_theta_tau_params
try:
if not donor_func(donor_atom, donor_hyds, acc_atom,
*tuple(arg_list + add_args)):
continue
except ConnectivityError as e:
session.logger.info(
"Skipping possible donor with bad geometry: %s\n%s\n"
% (donor_atom, e))
bad_connectivities += 1
continue
except AtomTypeError as e:
session.logger.warning(str(e))
#_problem = ("atom type", donor_atom, str(e), None)
continue
if verbose:
session.logger.info(
"\t%s satisfies donor criteria" % donor_atom)
# ensure hbond isn't precluded by metal-coordination...
if acc_atom in metal_coord:
from chimerax.geometry import angle
conflict = False
for metal in metal_coord[acc_atom]:
if angle(donor_atom._hb_coord,
acc_atom._hb_coord,
metal._hb_coord) < 90.0:
if verbose:
session.logger.info(
"\tH-bond conflicts with"
" metal coordination to %s" %
metal)
conflict = True
break
if conflict:
continue
hbonds.append((donor_atom, acc_atom))
if status:
session.logger.status("")
if bad_connectivities:
session.logger.warning(
"Skipped %d atom(s) with bad connectivities; see log for details"
% bad_connectivities)
if _problem:
if session.ui.is_gui:
# report a bug when atom matches multiple donor/acceptor descriptions
da, atom, grp1, grp2 = _problem
res_atoms = atom.residue.atoms
def res_atom_rep(a):
try:
i = res_atoms.index(a)
except ValueError:
return "other %s" % a.element.name
return "%2d" % (i + 1)
descript = "geometry class 1: %s\n\ngeometry class 2: %s" % (
repr(grp1), repr(grp2))
from chimerax.core.logger import report_exception
report_exception(
error_description=
"""At least one atom was classified into more than one acceptor or donor
geometry class. This indicates a problem in the
donr/acceptor classification mechanism and we would appreciate it if you
would use the bug-report button below to send us the information that
will allow us to improve the classification code.
residue name: %s
problem %s atom: %d
residue atoms:
%s
residue bonds:
%s
%s
""" % (atom.residue.name, da, res_atoms.index(atom) + 1,
"\n\t".join([
"%2d %-4s %-s (%s)" %
(en[0] + 1, en[1].name, en[1].idatm_type, str(en[1].coord))
for en in enumerate(res_atoms)
]), "\n\t".join([
"%s <-> %-s" %
(res_atom_rep(b.atoms[0]), res_atom_rep(b.atoms[1]))
for b in atom.residue.atoms.bonds
]), descript))
_problem = None
if _truncated:
if len(_truncated) > 20:
session.logger.warning(
"%d atoms were skipped as donors/acceptors due to missing"
" heavy-atom bond partners" % len(_truncated))
else:
session.logger.warning(
"The following atoms were skipped as donors/acceptors due to missing"
" heavy-atom bond partners: %s" %
"; ".join([str(a) for a in _truncated]))
_truncated = None
finally:
delattr(Atom, "_hb_coord")
return hbonds