def bond_with_H_length(heavy, geom):
element = heavy.element.name
if element == "C":
if geom == 4:
return 1.09
if geom == 3:
return 1.08
if geom == 2:
return 1.056
elif element == "N":
return N_H
elif element == "O":
# can't rely on water being in chain "water" anymore...
if heavy.num_bonds == 0 or heavy.num_bonds == 2 \
and len([nb for nb in heavy.neighbors if nb.element.number > 1]) == 0:
return 0.9572
return 0.96
elif element == "S":
return 1.336
from chimerax.atomic import Element
return Element.bond_length(heavy.element, Element.get_element(1))
def hyd_positions(heavy, include_lone_pairs=False):
"""Return list of positions for hydrogens attached to this atom.
If a hydrogen could be in one of several positions, don't return any of those.
"""
# first, find known attached atoms
bonded_heavys = []
hyds = []
for atom in heavy.neighbors:
if atom.element.number > 1:
bonded_heavys.append(atom)
else:
hyds.append(atom)
# convert to Points
hyd_locs = []
for hyd in hyds:
hyd_locs.append(hyd._hb_coord)
if hyd_locs and not include_lone_pairs:
# explicit hydrogens "win" over atom types
return hyd_locs
if heavy.idatm_type in type_info:
info = type_info[heavy.idatm_type]
geom = info.geometry
if include_lone_pairs:
subs = geom
else:
subs = info.substituents
bonded_locs = hyd_locs[:]
for b_heavy in bonded_heavys:
bonded_locs.append(b_heavy._hb_coord)
else:
return hyd_locs
known_subs = len(bonded_locs)
if known_subs >= subs or known_subs == 0:
return hyd_locs
# above eliminates 'single' geometry
if known_subs == 1 and geom == tetrahedral:
# rotamer
return hyd_locs
max_subs = geom
if max_subs - subs > 0:
# the "empty" bond could be anywhere
return hyd_locs
heavy_loc = heavy._hb_coord
bond_len = Element.bond_length(heavy.element, "H")
if geom == planar:
coplanar = []
for b_heavy in bonded_heavys:
try:
bh_geom = type_info[b_heavy.idatm_type].geometry
except KeyError:
bh_geom = None
if bh_geom != planar:
continue
for atom in b_heavy.neighbors:
if atom != heavy:
coplanar.append(atom._hb_coord)
else:
coplanar = None
hyd_locs = hyd_locs + list(
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))
return hyd_locs
def _find_donors(structure, d_params, limited_donors, generic_don_info):
don_atoms = []
don_data = []
std_donors = {}
for dp in d_params:
group_key, donorIndex, geom_type, tau_sym, arg_list, test_dist = dp
if group_key:
groups = find_group(group_key, [structure])
else:
# generic donors
groups = []
for atom in structure.atoms:
if atom in std_donors:
continue
if atom.element.number not in [7, 8, 16]:
continue
if limited_donors and atom not in limited_donors:
continue
# oxygen, nitrogen, or sulfur
try:
expect_bonds = type_info[atom.idatm_type].substituents
except KeyError:
expect_bonds = 0
num_bonds = atom.num_bonds
# screen out the partial terminal N that AddH can leave, since the geometry is
# problematic and the H direction isn't really determined
if atom.idatm_type == "Npl" and num_bonds == 2 \
and 1 in [n.element.number for n in atom.neighbors]:
continue
if num_bonds < expect_bonds:
groups.append([atom])
continue
for bonded in atom.neighbors:
if bonded.element.number == 1:
groups.append([atom])
break
if verbose:
for g in groups:
print("generic donor:", g[0])
if groups and geom_type == theta_tau:
# extend probe distance by H-bond length so that all relevant acceptors will be found
test_dist = test_dist + Element.bond_length(
groups[0][donorIndex].element, 'H')
for group in groups:
donor_atom = group[donorIndex]
if limited_donors and donor_atom not in limited_donors:
continue
if donor_atom in std_donors:
if group_key != std_donors[donor_atom] and not (
# conflicts of non-ring groups with ring
# groups not considered a problem (non-ring
# groups "win")
group_key[0] in _ring_funcs
and std_donors[donor_atom][0] not in _ring_funcs):
global _problem
_problem = ("donor", donor_atom, std_donors[donor_atom],
group_key)
continue
if donor_atom.is_missing_heavy_template_neighbors(
no_template_okay=True):
global _truncated
_truncated.add(donor_atom)
continue
std_donors[donor_atom] = group_key
don_atoms.append(donor_atom)
don_data.append((geom_type, tau_sym, arg_list, test_dist))
return don_atoms, don_data
# index of donor in group,
# type of donor geometry
# degree of tau symmetry
# argument tuple used when geometry-check function is called
#
# in argument tuple, conversions will occur before function gets called.
# namely:
# positive floats are assumed to be distances, and will be squared
# integers are assumed to be angles in degrees, and will be
# converted to radians
import sys
water = sys.intern("water")
theta_tau = sys.intern('theta_tau')
upsilon_tau = sys.intern('upsilon_tau')
OH_bond_dist = Element.bond_length("O", "H")
donor_params = [
# neutral carboxylic acid
[[['O3', ['Cac', H]], [1, 1, 0]], 0, upsilon_tau, 2,
(2.87, 103, -128, 140, -30, 2.87, 103, -128, 155, -30, 150, 2.87, 103,
-128, 140, -30, 150)],
# protonated nitrogen double-bonded to carbon
[
[['Npl', [['C2', [explicit_single_bond, explicit_single_bond]], H, H]],
[1, 1, 0, 0, 0, 0]],
0,
upsilon_tau,
4,
(
3.17,