def calculate_residue_phi_psi_angles(prev, current, next, deg=True):
"""Calculate phi-psi angles for a set of three residues. Returns (phi, psi)."""
phi = dihedral_angle(sites=extract_phi_sites(prev=prev, current=current),
deg=deg)
psi = dihedral_angle(sites=extract_psi_sites(current=current, next=next),
deg=deg)
return (phi, psi)
def should_be_flipped(residue_1, residue_2):
""" are these residues in similar flip orientation?"""
# assert residue_1.resname == residue_2.resname, "%s %s" % (
# residue_1.id_str(), residue_2.id_str())
if residue_1.resname != residue_2.resname:
# e.g. 1u54, 3srv: PTR mutation of TYR residues
return False
if residue_1.resname in flippable_sidechains:
tor_1_sites = []
for aname in flippable_sidechains[residue_1.resname][:4]:
a = residue_1.find_atom_by(name=aname)
if a is None:
return False
else:
tor_1_sites.append(a.xyz)
tor_23_sites = []
for aname in flippable_sidechains[residue_1.resname][:5]:
a = residue_2.find_atom_by(name=aname)
if a is None:
return False
else:
tor_23_sites.append(a.xyz)
tor1 = dihedral_angle(
sites=tor_1_sites,
deg=True)
tor2 = dihedral_angle(
sites=tor_23_sites[:4],
deg=True)
tor3 = dihedral_angle(
sites=tor_23_sites[:3]+[tor_23_sites[4]],
deg=True)
if tor1 is None or tor2 is None or tor3 is None:
return False
return abs(tor1-tor2) > abs(tor1-tor3)+5
return False
def should_be_flipped(residue_1, residue_2):
""" are these residues in similar flip orientation?"""
# assert residue_1.resname == residue_2.resname, "%s %s" % (
# residue_1.id_str(), residue_2.id_str())
if residue_1.resname != residue_2.resname:
# e.g. 1u54, 3srv: PTR mutation of TYR residues
return False
if residue_1.resname in flippable_sidechains:
tor_1_sites = []
for aname in flippable_sidechains[residue_1.resname][:4]:
a = residue_1.find_atom_by(name=aname)
if a is None:
return False
else:
tor_1_sites.append(a.xyz)
tor_23_sites = []
for aname in flippable_sidechains[residue_1.resname][:5]:
a = residue_2.find_atom_by(name=aname)
if a is None:
return False
else:
tor_23_sites.append(a.xyz)
tor1 = dihedral_angle(
sites=tor_1_sites,
deg=True)
tor2 = dihedral_angle(
sites=tor_23_sites[:4],
deg=True)
tor3 = dihedral_angle(
sites=tor_23_sites[:3]+[tor_23_sites[4]],
deg=True)
if tor1 is None or tor2 is None or tor3 is None:
return False
return abs(tor1-tor2) > abs(tor1-tor3)+5
return False
def should_be_flipped(residue_1, residue_2):
""" are these residues in similar flip orientation?"""
assert residue_1.resname == residue_2.resname
if residue_1.resname in flippable_sidechains:
tor_1_sites = []
for aname in flippable_sidechains[residue_1.resname][:4]:
a = residue_1.find_atom_by(name=aname)
if a is None:
return False
else:
tor_1_sites.append(a.xyz)
tor_23_sites = []
for aname in flippable_sidechains[residue_1.resname][:5]:
a = residue_2.find_atom_by(name=aname)
if a is None:
return False
else:
tor_23_sites.append(a.xyz)
tor1 = dihedral_angle(
sites=tor_1_sites,
deg=True)
tor2 = dihedral_angle(
sites=tor_23_sites[:4],
deg=True)
tor3 = dihedral_angle(
sites=tor_23_sites[:3]+[tor_23_sites[4]],
deg=True)
return abs(tor1-tor2) > abs(tor1-tor3)+5
return False
def get_peptide_bond_type(prev_Ca, prev_C, curr_N, curr_Ca):
"Return the type of peptide bond"
assert prev_Ca.name.strip() == 'CA'
assert prev_C.name.strip() == 'C'
assert curr_N.name.strip() == 'N'
assert curr_Ca.name.strip() == 'CA'
ang = dihedral_angle(
sites=[a.xyz for a in (prev_Ca, prev_C, curr_N, curr_Ca)], deg=True)
ang = numpy.round(ang, 2)
if curr_N.parent().resname == 'PRO':
cis, trans = ('PCIS', 'PTRANS')
else:
cis, trans = ('CIS', 'TRANS')
# Use lenient angle tolerances to detect CIS or TRANS
if angle_difference(a1=0, a2=ang, deg=True, abs_val=True) < 45:
bond_type = cis
elif angle_difference(a1=180, a2=ang, deg=True, abs_val=True) < 45:
bond_type = trans
else:
print 'WARNING: BOND IS NOT CIS OR TRANS (angle {:7}) for link between {} and {} - DEFAULTING TO TRANS'.format(
ang, prev_C.id_str(), curr_N.id_str())
bond_type = trans
return bond_type
def find_third_neighbors(self, dihedral_proxies):
""" Loop through dihedral angle proxies to find third neighbor
Fill in neighbors.b1 with iseq and angle proxy"""
for dp in dihedral_proxies:
for i_test in dp.i_seqs:
if (self.h_connectivity[i_test] is None
and not self.hd_sel[i_test]):
continue
ih = i_test
i1, i2, i3, i4 = dp.i_seqs
if (ih == i1):
i_third = i4
if (ih == i4):
i_third = i1
dihedral = dihedral_angle(sites=[
self.sites_cart[i1], self.sites_cart[i2],
self.sites_cart[i3], self.sites_cart[i4]
])
if dihedral is None:
return
dihedral_id = dp.angle_ideal
delta = geometry_restraints.angle_delta_deg(
angle_1=math.degrees(dihedral),
angle_2=dihedral_id,
periodicity=dp.periodicity)
dihedral_ideal = math.degrees(dihedral) + delta
b1 = {'iseq': i_third, 'dihedral_ideal': dihedral_ideal}
self.h_connectivity[ih].b1 = b1
self.assign_b1_for_H_atom_groups(ih=ih, i_third=i_third)
def get_omega_value(
self,
omega_cdl=False,
):
#
# this is very poor! there needs to be a better way to check for cis-
#
for i, residue in enumerate(self):
if i == 0: continue
if omega_cdl:
if len(self) == 3:
if i == 1: continue
else:
if i == 2: continue
ccn1, outl1 = get_c_ca_n(residue, return_subset=True)
ccn2, outl2 = get_c_ca_n(self[i - 1], return_subset=True)
ca1 = ccn1[1]
n = ccn1[2]
c = ccn2[0]
ca2 = ccn2[1]
omega_atoms = [ca1, n, c, ca2]
if None in omega_atoms: return None
omega = dihedral_angle(sites=[atom.xyz for atom in omega_atoms],
deg=True)
return omega
def add_c_terminal_oxygens_to_atom_group(ag,
use_capping_hydrogens=False,
append_to_end_of_model=False,
c_ca_n=None,
):
#
# do we need ANISOU
#
rc = []
atom_name=' OXT'
atom_element = 'O'
bond_length=1.231
if use_capping_hydrogens:
if ag.get_atom(atom_name.strip()): return []
atom_name=" HC "
atom_element="H"
bond_length=1.
if ag.get_atom(atom_name.strip()): return []
if c_ca_n is not None:
c, ca, n = c_ca_n
else:
c = ag.get_atom("C")
if c is None: return
ca = ag.get_atom("CA")
if ca is None: return
n = ag.get_atom("N")
if n is None: return
atom = ag.get_atom('O')
dihedral = dihedral_angle(sites=[atom.xyz,
c.xyz,
ca.xyz,
n.xyz,
],
deg=True)
ro2 = construct_xyz(c, bond_length,
ca, 120.,
n, dihedral,
period=2,
)
oxys = [' O ', atom_name]
for i in range(0,2):
name = oxys[i]
atom = ag.get_atom(name.strip())
if atom:
pass #atom.xyz = ro2[i]
else:
atom = iotbx.pdb.hierarchy.atom()
atom.name = name
atom.element = atom_element
atom.occ = c.occ
atom.b = c.b
atom.segid = ' '*4
atom.xyz = ro2[i]
if append_to_end_of_model:
chain = _add_atom_to_chain(atom, ag)
rc.append(chain)
else:
# add the atom to the hierarchy
ag.append_atom(atom)
return rc
def add_side_chain_acid_hydrogens_to_atom_group(
atom_group,
anchors=None,
configuration_index=0,
bond_length=0.95,
element='H',
):
"""Add hydrogen atoms to side-chain acid in place
Args:
atom_group (TYPE): Atom group
anchors (None, optional): Atoms that specify the acids moeity
configuration_index (int, optional): Configuration to return
"""
assert element in ['H', 'D']
c, o1, o2 = anchors
if configuration_index >= 2:
tmp = o1.name
o1.name = o2.name
o2.name = tmp
tmp = o1
o1 = o2
o2 = tmp
configuration_index = configuration_index % 2
if o2.name == ' OD2':
name = ' HD2'
atom = atom_group.get_atom('CB')
elif o2.name == ' OE2':
name = ' HE2'
atom = atom_group.get_atom('CG')
else:
assert 0
if element == 'D': name = name.replace('H', 'D')
dihedral = dihedral_angle(sites=[
atom.xyz,
c.xyz,
o1.xyz,
o2.xyz,
],
deg=True)
ro2 = construct_xyz(
o2,
bond_length,
c,
120.,
o1,
dihedral,
period=2,
)
i = configuration_index
atom = atom_group.get_atom(name.strip())
if atom:
pass #atom.xyz = ro2[i]
else:
atom = new_atom_with_inheritance(name, element, ro2[i], o2)
atom_group.append_atom(atom)
def get_dihedral_angle(atoms, round_coords=False):
# round here is to emulate rounding when dumping to pdb, to get more
# consistent result for rama outliers inside program and when calculating
# from resulted pdb file.
sites = []
if round_coords:
for x in atoms:
sites.append((round(x.xyz[0], 3), round(x.xyz[1], 3), round(x.xyz[2], 3)))
else:
sites = [x.xyz for x in atoms]
return dihedral_angle(
sites = sites,
deg=True)
def get_torsion(ag1, ag2, an1, an2, limits='-180-180'):
from scitbx.math import dihedral_angle
atoms = _get_atoms(ag1, an1) + _get_atoms(ag2, an2)
omega = dihedral_angle(sites=[atom.xyz for atom in atoms], deg=True)
if limits == '-180-180':
if omega > 180:
print(omega, limits)
assert 0
elif limits == '0-360':
if omega < 0:
omega += 360
# for atom in atoms: print atom.quote()
return omega
def add_main_chain_o_to_atom_group(ag, c_ca_n=None):
# cetral functuon
if c_ca_n is not None:
c, ca, n = c_ca_n
else:
c = ag.get_atom("C")
if c is None: return
ca = ag.get_atom("CA")
if ca is None: return
n = ag.get_atom("N")
if n is None: return
atom = ag.get_atom('O')
dihedral = dihedral_angle(sites=[
atom.xyz,
c.xyz,
ca.xyz,
n.xyz,
],
deg=True)
ro2 = construct_xyz(
c,
bond_length,
ca,
120.,
n,
dihedral,
period=2,
)
oxys = [' O ', atom_name]
for i in range(0, 2):
name = oxys[i]
atom = ag.get_atom(name.strip())
if atom:
pass #atom.xyz = ro2[i]
else:
atom = iotbx.pdb.hierarchy.atom()
atom.name = name
atom.element = atom_element
atom.occ = c.occ
atom.b = c.b
atom.segid = ' ' * 4
atom.xyz = ro2[i]
if append_to_end_of_model:
chain = _add_atom_to_chain(atom, ag)
rc.append(chain)
else:
# add the atom to the hierarchy
ag.append_atom(atom)
#for
assert atom
def get_dihedral_angle(atoms, round_coords=False):
# round here is to emulate rounding when dumping to pdb, to get more
# consistent result for rama outliers inside program and when calculating
# from resulted pdb file.
if atoms is None:
return None
sites = []
if round_coords:
for x in atoms:
sites.append((round(x.xyz[0], 3), round(x.xyz[1],
3), round(x.xyz[2], 3)))
else:
sites = [x.xyz for x in atoms]
return dihedral_angle(sites=sites, deg=True)
def check_for_plane_proxy(self, ih):
neighbors = self.h_connectivity[ih]
a0 = neighbors.a0['iseq']
a1 = neighbors.a1['iseq']
b1 = neighbors.b1['iseq']
if (neighbors.h1 and not neighbors.h2): # if there is only 1 H atom as second neighbor
ih2 = neighbors.h1['iseq']
if ('dihedral_ideal' not in neighbors.b1 or
'dihedral_ideal' not in self.h_connectivity[ih2].b1):
if ih in self.plane_h:
dihedral = dihedral_angle(
sites = [self.sites_cart[ih], self.sites_cart[a0],
self.sites_cart[a1],self.sites_cart[b1]])
neighbors.b1['dihedral_ideal'] = math.degrees(dihedral)
def get_omega_value(residue1, residue2, verbose=False):
ccn1, outl1 = get_c_ca_n(residue1, return_subset=True)
ccn2, outl2 = get_c_ca_n(residue2, return_subset=True)
ca1 = ccn1[1]
n = ccn1[2]
c = ccn2[0]
ca2 = ccn2[1]
omega_atoms = [ca1, n, c, ca2]
if verbose:
for atom in omega_atoms:
print(atom.quote())
if None in omega_atoms: return None
omega = dihedral_angle(sites=[atom.xyz for atom in omega_atoms], deg=True)
return omega
def get_ca_dihedrals(residues, verbose=False):
assert len(residues) >= 4
dihedrals = []
atoms = []
for residue in residues:
atoms.append(residue.find_atom_by(name=' CA '))
if len(atoms) == 4:
if verbose:
print('CAs')
for atom in atoms:
print(atom.quote())
dihedrals.append(
dihedral_angle(sites=[atom.xyz for atom in atoms], deg=True))
del atoms[0]
return dihedrals
def get_phi_psi_angles(residues, verbose=False):
assert len(residues) >= 3
dihedrals = []
for i in range(len(residues)):
if i < 2: continue
atoms = get_phi_psi_atoms(*tuple(residues[i - 2:i + 1]),
verbose=verbose)
if atoms is None: return None
for dihedral in atoms:
phi_or_psi = dihedral_angle(sites=[atom.xyz for atom in dihedral],
deg=True)
dihedrals.append(phi_or_psi)
if verbose:
print('dihedrals')
for phi_or_psi in dihedrals:
print('phi_or_psi', phi_or_psi)
return dihedrals
def get_phi_psi_angles(self,
only_psi_phi_pairs=True,
force_plus_one=False,
omega_cdl=False,
verbose=False,
):
atoms = self.get_phi_psi_atoms(only_psi_phi_pairs=only_psi_phi_pairs,
force_plus_one=force_plus_one,
omega_cdl=omega_cdl,
)
dihedrals = []
for dihedral in atoms:
phi_or_psi=dihedral_angle(sites=[atom.xyz for atom in dihedral], deg=True)
dihedrals.append(phi_or_psi)
if verbose:
for phi_or_psi in dihedrals:
print 'phi_or_psi',phi_or_psi
return dihedrals
def get_phi_psi_angles(self,
only_psi_phi_pairs=True,
force_plus_one=False,
omega_cdl=False,
verbose=False,
):
atoms = self.get_phi_psi_atoms(only_psi_phi_pairs=only_psi_phi_pairs,
force_plus_one=force_plus_one,
omega_cdl=omega_cdl,
)
if atoms is None: return None
dihedrals = []
for dihedral in atoms:
phi_or_psi=dihedral_angle(sites=[atom.xyz for atom in dihedral], deg=True)
dihedrals.append(phi_or_psi)
if verbose:
for phi_or_psi in dihedrals:
print 'phi_or_psi',phi_or_psi
return dihedrals
def cis_group(self, limit=45., verbose=False):
cis_peptide_bond = False
for i, residue in enumerate(self):
if i==0: continue
if i==2: continue # only check the middle omega angle
ccn1, outl1 = get_c_ca_n(residue)
ccn2, outl2 = get_c_ca_n(self[i-1])
ca1 = ccn1[1]
n = ccn1[2]
c = ccn2[0]
ca2 = ccn2[1]
omega_atoms = [ca1, n, c, ca2]
omega = dihedral_angle(sites=[atom.xyz for atom in omega_atoms], deg=True)
if (180.-abs(omega))>limit:
cis_peptide_bond = True
break
if verbose:
if cis_peptide_bond:
print 'cis peptide bond', cis_peptide_bond, omega
print self
return cis_peptide_bond
def get_omega_value(self,
omega_cdl=False,
):
#
# this is very poor! there needs to be a better way to check for cis-
#
for i, residue in enumerate(self):
if i==0: continue
if omega_cdl:
if len(self)==3:
if i==1: continue
else:
if i==2: continue
ccn1, outl1 = get_c_ca_n(residue, return_subset=True)
ccn2, outl2 = get_c_ca_n(self[i-1], return_subset=True)
ca1 = ccn1[1]
n = ccn1[2]
c = ccn2[0]
ca2 = ccn2[1]
omega_atoms = [ca1, n, c, ca2]
if None in omega_atoms: return None
omega = dihedral_angle(sites=[atom.xyz for atom in omega_atoms], deg=True)
return omega
def process_1_neighbor(self, neighbors):
ih = neighbors.ih
# if used for hydrogenate, make sure that first we use the H with dihedral angle
# However, this needs some tweaking for neutron H/D situations
if (neighbors.number_h_neighbors == 2):
i_h1, i_h2 = neighbors.h1['iseq'], neighbors.h2['iseq']
if ('dihedral_ideal' in neighbors.b1):
neighbors = self.h_connectivity[ih]
elif ('dihedral_ideal' in self.h_connectivity[i_h1].b1):
if self.h_parameterization[i_h1] is None:
neighbors = self.h_connectivity[i_h1]
elif ('dihedral_ideal' in self.h_connectivity[i_h2].b1):
if self.h_parameterization[i_h2] is None:
neighbors = self.h_connectivity[i_h2]
ih = neighbors.ih
#print(self.site_labels[ih])
i_a0 = neighbors.a0['iseq']
rh = matrix.col(self.sites_cart[ih])
r0 = matrix.col(self.sites_cart[i_a0])
if self.use_ideal_bonds_angles:
disth = neighbors.a0['dist_ideal']
else:
disth = (r0 - rh).length()
if (not neighbors.a1 or not neighbors.b1):
self.unk_list.append(ih)
return
i_a1 = neighbors.a1['iseq']
i_b1 = neighbors.b1['iseq']
r1 = matrix.col(self.sites_cart[i_a1])
rb1 = matrix.col(self.sites_cart[i_b1])
self.check_if_atoms_superposed(rh, r0, ih, i_a0)
self.check_if_atoms_superposed(r1, r0, i_a1, i_a0)
uh0 = (rh - r0).normalize()
u10 = (r1 - r0).normalize()
dihedral = dihedral_angle(sites=[
self.sites_cart[ih], self.sites_cart[i_a0], self.sites_cart[i_a1],
self.sites_cart[i_b1]
])
if self.use_ideal_bonds_angles:
alpha = math.radians(neighbors.a1['angle_ideal'])
#allow for rotation even for idealize = True
phi = dihedral
if self.use_ideal_dihedral:
#phi = math.radians(b1.dihedral_ideal)
if 'dihedral_ideal' in neighbors.b1:
phi = math.radians(neighbors.b1['dihedral_ideal'])
else:
alpha = (u10).angle(uh0)
phi = dihedral
#print(math.degrees(phi))
u1 = (r0 - r1).normalize()
rb10 = rb1 - r1
# TODO check needed?
u2 = (rb10 - ((rb10).dot(u1)) * u1).normalize()
u3 = u1.cross(u2)
if (neighbors.number_h_neighbors == 0):
self.h_parameterization[ih] = riding_coefficients(htype='alg1b',
ih=ih,
a0=i_a0,
a1=i_a1,
a2=i_b1,
a3=-1,
a=alpha,
b=phi,
h=0,
n=0,
disth=disth)
if (neighbors.number_h_neighbors == 2):
i_h1, i_h2 = neighbors.h1['iseq'], neighbors.h2['iseq']
i_h1, i_h2 = self.check_propeller_order(i_a0=i_a0,
i_a1=i_a1,
ih=ih,
i_h1=i_h1,
i_h2=i_h2)
for nprop, hprop in zip([0, 1, 2], [ih, i_h1, i_h2]):
self.h_parameterization[hprop] = riding_coefficients(
htype='prop',
ih=hprop,
a0=i_a0,
a1=i_a1,
a2=i_b1,
a3=-1,
a=alpha,
n=nprop,
b=phi,
h=0,
disth=disth)
def process_1_neighbor_type_arg(self, neighbors):
"""
alg1a: X-H2 planar groups, such as in ARG, ASN, GLN
requires that dihedral angle restraint exists for at least one H atom
"""
ih = neighbors.ih
i_h1 = neighbors.h1['iseq']
i_a0 = neighbors.a0['iseq']
rh = matrix.col(self.sites_cart[ih])
r0 = matrix.col(self.sites_cart[i_a0])
if self.use_ideal_bonds_angles:
disth = neighbors.a0['dist_ideal']
else:
disth = (r0 - rh).length()
i_a1 = neighbors.a1['iseq']
r1 = matrix.col(self.sites_cart[i_a1])
if ('dihedral_ideal' in neighbors.b1):
ih_dihedral = ih
ih_no_dihedral = i_h1
else:
if ('dihedral_ideal' in self.h_connectivity[i_h1].b1):
ih_dihedral = i_h1
ih_no_dihedral = ih
else:
self.unk_list.append(ih)
return
i_b1 = self.h_connectivity[ih_dihedral].b1['iseq']
rb1 = matrix.col(self.sites_cart[i_b1])
# check if angle is typical for propeller
# catches case of missing propeller atom
if (neighbors.h1['angle_ideal'] > 107
and neighbors.h1['angle_ideal'] < 111):
self.unk_list.append(ih)
else:
dihedral = dihedral_angle(sites=[
self.sites_cart[i_b1], self.sites_cart[i_a1],
self.sites_cart[i_a0], self.sites_cart[ih_dihedral]
])
self.check_if_atoms_superposed(rh, r0, ih, i_a0)
self.check_if_atoms_superposed(r1, r0, i_a1, i_a0)
uh0 = (rh - r0).normalize()
u10 = (r1 - r0).normalize()
if self.use_ideal_bonds_angles:
alpha = math.radians(neighbors.a1['angle_ideal'])
phi = math.radians(
self.h_connectivity[ih_dihedral].b1['dihedral_ideal'])
else:
alpha = (u10).angle(uh0)
phi = dihedral
u1 = (r0 - r1).normalize()
rb10 = rb1 - r1
# TODO check needed?
u2 = (rb10 - ((rb10).dot(u10)) * u10).normalize()
u3 = u1.cross(u2)
for ih_alg1a, phi_alg1a in zip([ih_dihedral, ih_no_dihedral],
[phi, phi + math.pi]):
if self.h_parameterization[ih_alg1a] is None:
self.h_parameterization[ih_alg1a] = riding_coefficients(
htype='alg1a',
ih=ih_alg1a,
a0=i_a0,
a1=i_a1,
a2=i_b1,
a3=-1,
a=alpha,
b=phi_alg1a,
n=0,
h=0,
disth=disth)
def determine_H_neighbors(geometry_restraints, bond_proxies, angle_proxies,
dihedral_proxies, hd_selection, sites_cart, atoms):
fsc2=geometry_restraints.shell_sym_tables[2].full_simple_connectivity()
fsc1=geometry_restraints.shell_sym_tables[1].full_simple_connectivity()
#fsc0=geometry_restraints.shell_sym_tables[0].full_simple_connectivity()
# Maybe there is better way to get number of atoms?
n_atoms = len(sites_cart)
connectivity = {}
# loop through bond proxies to find H atom and parent atom
for bproxy in bond_proxies:
i_seq, j_seq = bproxy.i_seqs
is_i_hd = hd_selection[i_seq]
is_j_hd = hd_selection[j_seq]
if(not is_i_hd and not is_j_hd): continue
elif(is_i_hd and is_j_hd): assert 0
else:
if (is_i_hd): ih, i_parent = i_seq, j_seq
elif(is_j_hd): ih, i_parent = j_seq, i_seq
else:
raise Sorry("Something went wrong in bond proxies")
rh = matrix.col(sites_cart[ih])
r0 = matrix.col(sites_cart[i_parent])
dist = (r0 - rh).length()
parent = atom_info(
iseq = i_parent,
dist_ideal = bproxy.distance_ideal,
dist = dist)
altloc_h = atoms[ih].parent().altloc
connectivity[ih]=[parent]
# this is connectivity[ih][1] --> list of second non-H neighbours
connectivity[ih].append([])
# this is connectivity[ih][2] --> list of second H/D neighbours
connectivity[ih].append([])
# find second neighbors
second_neighbors = list(fsc1[ih])
count_H = 0
altconf_dict = {}
for i_second in second_neighbors:
iselection = flex.size_t([ih,i_parent,i_second])
ap = angle_proxies.proxy_select(
n_seq = n_atoms,
iselection = iselection)
# check if angle proxy exists = check that list ap is not empty
if ap:
altloc_i_second = atoms[i_second].parent().altloc
#rint atoms[i_second].name, atoms[i_second].parent().altloc, atoms[i_second].parent().parent().resseq
#ag_isecond = atoms[i_second].parent().parent().atom_groups()
if ((altloc_i_second != altloc_h and altloc_i_second != 'A') and altloc_h ==''):
continue
neighbor = atom_info(
iseq = i_second,
angle_ideal = ap[0].angle_ideal)
if (hd_selection[i_second]):
connectivity[ih][2].append(neighbor)
count_H = count_H + 1
else:
connectivity[ih][1].append(neighbor)
(connectivity[ih][0]).count_H = count_H
# find third neighbors, if necessary
if (len(connectivity[ih][1]) == 1):
connectivity[ih].append([])
i_second = ((connectivity[ih][1])[0]).iseq
third_neighbors = list(fsc2[ih])
third_no_dihedrals = []
for i_third in third_neighbors:
if (not hd_selection[i_third]):
iselection = flex.size_t([i_parent,i_second,i_third])
ap = angle_proxies.proxy_select(
n_seq = n_atoms,
iselection = iselection)
if ap:
iselection_dihe = flex.size_t([ih,i_parent,i_second,i_third])
dp = dihedral_proxies.proxy_select(
n_seq = n_atoms,
iselection = iselection_dihe)
if dp:
dihedral_id = dp[0].angle_ideal
dihedral = dihedral_angle(
sites=[sites_cart[i_third], sites_cart[i_second],
sites_cart[i_parent],sites_cart[ih]])
sites_cart_dihe = sites_cart.select(iselection_dihe).deep_copy()
delta = dp.deltas(sites_cart=sites_cart_dihe)[0]
dihedral_ideal = math.degrees(dihedral) + delta
neighbor = atom_info(
iseq = i_third,
dihedral = dihedral,
dihedral_ideal = dihedral_ideal)
#print dihedral_id, delta, math.degrees(dihedral), dihedral_ideal
connectivity[ih][3].append(neighbor)
else:
neighbor = atom_info(
iseq = i_third)
third_no_dihedrals.append(neighbor)
if (not connectivity[ih][3]):
connectivity[ih][3] = third_no_dihedrals
if (len(connectivity[ih][1]) == 2):
reduced_neighbs = connectivity[ih][1]
ix = i_parent
iy = (reduced_neighbs[0]).iseq
iz = (reduced_neighbs[1]).iseq
iselection = flex.size_t([ix,iy,iz])
(connectivity[ih][0]).angle_ideal = angle_proxies.proxy_select(
n_seq = n_atoms,
iselection = iselection)[0].angle_ideal
if (len(connectivity[ih][1]) == 3):
# for tetrahedral, all 3 ideal angles are needed
reduced_neighbs = connectivity[ih][1]
angles = []
ix = i_parent
_list = [(0,1),(1,2),(2,0)]
for _i,_j in _list:
iy = (reduced_neighbs[_i]).iseq
iz = (reduced_neighbs[_j]).iseq
iselection = flex.size_t([ix,iy,iz])
ap = angle_proxies.proxy_select(
n_seq = n_atoms,
iselection = iselection)
if ap:
angles.append(ap[0].angle_ideal)
(connectivity[ih][0]).angle_ideal = angles
return connectivity
def get_h_parameterization(h_connectivity, sites_cart, use_ideal_bonds_angles):
h_parameterization = {}
n_atoms = len(sites_cart)
for ih in h_connectivity.keys():
#if (ih != 22):
# continue
#for debugging
#print 'atom:', names[ih]+' ('+str(ih)+ ') residue:', \
# atoms_list[ih].resseq, 'chain', atoms_list[ih].chain_id
# if entry exists already, skip it
if ih in h_parameterization.keys():
continue
a0 = h_connectivity[ih][0]
count_H = a0.count_H
reduced_neighbs = h_connectivity[ih][1]
n_red_neigbs = len(reduced_neighbs)
rh = matrix.col(sites_cart[ih])
r0 = matrix.col(sites_cart[a0.iseq])
if use_ideal_bonds_angles:
dist_h = a0.dist_ideal
else:
dist_h = (r0 - rh).length()
# alg2a, 2tetra, 2neigbs
if (n_red_neigbs == 2):
a1, a2 = reduced_neighbs[0], reduced_neighbs[1]
# if H is second neighbor, gets its index
if (count_H == 1):
hlist = h_connectivity[ih][2]
if hlist:
ih2 = (hlist[0])
i_h2 = (hlist[0]).iseq
else:
ih2 = None
sumang, a, b, h, root = get_coefficients(
ih=ih,
a0=a0,
a1=a1,
a2=a2,
ih2=ih2,
use_ideal_bonds_angles=use_ideal_bonds_angles,
sites_cart=sites_cart,
typeh='alg2')
h_parameterization[ih] = parameterization_info(a0=a0.iseq,
a1=a1.iseq,
a2=a2.iseq,
a=a,
b=b,
dist_h=dist_h)
# alg2a
if (sumang > (2 * math.pi + 0.05) and root < 0):
h_parameterization[ih].htype = 'unk_ideal'
elif (sumang < (2 * math.pi + 0.05)
and (sumang > 2 * math.pi - 0.05)):
h_parameterization[ih].htype = 'flat_2neigbs'
else:
if (count_H == 1):
# 2 tetragonal geometry
h_parameterization[ih].htype = '2tetra'
h_parameterization[ih].alpha = h
h_parameterization[i_h2] = parameterization_info(
a0=a0.iseq,
a1=a1.iseq,
a2=a2.iseq,
a=a,
b=b,
alpha=-h,
dist_h=dist_h,
htype='2tetra')
else:
# 2neigbs
h_parameterization[ih].h = h
h_parameterization[ih].htype = '2neigbs'
# tetragonal geometry: 3neigbs
elif (n_red_neigbs == 3 and count_H == 0):
a1, a2, a3 = reduced_neighbs[0], reduced_neighbs[
1], reduced_neighbs[2]
a, b, h = get_coefficients_alg3(
rh=rh,
a0=a0,
a1=a1,
a2=a2,
a3=a3,
use_ideal_bonds_angles=use_ideal_bonds_angles,
sites_cart=sites_cart)
h_parameterization[ih] = parameterization_info(a0=a0.iseq,
a1=a1.iseq,
a2=a2.iseq,
a3=a3.iseq,
a=a,
b=b,
h=h,
dist_h=dist_h,
htype='3neigbs')
# alg1a: X-H2 planar groups, such as in ARG, ASN, GLN
# requires that dihedral angle restraint exists for at least one H atom
elif (n_red_neigbs == 1 and count_H == 1
and len(h_connectivity[ih]) == 4):
b1 = None
a1 = reduced_neighbs[0]
r1 = matrix.col(sites_cart[a1.iseq])
hlist = h_connectivity[ih][2]
ih_2 = hlist[0].iseq
for b1_test in h_connectivity[ih][3]:
if (b1_test.dihedral_ideal is None):
continue
else:
b1 = b1_test
if (b1 == None):
for b1_test in h_connectivity[ih_2][3]:
if (b1_test.dihedral_ideal is None):
continue
else:
b1 = b1_test
ih, ih_2 = ih_2, ih
if (b1 == None):
h_parameterization[ih] = parameterization_info(htype='unk',
a0=a0.iseq)
continue
# check if angle is typical for propeller
# catches case of missing propeller atom
if (hlist[0].angle_ideal > 107 and hlist[0].angle_ideal < 111):
h_parameterization[ih] = parameterization_info(htype='unk',
a0=a0.iseq)
h_parameterization[ih_2] = parameterization_info(htype='unk',
a0=a0.iseq)
continue
dihedral = dihedral_angle(sites=[
sites_cart[b1.iseq], sites_cart[a1.iseq], sites_cart[a0.iseq],
sites_cart[ih]
])
#print 'dihedrals', a0.dihedral, dihedral, a0.dihedral_ideal
rb1 = matrix.col(sites_cart[b1.iseq])
uh0 = (rh - r0).normalize()
u10 = (r1 - r0).normalize()
if use_ideal_bonds_angles:
alpha = math.radians(a1.angle_ideal)
phi = math.radians(b1.dihedral_ideal)
#phi = dihedral
else:
alpha = (u10).angle(uh0)
#phi = a0.dihedral
phi = dihedral
u1 = (r0 - r1).normalize()
rb10 = rb1 - r1
u2 = (rb10 - ((rb10).dot(u10)) * u10).normalize()
u3 = u1.cross(u2)
#print names[ih], names[b1.iseq], names[a1.iseq]
if ih not in h_parameterization:
h_parameterization[ih] = parameterization_info(htype='alg1a',
a0=a0.iseq,
a1=a1.iseq,
a2=b1.iseq,
phi=phi,
n=0,
alpha=alpha,
dist_h=dist_h)
if ih_2 not in h_parameterization:
h_parameterization[ih_2] = parameterization_info(htype='alg1a',
a0=a0.iseq,
a1=a1.iseq,
a2=b1.iseq,
phi=phi +
math.pi,
n=0,
alpha=alpha,
dist_h=dist_h)
# case 1b
# a0.dihedral = dihedral angle between angle ideal and actual position
elif (n_red_neigbs == 1 and (count_H == 0 or count_H == 2)):
if (len(h_connectivity[ih]) != 4):
continue
a1 = reduced_neighbs[0]
b1 = (h_connectivity[ih][3])[0]
r1 = matrix.col(sites_cart[a1.iseq])
rb1 = matrix.col(sites_cart[b1.iseq])
uh0 = (rh - r0).normalize()
u10 = (r1 - r0).normalize()
dihedral = dihedral_angle(sites=[
sites_cart[ih], sites_cart[a0.iseq], sites_cart[a1.iseq],
sites_cart[b1.iseq]
])
if use_ideal_bonds_angles:
alpha = math.radians(a1.angle_ideal)
#phi = math.radians(b1.dihedral_ideal)
#allow for rotation even for idealize = True
phi = dihedral
else:
alpha = (u10).angle(uh0)
phi = dihedral
u1 = (r0 - r1).normalize()
rb10 = rb1 - r1
u2 = (rb10 - ((rb10).dot(u1)) * u1).normalize()
u3 = u1.cross(u2)
h_parameterization[ih] = parameterization_info(htype='alg1b',
a0=a0.iseq,
a1=a1.iseq,
a2=b1.iseq,
phi=phi,
n=0,
alpha=alpha,
dist_h=dist_h)
if (count_H == 2):
h_parameterization[ih].htype = 'prop'
hlist = h_connectivity[ih][2]
ih_2, ih_3 = hlist[0].iseq, hlist[1].iseq
h_parameterization[ih_2] = parameterization_info(htype='prop',
a0=a0.iseq,
a1=a1.iseq,
a2=b1.iseq,
phi=phi,
n=1,
alpha=alpha,
dist_h=dist_h)
# check if order is reversed
ih_2_coord = compute_H_position(sites_cart=sites_cart,
ih=ih_2,
hp=h_parameterization[ih_2])
h_parameterization[ih_3] = parameterization_info(htype='prop',
a0=a0.iseq,
a1=a1.iseq,
a2=b1.iseq,
phi=phi,
n=2,
alpha=alpha,
dist_h=dist_h)
if ((ih_2_coord - matrix.col(sites_cart[ih_3])).length() <
(ih_2_coord - matrix.col(sites_cart[ih_2])).length()):
h_parameterization[ih_2].n = 2
h_parameterization[ih_3].n = 1
else:
h_parameterization[ih] = parameterization_info(htype='unk',
a0=a0.iseq)
return h_parameterization
def get_h_parameterization(connectivity, sites_cart, idealize):
h_parameterization = {}
for ih in connectivity.keys():
#for debugging
#print 'atom:', names[ih]+' ('+str(ih)+ ') residue:', \
# atoms_list[ih].resseq, 'chain', atoms_list[ih].chain_id
# if entry exists already, skip it
if ih in h_parameterization:
continue
a0 = connectivity[ih][0]
count_H = a0.count_H
reduced_neighbs = connectivity[ih][1]
n_red_neigbs = len(reduced_neighbs)
rh = matrix.col(sites_cart[ih])
r0 = matrix.col(sites_cart[a0.iseq])
if idealize:
dist_h = a0.dist_ideal
else:
dist_h = (r0 - rh).length()
# alg2a, 2tetra, 2neigbs
if(n_red_neigbs == 2):
a1, a2 = reduced_neighbs[0], reduced_neighbs[1]
# if H is second neighbor, gets its index
if (count_H == 1):
hlist = connectivity[ih][2]
if hlist:
ih2 = (hlist[0])
i_h2 = (hlist[0]).iseq
else:
ih2 = None
sumang, a, b, h, root = get_coefficients(
ih = ih,
a0 = a0,
a1 = a1,
a2 = a2,
ih2 = ih2,
idealize = idealize,
sites_cart = sites_cart,
typeh = 'alg2')
h_parameterization[ih] = parameterization_info(
a0 = a0.iseq,
a1 = a1.iseq,
a2 = a2.iseq,
a = a,
b = b,
dist_h = dist_h)
# alg2a
if (sumang > (2*math.pi + 0.05) and root < 0):
h_parameterization[ih].htype = 'unk_ideal'
elif (sumang < (2*math.pi + 0.05) and (sumang > 2*math.pi - 0.05)):
h_parameterization[ih].htype = 'flat_2neigbs'
else:
if (count_H == 1):
# 2 tetragonal geometry
h_parameterization[ih].htype = '2tetra'
h_parameterization[ih].alpha = h
h_parameterization[i_h2] = parameterization_info(
a0 = a0.iseq,
a1 = a1.iseq,
a2 = a2.iseq,
a = a,
b = b,
alpha = -h,
dist_h = dist_h,
htype = '2tetra')
else:
# 2neigbs
h_parameterization[ih].h = h
h_parameterization[ih].htype = '2neigbs'
# tetragonal geometry: 3neigbs
elif (n_red_neigbs == 3 and count_H == 0):
a1, a2, a3 = reduced_neighbs[0], reduced_neighbs[1], reduced_neighbs[2]
a, b, h = get_coefficients_alg3(
rh = rh,
a0 = a0,
a1 = a1,
a2 = a2,
a3 = a3,
idealize = idealize,
sites_cart = sites_cart)
h_parameterization[ih] = parameterization_info(
a0 = a0.iseq,
a1 = a1.iseq,
a2 = a2.iseq,
a3 = a3.iseq,
a = a,
b = b,
h = h,
dist_h = dist_h,
htype = '3neigbs')
# alg1a: X-H2 planar groups, such as in ARG, ASN, GLN
# requires that dihedral angle restraint exists
elif(n_red_neigbs == 1 and count_H == 1 and len(connectivity[ih])==4):
a1 = reduced_neighbs[0]
r1 = matrix.col(sites_cart[a1.iseq])
hlist = connectivity[ih][2]
ih_2 = hlist[0].iseq
#if(len(connectivity[ih])!=4):
# continue
b1 = (connectivity[ih][3])[0]
if (b1.dihedral_ideal == None):
continue
#iseq_b1 = b1.iseq
dihedral = dihedral_angle(
sites=[sites_cart[b1.iseq], sites_cart[a1.iseq],
sites_cart[a0.iseq],sites_cart[ih]])
#print 'dihedrals', a0.dihedral, dihedral, a0.dihedral_ideal
rb1 = matrix.col(sites_cart[b1.iseq])
uh0 = (rh - r0).normalize()
u10 = (r1 - r0).normalize()
if idealize:
alpha = math.radians(a1.angle_ideal)
phi = math.radians(b1.dihedral_ideal)
#phi = dihedral
else:
alpha = (u10).angle(uh0)
#phi = a0.dihedral
phi = dihedral
u1 = (r0 - r1).normalize()
rb10 = rb1 - r1
u2 = (rb10 - ((rb10).dot(u10)) * u10).normalize()
u3 = u1.cross(u2)
h_parameterization[ih] = parameterization_info(
htype = 'alg1a',
a0 = a0.iseq,
a1 = a1.iseq,
a2 = b1.iseq,
phi = phi,
n = 0,
alpha = alpha,
dist_h = dist_h)
h_parameterization[ih_2] = parameterization_info(
htype = 'alg1a',
a0 = a0.iseq,
a1 = a1.iseq,
a2 = b1.iseq,
phi = phi+math.pi,
n = 0,
alpha = alpha,
dist_h = dist_h)
# case 1b
# a0.dihedral = dihedral angle between angle ideal and actual position
elif(n_red_neigbs == 1 and (count_H == 0 or count_H ==2)):
#if(count_H == 0 and len(connectivity[ih])!=4):
# print 'the culprit is ', ih, names[ih], atoms_list[ih].resseq
if (len(connectivity[ih])!=4):
continue
a1 = reduced_neighbs[0]
b1 = (connectivity[ih][3])[0]
r1 = matrix.col(sites_cart[a1.iseq])
rb1 = matrix.col(sites_cart[b1.iseq])
uh0 = (rh - r0).normalize()
u10 = (r1 - r0).normalize()
dihedral = dihedral_angle(
sites=[sites_cart[ih], sites_cart[a0.iseq],
sites_cart[a1.iseq],sites_cart[b1.iseq]])
if idealize:
alpha = math.radians(a1.angle_ideal)
#phi = math.radians(b1.dihedral_ideal)
#allow for rotation even for idealize = True
phi = dihedral
else:
alpha = (u10).angle(uh0)
phi = dihedral
u1 = (r0 - r1).normalize()
rb10 = rb1 - r1
u2 = (rb10 - ((rb10).dot(u1)) * u1).normalize()
u3 = u1.cross(u2)
h_parameterization[ih] = parameterization_info(
htype = 'alg1b',
a0 = a0.iseq,
a1 = a1.iseq,
a2 = b1.iseq,
phi = phi,
n = 0,
alpha = alpha,
dist_h = dist_h)
if (count_H == 2):
h_parameterization[ih].htype = 'prop'
hlist = connectivity[ih][2]
# TO DO: Can the order be reversed? To be kept in mind!!
ih_2, ih_3 = hlist[0].iseq, hlist[1].iseq
h_parameterization[ih_2] = parameterization_info(
htype = 'prop',
a0 = a0.iseq,
a1 = a1.iseq,
a2 = b1.iseq,
phi = phi,
n = 1,
alpha = alpha,
dist_h = dist_h)
ih_2_coord = generate_H_positions(
sites_cart = sites_cart,
ih = ih_2,
para_info = h_parameterization[ih_2]).rH_gen
h_parameterization[ih_3] = parameterization_info(
htype = 'prop',
a0 = a0.iseq,
a1 = a1.iseq,
a2 = b1.iseq,
phi = phi,
n = 2,
alpha = alpha,
dist_h = dist_h)
if ((ih_2_coord - matrix.col(sites_cart[ih_3])).length() <
(ih_2_coord - matrix.col(sites_cart[ih_2])).length() ):
h_parameterization[ih_2].n = 2
h_parameterization[ih_3].n = 1
else:
a1 = reduced_neighbs[0]
h_parameterization[ih] = parameterization_info(
htype = 'unk',
a0 = a0.iseq,
a1 = a1.iseq)
return h_parameterization
def get_dihedral_angle(atoms):
from scitbx.math import dihedral_angle
return dihedral_angle(
sites = [x.xyz for x in atoms],
deg=True)
def add_n_terminal_hydrogens_to_atom_group(ag,
use_capping_hydrogens=False,
append_to_end_of_model=False,
retain_original_hydrogens=True,
n_ca_c=None,
):
rc=[]
if n_ca_c is not None:
n, ca, c = n_ca_c
else:
n = ag.get_atom("N")
if n is None: return 'no N'
ca = ag.get_atom("CA")
if ca is None: return 'no CA'
c = ag.get_atom("C")
if c is None: return 'no C'
atom = ag.get_atom('H')
dihedral=120.
if atom:
dihedral = dihedral_angle(sites=[atom.xyz,
n.xyz,
ca.xyz,
c.xyz,
],
deg=True)
if retain_original_hydrogens: pass
else:
if ag.get_atom("H"): # maybe needs to be smarter or actually work
ag.remove_atom(ag.get_atom('H'))
#if use_capping_hydrogens and 0:
# for i, atom in enumerate(ag.atoms()):
# if atom.name == ' H3 ':
# ag.remove_atom(i)
# break
# add H1
rh3 = construct_xyz(n, 0.9,
ca, 109.5,
c, dihedral,
)
# this could be smarter
possible = ['H', 'H1', 'H2', 'H3', 'HT1', 'HT2']
h_count = 0
for h in possible:
if ag.get_atom(h): h_count+=1
number_of_hydrogens=3
if use_capping_hydrogens:
number_of_hydrogens-=1
#if ag.atoms()[0].parent().resname=='PRO':
# number_of_hydrogens=-1
# # should name the hydrogens correctly
if h_count>=number_of_hydrogens: return []
for i in range(0, number_of_hydrogens):
name = " H%d " % (i+1)
if retain_original_hydrogens:
if i==0 and ag.get_atom('H'): continue
if ag.get_atom(name.strip()): continue
if ag.resname=='PRO':
if i==0:
continue
atom = iotbx.pdb.hierarchy.atom()
atom.name = name
atom.element = "H"
atom.xyz = rh3[i]
atom.occ = n.occ
atom.b = n.b
atom.segid = ' '*4
if append_to_end_of_model and i+1==number_of_hydrogens:
rg = _add_atom_to_chain(atom, ag)
rc.append(rg)
else:
ag.append_atom(atom)
return rc
def determine_H_neighbors(geometry_restraints, pdb_hierarchy):
atoms = pdb_hierarchy.atoms()
sites_cart = atoms.extract_xyz()
bond_proxies_simple, asu = geometry_restraints.get_all_bond_proxies(
sites_cart=sites_cart)
angle_proxies = geometry_restraints.get_all_angle_proxies()
dihedral_proxies = geometry_restraints.dihedral_proxies # this should be function in GRM, like previous
fsc2 = geometry_restraints.shell_sym_tables[2].full_simple_connectivity()
fsc1 = geometry_restraints.shell_sym_tables[1].full_simple_connectivity()
#fsc0=geometry_restraints.shell_sym_tables[0].full_simple_h_connectivity()
# Maybe there is better way to get number of atoms?
n_atoms = len(sites_cart)
h_connectivity = {}
double_H = {}
number_h = 0
# -------------------------------------------------------------
# loop through bond proxies to find H atom and parent atom (A0)
# -------------------------------------------------------------
for bproxy in bond_proxies_simple:
i_seq, j_seq = bproxy.i_seqs
is_i_hd = atoms[i_seq].element_is_hydrogen()
is_j_hd = atoms[j_seq].element_is_hydrogen()
if (not is_i_hd and not is_j_hd): continue
elif (is_i_hd and is_j_hd): assert 0
else:
if (is_i_hd): ih, i_parent = i_seq, j_seq
elif (is_j_hd): ih, i_parent = j_seq, i_seq
else:
raise Sorry("Something went wrong in bond proxies")
rh = matrix.col(sites_cart[ih])
r0 = matrix.col(sites_cart[i_parent])
dist = (r0 - rh).length()
parent = atom_info(iseq=i_parent,
dist_ideal=bproxy.distance_ideal,
dist=dist)
altloc_h = atoms[ih].parent().altloc
#print 'atom:', atoms[ih].name+' ('+str(ih)+ ') residue:', \
# atoms[ih].parent().parent().resseq
i_parent_altloc = atoms[i_parent].parent().altloc
# number_h = number_h + 1
# ---------------------------------------------------------
# if entry exists already == H has two bonds
# use the first atom encountered, ignore all others
if (ih in h_connectivity):
double_H[ih] = [(h_connectivity[ih][0]).iseq, i_parent]
continue
# ---------------------------------------------------------
number_h = number_h + 1
# h_connectivity[ih][0] --> parent atom
h_connectivity[ih] = [parent]
# h_connectivity[ih][1] --> list of second non-H neighbours
h_connectivity[ih].append([])
# h_connectivity[ih][2] --> list of second H/D neighbours
h_connectivity[ih].append([])
# compute total list of second neighbors
second_neighbors = list(fsc1[ih])
count_H = 0
altloc_dict = {}
# loop to find second neighbors (ignore those where angle proxies don't
# exist, and choose same altloc for all second neighbors)
for i_second in second_neighbors:
iselection = flex.size_t([ih, i_parent, i_second])
ap = angle_proxies.proxy_select(n_seq=n_atoms,
iselection=iselection)
if (ap):
angle_ideal = ap[0].angle_ideal
if (i_second in altloc_dict.keys()):
continue
altloc_dict_temp = {}
i_second_altloc = atoms[i_second].parent().altloc
# make sure that all second neighbors belong to same altloc
if (h_connectivity[ih][1] and atoms[
(h_connectivity[ih][1])[0].iseq].parent().altloc != ''):
iseq_previous = (h_connectivity[ih][1])[0].iseq
overall_altloc = atoms[iseq_previous].parent().altloc
if (i_second_altloc != '' and altloc_h == ''
and i_second_altloc != overall_altloc):
continue
# if no previous altloc, chose that which has highest occ
elif (i_second_altloc != '' and altloc_h == ''
and i_parent_altloc != i_second_altloc):
altloc_dict_temp = make_altloc_dict(
atoms=atoms,
index=i_second,
altloc_dict_temp=altloc_dict_temp,
neighbors=second_neighbors,
altloc=i_second_altloc)
if (i_second in altloc_dict_temp.keys()):
i_second = max(altloc_dict_temp,
key=lambda k: altloc_dict_temp[k])
iselection = flex.size_t([ih, i_parent, i_second])
ap = angle_proxies.proxy_select(n_seq=n_atoms,
iselection=iselection)
if ap:
angle_ideal = ap[0].angle_ideal
altloc_dict.update(altloc_dict_temp)
neighbor = atom_info(iseq=i_second, angle_ideal=angle_ideal)
is_same_hd = is_same_element(iseq1=ih,
iseq2=i_second,
atoms=atoms)
if ((atoms[i_second].element_is_hydrogen() and is_same_hd)
or (atoms[i_second].element_is_hydrogen()
and i_second_altloc == '')):
h_connectivity[ih][2].append(neighbor)
count_H = count_H + 1
elif (not atoms[i_second].element_is_hydrogen()):
h_connectivity[ih][1].append(neighbor)
(h_connectivity[ih][0]).count_H = count_H
# ---------------------------------------------------------
# find third neighbors, if necessary
# ---------------------------------------------------------
# possibly, code for second and third neighbors can be transformed
# to a function - TODO
if (len(h_connectivity[ih][1]) == 1):
h_connectivity[ih].append([])
i_second = ((h_connectivity[ih][1])[0]).iseq
third_neighbors = list(fsc2[ih])
altloc_dict_third = {}
for i_third in third_neighbors:
if (not atoms[i_third].element_is_hydrogen()):
iselection = flex.size_t([i_parent, i_second, i_third])
ap = angle_proxies.proxy_select(n_seq=n_atoms,
iselection=iselection)
if ap:
if (i_third in altloc_dict_third.keys()):
continue
altloc_dict_third_temp = {}
i_third_altloc = atoms[i_third].parent().altloc
# make sure that all third neighbors belong to the same altloc
if (h_connectivity[ih][3]
and atoms[(h_connectivity[ih][3]
)[0].iseq].parent().altloc != ''):
iseq_previous_third = (
h_connectivity[ih][3])[0].iseq
overall_altloc_third = atoms[
iseq_previous_third].parent().altloc
if (i_third_altloc != '' and altloc_h == '' and
i_third_altloc != overall_altloc_third):
continue
elif (i_third_altloc != '' and altloc_h == ''):
altloc_dict_third_temp = make_altloc_dict(
atoms=atoms,
index=i_third,
altloc_dict_temp=altloc_dict_third_temp,
neighbors=third_neighbors,
altloc=i_third_altloc)
if (i_third in altloc_dict_third_temp.keys()):
i_third = max(
altloc_dict_third_temp,
key=lambda k: altloc_dict_third_temp[k])
altloc_dict_third.update(altloc_dict_third_temp)
# get dihedral angle between H, A0, A1 and third neighbor(B1, B2)
iselection_dihe = flex.size_t(
[ih, i_parent, i_second, i_third])
dp = dihedral_proxies.proxy_select(
n_seq=n_atoms, iselection=iselection_dihe)
dihedral = dihedral_angle(sites=[
sites_cart[i_third], sites_cart[i_second],
sites_cart[i_parent], sites_cart[ih]
])
sites_cart_dihe = sites_cart.select(
iselection_dihe).deep_copy()
if dp:
dihedral_id = dp[0].angle_ideal
delta = dp.deltas(sites_cart=sites_cart_dihe)[0]
dihedral_ideal = math.degrees(dihedral) + delta
else:
dihedral_ideal = None
neighbor = atom_info(iseq=i_third,
dihedral=dihedral,
dihedral_ideal=dihedral_ideal)
h_connectivity[ih][3].append(neighbor)
# get ideal angles involving parent and other non-H second neighbors
n_sec_neigbs = len(h_connectivity[ih][1])
if (n_sec_neigbs == 2 or n_sec_neigbs == 3):
reduced_neighbs = h_connectivity[ih][1]
angles = []
ix = i_parent
if (n_sec_neigbs == 2):
_list = [(0, 1)]
else:
_list = [(0, 1), (1, 2), (2, 0)]
for _i, _j in _list:
iy = (reduced_neighbs[_i]).iseq
iz = (reduced_neighbs[_j]).iseq
iselection = flex.size_t([ix, iy, iz])
ap = angle_proxies.proxy_select(n_seq=n_atoms,
iselection=iselection)
if ap:
angles.append(ap[0].angle_ideal)
else:
raise Sorry("Expected ideal angles are missing. \
Second neigbs - parent atom.")
(h_connectivity[ih][0]).angle_ideal = angles
#
return group_args(h_connectivity=h_connectivity,
double_H=double_H,
number_h=number_h)
def process_1_neighbor(self, neighbors):
ih = neighbors.ih
i_a0 = neighbors.a0['iseq']
rh = matrix.col(self.sites_cart[ih])
r0 = matrix.col(self.sites_cart[i_a0])
if self.use_ideal_bonds_angles:
disth = neighbors.a0['dist_ideal']
else:
disth = (r0 - rh).length()
i_a1 = neighbors.a1['iseq']
i_b1 = neighbors.b1['iseq']
r1 = matrix.col(self.sites_cart[i_a1])
rb1 = matrix.col(self.sites_cart[i_b1])
uh0 = (rh - r0).normalize()
u10 = (r1 - r0).normalize()
dihedral = dihedral_angle(sites=[
self.sites_cart[ih], self.sites_cart[i_a0], self.sites_cart[i_a1],
self.sites_cart[i_b1]
])
if self.use_ideal_bonds_angles:
alpha = math.radians(neighbors.a1['angle_ideal'])
#allow for rotation even for idealize = True
#phi = math.radians(b1.dihedral_ideal)
phi = dihedral
else:
alpha = (u10).angle(uh0)
phi = dihedral
u1 = (r0 - r1).normalize()
rb10 = rb1 - r1
u2 = (rb10 - ((rb10).dot(u1)) * u1).normalize()
u3 = u1.cross(u2)
if (neighbors.number_h_neighbors == 0):
self.h_parameterization[ih] = riding_coefficients(htype='alg1b',
ih=ih,
a0=i_a0,
a1=i_a1,
a2=i_b1,
a3=0,
a=alpha,
b=phi,
h=0,
n=0,
disth=disth)
if (neighbors.number_h_neighbors == 2):
i_h1, i_h2 = neighbors.h1['iseq'], neighbors.h2['iseq']
i_h1, i_h2 = self.check_propeller_order(i_a0=i_a0,
i_a1=i_a1,
ih=ih,
i_h1=i_h1,
i_h2=i_h2)
for nprop, hprop in zip([0, 1, 2], [ih, i_h1, i_h2]):
self.h_parameterization[hprop] = riding_coefficients(
htype='prop',
ih=hprop,
a0=i_a0,
a1=i_a1,
a2=i_b1,
a3=0,
a=alpha,
n=nprop,
b=phi,
h=0,
disth=disth)