def set_ion_determinants(conformation_container, version):
"""Add ion determinants and perturbations.
Args:
conformation_container: conformation to set
version: version object
"""
for titratable_group in conformation_container.get_titratable_groups():
for ion_group in conformation_container.get_ions():
dist_sq = squared_distance(titratable_group, ion_group)
if dist_sq < version.parameters.coulomb_cutoff2_squared:
weight = version.calculate_pair_weight(
titratable_group.num_volume, ion_group.num_volume)
# the pKa of both acids and bases are shifted up by negative
# ions (and vice versa)
value = (-ion_group.charge * version.calculate_coulomb_energy(
math.sqrt(dist_sq), weight))
new_det = Determinant(ion_group, value)
titratable_group.determinants['coulomb'].append(new_det)
def radial_volume_desolvation(parameters, group):
"""Calculate desolvation terms for group.
Args:
parameters: parameters for desolvation calculation
group: group of atoms for calculation
"""
all_atoms = group.atom.conformation_container.get_non_hydrogen_atoms()
volume = 0.0
group.num_volume = 0
min_dist_4th = MIN_DISTANCE_4TH
for atom in all_atoms:
# ignore atoms in the same residue
if (atom.res_num == group.atom.res_num
and atom.chain_id == group.atom.chain_id):
continue
sq_dist = squared_distance(group, atom)
# desolvation
if sq_dist < parameters.desolv_cutoff_squared:
# use a default relative volume of 1.0 if the volume of the element
# is not found in parameters
# insert check for methyl groups
if atom.element == 'C' and atom.name not in ['CA', 'C']:
dvol = parameters.VanDerWaalsVolume['C4']
else:
dvol = parameters.VanDerWaalsVolume.get(atom.element, 1.0)
dv_inc = dvol / max(min_dist_4th, sq_dist * sq_dist)
volume += dv_inc
# buried
if sq_dist < parameters.buried_cutoff_squared:
group.num_volume += 1
group.buried = calculate_weight(parameters, group.num_volume)
scale_factor = calculate_scale_factor(parameters, group.buried)
volume_after_allowance = max(0.00,
volume - parameters.desolvationAllowance)
group.energy_volume = (group.charge * parameters.desolvationPrefactor *
volume_after_allowance * scale_factor)
def assign_sybyl_type(atom):
"""Assign Sybyl type to atom.
Args:
atom: atom to assign
"""
# check if we already have assigned a name to this atom
if atom.sybyl_assigned:
return
# find some properties of the atom
ring_atoms = is_ring_member(atom)
aromatic = is_aromatic_ring(ring_atoms)
planar = is_planar(atom)
bonded_elements = {}
for i, bonded_atom in enumerate(atom.bonded_atoms):
bonded_elements[i] = bonded_atom.element
# Aromatic carbon/nitrogen
if aromatic:
for ring_atom in ring_atoms:
if ring_atom.element in ['C', 'N']:
set_type(ring_atom, ring_atom.element + '.ar')
return
# check for amide
if atom.element in ['O', 'N', 'C']:
o_atom = None
n_atom = None
c_atom = None
# oxygen, nitrogen
if atom.element in ['O', 'N']:
for bonded_elem in atom.get_bonded_elements('C'):
for bonded_atom in bonded_elem.bonded_atoms:
if (bonded_atom.element == 'N' and atom.element == 'O'):
o_atom = atom
c_atom = bonded_elem
n_atom = bonded_atom
elif (bonded_atom.element == 'O' and atom.element == 'N'):
n_atom = atom
c_atom = bonded_elem
o_atom = bonded_atom
# carbon
if atom.element == 'C':
nitrogens = atom.get_bonded_elements('N')
oxygens = atom.get_bonded_elements('O')
if len(nitrogens) == 1 and len(oxygens) == 1:
c_atom = atom
n_atom = nitrogens[0]
o_atom = oxygens[0]
if c_atom and n_atom and o_atom:
# make sure that the Nitrogen is not aromatic and that it has two
# heavy atom bonds
if (not is_aromatic_ring(is_ring_member(n_atom))
and len(n_atom.get_bonded_heavy_atoms()) == 2):
set_type(n_atom, 'N.am')
set_type(c_atom, 'C.2')
set_type(o_atom, 'O.2')
return
if atom.element == 'C':
# check for carboxyl
if (len(atom.bonded_atoms) == 3
and list(bonded_elements.values()).count('O') == 2):
index1 = list(bonded_elements.values()).index('O')
index2 = list(bonded_elements.values()).index('O', index1 + 1)
if (len(atom.bonded_atoms[index1].bonded_atoms) == 1
and len(atom.bonded_atoms[index2].bonded_atoms) == 1):
set_type(atom.bonded_atoms[index1], 'O.co2-')
set_type(atom.bonded_atoms[index2], 'O.co2')
set_type(atom, 'C.2')
return
# sp carbon
if len(atom.bonded_atoms) <= 2:
for bonded_atom in atom.bonded_atoms:
if (squared_distance(atom, bonded_atom) <
MAX_C_TRIPLE_BOND_SQUARED):
set_type(atom, 'C.1')
set_type(bonded_atom, bonded_atom.element + '.1')
if atom.sybyl_assigned:
return
# sp2 carbon
if planar:
set_type(atom, 'C.2')
# check for N.pl3
for bonded_atom in atom.bonded_atoms:
if bonded_atom.element == 'N':
if (len(bonded_atom.bonded_atoms) < 3
or is_planar(bonded_atom)):
set_type(bonded_atom, 'N.pl3')
return
# sp3 carbon
set_type(atom, 'C.3')
return
# Nitrogen
if atom.element == 'N':
# check for planar N
if len(atom.bonded_atoms) == 1:
if is_planar(atom.bonded_atoms[0]):
set_type(atom, 'N.pl3')
return
if planar:
set_type(atom, 'N.pl3')
return
set_type(atom, 'N.3')
return
# Oxygen
if atom.element == 'O':
set_type(atom, 'O.3')
if len(atom.bonded_atoms) == 1:
# check for carboxyl
if atom.bonded_atoms[0].element == 'C':
the_carbon = atom.bonded_atoms[0]
if (len(the_carbon.bonded_atoms) == 3
and the_carbon.count_bonded_elements('O') == 2):
[oxy1, oxy2] = the_carbon.get_bonded_elements('O')
if (len(oxy1.bonded_atoms) == 1
and len(oxy2.bonded_atoms) == 1):
set_type(oxy1, 'O.co2-')
set_type(oxy2, 'O.co2')
set_type(the_carbon, 'C.2')
return
# check for X=O
if (squared_distance(atom, atom.bonded_atoms[0]) <
MAX_C_DOUBLE_BOND_SQUARED):
set_type(atom, 'O.2')
if atom.bonded_atoms[0].element == 'C':
set_type(atom.bonded_atoms[0], 'C.2')
return
# Sulphur
if atom.element == 'S':
# check for SO2
if list(bonded_elements.values()).count('O') == 2:
index1 = list(bonded_elements.values()).index('O')
index2 = list(bonded_elements.values()).index('O', index1 + 1)
set_type(atom.bonded_atoms[index1], 'O.2')
set_type(atom.bonded_atoms[index2], 'O.2')
set_type(atom, 'S.o2')
return
# check for SO4
if list(bonded_elements.values()).count('O') == 4:
no_o2 = 0
for i in range(len(atom.bonded_atoms)):
if len(atom.bonded_atoms[i].bonded_atoms) == 1 and no_o2 < 2:
set_type(atom.bonded_atoms[i], 'O.2')
no_o2 += 1
else:
set_type(atom.bonded_atoms[i], 'O.3')
set_type(atom, 'S.3')
return
# Phosphorus
if atom.element == 'P':
set_type(atom, 'P.3')
# check for phosphate group
bonded_oxygens = atom.get_bonded_elements('O')
for o_atom in bonded_oxygens:
set_type(o_atom, 'O.3')
return
element = atom.element.capitalize()
set_type(atom, element)