def trigonal(self, atom):
"""Add hydrogens in trigonal geometry.
Args:
atom: atom to protonate
"""
debug('TRIGONAL - {0:d} bonded atoms'.format(len(atom.bonded_atoms)))
rot_angle = math.radians(120.0)
cvec = Vector(atom1=atom)
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
avec = Vector(atom1=atom, atom2=atom.bonded_atoms[0])
# use plane of bonded trigonal atom - e.g. arg
self.set_steric_number_and_lone_pairs(atom.bonded_atoms[0])
if (atom.bonded_atoms[0].steric_number == 3
and len(atom.bonded_atoms[0].bonded_atoms) > 1):
# use other atoms bonded to the neighbour to establish the
# plane, if possible
other_atom_indices = []
for i, bonded_atom in enumerate(
atom.bonded_atoms[0].bonded_atoms):
if bonded_atom != atom:
other_atom_indices.append(i)
vec1 = Vector(atom1=atom, atom2=atom.bonded_atoms[0])
vec2 = Vector(atom1=atom.bonded_atoms[0],
atom2=atom.bonded_atoms[0].bonded_atoms[
other_atom_indices[0]])
axis = vec1**vec2
# this is a trick to make sure that the order of atoms doesn't
# influence the final postions of added protons
if len(other_atom_indices) > 1:
vec3 = Vector(atom1=atom.bonded_atoms[0],
atom2=atom.bonded_atoms[0].bonded_atoms[
other_atom_indices[1]])
axis2 = vec1**vec3
if axis * axis2 > 0:
axis = axis + axis2
else:
axis = axis - axis2
else:
axis = avec.orthogonal()
avec = rotate_vector_around_an_axis(rot_angle, axis, avec)
avec = self.set_bond_distance(avec, atom.element)
self.add_proton(atom, cvec + avec)
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
avec1 = Vector(atom1=atom, atom2=atom.bonded_atoms[0]).rescale(1.0)
avec2 = Vector(atom1=atom, atom2=atom.bonded_atoms[1]).rescale(1.0)
new_a = -avec1 - avec2
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, cvec + new_a)
def add_protons(self, atom):
# decide which method to use
debug('PROTONATING',atom)
if atom.steric_number in list(self.protonation_methods.keys()):
self.protonation_methods[atom.steric_number](atom)
else:
warning('Do not have a method for protonating', atom, '(steric number: %d)' % atom.steric_number)
return
def add_protons(self, atom):
# decide which method to use
debug('PROTONATING', atom)
if atom.steric_number in list(self.protonation_methods.keys()):
self.protonation_methods[atom.steric_number](atom)
else:
warning('Do not have a method for protonating', atom,
'(steric number: %d)' % atom.steric_number)
return
def add_protons(self, atom):
"""Add protons to atom.
Args:
atom: atom for calculation
"""
# decide which method to use
debug('PROTONATING', atom)
if atom.steric_number in list(self.protonation_methods.keys()):
self.protonation_methods[atom.steric_number](atom)
else:
warning('Do not have a method for protonating', atom,
'(steric number: {0:d})'.format(atom.steric_number))
def protonate(self, molecules):
"""Protonate all atoms in the molecular container.
Args:
molecules: molecular containers
"""
debug('----- Protonation started -----')
# Remove all currently present hydrogen atoms
self.remove_all_hydrogen_atoms(molecules)
# protonate all atoms
for name in molecules.conformation_names:
non_h_atoms = (
molecules.conformations[name].get_non_hydrogen_atoms())
for atom in non_h_atoms:
self.protonate_atom(atom)
def tetrahedral(self, atom):
debug('TETRAHEDRAL - %d bonded atoms' % (len(atom.bonded_atoms)))
rot_angle = math.radians(109.5)
# sanity check
# if atom.number_of_protons_to_add + len(atom.bonded_atoms) != 4:
# self.display 'Error: Attempting tetrahedral structure with %d bonds'%(atom.number_of_protons_to_add +
# len(atom.bonded_atoms))
c = vector(atom1=atom)
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
a = vector(atom1=atom, atom2=atom.bonded_atoms[0])
axis = a.orthogonal()
a = rotate_vector_around_an_axis(rot_angle, axis, a)
a = self.set_bond_distance(a, atom.element)
self.add_proton(atom, c + a)
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
a1 = vector(atom1=atom, atom2=atom.bonded_atoms[0]).rescale(1.0)
a2 = vector(atom1=atom, atom2=atom.bonded_atoms[1]).rescale(1.0)
axis = a1 + a2
new_a = rotate_vector_around_an_axis(math.radians(90), axis, -a1)
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, c + new_a)
# 3 bonds
if len(atom.bonded_atoms) == 3 and atom.number_of_protons_to_add > 0:
a1 = vector(atom1=atom, atom2=atom.bonded_atoms[0]).rescale(1.0)
a2 = vector(atom1=atom, atom2=atom.bonded_atoms[1]).rescale(1.0)
a3 = vector(atom1=atom, atom2=atom.bonded_atoms[2]).rescale(1.0)
new_a = -a1 - a2 - a3
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, c + new_a)
return
def tetrahedral(self, atom):
debug('TETRAHEDRAL - %d bonded atoms'%(len(atom.bonded_atoms)))
rot_angle = math.radians(109.5)
# sanity check
# if atom.number_of_protons_to_add + len(atom.bonded_atoms) != 4:
# self.display 'Error: Attempting tetrahedral structure with %d bonds'%(atom.number_of_protons_to_add +
# len(atom.bonded_atoms))
c = vector(atom1 = atom)
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
a = vector(atom1 = atom, atom2 = atom.bonded_atoms[0])
axis = a.orthogonal()
a = rotate_vector_around_an_axis(rot_angle, axis, a)
a = self.set_bond_distance(a, atom.element)
self.add_proton(atom, c+a)
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
a1 = vector(atom1 = atom, atom2 = atom.bonded_atoms[0]).rescale(1.0)
a2 = vector(atom1 = atom, atom2 = atom.bonded_atoms[1]).rescale(1.0)
axis = a1 + a2
new_a = rotate_vector_around_an_axis(math.radians(90), axis, -a1)
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, c+new_a)
# 3 bonds
if len(atom.bonded_atoms) == 3 and atom.number_of_protons_to_add > 0:
a1 = vector(atom1 = atom, atom2 = atom.bonded_atoms[0]).rescale(1.0)
a2 = vector(atom1 = atom, atom2 = atom.bonded_atoms[1]).rescale(1.0)
a3 = vector(atom1 = atom, atom2 = atom.bonded_atoms[2]).rescale(1.0)
new_a = -a1-a2-a3
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, c+new_a)
return
def add_proton(atom, position):
"""Add a proton to an atom at a specific position.
Args:
atom: atom to protonate
position: position for proton
"""
# Create the new proton
new_h = propka.atom.Atom()
new_h.set_property(
numb=None,
name='H{0:s}'.format(atom.name[1:]),
res_name=atom.res_name,
chain_id=atom.chain_id,
res_num=atom.res_num,
x=round(position.x, 3), # round of to three decimal points to
# avoid round-off differences in input file
y=round(position.y, 3),
z=round(position.z, 3),
occ=None,
beta=None)
new_h.element = 'H'
new_h.type = atom.type
new_h.bonded_atoms = [atom]
new_h.charge = 0
new_h.steric_number = 0
new_h.number_of_lone_pairs = 0
new_h.number_of_protons_to_add = 0
new_h.num_pi_elec_2_3_bonds = 0
new_h.is_protonates = True
atom.bonded_atoms.append(new_h)
atom.number_of_protons_to_add -= 1
atom.conformation_container.add_atom(new_h)
# update names of all protons on this atom
new_h.residue_label = "{0:<3s}{1:>4d}{2:>2s}".format(
new_h.name, new_h.res_num, new_h.chain_id)
no_protons = atom.count_bonded_elements('H')
if no_protons > 1:
i = 1
for proton in atom.get_bonded_elements('H'):
proton.name = 'H{0:s}{1:d}'.format(atom.name[1:], i)
proton.residue_label = "{0:<3s}{1:>4d}{2:>2s}".format(
proton.name, proton.res_num, proton.chain_id)
i += 1
debug('added', new_h, 'to', atom)
def protonate(self, molecules):
""" Will protonate all atoms in the molecular container """
debug('----- Protonation started -----')
# Remove all currently present hydrogen atoms
self.remove_all_hydrogen_atoms(molecules)
# protonate all atoms
for name in molecules.conformation_names:
non_H_atoms = molecules.conformations[name].get_non_hydrogen_atoms()
for atom in non_H_atoms:
self.protonate_atom(atom)
# fix hydrogen names
#self.set_proton_names(non_H_atoms)
return
def set_charge(self, atom):
# atom is a protein atom
if atom.type == 'atom':
key = '%3s-%s' % (atom.resName, atom.name)
if atom.terminal:
debug(atom.terminal)
key = atom.terminal
if key in list(self.standard_charges.keys()):
atom.charge = self.standard_charges[key]
debug('Charge', atom, atom.charge)
atom.charge_set = True
# atom is a ligand atom
elif atom.type == 'hetatm':
if atom.sybyl_type in list(self.sybyl_charges.keys()):
atom.charge = self.sybyl_charges[atom.sybyl_type]
atom.sybyl_type = atom.sybyl_type.replace('-', '')
atom.charge_set = True
return
def set_charge(self, atom):
# atom is a protein atom
if atom.type=='atom':
key = '%3s-%s'%(atom.resName, atom.name)
if atom.terminal:
debug(atom.terminal)
key=atom.terminal
if key in list(self.standard_charges.keys()):
atom.charge = self.standard_charges[key]
debug('Charge', atom, atom.charge)
atom.charge_set = True
# atom is a ligand atom
elif atom.type=='hetatm':
if atom.sybyl_type in list(self.sybyl_charges.keys()):
atom.charge = self.sybyl_charges[atom.sybyl_type]
atom.sybyl_type = atom.sybyl_type.replace('-','')
atom.charge_set = True
return
def protonate(self, molecules):
""" Will protonate all atoms in the molecular container """
debug('----- Protonation started -----')
# Remove all currently present hydrogen atoms
self.remove_all_hydrogen_atoms(molecules)
# protonate all atoms
for name in molecules.conformation_names:
non_H_atoms = molecules.conformations[name].get_non_hydrogen_atoms(
)
for atom in non_H_atoms:
self.protonate_atom(atom)
# fix hydrogen names
#self.set_proton_names(non_H_atoms)
return
def add_proton(self, atom, position):
# Create the new proton
new_H = propka.atom.Atom()
new_H.setProperty(
numb=None,
name='H%s' % atom.name[1:],
resName=atom.resName,
chainID=atom.chainID,
resNumb=atom.resNumb,
x=round(position.x, 3), # round of to three digimal points
y=round(position.y, 3), # to avoid round-off differences
z=round(position.z, 3), # when input file
occ=None,
beta=None)
new_H.element = 'H'
new_H.type = atom.type
new_H.bonded_atoms = [atom]
new_H.charge = 0
new_H.steric_number = 0
new_H.number_of_lone_pairs = 0
new_H.number_of_protons_to_add = 0
new_H.number_of_pi_electrons_in_double_and_triple_bonds = 0
new_H.is_protonates = True
atom.bonded_atoms.append(new_H)
atom.number_of_protons_to_add -= 1
atom.conformation_container.add_atom(new_H)
# update names of all protons on this atom
new_H.residue_label = "%-3s%4d%2s" % (new_H.name, new_H.resNumb,
new_H.chainID)
no_protons = atom.count_bonded_elements('H')
if no_protons > 1:
i = 1
for proton in atom.get_bonded_elements('H'):
proton.name = 'H%s%d' % (atom.name[1:], i)
proton.residue_label = "%-3s%4d%2s" % (
proton.name, proton.resNumb, proton.chainID)
i += 1
debug('added', new_H, 'to', atom)
return
def add_proton(self, atom, position):
# Create the new proton
new_H = propka.atom.Atom()
new_H.setProperty(numb = None,
name = 'H%s'%atom.name[1:],
resName = atom.resName,
chainID = atom.chainID,
resNumb = atom.resNumb,
x = round(position.x,3), # round of to three digimal points
y = round(position.y,3), # to avoid round-off differences
z = round(position.z,3), # when input file
occ = None,
beta = None)
new_H.element = 'H'
new_H.type = atom.type
new_H.bonded_atoms = [atom]
new_H.charge = 0
new_H.steric_number = 0
new_H.number_of_lone_pairs = 0
new_H.number_of_protons_to_add = 0
new_H.number_of_pi_electrons_in_double_and_triple_bonds = 0
new_H.is_protonates = True
atom.bonded_atoms.append(new_H)
atom.number_of_protons_to_add -=1
atom.conformation_container.add_atom(new_H)
# update names of all protons on this atom
new_H.residue_label = "%-3s%4d%2s" % (new_H.name,new_H.resNumb, new_H.chainID)
no_protons = atom.count_bonded_elements('H')
if no_protons > 1:
i = 1
for proton in atom.get_bonded_elements('H'):
proton.name = 'H%s%d'%(atom.name[1:],i)
proton.residue_label = "%-3s%4d%2s" % (proton.name,proton.resNumb, proton.chainID)
i+=1
debug('added',new_H, 'to',atom)
return
def tetrahedral(self, atom):
"""Protonate atom in tetrahedral geometry.
Args:
atom: atom to protonate.
"""
debug('TETRAHEDRAL - {0:d} bonded atoms'.format(len(
atom.bonded_atoms)))
# TODO - might be good to move tetrahedral angle to constant
rot_angle = math.radians(109.5)
cvec = Vector(atom1=atom)
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
avec = Vector(atom1=atom, atom2=atom.bonded_atoms[0])
axis = avec.orthogonal()
avec = rotate_vector_around_an_axis(rot_angle, axis, avec)
avec = self.set_bond_distance(avec, atom.element)
self.add_proton(atom, cvec + avec)
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
avec1 = Vector(atom1=atom, atom2=atom.bonded_atoms[0]).rescale(1.0)
avec2 = Vector(atom1=atom, atom2=atom.bonded_atoms[1]).rescale(1.0)
axis = avec1 + avec2
new_a = rotate_vector_around_an_axis(math.radians(90), axis,
-avec1)
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, cvec + new_a)
# 3 bonds
if len(atom.bonded_atoms) == 3 and atom.number_of_protons_to_add > 0:
avec1 = Vector(atom1=atom, atom2=atom.bonded_atoms[0]).rescale(1.0)
avec2 = Vector(atom1=atom, atom2=atom.bonded_atoms[1]).rescale(1.0)
avec3 = Vector(atom1=atom, atom2=atom.bonded_atoms[2]).rescale(1.0)
new_a = -avec1 - avec2 - avec3
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, cvec + new_a)
def set_charge(self, atom):
"""Set charge for atom.
Args:
atom: atom to be charged
"""
# atom is a protein atom
if atom.type == 'atom':
key = '{0:3s}-{1:s}'.format(atom.res_name, atom.name)
if atom.terminal:
debug(atom.terminal)
key = atom.terminal
if key in self.standard_charges:
atom.charge = self.standard_charges[key]
debug('Charge', atom, atom.charge)
atom.charge_set = True
# atom is a ligand atom
elif atom.type == 'hetatm':
if atom.sybyl_type in self.sybyl_charges:
atom.charge = self.sybyl_charges[atom.sybyl_type]
atom.sybyl_type = atom.sybyl_type.replace('-', '')
atom.charge_set = True
def trigonal(self, atom):
debug('TRIGONAL - %d bonded atoms' % (len(atom.bonded_atoms)))
rot_angle = math.radians(120.0)
c = vector(atom1=atom)
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
a = vector(atom1=atom, atom2=atom.bonded_atoms[0])
# use plane of bonded trigonal atom - e.g. arg
self.set_steric_number_and_lone_pairs(atom.bonded_atoms[0])
if atom.bonded_atoms[0].steric_number == 3 and len(
atom.bonded_atoms[0].bonded_atoms) > 1:
# use other atoms bonded to the neighbour to establish the plane, if possible
other_atom_indices = []
for i in range(len(atom.bonded_atoms[0].bonded_atoms)):
if atom.bonded_atoms[0].bonded_atoms[i] != atom:
other_atom_indices.append(i)
v1 = vector(atom1=atom, atom2=atom.bonded_atoms[0])
v2 = vector(atom1=atom.bonded_atoms[0],
atom2=atom.bonded_atoms[0].bonded_atoms[
other_atom_indices[0]])
axis = v1**v2
# this is a trick to make sure that the order of atoms doesn't influence
# the final postions of added protons
if len(other_atom_indices) > 1:
v3 = vector(atom1=atom.bonded_atoms[0],
atom2=atom.bonded_atoms[0].bonded_atoms[
other_atom_indices[1]])
axis2 = v1**v3
if axis * axis2 > 0:
axis = axis + axis2
else:
axis = axis - axis2
else:
axis = a.orthogonal()
a = rotate_vector_around_an_axis(rot_angle, axis, a)
a = self.set_bond_distance(a, atom.element)
self.add_proton(atom, c + a)
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
a1 = vector(atom1=atom, atom2=atom.bonded_atoms[0]).rescale(1.0)
a2 = vector(atom1=atom, atom2=atom.bonded_atoms[1]).rescale(1.0)
new_a = -a1 - a2
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, c + new_a)
return
def set_steric_number_and_lone_pairs(self, atom):
# If we already did this, there is no reason to do it again
if atom.steric_number_and_lone_pairs_set:
return
debug('='*10)
debug('Setting steric number and lone pairs for',atom)
# costumly set the N backbone atoms up for peptide bond trigonal planer shape
#if atom.name == 'N' and len(atom.bonded_atoms) == 2:
# atom.steric_number = 3
# atom.number_of_lone_pairs = 0
# self.display 'Peptide bond: steric number is %d and number of lone pairs is %s'%(atom.steric_number,
# atom.number_of_lone_pairs)
# return
atom.steric_number = 0
debug('%65s: %4d'%('Valence electrons',self.valence_electrons[atom.element]))
atom.steric_number += self.valence_electrons[atom.element]
debug('%65s: %4d'%('Number of bonds',len(atom.bonded_atoms)))
atom.steric_number += len(atom.bonded_atoms)
debug('%65s: %4d'%('Number of hydrogen atoms to add',atom.number_of_protons_to_add))
atom.steric_number += atom.number_of_protons_to_add
debug('%65s: %4d'%('Number of pi-electrons in double and triple bonds(-)',atom.number_of_pi_electrons_in_double_and_triple_bonds))
atom.steric_number -= atom.number_of_pi_electrons_in_double_and_triple_bonds
debug('%65s: %4d'%('Number of pi-electrons in conjugated double and triple bonds(-)',atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds))
atom.steric_number -= atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds
debug('%65s: %4d'%('Number of donated co-ordinated bonds',0))
atom.steric_number += 0
debug('%65s: %4.1f'%('Charge(-)',atom.charge))
atom.steric_number -= atom.charge
atom.steric_number = math.floor(atom.steric_number/2.0)
atom.number_of_lone_pairs = atom.steric_number - len(atom.bonded_atoms) - atom.number_of_protons_to_add
debug('-'*70)
debug('%65s: %4d'%('Steric number',atom.steric_number))
debug('%65s: %4d'%('Number of lone pairs',atom.number_of_lone_pairs))
atom.steric_number_and_lone_pairs_set = True
return
def trigonal(self, atom):
debug('TRIGONAL - %d bonded atoms'%(len(atom.bonded_atoms)))
rot_angle = math.radians(120.0)
c = vector(atom1 = atom)
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
a = vector(atom1 = atom, atom2 = atom.bonded_atoms[0])
# use plane of bonded trigonal atom - e.g. arg
self.set_steric_number_and_lone_pairs(atom.bonded_atoms[0])
if atom.bonded_atoms[0].steric_number == 3 and len(atom.bonded_atoms[0].bonded_atoms)>1:
# use other atoms bonded to the neighbour to establish the plane, if possible
other_atom_indices = []
for i in range(len(atom.bonded_atoms[0].bonded_atoms)):
if atom.bonded_atoms[0].bonded_atoms[i] != atom:
other_atom_indices.append(i)
v1 = vector(atom1 = atom, atom2 = atom.bonded_atoms[0])
v2 = vector(atom1 = atom.bonded_atoms[0],
atom2 = atom.bonded_atoms[0].bonded_atoms[other_atom_indices[0]])
axis = v1**v2
# this is a trick to make sure that the order of atoms doesn't influence
# the final postions of added protons
if len(other_atom_indices)>1:
v3 = vector(atom1 = atom.bonded_atoms[0],
atom2 = atom.bonded_atoms[0].bonded_atoms[other_atom_indices[1]])
axis2 = v1**v3
if axis * axis2>0:
axis = axis+axis2
else:
axis = axis-axis2
else:
axis = a.orthogonal()
a = rotate_vector_around_an_axis(rot_angle, axis, a)
a = self.set_bond_distance(a, atom.element)
self.add_proton(atom, c+a)
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
a1 = vector(atom1 = atom, atom2 = atom.bonded_atoms[0]).rescale(1.0)
a2 = vector(atom1 = atom, atom2 = atom.bonded_atoms[1]).rescale(1.0)
new_a = -a1 - a2
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, c+new_a)
return
def set_steric_number_and_lone_pairs(self, atom):
"""Set steric number and lone pairs for atom.
Args:
atom: atom for calculation
"""
# If we already did this, there is no reason to do it again
if atom.steric_num_lone_pairs_set:
return
debug('=' * 10)
debug('Setting steric number and lone pairs for', atom)
atom.steric_number = 0
debug('{0:>65s}: {1:>4d}'.format('Valence electrons',
self.valence_electrons[atom.element]))
atom.steric_number += self.valence_electrons[atom.element]
debug('{0:>65s}: {1:>4d}'.format('Number of bonds',
len(atom.bonded_atoms)))
atom.steric_number += len(atom.bonded_atoms)
debug('{0:>65s}: {1:>4d}'.format('Number of hydrogen atoms to add',
atom.number_of_protons_to_add))
atom.steric_number += atom.number_of_protons_to_add
debug('{0:>65s}: {1:>4d}'.format(
'Number of pi-electrons in double and triple bonds(-)',
atom.num_pi_elec_2_3_bonds))
atom.steric_number -= atom.num_pi_elec_2_3_bonds
debug('{0:>65s}: {1:>4d}'.format(
'Number of pi-electrons in conjugated double and triple bonds(-)',
atom.num_pi_elec_conj_2_3_bonds))
atom.steric_number -= atom.num_pi_elec_conj_2_3_bonds
debug('{0:>65s}: {1:>4d}'.format(
'Number of donated co-ordinated bonds', 0))
atom.steric_number += 0
debug('{0:>65s}: {1:>4.1f}'.format('Charge(-)', atom.charge))
atom.steric_number -= atom.charge
atom.steric_number = math.floor(atom.steric_number / 2.0)
atom.number_of_lone_pairs = (atom.steric_number -
len(atom.bonded_atoms) -
atom.number_of_protons_to_add)
debug('-' * 70)
debug('{0:>65s}: {1:>4d}'.format('Steric number', atom.steric_number))
debug('{0:>65s}: {1:>4d}'.format('Number of lone pairs',
atom.number_of_lone_pairs))
atom.steric_num_lone_pairs_set = True
def set_number_of_protons_to_add(self, atom):
"""Set the number of protons to add to this atom.
Args:
atom: atom for calculation
"""
debug('*' * 10)
debug('Setting number of protons to add for', atom)
atom.number_of_protons_to_add = 8
debug(" 8")
atom.number_of_protons_to_add -= self.valence_electrons[atom.element]
debug('Valence electrons: {0:>4d}'.format(
-self.valence_electrons[atom.element]))
atom.number_of_protons_to_add -= len(atom.bonded_atoms)
debug('Number of bonds: {0:>4d}'.format(-len(atom.bonded_atoms)))
atom.number_of_protons_to_add -= atom.num_pi_elec_2_3_bonds
debug('Pi electrons: {0:>4d}'.format(-atom.num_pi_elec_2_3_bonds))
atom.number_of_protons_to_add += int(atom.charge)
debug('Charge: {0:>4.1f}'.format(atom.charge))
debug('-' * 10)
debug(atom.number_of_protons_to_add)
def addDeterminants(iterative_interactions, version, options=None):
"""
The iterative pKa scheme. Later it is all added in 'calculateTotalPKA'
"""
# --- setup ---
iteratives = []
done_group = []
# creating iterative objects with references to their real group counterparts
for interaction in iterative_interactions:
pair = interaction[0]
for group in pair:
if group in done_group:
#print "done already"
""" do nothing - already have an iterative object for this group """
else:
newIterative = Iterative(group)
iteratives.append(newIterative)
done_group.append(group)
# Initialize iterative scheme
debug("\n --- pKa iterations (%d groups, %d interactions) ---" %
(len(iteratives), len(iterative_interactions)))
converged = False
iteration = 0
# set non-iterative pka values as first step
for itres in iteratives:
itres.pKa_iter.append(itres.pKa_NonIterative)
# --- starting pKa iterations ---
while converged == False:
# initialize pKa_new
iteration += 1
for itres in iteratives:
itres.determinants = {
'sidechain': [],
'backbone': [],
'coulomb': []
}
itres.pKa_new = itres.pKa_NonIterative
# Adding interactions to temporary determinant container
for interaction in iterative_interactions:
pair = interaction[0]
values = interaction[1]
annihilation = interaction[2]
#print "len(interaction) = %d" % (len(interaction))
object1, object2 = findIterative(pair, iteratives)
Q1 = object1.Q
Q2 = object2.Q
if Q1 < 0.0 and Q2 < 0.0:
""" both are acids """
addIterativeAcidPair(object1, object2, interaction)
elif Q1 > 0.0 and Q2 > 0.0:
""" both are bases """
addIterativeBasePair(object1, object2, interaction)
else:
""" one of each """
addIterativeIonPair(object1, object2, interaction, version)
# Calculating pKa_new values
for itres in iteratives:
for type in ['sidechain', 'backbone', 'coulomb']:
for determinant in itres.determinants[type]:
itres.pKa_new += determinant[1]
# Check convergence
converged = True
for itres in iteratives:
if itres.pKa_new == itres.pKa_old:
itres.converged = True
else:
itres.converged = False
converged = False
# reset pKa_old & storing pKa_new in pKa_iter
for itres in iteratives:
itres.pKa_old = itres.pKa_new
itres.pKa_iter.append(itres.pKa_new)
if iteration == 10:
info("did not converge in %d iterations" % (iteration))
break
# --- Iterations finished ---
# printing pKa iterations
# formerly was conditioned on if options.verbosity >= 2 - now unnecessary
str = "%12s" % (" ")
for index in range(0, iteration + 1):
str += "%8d" % (index)
debug(str)
for itres in iteratives:
str = "%s " % (itres.label)
for pKa in itres.pKa_iter:
str += "%8.2lf" % (pKa)
if itres.converged == False:
str += " *"
debug(str)
# creating real determinants and adding them to group object
for itres in iteratives:
for type in ['sidechain', 'backbone', 'coulomb']:
for interaction in itres.determinants[type]:
#info('done',itres.group.label,interaction[0],interaction[1])
value = interaction[1]
if value > 0.005 or value < -0.005:
g = interaction[0]
newDeterminant = Determinant(g, value)
itres.group.determinants[type].append(newDeterminant)
def addDeterminants(iterative_interactions, version, options=None):
"""
The iterative pKa scheme. Later it is all added in 'calculateTotalPKA'
"""
# --- setup ---
iteratives = []
done_group = []
# creating iterative objects with references to their real group counterparts
for interaction in iterative_interactions:
pair = interaction[0]
for group in pair:
if group in done_group:
#print "done already"
""" do nothing - already have an iterative object for this group """
else:
newIterative = Iterative(group)
iteratives.append(newIterative)
done_group.append(group)
# Initialize iterative scheme
debug("\n --- pKa iterations (%d groups, %d interactions) ---" %
(len(iteratives), len(iterative_interactions)))
converged = False
iteration = 0
# set non-iterative pka values as first step
for itres in iteratives:
itres.pKa_iter.append(itres.pKa_NonIterative)
# --- starting pKa iterations ---
while converged == False:
# initialize pKa_new
iteration += 1
for itres in iteratives:
itres.determinants = {'sidechain':[],'backbone':[],'coulomb':[]}
itres.pKa_new = itres.pKa_NonIterative
# Adding interactions to temporary determinant container
for interaction in iterative_interactions:
pair = interaction[0]
values = interaction[1]
annihilation = interaction[2]
#print "len(interaction) = %d" % (len(interaction))
object1, object2 = findIterative(pair, iteratives)
Q1 = object1.Q
Q2 = object2.Q
if Q1 < 0.0 and Q2 < 0.0:
""" both are acids """
addIterativeAcidPair(object1, object2, interaction)
elif Q1 > 0.0 and Q2 > 0.0:
""" both are bases """
addIterativeBasePair(object1, object2, interaction)
else:
""" one of each """
addIterativeIonPair(object1, object2, interaction, version)
# Calculating pKa_new values
for itres in iteratives:
for type in ['sidechain','backbone','coulomb']:
for determinant in itres.determinants[type]:
itres.pKa_new += determinant[1]
# Check convergence
converged = True
for itres in iteratives:
if itres.pKa_new == itres.pKa_old:
itres.converged = True
else:
itres.converged = False
converged = False
# reset pKa_old & storing pKa_new in pKa_iter
for itres in iteratives:
itres.pKa_old = itres.pKa_new
itres.pKa_iter.append(itres.pKa_new)
if iteration == 10:
info("did not converge in %d iterations" % (iteration))
break
# --- Iterations finished ---
# printing pKa iterations
# formerly was conditioned on if options.verbosity >= 2 - now unnecessary
str = "%12s" % (" ")
for index in range(0, iteration+1 ):
str += "%8d" % (index)
debug(str)
for itres in iteratives:
str = "%s " % (itres.label)
for pKa in itres.pKa_iter:
str += "%8.2lf" % (pKa)
if itres.converged == False:
str += " *"
debug(str)
# creating real determinants and adding them to group object
for itres in iteratives:
for type in ['sidechain','backbone','coulomb']:
for interaction in itres.determinants[type]:
#info('done',itres.group.label,interaction[0],interaction[1])
value = interaction[1]
if value > 0.005 or value < -0.005:
g = interaction[0]
newDeterminant = Determinant(g, value)
itres.group.determinants[type].append(newDeterminant)
def add_determinants(iterative_interactions, version, _=None):
"""Add determinants iteratively.
The iterative pKa scheme. Later it is all added in 'calculateTotalPKA'
Args:
iterative_interactions: list of iterative interactions
version: version object
_: options object
"""
# --- setup ---
iteratives = []
done_group = []
# create iterative objects with references to their real group counterparts
for interaction in iterative_interactions:
pair = interaction[0]
for group in pair:
if group in done_group:
# do nothing - already have an iterative object for this group
pass
else:
new_iterative = Iterative(group)
iteratives.append(new_iterative)
done_group.append(group)
# Initialize iterative scheme
debug(
"\n --- pKa iterations ({0:d} groups, {1:d} interactions) ---".format(
len(iteratives), len(iterative_interactions)))
converged = False
iteration = 0
# set non-iterative pka values as first step
for iter_ in iteratives:
iter_.pka_iter.append(iter_.pka_noniterative)
# --- starting pKa iterations ---
while not converged:
# initialize pka_new
iteration += 1
for itres in iteratives:
itres.determinants = {'sidechain': [], 'backbone': [],
'coulomb': []}
itres.pka_new = itres.pka_noniterative
# Adding interactions to temporary determinant container
for interaction in iterative_interactions:
pair = interaction[0]
object1, object2 = find_iterative(pair, iteratives)
q1 = object1.q
q2 = object2.q
if q1 < 0.0 and q2 < 0.0:
# both are acids
add_iterative_acid_pair(object1, object2, interaction)
elif q1 > 0.0 and q2 > 0.0:
# both are bases
add_iterative_base_pair(object1, object2, interaction)
else:
# one of each
add_iterative_ion_pair(object1, object2, interaction, version)
# Calculating pka_new values
for itres in iteratives:
for type_ in ['sidechain', 'backbone', 'coulomb']:
for determinant in itres.determinants[type_]:
itres.pka_new += determinant[1]
# Check convergence
converged = True
for itres in iteratives:
if itres.pka_new == itres.pka_old:
itres.converged = True
else:
itres.converged = False
converged = False
# reset pka_old & storing pka_new in pka_iter
for itres in iteratives:
itres.pka_old = itres.pka_new
itres.pka_iter.append(itres.pka_new)
if iteration == 10:
info("did not converge in {0:d} iterations".format(iteration))
break
# printing pKa iterations
# formerly was conditioned on if options.verbosity >= 2 - now unnecessary
str_ = ' '
for index in range(iteration+1):
str_ += "{0:>8d}".format(index)
debug(str_)
for itres in iteratives:
str_ = "{0:s} ".format(itres.label)
for pka in itres.pka_iter:
str_ += "{0:>8.2f}".format(pka)
if not itres.converged:
str_ += " *"
debug(str_)
# creating real determinants and adding them to group object
for itres in iteratives:
for type_ in ['sidechain', 'backbone', 'coulomb']:
for interaction in itres.determinants[type_]:
#info('done',itres.group.label,interaction[0],interaction[1])
value = interaction[1]
if value > UNK_MIN_VALUE or value < -UNK_MIN_VALUE:
group = interaction[0]
new_det = Determinant(group, value)
itres.group.determinants[type_].append(new_det)
def set_number_of_protons_to_add(self, atom):
debug('*'*10)
debug('Setting number of protons to add for',atom)
atom.number_of_protons_to_add = 8
debug(' %4d'%8)
atom.number_of_protons_to_add -= self.valence_electrons[atom.element]
debug('Valence eletrons: %4d'%-self.valence_electrons[atom.element])
atom.number_of_protons_to_add -= len(atom.bonded_atoms)
debug('Number of bonds: %4d'%- len(atom.bonded_atoms))
atom.number_of_protons_to_add -= atom.number_of_pi_electrons_in_double_and_triple_bonds
debug('Pi electrons: %4d'%-atom.number_of_pi_electrons_in_double_and_triple_bonds)
atom.number_of_protons_to_add += int(atom.charge)
debug('Charge: %4.1f'%atom.charge)
debug('-'*10)
debug(atom.number_of_protons_to_add)
return
def set_number_of_protons_to_add(self, atom):
debug('*' * 10)
debug('Setting number of protons to add for', atom)
atom.number_of_protons_to_add = 8
debug(' %4d' % 8)
atom.number_of_protons_to_add -= self.valence_electrons[atom.element]
debug('Valence eletrons: %4d' % -self.valence_electrons[atom.element])
atom.number_of_protons_to_add -= len(atom.bonded_atoms)
debug('Number of bonds: %4d' % -len(atom.bonded_atoms))
atom.number_of_protons_to_add -= atom.number_of_pi_electrons_in_double_and_triple_bonds
debug('Pi electrons: %4d' %
-atom.number_of_pi_electrons_in_double_and_triple_bonds)
atom.number_of_protons_to_add += int(atom.charge)
debug('Charge: %4.1f' % atom.charge)
debug('-' * 10)
debug(atom.number_of_protons_to_add)
return
def set_steric_number_and_lone_pairs(self, atom):
# If we already did this, there is no reason to do it again
if atom.steric_number_and_lone_pairs_set:
return
debug('=' * 10)
debug('Setting steric number and lone pairs for', atom)
# costumly set the N backbone atoms up for peptide bond trigonal planer shape
#if atom.name == 'N' and len(atom.bonded_atoms) == 2:
# atom.steric_number = 3
# atom.number_of_lone_pairs = 0
# self.display 'Peptide bond: steric number is %d and number of lone pairs is %s'%(atom.steric_number,
# atom.number_of_lone_pairs)
# return
atom.steric_number = 0
debug('%65s: %4d' %
('Valence electrons', self.valence_electrons[atom.element]))
atom.steric_number += self.valence_electrons[atom.element]
debug('%65s: %4d' % ('Number of bonds', len(atom.bonded_atoms)))
atom.steric_number += len(atom.bonded_atoms)
debug(
'%65s: %4d' %
('Number of hydrogen atoms to add', atom.number_of_protons_to_add))
atom.steric_number += atom.number_of_protons_to_add
debug('%65s: %4d' %
('Number of pi-electrons in double and triple bonds(-)',
atom.number_of_pi_electrons_in_double_and_triple_bonds))
atom.steric_number -= atom.number_of_pi_electrons_in_double_and_triple_bonds
debug(
'%65s: %4d' %
('Number of pi-electrons in conjugated double and triple bonds(-)',
atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds))
atom.steric_number -= atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds
debug('%65s: %4d' % ('Number of donated co-ordinated bonds', 0))
atom.steric_number += 0
debug('%65s: %4.1f' % ('Charge(-)', atom.charge))
atom.steric_number -= atom.charge
atom.steric_number = math.floor(atom.steric_number / 2.0)
atom.number_of_lone_pairs = atom.steric_number - len(
atom.bonded_atoms) - atom.number_of_protons_to_add
debug('-' * 70)
debug('%65s: %4d' % ('Steric number', atom.steric_number))
debug('%65s: %4d' %
('Number of lone pairs', atom.number_of_lone_pairs))
atom.steric_number_and_lone_pairs_set = True
return
