def __init__(self):
self.name = "new-school protonator"
self.valence_electrons = {'H':1,
'C':4,
'N':5,
'O':6,
'F':7,
'P':5,
'S':6,
'CL':7}
self.standard_charges= {'ARG-NH1':1.0,
'ASP-OD2':-1.0,
'GLU-OE2':-1.0,
'HIS-NE2':0.0,
'LYS-NZ':1.0,
'NTERM':1.0,
'CTERM':-1.0}
self.sybyl_charges = {'N.pl3':+1,
'N.3':+1,
'N.4':+1,
'N.ar':+1,
'O.co2+':-1}
# self.standard_conjugate_charges= {'ARG-NH1':1.0}
self.bond_lengths = {'C':1.09,
'N':1.01,
'O':0.96,
'F':0.92,
'Cl':1.27,
'Br':1.41,
'I':1.61}
self.ions = ['NA','CA']
# protonation_methods[steric_number] = method
self.protonation_methods = {4:self.tetrahedral,
3:self.trigonal}
self.my_bond_maker = bonds.bondmaker()
return
def assign_atom_names(self):
"""Assigns sybyl names to ligand atoms based on elements and coordinates """
# find bonding atoms
self.my_bond_maker = bonds.bondmaker()
self.my_bond_maker.find_bonds_for_atoms(self.atoms)
for atom in self.atoms:
# check if we already have assigned a name to this atom
if hasattr(atom,'sybyl_assigned'):
print(atom.name,'already assigned')
continue
# find some properties of the atom
ring_atoms = self.is_ring_member(atom)
aromatic = self.is_aromatic_ring(ring_atoms)
planar = self.is_planar(atom)
bonded_elements = {}
for i in range(len(atom.bonded_atoms)):
bonded_elements[i]=atom.bonded_atoms[i].get_element()
# Aromatic carbon/nitrogen
if aromatic:
for ra in ring_atoms:
if ra.get_element() in ['C','N']:
self.set_type(ra, ra.get_element()+'.ar')
continue
# check for amide
if atom.get_element() in ['O','N']:
amide = 0
for b in atom.bonded_atoms:
if b.element == 'C':
for bb in b.bonded_atoms:
if (bb.get_element() =='N' and atom.get_element() == 'O'):
self.set_type(bb,'N.am')
self.set_type(b,'C.2')
self.set_type(atom,'O.2')
amide = 1
if (bb.get_element() =='O' and atom.get_element() == 'N'):
self.set_type(atom,'N.am')
self.set_type(b,'C.2')
self.set_type(bb,'O.2')
amide = 1
if amide==1:
continue
if atom.get_element()=='C':
# check for amide
if 'O' in bonded_elements.values() and 'N' in bonded_elements.values():
self.set_type(atom,'C.2')
for b in atom.bonded_atoms:
if b.get_element()=='N':
self.set_type(b,'N.am')
if b.get_element()=='O':
self.set_type(b,'O.2')
continue
# check for carboxyl
if len(atom.bonded_atoms)==3 and list(bonded_elements.values()).count('O')==2:
i1 = list(bonded_elements.values()).index('O')
i2 = list(bonded_elements.values()).index('O',i1+1)
if len(atom.bonded_atoms[i1].bonded_atoms)==1 and len(atom.bonded_atoms[i2].bonded_atoms)==1:
self.set_type(atom.bonded_atoms[i1],'O.co2+')
self.set_type(atom.bonded_atoms[i2],'O.co2')
self.set_type(atom,'C.2')
continue
# sp carbon
if len(atom.bonded_atoms)<=2:
for b in atom.bonded_atoms:
if self.my_bond_maker.squared_distance(atom, b) < max_C_triple_bond_squared:
self.set_type(atom,'C.1')
self.set_type(b,b.get_element()+'.1')
if hasattr(atom,'sybyl_assigned'):
continue
# sp2 carbon
if planar:
self.set_type(atom,'C.2')
# check for N.pl3
for b in atom.bonded_atoms:
if b.get_element()=='N':
if len(b.bonded_atoms)<3 or self.is_planar(b):
self.set_type(b,'N.pl3')
continue
# sp3 carbon
self.set_type(atom, 'C.3')
continue
# Nitrogen
if atom.get_element() == 'N':
# check for planar N
if len(atom.bonded_atoms)==1:
if self.is_planar(atom.bonded_atoms[0]):
self.set_type(atom,'N.pl3')
continue
if planar:
self.set_type(atom,'N.pl3')
continue
self.set_type(atom,'N.3')
continue
# Oxygen
if atom.get_element() == 'O':
self.set_type(atom,'O.3')
# check for X=O
if len(atom.bonded_atoms) == 1:
if self.my_bond_maker.squared_distance(atom, atom.bonded_atoms[0]) < max_C_double_bond_squared:
self.set_type(atom,'O.2')
if atom.bonded_atoms[0].get_element()=='C':
self.set_type(atom.bonded_atoms[0],'C.2')
continue
# Sulphur
if atom.get_element() == 'S':
#check for SO2
if list(bonded_elements.values()).count('O')==2:
i1 = list(bonded_elements.values()).index('O')
i2 = list(bonded_elements.values()).index('O',i1+1)
self.set_type(atom.bonded_atoms[i1],'O.2')
self.set_type(atom.bonded_atoms[i2],'O.2')
self.set_type(atom,'S.o2')
continue
# 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:
self.set_type(atom.bonded_atoms[i],'O.2')
no_O2+=1
else:
self.set_type(atom.bonded_atoms[i],'O.3')
self.set_type(atom,'S.3')
continue
element = atom.get_element().capitalize()
self.set_type(atom,element)
#print('Using element as type for %s'%atom.get_element())
return
def assign_atom_names(self):
"""
Assigns sybyl names to ligand atoms based on elements and coordinates
copied from propka/ligand.py
modified:
P -> P3
O.co2+ - > O.co2
"""
# find bonding atoms
self.my_bond_maker = bonds.bondmaker()
self.my_bond_maker.find_bonds_for_atoms(self.atoms)
for atom in self.atoms:
# check if we already have assigned a name to this atom
if hasattr(atom, 'sybyl_assigned'):
print(atom.resName, atom.numb, atom.name, 'alreadyassigned')
continue
# find some properties of the atom
ring_atoms = self.is_ring_member(atom)
aromatic = self.is_aromatic_ring(ring_atoms)
planar = self.is_planar(atom)
bonded_elements = {}
for i in range(len(atom.bonded_atoms)):
bonded_elements[i] = atom.bonded_atoms[i].get_element()
# Aromatic carbon/nitrogen
if aromatic:
#print "--- if aromatic",atom.resName, atom.numb, atom.name, atom.get_element()
#for ra in ring_atoms:
# if ra.get_element() in ['C', 'N']:
# self.set_type(ra, ra.get_element() + '.ar')
#continue
'''SH: In the original version, if a ring is planar (eg., 4FXF_D_FBP_606)
but contains other atoms than C or N the loop breaks without assigning these atoms
'''
if atom.get_element() in ['C', 'N']:
self.set_type(atom, atom.get_element() + '.ar')
continue
# check for amide
if atom.get_element() in ['O', 'N']:
amide = 0
for b in atom.bonded_atoms:
if b.element == 'C':
for bb in b.bonded_atoms:
if (bb.get_element() == 'N'
and atom.get_element() == 'O'):
self.set_type(bb, 'N.am')
self.set_type(b, 'C.2')
self.set_type(atom, 'O.2')
amide = 1
if (bb.get_element() == 'O'
and atom.get_element() == 'N'):
self.set_type(atom, 'N.am')
self.set_type(b, 'C.2')
self.set_type(bb, 'O.2')
amide = 1
if amide == 1:
continue
if atom.get_element() == 'C':
# check for amide
if 'O' in bonded_elements.values(
) and 'N' in bonded_elements.values():
self.set_type(atom, 'C.2')
for b in atom.bonded_atoms:
if b.get_element() == 'N':
self.set_type(b, 'N.am')
if b.get_element() == 'O':
self.set_type(b, 'O.2')
continue
# check for carboxyl
if len(atom.bonded_atoms) == 3 and list(
bonded_elements.values()).count('O') == 2:
i1 = list(bonded_elements.values()).index('O')
i2 = list(bonded_elements.values()).index('O', i1 + 1)
if len(atom.bonded_atoms[i1].bonded_atoms) == 1 and len(
atom.bonded_atoms[i2].bonded_atoms) == 1:
#self.set_type(atom.bonded_atoms[i1], 'O.co2+')
self.set_type(atom.bonded_atoms[i1],
'O.co2') #SH: problems in 1a3w
self.set_type(atom.bonded_atoms[i2], 'O.co2')
self.set_type(atom, 'C.2')
continue
# sp carbon
if len(atom.bonded_atoms) <= 2:
for b in atom.bonded_atoms:
if self.my_bond_maker.squared_distance(
atom, b) < max_C_triple_bond_squared:
self.set_type(atom, 'C.1')
self.set_type(b, b.get_element() + '.1')
if hasattr(atom, 'sybyl_assigned'):
continue
# sp2 carbon
if planar:
self.set_type(atom, 'C.2')
# check for N.pl3
for b in atom.bonded_atoms:
if b.get_element() == 'N':
if len(b.bonded_atoms) < 3 or self.is_planar(b):
self.set_type(b, 'N.pl3')
continue
# sp3 carbon
self.set_type(atom, 'C.3')
continue
# Nitrogen
if atom.get_element() == 'N':
# check for planar N
if len(atom.bonded_atoms) == 1:
if self.is_planar(atom.bonded_atoms[0]):
self.set_type(atom, 'N.pl3')
continue
if planar:
self.set_type(atom, 'N.pl3')
continue
self.set_type(atom, 'N.3')
continue
# Oxygen
if atom.get_element() == 'O':
self.set_type(atom, 'O.3')
# check for X=O
if len(atom.bonded_atoms) == 1:
if self.my_bond_maker.squared_distance(
atom,
atom.bonded_atoms[0]) < max_C_double_bond_squared:
self.set_type(atom, 'O.2')
if atom.bonded_atoms[0].get_element() == 'C':
self.set_type(atom.bonded_atoms[0], 'C.2')
continue
# Sulphur
if atom.get_element() == 'S':
#check for SO2
if list(bonded_elements.values()).count('O') == 2:
i1 = list(bonded_elements.values()).index('O')
i2 = list(bonded_elements.values()).index('O', i1 + 1)
self.set_type(atom.bonded_atoms[i1], 'O.2')
self.set_type(atom.bonded_atoms[i2], 'O.2')
self.set_type(atom, 'S.o2')
continue
# 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:
self.set_type(atom.bonded_atoms[i], 'O.2')
no_O2 += 1
else:
self.set_type(atom.bonded_atoms[i], 'O.3')
self.set_type(atom, 'S.3')
continue
# Phosphorous (phosphorous sp3)
#@attention: This was added and may not consider all types of phosphorous
if atom.get_element() == 'P':
self.set_type(atom, 'P.3')
continue
element = atom.get_element().capitalize()
self.set_type(atom, element)
#pka_print('Using element as type for %s'%atom.get_element())
return
def assign_atom_names(self):
"""Assigns sybyl names to ligand atoms based on elements and coordinates """
# find bonding atoms
self.my_bond_maker = bonds.bondmaker()
self.my_bond_maker.find_bonds_for_atoms(self.atoms)
for atom in self.atoms:
# check if we already have assigned a name to this atom
if hasattr(atom, 'sybyl_assigned'):
print(atom.name, 'already assigned')
continue
# find some properties of the atom
ring_atoms = self.is_ring_member(atom)
aromatic = self.is_aromatic_ring(ring_atoms)
planar = self.is_planar(atom)
bonded_elements = {}
for i in range(len(atom.bonded_atoms)):
bonded_elements[i] = atom.bonded_atoms[i].get_element()
# Aromatic carbon/nitrogen
if aromatic:
for ra in ring_atoms:
if ra.get_element() in ['C', 'N']:
self.set_type(ra, ra.get_element() + '.ar')
continue
# check for amide
if atom.get_element() in ['O', 'N']:
amide = 0
for b in atom.bonded_atoms:
if b.element == 'C':
for bb in b.bonded_atoms:
if (bb.get_element() == 'N'
and atom.get_element() == 'O'):
self.set_type(bb, 'N.am')
self.set_type(b, 'C.2')
self.set_type(atom, 'O.2')
amide = 1
if (bb.get_element() == 'O'
and atom.get_element() == 'N'):
self.set_type(atom, 'N.am')
self.set_type(b, 'C.2')
self.set_type(bb, 'O.2')
amide = 1
if amide == 1:
continue
if atom.get_element() == 'C':
# check for amide
if 'O' in bonded_elements.values(
) and 'N' in bonded_elements.values():
self.set_type(atom, 'C.2')
for b in atom.bonded_atoms:
if b.get_element() == 'N':
self.set_type(b, 'N.am')
if b.get_element() == 'O':
self.set_type(b, 'O.2')
continue
# check for carboxyl
if len(atom.bonded_atoms) == 3 and list(
bonded_elements.values()).count('O') == 2:
i1 = list(bonded_elements.values()).index('O')
i2 = list(bonded_elements.values()).index('O', i1 + 1)
if len(atom.bonded_atoms[i1].bonded_atoms) == 1 and len(
atom.bonded_atoms[i2].bonded_atoms) == 1:
self.set_type(atom.bonded_atoms[i1], 'O.co2+')
self.set_type(atom.bonded_atoms[i2], 'O.co2')
self.set_type(atom, 'C.2')
continue
# sp carbon
if len(atom.bonded_atoms) <= 2:
for b in atom.bonded_atoms:
if self.my_bond_maker.squared_distance(
atom, b) < max_C_triple_bond_squared:
self.set_type(atom, 'C.1')
self.set_type(b, b.get_element() + '.1')
if hasattr(atom, 'sybyl_assigned'):
continue
# sp2 carbon
if planar:
self.set_type(atom, 'C.2')
# check for N.pl3
for b in atom.bonded_atoms:
if b.get_element() == 'N':
if len(b.bonded_atoms) < 3 or self.is_planar(b):
self.set_type(b, 'N.pl3')
continue
# sp3 carbon
self.set_type(atom, 'C.3')
continue
# Nitrogen
if atom.get_element() == 'N':
# check for planar N
if len(atom.bonded_atoms) == 1:
if self.is_planar(atom.bonded_atoms[0]):
self.set_type(atom, 'N.pl3')
continue
if planar:
self.set_type(atom, 'N.pl3')
continue
self.set_type(atom, 'N.3')
continue
# Oxygen
if atom.get_element() == 'O':
self.set_type(atom, 'O.3')
# check for X=O
if len(atom.bonded_atoms) == 1:
if self.my_bond_maker.squared_distance(
atom,
atom.bonded_atoms[0]) < max_C_double_bond_squared:
self.set_type(atom, 'O.2')
if atom.bonded_atoms[0].get_element() == 'C':
self.set_type(atom.bonded_atoms[0], 'C.2')
continue
# Sulphur
if atom.get_element() == 'S':
#check for SO2
if list(bonded_elements.values()).count('O') == 2:
i1 = list(bonded_elements.values()).index('O')
i2 = list(bonded_elements.values()).index('O', i1 + 1)
self.set_type(atom.bonded_atoms[i1], 'O.2')
self.set_type(atom.bonded_atoms[i2], 'O.2')
self.set_type(atom, 'S.o2')
continue
# 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:
self.set_type(atom.bonded_atoms[i], 'O.2')
no_O2 += 1
else:
self.set_type(atom.bonded_atoms[i], 'O.3')
self.set_type(atom, 'S.3')
continue
element = atom.get_element().capitalize()
self.set_type(atom, element)
#print('Using element as type for %s'%atom.get_element())
return
def assign_atom_names(self):
"""
Assigns sybyl names to ligand atoms based on elements and coordinates
copied from propka/ligand.py
modified:
P -> P3
O.co2+ - > O.co2
"""
# find bonding atoms
self.my_bond_maker = bonds.bondmaker()
self.my_bond_maker.find_bonds_for_atoms(self.atoms)
for atom in self.atoms:
# check if we already have assigned a name to this atom
if hasattr(atom, 'sybyl_assigned'):
print(atom.resName, atom.numb, atom.name, 'alreadyassigned')
continue
# find some properties of the atom
ring_atoms = self.is_ring_member(atom)
aromatic = self.is_aromatic_ring(ring_atoms)
planar = self.is_planar(atom)
bonded_elements = {}
for i in range(len(atom.bonded_atoms)):
bonded_elements[i] = atom.bonded_atoms[i].get_element()
# Aromatic carbon/nitrogen
if aromatic:
#print "--- if aromatic",atom.resName, atom.numb, atom.name, atom.get_element()
#for ra in ring_atoms:
# if ra.get_element() in ['C', 'N']:
# self.set_type(ra, ra.get_element() + '.ar')
#continue
'''SH: In the original version, if a ring is planar (eg., 4FXF_D_FBP_606)
but contains other atoms than C or N the loop breaks without assigning these atoms
'''
if atom.get_element() in ['C', 'N']:
self.set_type(atom, atom.get_element() + '.ar')
continue
# check for amide
if atom.get_element() in ['O', 'N']:
amide = 0
for b in atom.bonded_atoms:
if b.element == 'C':
for bb in b.bonded_atoms:
if (bb.get_element() == 'N' and atom.get_element() == 'O'):
self.set_type(bb, 'N.am')
self.set_type(b, 'C.2')
self.set_type(atom, 'O.2')
amide = 1
if (bb.get_element() == 'O' and atom.get_element() == 'N'):
self.set_type(atom, 'N.am')
self.set_type(b, 'C.2')
self.set_type(bb, 'O.2')
amide = 1
if amide == 1:
continue
if atom.get_element() == 'C':
# check for amide
if 'O' in bonded_elements.values() and 'N' in bonded_elements.values():
self.set_type(atom, 'C.2')
for b in atom.bonded_atoms:
if b.get_element() == 'N':
self.set_type(b, 'N.am')
if b.get_element() == 'O':
self.set_type(b, 'O.2')
continue
# check for carboxyl
if len(atom.bonded_atoms) == 3 and list(bonded_elements.values()).count('O') == 2:
i1 = list(bonded_elements.values()).index('O')
i2 = list(bonded_elements.values()).index('O', i1 + 1)
if len(atom.bonded_atoms[i1].bonded_atoms) == 1 and len(atom.bonded_atoms[i2].bonded_atoms) == 1:
#self.set_type(atom.bonded_atoms[i1], 'O.co2+')
self.set_type(atom.bonded_atoms[i1], 'O.co2') #SH: problems in 1a3w
self.set_type(atom.bonded_atoms[i2], 'O.co2')
self.set_type(atom, 'C.2')
continue
# sp carbon
if len(atom.bonded_atoms) <= 2:
for b in atom.bonded_atoms:
if self.my_bond_maker.squared_distance(atom, b) < max_C_triple_bond_squared:
self.set_type(atom, 'C.1')
self.set_type(b, b.get_element() + '.1')
if hasattr(atom, 'sybyl_assigned'):
continue
# sp2 carbon
if planar:
self.set_type(atom, 'C.2')
# check for N.pl3
for b in atom.bonded_atoms:
if b.get_element() == 'N':
if len(b.bonded_atoms) < 3 or self.is_planar(b):
self.set_type(b, 'N.pl3')
continue
# sp3 carbon
self.set_type(atom, 'C.3')
continue
# Nitrogen
if atom.get_element() == 'N':
# check for planar N
if len(atom.bonded_atoms) == 1:
if self.is_planar(atom.bonded_atoms[0]):
self.set_type(atom, 'N.pl3')
continue
if planar:
self.set_type(atom, 'N.pl3')
continue
self.set_type(atom, 'N.3')
continue
# Oxygen
if atom.get_element() == 'O':
self.set_type(atom, 'O.3')
# check for X=O
if len(atom.bonded_atoms) == 1:
if self.my_bond_maker.squared_distance(atom, atom.bonded_atoms[0]) < max_C_double_bond_squared:
self.set_type(atom, 'O.2')
if atom.bonded_atoms[0].get_element() == 'C':
self.set_type(atom.bonded_atoms[0], 'C.2')
continue
# Sulphur
if atom.get_element() == 'S':
#check for SO2
if list(bonded_elements.values()).count('O') == 2:
i1 = list(bonded_elements.values()).index('O')
i2 = list(bonded_elements.values()).index('O', i1 + 1)
self.set_type(atom.bonded_atoms[i1], 'O.2')
self.set_type(atom.bonded_atoms[i2], 'O.2')
self.set_type(atom, 'S.o2')
continue
# 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:
self.set_type(atom.bonded_atoms[i], 'O.2')
no_O2 += 1
else:
self.set_type(atom.bonded_atoms[i], 'O.3')
self.set_type(atom, 'S.3')
continue
# Phosphorous (phosphorous sp3)
#@attention: This was added and may not consider all types of phosphorous
if atom.get_element() == 'P':
self.set_type(atom, 'P.3')
continue
element = atom.get_element().capitalize()
self.set_type(atom, element)
#pka_print('Using element as type for %s'%atom.get_element())
return
