def assign_bond_order1(self, atoms, bonds):
""" """
hyb_val = [0,3,2,1]
converter = TypeConverter("HYB")
for a in atoms:
hyb = converter.convert(a.babel_type, 'dummy')
a._redo = hyb_val[int(hyb)]
#print a.full_name(), a.babel_type, hyb, a._redo
for b in bonds:
# initialize bondOrder attribute
if b.bondOrder is None:
b.bondOrder = 1
sum_code = b.atom1._redo + b.atom2._redo
#print b, sum_code
if sum_code == 6:
b.bondOrder = 3
elif sum_code == 4:
b.bondOrder = 2
else:
b.bondOrder = 1
if self.is_carboxyl(b):
b.bondOrder = 2
if b.bondOrder < 1 or b.bondOrder > 3:
print "Bond %s is wierd - Bond order is %d\n" % \
(b, b.bondOrder)
self.check_for_conjugation(atoms)
# cleanup
for a in atoms:
delattr(a, '_redo')
def find_aromatic_rings(self):
""" """
converter = TypeConverter("HYB")
for r in self.rings.rings:
is_aromatic = 0
if len(r['atoms']) == 5 or len(r['atoms']) == 6:
is_aromatic = 1
for a in r['atoms']:
# check to see if the atom is sp2
# if not, the ring isn't aromatic
hyb_str = converter.convert(a.babel_type, 'all_caps')
hyb = int(hyb_str)
if hyb != 2:
is_aromatic = 0
break
# check to see if the atom has 3 bonds to
# heavy atoms in the same ring.
# If not, the ring isn't aromatic
if self.count_arom_atm_bonds(a, r) != 3:
is_aromatic = 0
break
if is_aromatic:
r['aromatic'] = 1
for a in r['atoms']: a.arom_atm = 1
def find_aromatic_rings(self):
""" """
converter = TypeConverter("HYB")
for r in self.rings.rings:
is_aromatic = 0
if len(r['atoms']) == 5 or len(r['atoms']) == 6:
is_aromatic = 1
for a in r['atoms']:
# check to see if the atom is sp2
# if not, the ring isn't aromatic
hyb_str = converter.convert(a.babel_type, 'all_caps')
hyb = int(hyb_str)
if hyb != 2:
is_aromatic = 0
break
# check to see if the atom has 3 bonds to
# heavy atoms in the same ring.
# If not, the ring isn't aromatic
if self.count_arom_atm_bonds(a, r) != 3:
is_aromatic = 0
break
if is_aromatic:
r['aromatic'] = 1
for a in r['atoms']:
a.arom_atm = 1
def assign_bond_order1(self, atoms, bonds):
""" """
hyb_val = [0, 3, 2, 1]
converter = TypeConverter("HYB")
for a in atoms:
hyb = converter.convert(a.babel_type, 'dummy')
a._redo = hyb_val[int(hyb)]
#print a.full_name(), a.babel_type, hyb, a._redo
for b in bonds:
# initialize bondOrder attribute
if b.bondOrder is None:
b.bondOrder = 1
sum_code = b.atom1._redo + b.atom2._redo
#print b, sum_code
if sum_code == 6:
b.bondOrder = 3
elif sum_code == 4:
b.bondOrder = 2
else:
b.bondOrder = 1
if self.is_carboxyl(b):
b.bondOrder = 2
if b.bondOrder < 1 or b.bondOrder > 3:
print "Bond %s is wierd - Bond order is %d\n" % \
(b, b.bondOrder)
self.check_for_conjugation(atoms)
# cleanup
for a in atoms:
delattr(a, '_redo')
def lookup_sigma_params(self, atoms):
""" """
converter = TypeConverter("MAP")
for a in atoms:
type = converter.convert(a.babel_type)
if type[:2] in self.par.keys():
a._gast_par = self.par[type]
else:
print "Sorry, there are no Gasteiger parameters available for atom %s" % a.full_name()
a._gast_par = [0.0, 0.0, 0.0, 1.0]
def assign_hybrid_radii(self, atoms):
""" """
converter = TypeConverter("XYZ")
for a in atoms:
atm_type = converter.convert(a.babel_type, 'zero')
if atm_type == 0:
atm_type = a.babel_type
atm_type = converter.clean_atom_type(atm_type)
a.babel_cov_rad = babel_elements[atm_type]['cov_rad']
a.babel_bond_ord_rad = babel_elements[atm_type]['bond_ord_rad']
a.babel_max_bonds = babel_elements[atm_type]['max_bonds']
def lookup_sigma_params(self, atoms):
""" """
converter = TypeConverter("MAP")
for a in atoms:
type = converter.convert(a.babel_type)
if type[:2] in self.par.keys():
a._gast_par = self.par[type]
else:
print "Sorry, there are no Gasteiger parameters available for atom %s" % a.full_name(
)
a._gast_par = [0.0, 0.0, 0.0, 1.0]
def assign_hybrid_radii(self, atoms):
""" """
converter = TypeConverter("XYZ")
for a in atoms:
atm_type = converter.convert(a.babel_type, 'zero')
if atm_type == 0:
atm_type = a.babel_type
atm_type = converter.clean_atom_type(atm_type)
a.babel_cov_rad = babel_elements[atm_type]['cov_rad']
a.babel_bond_ord_rad = babel_elements[atm_type]['bond_ord_rad']
a.babel_max_bonds = babel_elements[atm_type]['max_bonds']
def count_missing_hydrogens(self, atoms):
""" """
missing = 0
converter = TypeConverter("HAD")
for a in atoms:
temp_type = converter.convert(a.babel_type, 'zero')
if temp_type == 0:
print "Unable to assign valence to atom %s type = %s" % \
(a.full_name(), a.babel_type)
type_valence = int(temp_type)
val = len(a.bonds)
if val < type_valence and val > 0:
missing = missing + type_valence - val
return missing
def count_missing_hydrogens(self, atoms):
""" """
missing = 0
converter = TypeConverter("HAD")
for a in atoms:
temp_type = converter.convert(a.babel_type, 'zero')
if temp_type == 0:
print "Unable to assign valence to atom %s type = %s" % \
(a.full_name(), a.babel_type)
type_valence = int(temp_type)
val = len(a.bonds)
if val < type_valence and val > 0:
missing = missing + type_valence - val
return missing
def estimate_bond_order2(self, bonds):
""" """
converter = TypeConverter("HYB")
for b in bonds:
bo = 1
a1 = b.atom1
a2 = b.atom2
dist = distance(a1.coords, a2.coords)
cov_sum = a1.babel_bond_ord_rad + a2.babel_bond_ord_rad
ratio = dist/cov_sum
start_type = converter.convert(a1.babel_type, "all_caps")
end_type = converter.convert(a2.babel_type, "all_caps")
if ratio <= DOUBLE_TRIPLE_CUTOFF:
if start_type[0] == '1' and end_type[0] == '1':
bo = 3
elif ratio <= SINGLE_DOUBLE_CUTOFF:
if start_type[0] == '2' and end_type[0] == '2':
bo = 2
b.bondOrder = bo
def estimate_bond_order2(self, bonds):
""" """
converter = TypeConverter("HYB")
for b in bonds:
bo = 1
a1 = b.atom1
a2 = b.atom2
dist = distance(a1.coords, a2.coords)
cov_sum = a1.babel_bond_ord_rad + a2.babel_bond_ord_rad
ratio = dist / cov_sum
start_type = converter.convert(a1.babel_type, "all_caps")
end_type = converter.convert(a2.babel_type, "all_caps")
if ratio <= DOUBLE_TRIPLE_CUTOFF:
if start_type[0] == '1' and end_type[0] == '1':
bo = 3
elif ratio <= SINGLE_DOUBLE_CUTOFF:
if start_type[0] == '2' and end_type[0] == '2':
bo = 2
b.bondOrder = bo
def countMissingBonds(atoms):
converter = TypeConverter('HYB')
needDBatoms = []
canHaveDBatoms = []
for a in atoms:
a._needsDB = 0
a._canHaveDB = 0
hyb = int(converter.convert(a.babel_type, 'all_caps'))
if hyb != 2: continue
if a.babel_type[0] == 'C':
sum = 0
for b in a.bonds:
sum = sum + b.bondOrder
if sum == 3:
if len(a.bonds) == 3:
a._needsDB = 1
needDBatoms.append(a)
elif len(a.bonds) == 2: # ==C-- or ==C/
a1 = a.bonds[0].atom1
if a1 == a: a1 = a.bonds[0].atom2
a3 = a.bonds[1].atom1
if a3 == a: a3 = a.bonds[1].atom2
ang = bond_angle(a1.coords, a.coords, a3.coords)
if math.fabs(ang - 180) < 10: # ==C--
a._needDB = 1
needDBatoms.append(a)
elif sum == 2:
if len(a.bonds) == 2:
a1 = a.bonds[0].atom1
if a1 == a: a1 = a.bonds[0].atom2
a3 = a.bonds[1].atom1
if a3 == a: a3 = a.bonds[1].atom2
ang = bond_angle(a1.coords, a.coords, a3.coords)
if math.fabs(ang - 180) < 10:
a._needsDB = 2
needDBatoms.append(a)
else:
a._needsDB = 1
needDBatoms.append(a)
elif sum == 1:
a._needsDB = 1
needDBatoms.append(a)
elif a.babel_type[0] == 'N':
sum = 0
for b in a.bonds:
sum = sum + b.bondOrder
if sum == 2 and len(a.bonds) == 2:
canHaveDBatoms.append(a)
a._canHaveDB = 1
elif a.babel_type[0] == 'O':
sum = 0
for b in a.bonds:
sum = sum + b.bondOrder
if sum == 1:
canHaveDBatoms.append(a)
a._canHaveDB = 1
return needDBatoms, canHaveDBatoms
def place_hydrogens2(self, atoms, num_H_to_add):
""" """
Hat = []
converter = TypeConverter("HYB")
for a in atoms:
type_name = converter.convert(a.babel_type, 'zero')
hyb = int(type_name)
code = a.babel_atomic_number * 10 + hyb
to_add = a._redo
if code == 63: # sp3 carbon
if to_add == 1:
Hat = Hat + self.add_tertiary_hydrogen(a, SP3_C_H_DIST)
elif to_add == 2:
Hat = Hat + self.add_methylene_hydrogens(a, SP3_C_H_DIST)
elif to_add == 3:
Hat = Hat + self.add_methyl_hydrogen(a, SP3_C_H_DIST)
Hat = Hat + self.add_methylene_hydrogens(
a, SP3_C_H_DIST, Hat[-1])
elif code == 73: # sp3 nitrogen
if to_add == 1:
if a.babel_type == "N3+":
Hat = Hat + self.add_tertiary_hydrogen(a, SP3_N_H_DIST)
else:
Hat = Hat + self.add_sp3_N_hydrogen(a, SP3_N_H_DIST)
elif to_add == 2:
Hat = Hat + self.add_methylene_hydrogens(a, SP3_N_H_DIST)
elif to_add == 3:
Hat = Hat + self.add_methyl_hydrogen(a, SP3_N_H_DIST)
Hat = Hat + self.add_methylene_hydrogens(
a, SP3_N_H_DIST, Hat[-1])
elif code == 62: # sp2 carbon
if to_add == 1:
Hat = Hat + self.add_sp2_hydrogen(a, SP2_C_H_DIST)
elif code == 72: # sp2 nitrogen
if to_add == 1:
Hat = Hat + self.add_sp2_hydrogen(a, SP2_N_H_DIST)
elif code == 61: # sp carbon
if to_add == 1:
Hat = Hat + self.add_sp_hydrogen(a, SP_C_H_DIST)
elif code == 83: # sp3 oxygen
if to_add == 1:
Hat = Hat + self.add_methyl_hydrogen(a, SP3_O_H_DIST)
# save vinyl and amide protons for last,
# this way we know where to put them
for a in atoms:
type_name = converter.convert(a.babel_type, 'zero')
hyb = int(type_name)
code = a.babel_atomic_number * 10 + hyb
to_add = a._redo
if code == 62: # sp2 carbon
if to_add == 2:
Hat = Hat + self.add_vinyl_hydrogens(a, SP2_C_H_DIST)
elif code == 72: # sp2 nitrogens
if to_add == 2:
Hat = Hat + self.add_vinyl_hydrogens(a, SP2_N_H_DIST)
return Hat
def countMissingBonds(atoms):
converter = TypeConverter('HYB')
needDBatoms = []
canHaveDBatoms = []
for a in atoms:
a._needsDB = 0
a._canHaveDB = 0
hyb = int(converter.convert(a.babel_type, 'all_caps'))
if hyb != 2: continue
if a.babel_type[0] == 'C':
sum = 0
for b in a.bonds:
sum = sum + b.bondOrder
if sum == 3:
if len(a.bonds)==3:
a._needsDB = 1
needDBatoms.append(a)
elif len(a.bonds)==2: # ==C-- or ==C/
a1 = a.bonds[0].atom1
if a1==a: a1 = a.bonds[0].atom2
a3 = a.bonds[1].atom1
if a3==a: a3 = a.bonds[1].atom2
ang = bond_angle( a1.coords, a.coords, a3.coords )
if math.fabs(ang-180) < 10: # ==C--
a._needDB = 1
needDBatoms.append(a)
elif sum == 2:
if len(a.bonds)==2:
a1 = a.bonds[0].atom1
if a1==a: a1 = a.bonds[0].atom2
a3 = a.bonds[1].atom1
if a3==a: a3 = a.bonds[1].atom2
ang = bond_angle( a1.coords, a.coords, a3.coords )
if math.fabs(ang-180) < 10:
a._needsDB = 2
needDBatoms.append(a)
else:
a._needsDB = 1
needDBatoms.append(a)
elif sum == 1:
a._needsDB = 1
needDBatoms.append(a)
elif a.babel_type[0] == 'N':
sum = 0
for b in a.bonds:
sum = sum + b.bondOrder
if sum == 2 and len(a.bonds)==2:
canHaveDBatoms.append(a)
a._canHaveDB = 1
elif a.babel_type[0] == 'O':
sum = 0
for b in a.bonds:
sum = sum + b.bondOrder
if sum == 1:
canHaveDBatoms.append(a)
a._canHaveDB = 1
return needDBatoms, canHaveDBatoms
def place_hydrogens2(self, atoms, num_H_to_add):
""" """
Hat = []
converter = TypeConverter("HYB")
for a in atoms:
type_name = converter.convert(a.babel_type, 'zero')
hyb = int(type_name)
code = a.babel_atomic_number * 10 + hyb
to_add = a._redo
if code == 63: # sp3 carbon
if to_add==1:
Hat = Hat + self.add_tertiary_hydrogen(a, SP3_C_H_DIST)
elif to_add==2:
Hat = Hat + self.add_methylene_hydrogens(a ,SP3_C_H_DIST)
elif to_add==3:
Hat = Hat + self.add_methyl_hydrogen(a, SP3_C_H_DIST)
Hat = Hat + self.add_methylene_hydrogens(a, SP3_C_H_DIST,
Hat[-1])
elif code == 73: # sp3 nitrogen
if to_add==1:
if a.babel_type=="N3+":
Hat = Hat + self.add_tertiary_hydrogen(a, SP3_N_H_DIST)
else:
Hat = Hat + self.add_sp3_N_hydrogen(a, SP3_N_H_DIST)
elif to_add==2:
Hat = Hat + self.add_methylene_hydrogens(a ,SP3_N_H_DIST)
elif to_add==3:
Hat = Hat + self.add_methyl_hydrogen(a, SP3_N_H_DIST)
Hat = Hat + self.add_methylene_hydrogens(a ,SP3_N_H_DIST,
Hat[-1])
elif code == 62: # sp2 carbon
if to_add==1:
Hat = Hat + self.add_sp2_hydrogen(a ,SP2_C_H_DIST)
elif code == 72: # sp2 nitrogen
if to_add==1:
Hat = Hat + self.add_sp2_hydrogen(a ,SP2_N_H_DIST)
elif code == 61: # sp carbon
if to_add==1:
Hat = Hat + self.add_sp_hydrogen(a ,SP_C_H_DIST)
elif code == 83: # sp3 oxygen
if to_add==1:
Hat = Hat + self.add_methyl_hydrogen(a, SP3_O_H_DIST)
# save vinyl and amide protons for last,
# this way we know where to put them
for a in atoms:
type_name = converter.convert(a.babel_type, 'zero')
hyb = int(type_name)
code = a.babel_atomic_number * 10 + hyb
to_add = a._redo
if code == 62: # sp2 carbon
if to_add==2:
Hat = Hat + self.add_vinyl_hydrogens(a ,SP2_C_H_DIST)
elif code == 72: # sp2 nitrogens
if to_add==2:
Hat = Hat + self.add_vinyl_hydrogens(a ,SP2_N_H_DIST)
return Hat