diff --git a/propka/ligand.py b/propka/ligand.py index 2be158d..3386793 100644 --- a/propka/ligand.py +++ b/propka/ligand.py @@ -123,20 +123,22 @@ def assign_sybyl_type(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: + # 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: + 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: + 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') @@ -144,7 +146,8 @@ def assign_sybyl_type(atom): # 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: + 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: @@ -155,8 +158,8 @@ def assign_sybyl_type(atom): # 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): + if (len(bonded_atom.bonded_atoms) < 3 + or is_planar(bonded_atom)): set_type(bonded_atom, 'N.pl3') return # sp3 carbon @@ -181,16 +184,18 @@ def assign_sybyl_type(atom): # 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: + 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: + 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: + 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') @@ -262,8 +267,8 @@ def identify_ring(this_atom, original_atom, number, past_atoms): these_return_atoms = identify_ring(atom, original_atom, number, past_atoms) if len(these_return_atoms) > 0: - if len(return_atoms) > len(these_return_atoms) \ - or len(return_atoms) == 0: + if (len(return_atoms) > len(these_return_atoms) + or len(return_atoms) == 0): return_atoms = these_return_atoms return return_atoms