diff --git a/propka/iterative.py b/propka/iterative.py index d14d86f..5bafc8e 100644 --- a/propka/iterative.py +++ b/propka/iterative.py @@ -10,12 +10,14 @@ from propka.lib import info, debug UNK_MIN_VALUE = 0.005 -def add_to_determinant_list(group1, group2, distance, iterative_interactions, version): +def add_to_determinant_list(group1, group2, distance, iterative_interactions, + version): """Add iterative determinantes to the list. [[R1, R2], [side-chain, coulomb], [A1, A2]], ... - NOTE - the sign is determined when the interaction is added to the iterative object! + NOTE - sign is determined when the interaction is added to the iterative + object! NOTE - distance < coulomb_cutoff here Args: @@ -141,14 +143,18 @@ def add_iterative_ion_pair(object1, object2, interaction, version): q2 = object2.q comp1 = object1.pka_old + annihilation[0] + q1*coulomb_value comp2 = object2.pka_old + annihilation[1] + q2*coulomb_value - if object1.res_name not in version.parameters.exclude_sidechain_interactions: + if (object1.res_name + not in version.parameters.exclude_sidechain_interactions): comp1 += q1*hbond_value - if object2.res_name not in version.parameters.exclude_sidechain_interactions: + if (object2.res_name + not in version.parameters.exclude_sidechain_interactions): comp2 += q2*hbond_value if q1 == -1.0 and comp1 < comp2: - add_term = True # pKa(acid) < pKa(base) + # pKa(acid) < pKa(base) + add_term = True elif q1 == 1.0 and comp1 > comp2: - add_term = True # pKa(base) > pKa(acid) + # pKa(base) > pKa(acid) + add_term = True else: add_term = False annihilation[0] = 0.00 @@ -167,12 +173,14 @@ def add_iterative_ion_pair(object1, object2, interaction, version): # Side-chain if hbond_value > UNK_MIN_VALUE: # residue1 - if object1.res_name not in version.parameters.exclude_sidechain_interactions: + if (object1.res_name + not in version.parameters.exclude_sidechain_interactions): interaction = [object2, q1*hbond_value] annihilation[0] += -q1*hbond_value object1.determinants['sidechain'].append(interaction) # residue2 - if object2.res_name not in version.parameters.exclude_sidechain_interactions: + if (object2.res_name + not in version.parameters.exclude_sidechain_interactions): interaction = [object1, q2*hbond_value] annihilation[1] += -q2*hbond_value object2.determinants['sidechain'].append(interaction) @@ -191,7 +199,7 @@ def add_determinants(iterative_interactions, version, _=None): # --- setup --- iteratives = [] done_group = [] - # creating iterative objects with references to their real group counterparts + # create iterative objects with references to their real group counterparts for interaction in iterative_interactions: pair = interaction[0] for group in pair: @@ -354,8 +362,9 @@ class Iterative: return self.label == other.label else: # For heterogene atoms we also need to check the residue number - return self.label == other.label \ - and self.atom.res_num == other.atom.res_num + return ( + self.label == other.label + and self.atom.res_num == other.atom.res_num) def __hash__(self): """Needed to use objects in sets."""