From 1ce44b77bf0536a21da2a7e7937f8fc5d0e8acbd Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Mon, 25 May 2020 17:33:16 -0700 Subject: [PATCH] Clean up line breaks in calculations.py See https://github.com/jensengroup/propka-3.1/issues/43. --- propka/calculations.py | 64 ++++++++++++++++++++++-------------------- 1 file changed, 34 insertions(+), 30 deletions(-) diff --git a/propka/calculations.py b/propka/calculations.py index 711cd60..b507764 100644 --- a/propka/calculations.py +++ b/propka/calculations.py @@ -259,14 +259,14 @@ def add_amd_hydrogen(residue): o_atom = None n_atom = None for atom in residue: - if (atom.res_name == "GLN" and atom.name == "CD") \ - or (atom.res_name == "ASN" and atom.name == "CG"): + if ((atom.res_name == "GLN" and atom.name == "CD") + or (atom.res_name == "ASN" and atom.name == "CG")): c_atom = atom - elif (atom.res_name == "GLN" and atom.name == "OE1") \ - or (atom.res_name == "ASN" and atom.name == "OD1"): + elif ((atom.res_name == "GLN" and atom.name == "OE1") + or (atom.res_name == "ASN" and atom.name == "OD1")): o_atom = atom - elif (atom.res_name == "GLN" and atom.name == "NE2") \ - or (atom.res_name == "ASN" and atom.name == "ND2"): + elif ((atom.res_name == "GLN" and atom.name == "NE2") + or (atom.res_name == "ASN" and atom.name == "ND2")): n_atom = atom if (c_atom is None) or (o_atom is None) or (n_atom is None): errstr = "Unable to find all atoms for %s %s" % (residue[0].res_name, @@ -445,8 +445,8 @@ def radial_volume_desolvation(parameters, group): min_dist_4th = MIN_DISTANCE_4TH for atom in all_atoms: # ignore atoms in the same residue - if atom.res_num == group.atom.res_num \ - and atom.chain_id == group.atom.chain_id: + if (atom.res_num == group.atom.res_num + and atom.chain_id == group.atom.chain_id): continue sq_dist = squared_distance(group, atom) # desolvation @@ -466,8 +466,9 @@ def radial_volume_desolvation(parameters, group): group.buried = calculate_weight(parameters, group.num_volume) scale_factor = calculate_scale_factor(parameters, group.buried) volume_after_allowance = max(0.00, volume-parameters.desolvationAllowance) - group.energy_volume = group.charge * parameters.desolvationPrefactor \ - * volume_after_allowance * scale_factor + group.energy_volume = ( + group.charge * parameters.desolvationPrefactor + * volume_after_allowance * scale_factor) def calculate_scale_factor(parameters, weight): @@ -494,8 +495,9 @@ def calculate_weight(parameters, num_volume): Returns: desolvation weight """ - weight = float(num_volume - parameters.Nmin) \ - / float(parameters.Nmax - parameters.Nmin) + weight = ( + float(num_volume - parameters.Nmin) + / float(parameters.Nmax - parameters.Nmin)) weight = min(1.0, weight) weight = max(0.0, weight) return weight @@ -647,8 +649,8 @@ def hydrogen_bond_interaction(group1, group2, version): # Do nothing, value should have been assigned. pass else: - value = version.calculate_side_chain_energy(dist, dpka_max, cutoff, weight, - f_angle) + value = version.calculate_side_chain_energy( + dist, dpka_max, cutoff, weight, f_angle) return value @@ -712,15 +714,16 @@ def coulomb_energy(dist, weight, parameters): """ diel = UNK_DIELECTRIC1 - (UNK_DIELECTRIC1 - UNK_DIELECTRIC2)*weight dist = max(dist, parameters.coulomb_cutoff1) - scale = (dist - parameters.coulomb_cutoff2)/(parameters.coulomb_cutoff1 \ - - parameters.coulomb_cutoff2) + scale = ( + (dist - parameters.coulomb_cutoff2) + / (parameters.coulomb_cutoff1 - parameters.coulomb_cutoff2)) scale = max(0.0, scale) scale = min(1.0, scale) dpka = UNK_PKA_SCALING1/(diel*dist)*scale return abs(dpka) -def backbone_reorganization(parameters, conformation): +def backbone_reorganization(_, conformation): """Perform calculations related to backbone reorganizations. NOTE - this was described in the code as "adding test stuff" @@ -728,7 +731,7 @@ def backbone_reorganization(parameters, conformation): TODO - figure out why a similar function exists in version.py Args: - parameters: not used + _: not used conformation: specific molecule conformation """ titratable_groups = conformation.get_backbone_reorganisation_groups() @@ -744,9 +747,10 @@ def backbone_reorganization(parameters, conformation): atom3=bbc_group.atom, center=center) if dist < UNK_BACKBONE_DISTANCE1 and f_angle > UNK_FANGLE_MIN: - value = 1.0 - (dist-UNK_BACKBONE_DISTANCE2) \ - / (UNK_BACKBONE_DISTANCE1-UNK_BACKBONE_DISTANCE2) - dpka += UNK_PKA_SCALING2*min(1.0, value) + value = ( + 1.0 - (dist-UNK_BACKBONE_DISTANCE2) + / (UNK_BACKBONE_DISTANCE1-UNK_BACKBONE_DISTANCE2)) + dpka += UNK_PKA_SCALING2 * min(1.0, value) titratable_group.energy_local = dpka*weight @@ -774,14 +778,14 @@ def check_exceptions(version, group1, group2): exception, value = check_coo_coo_exception(group1, group2, version) elif (res_type1 == "CYS") and (res_type2 == "CYS"): exception, value = check_cys_cys_exception(group1, group2, version) - elif (res_type1 == "COO") and (res_type2 == "HIS") or \ - (res_type1 == "HIS") and (res_type2 == "COO"): + elif ((res_type1 == "COO") and (res_type2 == "HIS") + or (res_type1 == "HIS") and (res_type2 == "COO")): exception, value = check_coo_his_exception(group1, group2, version) - elif (res_type1 == "OCO") and (res_type2 == "HIS") or \ - (res_type1 == "HIS") and (res_type2 == "OCO"): + elif ((res_type1 == "OCO") and (res_type2 == "HIS") + or (res_type1 == "HIS") and (res_type2 == "OCO")): exception, value = check_oco_his_exception(group1, group2, version) - elif (res_type1 == "CYS") and (res_type2 == "HIS") or \ - (res_type1 == "HIS") and (res_type2 == "CYS"): + elif ((res_type1 == "CYS") and (res_type2 == "HIS") + or (res_type1 == "HIS") and (res_type2 == "CYS")): exception, value = check_cys_his_exception(group1, group2, version) else: # do nothing, no exception for this pair @@ -933,8 +937,8 @@ def check_buried(num_volume1, num_volume2): Returns: True if interaction is buried, False otherwise """ - if (num_volume1 + num_volume2 <= COMBINED_NUM_BURIED_MAX) \ - and (num_volume1 <= SEPARATE_NUM_BURIED_MAX \ - or num_volume2 <= SEPARATE_NUM_BURIED_MAX): + if ((num_volume1 + num_volume2 <= COMBINED_NUM_BURIED_MAX) + and (num_volume1 <= SEPARATE_NUM_BURIED_MAX + or num_volume2 <= SEPARATE_NUM_BURIED_MAX)): return False return True