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Replace old formatting with new str.format()

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This commit is contained in:
Nathan Baker
2020-05-27 20:55:44 -07:00
parent 6e7c188dbd
commit 3266521d31
7 changed files with 62 additions and 53 deletions
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6
propka/bonds.py
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@@ -191,7 +191,7 @@ class BondMaker:
atoms: list of atoms to check for bonds
"""
for atom1 in atoms:
key = '%s-%s' % (atom1.res_name, atom1.name)
key = '{0:s}-{1:s}'.format(atom1.res_name, atom1.name)
if key in list(self.num_pi_elec_bonds_sidechains.keys()):
atom1.num_pi_elec_2_3_bonds = (
self.num_pi_elec_bonds_sidechains[key])
@@ -235,7 +235,7 @@ class BondMaker:
self.num_pi_elec_conj_bonds_ligands[atom.sybyl_type])
# for protein
if atom.type == 'atom':
key = '%s-%s' % (atom.res_name, atom.name)
key = '{0:s}-{1:s}'.format(atom.res_name, atom.name)
if key in list(self.num_pi_elec_bonds_sidechains.keys()):
atom.num_pi_elec_2_3_bonds = (
self.num_pi_elec_bonds_sidechains[key])
@@ -300,7 +300,7 @@ class BondMaker:
sq_dist = propka.calculations.squared_distance(atom1, atom2)
if sq_dist > self.max_sq_distance:
return False
key = '%s-%s' % (atom1.element, atom2.element)
key = '{0:s}-{1:s}'.format(atom1.element, atom2.element)
h_count = key.count('H')
if sq_dist < self.h_dist_squared and h_count == 1:
return True