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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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16
propka/atom.py
View File

@@ -104,7 +104,7 @@ class Atom(object):
self.y = float(line[38:46].strip())
self.z = float(line[46:54].strip())
self.res_num = int(line[22:26].strip())
self.res_name = "%-3s" % (line[17:20].strip())
self.res_name = "{0:<3s}".format(line[17:20].strip())
self.chain_id = line[21]
# Set chain id to "_" if it is just white space.
if not self.chain_id.strip():
@@ -124,7 +124,7 @@ class Atom(object):
if len(self.name) == 4:
self.element = self.element[0]
if len(self.element) == 2:
self.element = '%1s%1s' % (
self.element = '{0:1s}{1:1s}'.format(
self.element[0], self.element[1].lower())
def set_group_type(self, type_):
@@ -278,15 +278,15 @@ class Atom(object):
Returns:
String with PDB line.
"""
res = 'CONECT%5d' % self.numb
res = 'CONECT{0:5d}'.format(self.numb)
bonded = []
for atom in self.bonded_atoms:
bonded.append(atom.numb)
bonded.sort()
for b in bonded:
res += '%5d' % b
for bond in bonded:
res += '{0:5d}'.format(bond)
res += '\n'
return res
@@ -316,12 +316,14 @@ class Atom(object):
self.occ = self.occ.replace('LG', 'non_titratable_ligand')
# try to initialise the group
try:
group_attr = "%s_group" % self.occ
group_attr = "{0:s}_group".format(self.occ)
group_attr = getattr(propka.group, group_attr)
self.group = group_attr(self)
except:
# TODO - be more specific with expection handling here
str_ = '%s in input_file is not recognized as a group' % self.occ
str_ = (
'{0:s} in input_file is not recognized as a group'.format(
self.occ))
raise Exception(str_)
# set the model pKa value
if self.beta != '-':

6
propka/bonds.py
View File

@@ -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

21
propka/calculations.py
View File

@@ -242,9 +242,9 @@ def add_trp_hydrogen(residue):
elif atom.name == "CE2":
ce_atom = atom
if (cd_atom is None) or (ne_atom is None) or (ce_atom is None):
errstr = "Unable to find all atoms for %s %s" % (
str_ = "Unable to find all atoms for {0:s} {1:s}".format(
residue[0].res_name, residue[0].res_num)
raise ValueError(errstr)
raise ValueError(str_)
he_atom = protonate_sp2(cd_atom, ne_atom, ce_atom)
he_atom.name = "HNE"
@@ -269,9 +269,9 @@ def add_amd_hydrogen(residue):
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" % (
str_ = "Unable to find all atoms for {0:s} {1:s}".format(
residue[0].res_name, residue[0].res_num)
raise ValueError(errstr)
raise ValueError(str_)
h1_atom = protonate_direction(n_atom, o_atom, c_atom)
h1_atom.name = "HN1"
h2_atom = protonate_average_direction(n_atom, c_atom, o_atom)
@@ -396,10 +396,10 @@ def make_new_h(atom, x, y, z):
new hydrogen atom
"""
new_h = propka.atom.Atom()
new_h.set_property(numb=None, name='H%s' % atom.name[1:],
res_name=atom.res_name, chain_id=atom.chain_id,
res_num=atom.res_num, x=x, y=y, z=z, occ=None,
beta=None)
new_h.set_property(
numb=None, name='H{0:s}'.format(atom.name[1:]),
res_name=atom.res_name, chain_id=atom.chain_id,
res_num=atom.res_num, x=x, y=y, z=z, occ=None, beta=None)
new_h.element = 'H'
new_h.bonded_atoms = [atom]
new_h.charge = 0
@@ -604,8 +604,9 @@ def hydrogen_bond_interaction(group1, group2, version):
atoms2 = group2.get_interaction_atoms(group1)
[closest_atom1, dist, closest_atom2] = get_smallest_distance(atoms1, atoms2)
if None in [closest_atom1, closest_atom2]:
warning('Side chain interaction failed for %s and %s' % (
group1.label, group2.label))
warning(
'Side chain interaction failed for {0:s} and {1:s}'.format(
group1.label, group2.label))
return None
# get the parameters
[dpka_max, cutoff] = version.get_hydrogen_bond_parameters(closest_atom1,

4
propka/conformation_container.py
View File

@@ -58,7 +58,7 @@ class ConformationContainer:
# if a group is coupled and we are reading a .propka_input file, then
# some more configuration might be needed
map_ = make_interaction_map(
'Covalent coupling map for %s' % self,
'Covalent coupling map for {0:s}'.format(str(self)),
self.get_covalently_coupled_groups(),
lambda g1, g2: g1 in g2.covalently_coupled_groups)
info(map_)
@@ -100,7 +100,7 @@ class ConformationContainer:
self.set_common_charge_centres()
# print coupling map
map_ = make_interaction_map(
'Covalent coupling map for %s' % self,
'Covalent coupling map for {0:s}'.format(str(self)),
self.get_covalently_coupled_groups(),
lambda g1, g2: g1 in g2.covalently_coupled_groups)
info(map_)

21
propka/coupled_groups.py
View File

@@ -193,7 +193,7 @@ class NonCovalentlyCoupledGroups:
conformation: conformation to print
"""
map_ = make_interaction_map(
'Non-covalent coupling map for %s' % conformation,
'Non-covalent coupling map for {0:s}'.format(str(conformation)),
conformation.get_non_covalently_coupled_groups(),
lambda g1, g2: g1 in g2.non_covalently_coupled_groups)
info(map_)
@@ -209,7 +209,8 @@ class NonCovalentlyCoupledGroups:
conformation: conformation to print
system: system to print
"""
info('System containing %d groups:' % len(system))
info(
'System containing {0:d} groups:'.format(len(system)))
# make list of interactions within this system
interactions = list(itertools.combinations(system, 2))
# print out coupling info for each interaction
@@ -233,8 +234,8 @@ class NonCovalentlyCoupledGroups:
# Tell the user what is swap in this combination
swap_info += 'Swapping the following interactions:\n'
for interaction in combination:
swap_info += ' %s %s\n' % (interaction[0].label,
interaction[1].label)
swap_info += ' {0:s} {1:s}\n'.format(
interaction[0].label, interaction[1].label)
# swap...
for interaction in combination:
self.swap_interactions([interaction[0]], [interaction[1]])
@@ -275,9 +276,9 @@ class NonCovalentlyCoupledGroups:
all_labels = [g.label for g in system]
str_ = ' ' + '-' * 113 + '\n'
for group in system:
str_ += self.tagged_format(' %-8s|' % tag,
group.get_determinant_string(),
all_labels)
str_ += self.tagged_format(
' {0:<8s}|'.format(tag), group.get_determinant_string(),
all_labels)
return str_ + '\n'
def swap_interactions(self, groups1, groups2, include_side_chain_hbs=True):
@@ -342,10 +343,10 @@ class NonCovalentlyCoupledGroups:
Returns:
tagged string
"""
str_ = "%s %s" % (tag, str_)
str_ = str_.replace('\n', '\n%s ' % tag)
str_ = "{0:s} {1:s}".format(tag, str_)
str_ = str_.replace('\n', '\n{0:s} '.format(tag))
for label in labels:
str_ = str_.replace(label, '\033[31m%s\033[30m' % label)
str_ = str_.replace(label, '\033[31m{0:s}\033[30m'.format(label))
return str_ + '\n'
@staticmethod

2
propka/determinant.py
View File

@@ -34,4 +34,4 @@ class Determinant:
self.value += value
def __str__(self):
return '%s: %8.2f' % (self.label, self.value)
return '{0:s}: {1:8.2f}'.format(self.label, self.value)

45
propka/group.py
View File

@@ -179,7 +179,7 @@ class Group:
# first check if there are any coupled groups at all
if len(self.covalently_coupled_groups) == 0:
return ''
line = 'CCOUPL%5d' % self.atom.numb
line = 'CCOUPL{0:5d}'.format(self.atom.numb)
# extract and sort numbers of coupled groups
coupled = []
for group in self.covalently_coupled_groups:
@@ -187,7 +187,7 @@ class Group:
coupled.sort()
# write 'em out
for num in coupled:
line += '%5d' % num
line += '{0:5d}'.format(num)
line += '\n'
return line
@@ -200,7 +200,7 @@ class Group:
# first check if there are any coupled groups at all
if len(self.non_covalently_coupled_groups) == 0:
return ''
line = 'NCOUPL%5d' % self.atom.numb
line = 'NCOUPL{0:5d}'.format(self.atom.numb)
# extract and sort numbers of coupled groups
coupled = []
for group in self.non_covalently_coupled_groups:
@@ -208,7 +208,7 @@ class Group:
coupled.sort()
# write 'em out
for num in coupled:
line += '%5d' % num
line += '{0:5d}'.format(num)
line += '\n'
return line
@@ -229,9 +229,10 @@ class Group:
def __iadd__(self, other):
if self.type != other.type:
errstr = ('Cannot add groups of different types (%s and %s)'
% (self.type, other.type))
raise Exception(errstr)
str_ = (
'Cannot add groups of different types '
'({0:s} and {1:s})'.format(self.type, other.type))
raise Exception(str_)
# add all values
self.pka_value += other.pka_value
self.num_volume += other.num_volume
@@ -343,9 +344,9 @@ class Group:
if not self.model_pka_set:
self.model_pka = self.parameters.model_pkas[self.residue_type]
# check if we should apply a custom model pka
key = (
'%s-%s'
% (self.atom.res_name.strip(), self.atom.name.strip()))
key = '{0:s}-{1:s}'.format(
self.atom.res_name.strip(),
self.atom.name.strip())
if key in self.parameters.custom_model_pkas.keys():
self.model_pka = self.parameters.custom_model_pkas[key]
self.model_pka_set = True
@@ -388,10 +389,10 @@ class Group:
ok = False
if not ok:
str_ = 'Missing atoms or failed protonation for '
str_ += ('%s (%s) -- please check the structure'
% (self.label, self.type))
str_ += '{0:s} ({1:s}) -- please check the structure'.format(
self.label, self.type)
warning(str_)
warning('%s' % self)
warning('{0:s}'.format(str(self)))
num_acid = sum(
[EXPECTED_ATOMS_ACID_INTERACTIONS[self.type][e]
for e in EXPECTED_ATOMS_ACID_INTERACTIONS[self.type].keys()])
@@ -399,15 +400,19 @@ class Group:
[EXPECTED_ATOMS_BASE_INTERACTIONS[self.type][e]
for e in EXPECTED_ATOMS_BASE_INTERACTIONS[self.type].keys()])
warning(
'Expected %d interaction atoms for acids, found:' % num_acid)
'Expected {0:d} interaction atoms for acids, found:'.format(
num_acid))
for i in range(len(self.interaction_atoms_for_acids)):
warning(
' %s' % self.interaction_atoms_for_acids[i])
' {0:s}'.format(
str(self.interaction_atoms_for_acids[i])))
warning(
'Expected %d interaction atoms for bases, found:' % num_base)
'Expected {0:d} interaction atoms for bases, found:'.format(
num_base))
for i in range(len(self.interaction_atoms_for_bases)):
warning(
' %s' % self.interaction_atoms_for_bases[i])
' {0:s}'.format(
str(self.interaction_atoms_for_bases[i])))
def get_interaction_atoms(self, interacting_group):
"""Get atoms involved in interaction with other group.
@@ -461,14 +466,14 @@ class Group:
number_of_coulomb)
str_ = ""
for line_number in range(number_of_lines):
str_ += "%s" % (self.label)
str_ += "{0:s}".format(self.label)
if line_number == 0:
str_ += " %6.2lf" %(self.pka_value)
str_ += " {0:6.2f}".format(self.pka_value)
if len(self.non_covalently_coupled_groups) > 0:
str_ += '*'
else:
str_ += ' '
str_ += " %4d%2s " % (int(100.0*self.buried), "%")
str_ += " {0:4d}{1:>2s} ".format(int(100.0*self.buried), "%")
str_ += " %6.2lf %4d" % (self.energy_volume, self.num_volume)
str_ += " %6.2lf %4d" % (self.energy_local, self.num_local)
else: