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Fix "Prefer format() over string interpolation operator" issue #592

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Fix "Prefer format() over string interpolation operator" issue #592

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47cd54d
Migrated `%` string formating
quantifiedcode-bot Dec 15, 2015
39c969e
Remove some bangs from formated string
jbarnoud Dec 16, 2015
256d168
Merge pull request #595 from jbarnoud/wrapped2_to3_fix-3
kain88-de Dec 16, 2015
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11 changes: 5 additions & 6 deletions package/MDAnalysis/analysis/align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -461,7 +461,7 @@ def rms_fit_trj(traj, reference, select='all', filename=None, rmsdfile=None, pre
ref_atoms, traj_atoms = get_matching_atoms(ref_atoms, traj_atoms,
tol_mass=tol_mass, strict=strict)

logger.info("RMS-fitting on %d atoms." % len(ref_atoms))
logger.info("RMS-fitting on {0:d} atoms.".format(len(ref_atoms)))
if mass_weighted:
# if performing a mass-weighted alignment/rmsd calculation
weight = ref_atoms.masses / ref_atoms.masses.mean()
Expand Down Expand Up @@ -667,8 +667,8 @@ def fasta2select(fastafilename, is_aligned=False,
raise
with open(alnfilename) as aln:
alignment = Bio.AlignIO.read(aln, "clustal", alphabet=protein_gapped)
logger.info("Using clustalw sequence alignment %r" % alnfilename)
logger.info("ClustalW Newick guide tree was also produced: %r" % treefilename)
logger.info("Using clustalw sequence alignment {0!r}".format(alnfilename))
logger.info("ClustalW Newick guide tree was also produced: {0!r}".format(treefilename))

nseq = len(alignment)
if nseq != 2:
Expand Down Expand Up @@ -922,9 +922,8 @@ def get_atoms_byres(g, match_mask=np.logical_not(mismatch_mask)):

logger.error("Atoms: reference | trajectory")
for ar, at in itertools.izip(ag1[mismatch_atomindex], ag2[mismatch_atomindex]):
logger.error("%4s %3d %3s %3s %6.3f | %4s %3d %3s %3s %6.3f" %
(ar.segid, ar.resid, ar.resname, ar.name, ar.mass,
at.segid, at.resid, at.resname, at.name, at.mass,))
logger.error("{0:4s} {1:3d} {2:3s} {3:3s} {4:6.3f} | {5:4s} {6:3d} {7:3s} {8:3s} {9:6.3f}".format(ar.segid, ar.resid, ar.resname, ar.name, ar.mass,
at.segid, at.resid, at.resname, at.name, at.mass))
errmsg = ("Inconsistent selections, masses differ by more than {0}; " + \
"mis-matching atoms are shown above.").format(tol_mass)
logger.error(errmsg)
Expand Down
17 changes: 8 additions & 9 deletions package/MDAnalysis/analysis/contacts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -243,7 +243,7 @@ def __init__(self, topology, trajectory, ref1=None, ref2=None, radius=8.0,
# don't bother if trajectory is empty (can lead to segfaults so better catch it)
stats = os.stat(trajectory)
if stats.st_size == 0:
warnings.warn('trajectory = %(trajectory)s is empty, skipping...' % vars())
warnings.warn('trajectory = {trajectory!s} is empty, skipping...'.format(**vars()))
self._skip = True
return
# under normal circumstances we do not skip
Expand Down Expand Up @@ -320,7 +320,7 @@ def run(self, store=True, force=False):
if self._skip or self.output_exists(force=force):
import warnings

warnings.warn("File %(output)r or %(output_bz2)r already exists, loading %(trajectory)r." % vars(self))
warnings.warn("File {output!r} or {output_bz2!r} already exists, loading {trajectory!r}.".format(**vars(self)))
try:
self.load(self.output)
except IOError:
Expand All @@ -329,8 +329,7 @@ def run(self, store=True, force=False):

outbz2 = bz2.BZ2File(self.output_bz2, mode='w', buffering=8192)
try:
outbz2.write("# q1-q2 analysis\n# nref1 = %d\n# nref2 = %d\n"
% (self.nref[0], self.nref[1]))
outbz2.write("# q1-q2 analysis\n# nref1 = {0:d}\n# nref2 = {1:d}\n".format(self.nref[0], self.nref[1]))
outbz2.write("# frame q1 q2 n1 n2\n")
records = []
for ts in self.u.trajectory:
Expand All @@ -343,7 +342,7 @@ def run(self, store=True, force=False):

if store:
records.append((frame, q1, q2, n1, n2))
outbz2.write("%(frame)4d %(q1)8.6f %(q2)8.6f %(n1)5d %(n2)5d\n" % vars())
outbz2.write("{frame:4d} {q1:8.6f} {q2:8.6f} {n1:5d} {n2:5d}\n".format(**vars()))
finally:
outbz2.close()
if store:
Expand Down Expand Up @@ -608,7 +607,7 @@ def run(self, store=True, force=False, start_frame=1, end_frame=None, step_value
return None

with openany(self.output, 'w') as out:
out.write("# q1 analysis\n# nref = %d\n" % (self.nref))
out.write("# q1 analysis\n# nref = {0:d}\n".format((self.nref)))
out.write("# frame q1 n1\n")
records = []
self.qavg *= 0 # average contact existence
Expand All @@ -627,7 +626,7 @@ def run(self, store=True, force=False, start_frame=1, end_frame=None, step_value
self.qavg += self.q
if store:
records.append((frame, q1, n1))
out.write("%(frame)4d %(q1)8.6f %(n1)5d\n" % vars())
out.write("{frame:4d} {q1:8.6f} {n1:5d}\n".format(**vars()))
if store:
self.timeseries = np.array(records).T
n_frames = len(range(total_frames)[start_frame:end_frame:step_value])
Expand Down Expand Up @@ -758,8 +757,8 @@ def plot_qavg(self, filename=None, **kwargs):
xlim(min(x), max(x))
ylim(min(y), max(y))

xlabel("residue from %r" % self.selection_strings[0])
ylabel("residue from %r" % self.selection_strings[1])
xlabel("residue from {0!r}".format(self.selection_strings[0]))
ylabel("residue from {0!r}".format(self.selection_strings[1]))

colorbar()

Expand Down
20 changes: 7 additions & 13 deletions package/MDAnalysis/analysis/density.py
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Original file line number Diff line number Diff line change
Expand Up @@ -370,8 +370,7 @@ def convert_density(self, unit='Angstrom'):
try:
self.grid *= units.get_conversion_factor('density', self.units['density'], unit)
except KeyError:
raise ValueError("The name of the unit (%r supplied) must be one of:\n%r" %
(unit, units.conversion_factor['density'].keys()))
raise ValueError("The name of the unit ({0!r} supplied) must be one of:\n{1!r}".format(unit, units.conversion_factor['density'].keys()))
self.units['density'] = unit

def __repr__(self):
Expand Down Expand Up @@ -478,8 +477,7 @@ def current_coordinates():
return group.coordinates()

coord = current_coordinates()
logger.info("Selected %d atoms out of %d atoms (%s) from %d total." %
(coord.shape[0], len(u.select_atoms(atomselection)), atomselection, len(u.atoms)))
logger.info("Selected {0:d} atoms out of {1:d} atoms ({2!s}) from {3:d} total.".format(coord.shape[0], len(u.select_atoms(atomselection)), atomselection, len(u.atoms)))

# mild warning; typically this is run on RMS-fitted trajectories and
# so the box information is rather meaningless
Expand Down Expand Up @@ -509,8 +507,7 @@ def current_coordinates():
h = grid.copy()

for ts in u.trajectory:
print("Histograming %6d atoms in frame %5d/%d [%5.1f%%]\r" % \
(len(coord), ts.frame, u.trajectory.n_frames, 100.0 * ts.frame / u.trajectory.n_frames),)
print("Histograming {0:6d} atoms in frame {1:5d}/{2:d} [{3:5.1f}%]\r".format(len(coord), ts.frame, u.trajectory.n_frames, 100.0 * ts.frame / u.trajectory.n_frames),)
coord = current_coordinates()
if len(coord) == 0:
continue
Expand Down Expand Up @@ -758,8 +755,7 @@ def __init__(self, pdb, delta=1.0, atomselection='resname HOH and name O',
u = as_Universe(pdb)
group = u.select_atoms(atomselection)
coord = group.coordinates()
logger.info("Selected %d atoms (%s) out of %d total." %
(coord.shape[0], atomselection, len(u.atoms)))
logger.info("Selected {0:d} atoms ({1!s}) out of {2:d} total.".format(coord.shape[0], atomselection, len(u.atoms)))
smin = np.min(coord, axis=0) - padding
smax = np.max(coord, axis=0) + padding

Expand Down Expand Up @@ -788,7 +784,7 @@ def __init__(self, pdb, delta=1.0, atomselection='resname HOH and name O',
else:
# histogram 'delta functions'
grid, self.edges = np.histogramdd(coord, bins=bins, range=arange, normed=False)
logger.info("Histogrammed %6d atoms from pdb." % len(group.atoms))
logger.info("Histogrammed {0:6d} atoms from pdb.".format(len(group.atoms)))
# just a convolution of the density with a Gaussian
self.g = self._smear_sigma(grid, sigma)

Expand Down Expand Up @@ -824,8 +820,7 @@ def _smear_sigma(self, grid, sigma):
for iwat in xrange(len(pos[0])): # super-ugly loop
p = tuple([wp[iwat] for wp in pos])
g += grid[p] * np.fromfunction(self._gaussian, grid.shape, dtype=np.int, p=p, sigma=sigma)
print("Smearing out atom position %4d/%5d with RMSF %4.2f A\r" % \
(iwat + 1, len(pos[0]), sigma),)
print("Smearing out atom position {0:4d}/{1:5d} with RMSF {2:4.2f} A\r".format(iwat + 1, len(pos[0]), sigma),)
return g

def _smear_rmsf(self, coordinates, grid, edges, rmsf):
Expand All @@ -838,8 +833,7 @@ def _smear_rmsf(self, coordinates, grid, edges, rmsf):
continue
g += np.fromfunction(self._gaussian_cartesian, grid.shape, dtype=np.int,
c=coord, sigma=rmsf[iwat])
print("Smearing out atom position %4d/%5d with RMSF %4.2f A\r" % \
(iwat + 1, N, rmsf[iwat]),)
print("Smearing out atom position {0:4d}/{1:5d} with RMSF {2:4.2f} A\r".format(iwat + 1, N, rmsf[iwat]),)
return g

def _gaussian(self, i, j, k, p, sigma):
Expand Down
31 changes: 15 additions & 16 deletions package/MDAnalysis/analysis/hbonds/hbond_analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -536,8 +536,8 @@ def __init__(self, universe, selection1='protein', selection2='all', selection1_
"heuristic": self._get_bonded_hydrogens_list, # pre 0.7.6
}
if not detect_hydrogens in self._get_bonded_hydrogens_algorithms:
raise ValueError("detect_hydrogens must be one of %r" %
self._get_bonded_hydrogens_algorithms.keys())
raise ValueError("detect_hydrogens must be one of {0!r}".format(
self._get_bonded_hydrogens_algorithms.keys()))
self.detect_hydrogens = detect_hydrogens

self.u = universe
Expand Down Expand Up @@ -566,7 +566,7 @@ def __init__(self, universe, selection1='protein', selection2='all', selection1_
if not (self.selection1 and self.selection2):
raise ValueError('HydrogenBondAnalysis: invalid selections')
elif self.selection1_type not in ('both', 'donor', 'acceptor'):
raise ValueError('HydrogenBondAnalysis: Invalid selection type %s' % self.selection1_type)
raise ValueError('HydrogenBondAnalysis: Invalid selection type {0!s}'.format(self.selection1_type))

self.timeseries = None # final result
self.timesteps = None # time for each frame
Expand Down Expand Up @@ -679,8 +679,7 @@ def _get_bonded_hydrogens_dist(self, atom):
"""
try:
return atom.residue.select_atoms(
"(name H* or name 1H* or name 2H* or name 3H* or type H) and around %f name %s" %
(self.r_cov[atom.name[0]], atom.name))
"(name H* or name 1H* or name 2H* or name 3H* or type H) and around {0:f} name {1!s}".format(self.r_cov[atom.name[0]], atom.name))
except NoDataError:
return []

Expand Down Expand Up @@ -760,18 +759,18 @@ def _update_selection_2(self):
self._s2_acceptors = {}
if self.selection1_type in ('donor', 'both'):
self._s2_acceptors = self._s2.select_atoms(
' or '.join(['name %s' % i for i in self.acceptors]))
self.logger_debug("Selection 2 acceptors: %d" % len(self._s2_acceptors))
' or '.join(['name {0!s}'.format(i) for i in self.acceptors]))
self.logger_debug("Selection 2 acceptors: {0:d}".format(len(self._s2_acceptors)))
if self.selection1_type in ('acceptor', 'both'):
self._s2_donors = self._s2.select_atoms(
' or '.join(['name %s' % i for i in self.donors]))
' or '.join(['name {0!s}'.format(i) for i in self.donors]))
self._s2_donors_h = {}
for i, d in enumerate(self._s2_donors):
tmp = self._get_bonded_hydrogens(d)
if tmp:
self._s2_donors_h[i] = tmp
self.logger_debug("Selection 2 donors: %d" % len(self._s2_donors))
self.logger_debug("Selection 2 donor hydrogens: %d" % len(self._s2_donors_h))
self.logger_debug("Selection 2 donors: {0:d}".format(len(self._s2_donors)))
self.logger_debug("Selection 2 donor hydrogens: {0:d}".format(len(self._s2_donors_h)))

def logger_debug(self, *args):
if self.verbose:
Expand Down Expand Up @@ -881,11 +880,11 @@ def _get_timestep():
dist = self.calc_eucl_distance(donor_atom, a)
if angle >= self.angle and dist <= self.distance:
self.logger_debug(
"S1-D: %s <-> S2-A: %s %f A, %f DEG" % (h.index + 1, a.index + 1, dist, angle))
"S1-D: {0!s} <-> S2-A: {1!s} {2:f} A, {3:f} DEG".format(h.index + 1, a.index + 1, dist, angle))
#self.logger_debug("S1-D: %r <-> S2-A: %r %f A, %f DEG" % (h, a, dist, angle))
frame_results.append(
[h.index + 1, a.index + 1, '%s%s:%s' % (h.resname, repr(h.resid), h.name),
'%s%s:%s' % (a.resname, repr(a.resid), a.name), dist, angle])
[h.index + 1, a.index + 1, '{0!s}{1!s}:{2!s}'.format(h.resname, repr(h.resid), h.name),
'{0!s}{1!s}:{2!s}'.format(a.resname, repr(a.resid), a.name), dist, angle])
already_found[(h.index + 1, a.index + 1)] = True
if self.selection1_type in ('acceptor', 'both') and len(self._s1_acceptors) > 0:
self.logger_debug("Selection 1 Acceptors <-> Donors")
Expand All @@ -904,11 +903,11 @@ def _get_timestep():
dist = self.calc_eucl_distance(donor_atom, a)
if angle >= self.angle and dist <= self.distance:
self.logger_debug(
"S1-A: %s <-> S2-D: %s %f A, %f DEG" % (a.index + 1, h.index + 1, dist, angle))
"S1-A: {0!s} <-> S2-D: {1!s} {2:f} A, {3:f} DEG".format(a.index + 1, h.index + 1, dist, angle))
#self.logger_debug("S1-A: %r <-> S2-D: %r %f A, %f DEG" % (a, h, dist, angle))
frame_results.append(
[h.index + 1, a.index + 1, '%s%s:%s' % (h.resname, repr(h.resid), h.name),
'%s%s:%s' % (a.resname, repr(a.resid), a.name), dist, angle])
[h.index + 1, a.index + 1, '{0!s}{1!s}:{2!s}'.format(h.resname, repr(h.resid), h.name),
'{0!s}{1!s}:{2!s}'.format(a.resname, repr(a.resid), a.name), dist, angle])
self.timeseries.append(frame_results)

logger.info("HBond analysis: complete; timeseries with %d hbonds in %s.timeseries",
Expand Down
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