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Replace old-style printf with str.format

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This commit is contained in:
Nathan Baker
2020-05-28 16:10:48 -07:00
parent 3266521d31
commit ba67f5149d
11 changed files with 231 additions and 202 deletions
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9
propka/coupled_groups.py
View File

@@ -371,11 +371,12 @@ class NonCovalentlyCoupledGroups:
"(difference: {shift1:>6.2f}, {shift2:>6.2f})" "(difference: {shift1:>6.2f}, {shift2:>6.2f})"
).format( ).format(
label1=group1.label, label2=group2.label, label1=group1.label, label2=group2.label,
coupl_fact=data['coupling_factor'], def_energy=data['default_energy'], coupl_fact=data['coupling_factor'],
def_energy=data['default_energy'],
swap_energy=data['swapped_energy'], swap_energy=data['swapped_energy'],
diff_energy=data['default_energy']-data['swapped_energy'], ph=data['pH'], diff_energy=data['default_energy']-data['swapped_energy'],
int_energy=data['interaction_energy'], pka1=group1.intrinsic_pka, ph=data['pH'], int_energy=data['interaction_energy'],
pka2=group2.intrinsic_pka, pka1=group1.intrinsic_pka, pka2=group2.intrinsic_pka,
diff_pka=group1.intrinsic_pka-group2.intrinsic_pka, diff_pka=group1.intrinsic_pka-group2.intrinsic_pka,
swap1=data['swapped_pka1'], swap2=data['swapped_pka2'], swap1=data['swapped_pka1'], swap2=data['swapped_pka2'],
shift1=data['pka_shift1'], shift2=data['pka_shift2']) shift1=data['pka_shift1'], shift2=data['pka_shift2'])

32
propka/group.py
View File

@@ -473,11 +473,13 @@ class Group:
str_ += '*' str_ += '*'
else: else:
str_ += ' ' str_ += ' '
str_ += " {0:4d}{1:>2s} ".format(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_ += " {0:6.2f} {1:4d}".format(
str_ += " %6.2lf %4d" % (self.energy_local, self.num_local) self.energy_volume, int(self.num_volume))
str_ += " {0:6.2f} {1:4d}".format(
self.energy_local, int(self.num_local))
else: else:
str_ += "%40s" % (" ") str_ += "{0:>40s}".format(" ")
# add the determinants # add the determinants
for type_ in ['sidechain', 'backbone', 'coulomb']: for type_ in ['sidechain', 'backbone', 'coulomb']:
str_ += self.get_determinant_for_string(type_, line_number) str_ += self.get_determinant_for_string(type_, line_number)
@@ -496,11 +498,11 @@ class Group:
string string
""" """
if number >= len(self.determinants[type_]): if number >= len(self.determinants[type_]):
empty_determinant = "%s%4d%2s" % ("XXX", 0, "X") return " 0.00 XXX 0 X"
return "%8.2lf %s" % (0.0, empty_determinant)
else: else:
determinant = self.determinants[type_][number] determinant = self.determinants[type_][number]
return "%8.2lf %s" % (determinant.value, determinant.label) return "{0:8.2f} {1:s}".format(
determinant.value, determinant.label)
def calculate_total_pka(self): def calculate_total_pka(self):
"""Calculate total pKa based on determinants associated with this """Calculate total pKa based on determinants associated with this
@@ -551,15 +553,16 @@ class Group:
penalty = '' penalty = ''
if self.coupled_titrating_group: if self.coupled_titrating_group:
penalty = ( penalty = (
' NB: Discarded due to coupling with %s' ' NB: Discarded due to coupling with {0:s}'.format(
% self.coupled_titrating_group.label) self.coupled_titrating_group.label))
fmt = ( fmt = (
" {g.label:>9s} {g.pka_value:8.2f} {g.model_pka:10.2f} " " {g.label:>9s} {g.pka_value:8.2f} {g.model_pka:10.2f} "
"{type:>18s} {penalty:s}\n") "{type:>18s} {penalty:s}\n")
return fmt.format(g=self, type=ligand_type, penalty=penalty) return fmt.format(g=self, type=ligand_type, penalty=penalty)
def __str__(self): def __str__(self):
return 'Group (%s) for %s' % (self.type, self.atom) str_ = 'Group ({0:s}) for {1:s}'.format(self.type, str(self.atom))
return str_
def calculate_folding_energy(self, parameters, ph=None, reference=None): def calculate_folding_energy(self, parameters, ph=None, reference=None):
"""Return the electrostatic energy of this residue at specified pH. """Return the electrostatic energy of this residue at specified pH.
@@ -1243,8 +1246,9 @@ def is_group(parameters, atom):
elif parameters.ligand_typing == 'groups': elif parameters.ligand_typing == 'groups':
ligand_group = is_ligand_group_by_groups(parameters, atom) ligand_group = is_ligand_group_by_groups(parameters, atom)
else: else:
raise Exception('Unknown ligand typing method \'%s\'' raise Exception(
% parameters.ligand_typing) 'Unknown ligand typing method \'{0.s}\''.format(
parameters.ligand_typing))
if ligand_group: if ligand_group:
return ligand_group return ligand_group
return None return None
@@ -1276,9 +1280,9 @@ def is_protein_group(parameters, atom):
if atom.count_bonded_elements('O') == 1: if atom.count_bonded_elements('O') == 1:
return BBCGroup(atom) return BBCGroup(atom)
### Filters for side chains based on PDB protein atom names ### Filters for side chains based on PDB protein atom names
key = '%s-%s' % (atom.res_name, atom.name) key = '{0:s}-{1:s}'.format(atom.res_name, atom.name)
if key in parameters.protein_group_mapping.keys(): if key in parameters.protein_group_mapping.keys():
class_str = "%sGroup" % parameters.protein_group_mapping[key] class_str = "{0:s}Group".format(parameters.protein_group_mapping[key])
group_class = globals()[class_str] group_class = globals()[class_str]
return group_class(atom) return group_class(atom)
return None return None

8
propka/hybrid36.py
View File

@@ -20,7 +20,7 @@ def decode(input_string):
Returns: Returns:
integer integer
""" """
value_error_message = "invalid literal for hybrid-36 conversion: '%s'" value_error_message = "invalid literal for hybrid-36 conversion: '{0:s}'"
original_input_string = input_string original_input_string = input_string
input_string = input_string.strip() input_string = input_string.strip()
@@ -33,7 +33,7 @@ def decode(input_string):
sign = 1 sign = 1
if len(input_string) == 0: if len(input_string) == 0:
raise ValueError(value_error_message % input_string) raise ValueError(value_error_message.format(input_string))
# See http://cci.lbl.gov/hybrid_36/ for documentation on the format. # See http://cci.lbl.gov/hybrid_36/ for documentation on the format.
@@ -49,13 +49,13 @@ def decode(input_string):
reference = (16 * 36 ** (num_chars - 1) + 10 ** num_chars) reference = (16 * 36 ** (num_chars - 1) + 10 ** num_chars)
_hybrid36_set = _HYBRID36_LOWER_SET _hybrid36_set = _HYBRID36_LOWER_SET
else: else:
raise ValueError(value_error_message % original_input_string) raise ValueError(value_error_message.format(original_input_string))
# Check the validity of the input string: ASCII characters should be # Check the validity of the input string: ASCII characters should be
# either all uppercase or all lowercase. # either all uppercase or all lowercase.
for char in input_string[1:]: for char in input_string[1:]:
if char not in _hybrid36_set: if char not in _hybrid36_set:
raise ValueError(value_error_message % original_input_string) raise ValueError(value_error_message.format(original_input_string))
# Convert with the int function. # Convert with the int function.
return sign * (int(input_string, 36) + reference) return sign * (int(input_string, 36) + reference)

15
propka/iterative.py
View File

@@ -211,8 +211,9 @@ def add_determinants(iterative_interactions, version, _=None):
iteratives.append(new_iterative) iteratives.append(new_iterative)
done_group.append(group) done_group.append(group)
# Initialize iterative scheme # Initialize iterative scheme
debug("\n --- pKa iterations (%d groups, %d interactions) ---" % debug(
(len(iteratives), len(iterative_interactions))) "\n --- pKa iterations ({0:d} groups, {1:d} interactions) ---".format(
len(iteratives), len(iterative_interactions)))
converged = False converged = False
iteration = 0 iteration = 0
# set non-iterative pka values as first step # set non-iterative pka values as first step
@@ -262,18 +263,18 @@ def add_determinants(iterative_interactions, version, _=None):
itres.pka_iter.append(itres.pka_new) itres.pka_iter.append(itres.pka_new)
if iteration == 10: if iteration == 10:
info("did not converge in %d iterations" % (iteration)) info("did not converge in {0:d} iterations".format(iteration))
break break
# printing pKa iterations # printing pKa iterations
# formerly was conditioned on if options.verbosity >= 2 - now unnecessary # formerly was conditioned on if options.verbosity >= 2 - now unnecessary
str_ = "%12s" % (" ") str_ = ' '
for index in range(iteration+1): for index in range(iteration+1):
str_ += "%8d" % (index) str_ += "{0:>8d}".format(index)
debug(str_) debug(str_)
for itres in iteratives: for itres in iteratives:
str_ = "%s " % (itres.label) str_ = "{0:s} ".format(itres.label)
for pka in itres.pka_iter: for pka in itres.pka_iter:
str_ += "%8.2lf" % (pka) str_ += "{0:>8.2f}".format(pka)
if not itres.converged: if not itres.converged:
str_ += " *" str_ += " *"
debug(str_) debug(str_)

15
propka/lib.py
View File

@@ -29,7 +29,7 @@ def open_file_for_reading(input_file):
try: try:
file_ = open(input_file, 'rt') file_ = open(input_file, 'rt')
except: except:
raise IOError('Cannot find file %s' % input_file) raise IOError('Cannot find file {0:s}'.format(input_file))
return file_ return file_
@@ -52,7 +52,7 @@ def open_file_for_writing(input_file):
try: try:
file_ = open(input_file, 'wt') file_ = open(input_file, 'wt')
except FileNotFoundError: except FileNotFoundError:
raise Exception('Could not open %s' % input_file) raise Exception('Could not open {0:s}'.format(input_file))
return file_ return file_
@@ -228,7 +228,7 @@ def build_parser(parser=None):
group.add_argument( group.add_argument(
"-p", "--parameters", dest="parameters", "-p", "--parameters", dest="parameters",
default=pkg_resources.resource_filename(__name__, "propka.cfg"), default=pkg_resources.resource_filename(__name__, "propka.cfg"),
help="set the parameter file [%(default)s]") help="set the parameter file [{default:s}]")
try: try:
group.add_argument( group.add_argument(
"--log-level", "--log-level",
@@ -306,7 +306,8 @@ def loadOptions(args):
try: try:
chain, resnum, inscode = parse_res_string(res_str) chain, resnum, inscode = parse_res_string(res_str)
except ValueError: except ValueError:
_LOGGER.critical('Invalid residue string: "%s"', res_str) _LOGGER.critical(
'Invalid residue string: "{0:s}"'.format(res_str))
sys.exit(1) sys.exit(1)
res_list.append((chain, resnum, inscode)) res_list.append((chain, resnum, inscode))
options.titrate_only = res_list options.titrate_only = res_list
@@ -332,9 +333,9 @@ def make_tidy_atom_label(name, element):
label = name label = name
else: # if less than 4 characters long, insert white space as needed else: # if less than 4 characters long, insert white space as needed
if len(element) == 1: if len(element) == 1:
label = ' %-3s' % name label = ' {0:<3s}'.format(name)
else: # The element should occupy the two first chars else: # The element should occupy the two first chars
label = '%-4s' % name label = '{0:<4s}'.format(name)
return label return label
@@ -365,7 +366,7 @@ def write_file(filename, lines):
""" """
file_ = open_file_for_writing(filename) file_ = open_file_for_writing(filename)
for line in lines: for line in lines:
file_.write("%s\n" % (line)) file_.write("{0:s}\n".format(line))
file_.close() file_.close()

18
propka/ligand_pka_values.py
View File

@@ -42,7 +42,7 @@ class LigandPkaValues:
map(lambda dir: os.path.join(dir, program), map(lambda dir: os.path.join(dir, program),
path))] path))]
if len(locs) == 0: if len(locs) == 0:
str_ = "'Error: Could not find %s." % program str_ = "'Error: Could not find {0:s}.".format(program)
str_ += ' Please make sure that it is found in the path.' str_ += ' Please make sure that it is found in the path.'
info(str_) info(str_)
sys.exit(-1) sys.exit(-1)
@@ -73,7 +73,7 @@ class LigandPkaValues:
max_ph: maximum pH value max_ph: maximum pH value
""" """
for name in molecule.conformation_names: for name in molecule.conformation_names:
filename = '%s_%s' % (molecule.name, name) filename = '{0:s}_{1:s}'.format(molecule.name, name)
self.get_marvin_pkas_for_conformation_container( self.get_marvin_pkas_for_conformation_container(
molecule.conformations[name], name=filename, molecule.conformations[name], name=filename,
reuse=molecule.options.reuse_ligand_mol2_file, reuse=molecule.options.reuse_ligand_mol2_file,
@@ -113,7 +113,7 @@ class LigandPkaValues:
# do one molecule at the time so we don't confuse marvin # do one molecule at the time so we don't confuse marvin
molecules = propka.lib.split_atoms_into_molecules(atoms) molecules = propka.lib.split_atoms_into_molecules(atoms)
for i, molecule in enumerate(molecules): for i, molecule in enumerate(molecules):
filename = '%s_%d.mol2' % (name, i+1) filename = '{0:s}_{1:d}.mol2'.format(name, i+1)
self.get_marvin_pkas_for_molecule( self.get_marvin_pkas_for_molecule(
molecule, filename=filename, reuse=reuse, num_pkas=num_pkas, molecule, filename=filename, reuse=reuse, num_pkas=num_pkas,
min_ph=min_ph, max_ph=max_ph) min_ph=min_ph, max_ph=max_ph)
@@ -136,8 +136,10 @@ class LigandPkaValues:
propka.pdb.write_mol2_for_atoms(atoms, filename) propka.pdb.write_mol2_for_atoms(atoms, filename)
# check that we actually have a file to work with # check that we actually have a file to work with
if not os.path.isfile(filename): if not os.path.isfile(filename):
errstr = ("Didn't find a user-modified file '%s' - generating one" errstr = (
% filename) "Didn't find a user-modified file '{0:s}' "
"- generating one".format(
filename))
warning(errstr) warning(errstr)
propka.pdb.write_mol2_for_atoms(atoms, filename) propka.pdb.write_mol2_for_atoms(atoms, filename)
# Marvin calculate pKa values # Marvin calculate pKa values
@@ -155,11 +157,11 @@ class LigandPkaValues:
'*********************************************') '*********************************************')
info('* Warning: Marvin execution failed: ' info('* Warning: Marvin execution failed: '
' *') ' *')
info('* %-100s *' % errors) info('* {0:<100s} *'.format(errors))
info('* ' info('* '
' *') ' *')
info('* Please edit the ligand mol2 file and re-run PropKa with ' info('* Please edit the ligand mol2 file and re-run PropKa with '
'the -l option: %29s *' % filename) 'the -l option: {0:>29s} *'.format(filename))
info('***********************************************************' info('***********************************************************'
'*********************************************') '*********************************************')
sys.exit(-1) sys.exit(-1)
@@ -169,7 +171,7 @@ class LigandPkaValues:
for i, index in enumerate(indices): for i, index in enumerate(indices):
atoms[index].marvin_pka = pkas[i] atoms[index].marvin_pka = pkas[i]
atoms[index].charge = {'a': -1, 'b': 1}[types[i]] atoms[index].charge = {'a': -1, 'b': 1}[types[i]]
info('%s model pKa: %.2f' % (atoms[index], pkas[i])) info('{0:s} model pKa: {1:<.2f}'.format(atoms[index], pkas[i]))
@staticmethod @staticmethod
def extract_pkas(output): def extract_pkas(output):

19
propka/molecular_container.py
View File

@@ -50,7 +50,8 @@ class Molecular_container:
self.version = version_class(parameters) self.version = version_class(parameters)
except AttributeError as err: except AttributeError as err:
print(err) print(err)
errstr = 'Error: Version %s does not exist' % parameters.version errstr = 'Error: Version {0:s} does not exist'.format(
parameters.version)
raise Exception(errstr) raise Exception(errstr)
# read the input file # read the input file
if input_file_extension[0:4] == '.pdb': if input_file_extension[0:4] == '.pdb':
@@ -89,7 +90,7 @@ class Molecular_container:
# do some additional set up # do some additional set up
self.additional_setup_when_reading_input_file() self.additional_setup_when_reading_input_file()
else: else:
info('Unrecognized input file:%s' % input_file) info('Unrecognized input file:{0:s}'.format(input_file))
sys.exit(-1) sys.exit(-1)
def top_up_conformations(self): def top_up_conformations(self):
@@ -152,8 +153,10 @@ class Molecular_container:
if group_to_add: if group_to_add:
avr_group += group_to_add avr_group += group_to_add
else: else:
str_ = ('Group %s could not be found in conformation %s.' str_ = (
% (group.atom.residue_label, name)) 'Group {0:s} could not be found in '
'conformation {0:s}.'.format(
group.atom.residue_label, name))
warning(str_) warning(str_)
# ... and store the average value # ... and store the average value
avr_group = avr_group / len(self.conformation_names) avr_group = avr_group / len(self.conformation_names)
@@ -178,16 +181,16 @@ class Molecular_container:
options: options object options: options object
""" """
# write out the average conformation # write out the average conformation
filename = os.path.join('%s.pka' % (self.name)) filename = os.path.join('{0:s}.pka'.format(self.name))
# if the display_coupled_residues option is true, write the results out # if the display_coupled_residues option is true, write the results out
# to an alternative pka file # to an alternative pka file
if self.options.display_coupled_residues: if self.options.display_coupled_residues:
filename = os.path.join('%s_alt_state.pka' % (self.name)) filename = os.path.join('{0:s}_alt_state.pka'.format(self.name))
if (hasattr(self.version.parameters, 'output_file_tag') if (hasattr(self.version.parameters, 'output_file_tag')
and len(self.version.parameters.output_file_tag) > 0): and len(self.version.parameters.output_file_tag) > 0):
filename = os.path.join( filename = os.path.join(
'%s_%s.pka' % (self.name, '{0:s}_{1:s}.pka'.format(
self.version.parameters.output_file_tag)) self.name, self.version.parameters.output_file_tag))
propka.output.write_pka( propka.output.write_pka(
self, self.version.parameters, filename=filename, self, self.version.parameters, filename=filename,
conformation='AVR', reference=reference) conformation='AVR', reference=reference)

93
propka/output.py
View File

@@ -5,9 +5,9 @@ from propka.lib import info
def print_header(): def print_header():
"""Print header section of output.""" """Print header section of output."""
str_ = "%s\n" % get_propka_header() str_ = "{0:s}\n".format(get_propka_header())
str_ += "%s\n" % get_references_header() str_ += "{0:s}\n".format(get_references_header())
str_ += "%s\n" % get_warning_header() str_ += "{0:s}\n".format(get_warning_header())
info(str_) info(str_)
@@ -25,10 +25,10 @@ def write_pdb(protein, pdbfile=None, filename=None, include_hydrogens=False,
if pdbfile is None: if pdbfile is None:
# opening file if not given # opening file if not given
if filename is None: if filename is None:
filename = "%s.pdb" % (protein.name) filename = "{0:s}.pdb".format(protein.name)
# TODO - this would be better as a context manager # TODO - this would be better as a context manager
pdbfile = open(filename, 'w') pdbfile = open(filename, 'w')
info("writing pdbfile %s" % (filename)) info("writing pdbfile {0:s}".format(filename))
close_file = True close_file = True
else: else:
# don't close the file, it was opened in a different place # don't close the file, it was opened in a different place
@@ -67,20 +67,20 @@ def write_pka(protein, parameters, filename=None, conformation='1A',
# TODO - the code immediately overrides the verbose argument; why? # TODO - the code immediately overrides the verbose argument; why?
verbose = True verbose = True
if filename is None: if filename is None:
filename = "%s.pka" % (protein.name) filename = "{0:s}.pka".format(protein.name)
# TODO - this would be much better with a context manager # TODO - this would be much better with a context manager
file_ = open(filename, 'w') file_ = open(filename, 'w')
if verbose: if verbose:
info("Writing %s" % (filename)) info("Writing {0:s}".format(filename))
# writing propka header # writing propka header
str_ = "%s\n" % get_propka_header() str_ = "{0:s}\n".format(get_propka_header())
str_ += "%s\n" % get_references_header() str_ += "{0:s}\n".format(get_references_header())
str_ += "%s\n" % get_warning_header() str_ += "{0:s}\n".format(get_warning_header())
# writing pKa determinant section # writing pKa determinant section
str_ += get_determinant_section(protein, conformation, parameters) str_ += get_determinant_section(protein, conformation, parameters)
# writing pKa summary section # writing pKa summary section
str_ += get_summary_section(protein, conformation, parameters) str_ += get_summary_section(protein, conformation, parameters)
str_ += "%s\n" % get_the_line() str_ += "{0:s}\n".format(get_the_line())
# printing Folding Profile # printing Folding Profile
str_ += get_folding_profile_section( str_ += get_folding_profile_section(
protein, conformation=conformation, reference=reference, protein, conformation=conformation, reference=reference,
@@ -109,17 +109,18 @@ def print_tm_profile(protein, reference="neutral", window=[0., 14., 1.],
_: Boolean for verbosity _: Boolean for verbosity
options: options object options: options object
""" """
profile = protein.getTmProfile(reference=reference, grid=[0., 14., 0.1], profile = protein.getTmProfile(
tms=tms, ref=ref, options=options) reference=reference, grid=[0., 14., 0.1], tms=tms, ref=ref,
options=options)
if profile is None: if profile is None:
str_ = "Could not determine Tm-profile\n" str_ = "Could not determine Tm-profile\n"
else: else:
str_ = " suggested Tm-profile for %s\n" % (protein.name) str_ = " suggested Tm-profile for {0:s}\n".format(protein.name)
for (ph, tm_) in profile: for (ph, tm_) in profile:
if (ph >= window[0] and ph <= window[1] if (ph >= window[0] and ph <= window[1]
and (ph%window[2] < 0.01 and (ph % window[2] < 0.01
or ph%window[2] > 0.99*window[2])): or ph % window[2] > 0.99*window[2])):
str_ += "%6.2lf%10.2lf\n" % (ph, tm_) str_ += "{0:>6.2f}{1:>10.2f}\n".format(ph, tm_)
info(str_) info(str_)
@@ -160,7 +161,7 @@ def get_determinant_section(protein, conformation, parameters):
string string
""" """
# getting the same order as in propka2.0 # getting the same order as in propka2.0
str_ = "%s\n" % get_determinants_header() str_ = "{0:s}\n".format(get_determinants_header())
# printing determinants # printing determinants
for chain in protein.conformations[conformation].chains: for chain in protein.conformations[conformation].chains:
for residue_type in parameters.write_out_order: for residue_type in parameters.write_out_order:
@@ -169,8 +170,9 @@ def get_determinant_section(protein, conformation, parameters):
if g.atom.chain_id == chain] if g.atom.chain_id == chain]
for group in groups: for group in groups:
if group.residue_type == residue_type: if group.residue_type == residue_type:
str_ += "%s" % group.get_determinant_string( str_ += "{0:s}".format(
parameters.remove_penalised_group) group.get_determinant_string(
parameters.remove_penalised_group))
# Add a warning in case of coupled residues # Add a warning in case of coupled residues
if (protein.conformations[conformation].non_covalently_coupled_groups if (protein.conformations[conformation].non_covalently_coupled_groups
and not protein.options.display_coupled_residues): and not protein.options.display_coupled_residues):
@@ -190,13 +192,14 @@ def get_summary_section(protein, conformation, parameters):
Returns: Returns:
string string
""" """
str_ = "%s\n" % get_summary_header() str_ = "{0:s}\n".format(get_summary_header())
# printing pKa summary # printing pKa summary
for residue_type in parameters.write_out_order: for residue_type in parameters.write_out_order:
for group in protein.conformations[conformation].groups: for group in protein.conformations[conformation].groups:
if group.residue_type == residue_type: if group.residue_type == residue_type:
str_ += "%s" % group.get_summary_string( str_ += "{0:s}".format(
parameters.remove_penalised_group) group.get_summary_string(
parameters.remove_penalised_group))
return str_ return str_
@@ -219,8 +222,8 @@ def get_folding_profile_section(protein, conformation='AVR',
""" """
str_ = get_the_line() str_ = get_the_line()
str_ += "\n" str_ += "\n"
str_ += "Free energy of %9s (kcal/mol) as a function" % direction str_ += "Free energy of {0:>9s} (kcal/mol) as a function".format(direction)
str_ += " of pH (using %s reference)\n" % reference str_ += " of pH (using {0:s} reference)\n".format(reference)
profile, [ph_opt, dg_opt], [dg_min, dg_max], [ph_min, ph_max] = ( profile, [ph_opt, dg_opt], [dg_min, dg_max], [ph_min, ph_max] = (
protein.get_folding_profile( protein.get_folding_profile(
conformation=conformation, reference=reference, conformation=conformation, reference=reference,
@@ -230,27 +233,28 @@ def get_folding_profile_section(protein, conformation='AVR',
else: else:
for (ph, dg) in profile: for (ph, dg) in profile:
if ph >= window[0] and ph <= window[1]: if ph >= window[0] and ph <= window[1]:
if ph%window[2] < 0.05 or ph%window[2] > 0.95: if ph % window[2] < 0.05 or ph % window[2] > 0.95:
str_ += "%6.2lf%10.2lf\n" % (ph, dg) str_ += "{0:>6.2f}{1:>10.2f}\n".format(ph, dg)
str_ += "\n" str_ += "\n"
if ph_opt is None or dg_opt is None: if ph_opt is None or dg_opt is None:
str_ += "Could not determine pH optimum\n" str_ += "Could not determine pH optimum\n"
else: else:
str_ += "The pH of optimum stability is %4.1lf" % ph_opt str_ += "The pH of optimum stability is {0:>4.1f}".format(ph_opt)
str_ += (" for which the free energy is %6.1lf kcal/mol at 298K\n" str_ += (
% dg_opt) " for which the free energy is {0:>6.1f} kcal/mol at 298K\n".format(
dg_opt))
if dg_min is None or dg_max is None: if dg_min is None or dg_max is None:
str_ += "Could not determine pH values where the free energy" str_ += "Could not determine pH values where the free energy"
str_ += " is within 80 %s of minimum\n" % ("%") str_ += " is within 80 %% of minimum\n"
else: else:
str_ += "The free energy is within 80 %% of maximum" str_ += "The free energy is within 80 %% of maximum"
str_ += " at pH %4.1lf to %4.1lf\n" % (dg_min, dg_max) str_ += " at pH {0:>4.1f} to {1:>4.1f}\n".format(dg_min, dg_max)
if ph_min is None or ph_max is None: if ph_min is None or ph_max is None:
str_ += "Could not determine the pH-range where the free" str_ += "Could not determine the pH-range where the free"
str_ += " energy is negative\n\n" str_ += " energy is negative\n\n"
else: else:
str_ += "The free energy is negative in the range" str_ += "The free energy is negative in the range"
str_ += " %4.1lf - %4.1lf\n\n" % (ph_min, ph_max) str_ += " {0:>4.1f} - {1:>4.1f}\n\n".format(ph_min, ph_max)
return str_ return str_
@@ -278,7 +282,7 @@ def get_charge_profile_section(protein, conformation='AVR', _=None):
if pi_pro is None or pi_mod is None: if pi_pro is None or pi_mod is None:
str_ += "Could not determine the pI\n\n" str_ += "Could not determine the pI\n\n"
else: else:
str_ += ("The pI is %5.2lf (folded) and %5.2lf (unfolded)\n") str_ += ("The pI is {0:>5.2f} (folded) and {1:>5.2f} (unfolded)\n")
return str_ return str_
@@ -290,7 +294,8 @@ def write_jackal_scap_file(mutation_data=None, filename="1xxx_scap.list",
""" """
with open(filename, 'w') as file_: with open(filename, 'w') as file_:
for chain_id, _, res_num, code2 in mutation_data: for chain_id, _, res_num, code2 in mutation_data:
str_ = "%s, %d, %s\n" % (chain_id, res_num, code2) str_ = "{chain:s}, {num:d}, {code:s}\n".format(
chain=chain_id, num=res_num, code=code2)
file_.write(str_) file_.write(str_)
@@ -302,9 +307,9 @@ def write_scwrl_sequence_file(sequence, filename="x-ray.seq", _=None):
with open(filename, 'w') as file_: with open(filename, 'w') as file_:
start = 0 start = 0
while len(sequence[start:]) > 60: while len(sequence[start:]) > 60:
file_.write("%s\n" % (sequence[start:start+60])) file_.write("{0:s}s\n".format(sequence[start:start+60]))
start += 60 start += 60
file_.write("%s\n" % (sequence[start:])) file_.write("{0:s}\n".format(sequence[start:]))
def get_propka_header(): def get_propka_header():
@@ -314,7 +319,7 @@ def get_propka_header():
string string
""" """
today = date.today() today = date.today()
str_ = "propka3.1 %93s\n" % (today) str_ = "propka3.1 {0:>93s}\n".format(today)
str_ += ("---------------------------------------------------------------" str_ += ("---------------------------------------------------------------"
"----------------------------------------\n") "----------------------------------------\n")
str_ += ("-- " str_ += ("-- "
@@ -468,19 +473,19 @@ def make_interaction_map(name, list_, interaction):
for i, group1 in enumerate(list_): for i, group1 in enumerate(list_):
for group2 in list_[i:]: for group2 in list_[i:]:
if interaction(group1, group2): if interaction(group1, group2):
res += 'Coupling: %9s - %9s\n' % (group1.label, res += 'Coupling: {0:>9s} - {1:>9s}\n'.format(
group2.label) group1.label, group2.label)
return res return res
# Name and map header # Name and map header
res = '%s\n%12s' % (name, '') res = '{0:s}\n{1:>12s}'.format(name, '')
for group in list_: for group in list_:
res += '%9s | ' % group.label res += '{0:>9s} | '.format(group.label)
# do the map # do the map
for group1 in list_: for group1 in list_:
res += '\n%-12s' % (group1.label) res += '\n{0:<12s}'.format(group1.label)
for group2 in list_: for group2 in list_:
tag = '' tag = ''
if interaction(group1, group2): if interaction(group1, group2):
tag = ' X ' tag = ' X '
res += '%10s| '%tag res += '{0:>10s}| '.format(tag)
return res return res

162
propka/parameters.py
View File

@@ -163,7 +163,8 @@ class Parameters:
value = float(words[1]) value = float(words[1])
setattr(self, words[0], value) setattr(self, words[0], value)
value_sq = value*value value_sq = value*value
setattr(self, "%s_squared" % words[0], value_sq) attr = "{0:s}_squared".format(words[0])
setattr(self, attr, value_sq)
def parse_parameter(self, words): def parse_parameter(self, words):
"""Parse field to parameters. """Parse field to parameters.
@@ -206,7 +207,7 @@ class Parameters:
"""Print interaction parameters.""" """Print interaction parameters."""
info('--------------- Model pKa values ----------------------') info('--------------- Model pKa values ----------------------')
for k in self.model_pkas: for k in self.model_pkas:
info('%3s %8.2f' % (k, self.model_pkas[k])) info('{0:>3s} {1:8.2f}'.format(k, self.model_pkas[k]))
info('') info('')
info('--------------- Interactions --------------------------') info('--------------- Interactions --------------------------')
@@ -243,21 +244,21 @@ class Parameters:
!= self.interaction_matrix[group1][group2]): != self.interaction_matrix[group1][group2]):
map_interaction += '* ' map_interaction += '* '
if (self.sidechain_cutoffs.get_value(group1, val)[0] if (self.sidechain_cutoffs.get_value(group1, val)[0]
!= self.sidechain_cutoffs.get_value(group1, != self.sidechain_cutoffs.get_value(
group2)[0] group1, group2)[0]
or self.sidechain_cutoffs.get_value(group1, or self.sidechain_cutoffs.get_value(
val)[1] group1, val)[1]
!= self.sidechain_cutoffs.get_value(group1, != self.sidechain_cutoffs.get_value(
group2)[1]): group1, group2)[1]):
map_interaction += '! ' map_interaction += '! '
else: else:
map_interaction += ' ' map_interaction += ' '
if (len(map_[group2]) == 0 if (len(map_[group2]) == 0
and (self.sidechain_cutoffs.get_value(group1, and (self.sidechain_cutoffs.get_value(
group2)[0] group1, group2)[0]
!= 3 != 3
or self.sidechain_cutoffs.get_value(group1, or self.sidechain_cutoffs.get_value(
group2)[1] group1, group2)[1]
!= 4)): != 4)):
map_interaction += '? ' map_interaction += '? '
info(interaction, map_interaction) info(interaction, map_interaction)
@@ -306,30 +307,32 @@ O2
lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO',
'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP',
'SH'] 'SH']
str_ = """ lines = [
\\begin{longtable}{lllll} "",
\\caption{Ligand interaction parameters. For interactions not listed, the default value of %s is applied.} "\\begin{{longtable}}{{lllll}}",
\\label{tab:ligand_interaction_parameters}\\\\ ("\\caption{{Ligand interaction parameters. For interactions not "
"listed, the default value of {0:s} is applied.}}").format(
\\toprule self.sidechain_cutoffs.default),
Group1 & Group2 & Interaction & c1 &c2 \\\\ "\\label{{tab:ligand_interaction_parameters}}\\\\",
\\midrule "\\toprule",
\\endfirsthead "Group1 & Group2 & Interaction & c1 &c2 \\\\",
"\\midrule",
\\multicolumn{5}{l}{\\emph{continued from the previous page}}\\\\ "\\endfirsthead",
\\toprule "",
Group1 & Group2 & Interaction & c1 &c2 \\\\ "\\multicolumn{{5}}{{l}}{\\emph{{continued from the previous page}}}\\\\",
\\midrule "\\toprule",
\\endhead "Group1 & Group2 & Interaction & c1 &c2 \\\\",
"\\midrule",
\\midrule "\\endhead",
\\multicolumn{5}{r}{\\emph{continued on the next page}}\\\\ "",
\\endfoot "\\midrule",
"\\multicolumn{{5}}{{r}}{\\emph{{continued on the next page}}}\\\\",
\\bottomrule "\\endfoot",
\\endlastfoot "",
"\\bottomrule",
""" % (self.sidechain_cutoffs.default) "\\endlastfoot",
""]
str_ = "\n".join(lines)
for group1 in agroups: for group1 in agroups:
for group2 in lgroups: for group2 in lgroups:
if self.interaction_matrix[group1][group2] == '-': if self.interaction_matrix[group1][group2] == '-':
@@ -347,7 +350,7 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
self.sidechain_cutoffs.get_value(group1, group2)[1]) self.sidechain_cutoffs.get_value(group1, group2)[1])
if group1 == group2: if group1 == group2:
break break
str_ += ' \\end{longtable}\n' str_ += ' \\end{{longtable}}\n'
info(str_) info(str_)
def print_interactions_latex(self): def print_interactions_latex(self):
@@ -357,42 +360,43 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32', 'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32',
'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM',
'N1', 'O2', 'OP', 'SH'] 'N1', 'O2', 'OP', 'SH']
str_ = """ lines = [
\\begin{longtable}{%s} "",
\\caption{Ligand interaction parameters. For interactions not listed, the default value of %s is applied.} "\\begin{longtable}{{{0:s}}}".format('l'*len(agroups)),
\\label{tab:ligand_interaction_parameters}\\\\ ("\\caption{{Ligand interaction parameters. For interactions not "
"listed, the default value of {0:s} is applied.}}").format(
\\toprule str(self.sidechain_cutoffs.default)),
Group1 & Group2 & Interaction & c1 &c2 \\\\ "\\label{{tab:ligand_interaction_parameters}}\\\\",
\\midrule "\\toprule",
\\endfirsthead "Group1 & Group2 & Interaction & c1 &c2 \\\\",
"\\midrule",
\\multicolumn{5}{l}{\\emph{continued from the previous page}}\\\\ "\\endfirsthead",
\\toprule "",
Group1 & Group2 & Interaction & c1 &c2 \\\\ "\\multicolumn{{5}}{{l}}{\\emph{{continued from the previous page}}}\\\\",
\\midrule "\\toprule",
\\endhead "Group1 & Group2 & Interaction & c1 &c2 \\\\",
"\\midrule",
\\midrule "\\endhead",
\\multicolumn{5}{r}{\\emph{continued on the next page}}\\\\ "",
\\endfoot "\\midrule",
"\\multicolumn{{5}}{{r}}{\\emph{{continued on the next page}}}\\\\",
\\bottomrule "\\endfoot",
\\endlastfoot "",
"\\bottomrule",
""" % ('l'*len(agroups), self.sidechain_cutoffs.default) "\\endlastfoot",
""
]
str_ = "\n".join(lines)
for group1 in agroups: for group1 in agroups:
for group2 in agroups: for group2 in agroups:
str_ += ('%3s & %3s & %1s & %4s & %4s\\\\ \n' fmt = '{g1:>3s} & {g2:>3s} & {mat:1s} & {val1:>4s} & {val2:>4s}\\\\ \n'
% (group1, group2, str_ += fmt.format(
self.interaction_matrix[group1][group2], group1, group2, self.interaction_matrix[group1][group2],
self.sidechain_cutoffs.get_value( str(self.sidechain_cutoffs.get_value(group1, group2)[0]),
group1, group2)[0], str(self.sidechain_cutoffs.get_value(group1, group2)[1]))
self.sidechain_cutoffs.get_value(
group1, group2)[1]))
if group1 == group2: if group1 == group2:
break break
str_ += ' \\end{longtable}\n' str_ += ' \\end{{longtable}}\n'
info(str_) info(str_)
@@ -450,7 +454,8 @@ class InteractionMatrix:
group: group to get group: group to get
""" """
if group not in self.dictionary.keys(): if group not in self.dictionary.keys():
str_ = '%s not found in interaction matrix %s' % (group, self.name) str_ = '{0:s} not found in interaction matrix {1:s}'.format(
group, self.name)
raise KeyError(str_) raise KeyError(str_)
return self.dictionary[group] return self.dictionary[group]
@@ -465,12 +470,12 @@ class InteractionMatrix:
def __str__(self): def __str__(self):
str_ = ' ' str_ = ' '
for key in self.ordered_keys: for key in self.ordered_keys:
str_ += '%3s ' % key str_ += '{0:>3s} '.format(key)
str_ += '\n' str_ += '\n'
for key1 in self.ordered_keys: for key1 in self.ordered_keys:
str_ += '%3s ' % key1 str_ += '{0:>3s} '.format(key1)
for key2 in self.ordered_keys: for key2 in self.ordered_keys:
str_ += '%3s ' % self[key1][key2] str_ += '{0:>3s} '.format(self[key1][key2])
str_ += '\n' str_ += '\n'
return str_ return str_
@@ -517,8 +522,9 @@ class PairwiseMatrix:
""" """
if key1 in self.dictionary and key2 in self.dictionary[key1]: if key1 in self.dictionary and key2 in self.dictionary[key1]:
if key1 != key2: if key1 != key2:
str_ = ('Parameter value for %s, %s defined more than once' str_ = (
% (key1, key2)) 'Parameter value for {0:s}, {1:s} defined more '
'than once'.format(key1, key2))
warning(str_) warning(str_)
if not key1 in self.dictionary: if not key1 in self.dictionary:
self.dictionary[key1] = {} self.dictionary[key1] = {}
@@ -547,7 +553,8 @@ class PairwiseMatrix:
matrix information matrix information
""" """
if group not in self.dictionary.keys(): if group not in self.dictionary.keys():
str_ = '%s not found in interaction matrix %s' % (group, self.name) str_ = '{0:s} not found in interaction matrix {1:s}'.format(
group, self.name)
raise KeyError(str_) raise KeyError(str_)
return self.dictionary[group] return self.dictionary[group]
@@ -563,5 +570,6 @@ class PairwiseMatrix:
str_ = '' str_ = ''
for key1 in self.keys(): for key1 in self.keys():
for key2 in self[key1].keys(): for key2 in self[key1].keys():
str_ += '%s %s %s\n' % (key1, key2, self[key1][key2]) str_ += '{0:s} {1:s} {2:s}\n'.format(
key1, key2, self[key1][key2])
return str_ return str_

38
propka/pdb.py
View File

@@ -58,23 +58,25 @@ def protein_precheck(conformations, names):
atoms_by_residue[res_id] = [atom] atoms_by_residue[res_id] = [atom]
for res_id, res_atoms in atoms_by_residue.items(): for res_id, res_atoms in atoms_by_residue.items():
res_name = res_atoms[0].res_name res_name = res_atoms[0].res_name
residue_label = '%3s%5s'%(res_name, res_id) residue_label = '{0:>3s}{1:>5s}'.format(res_name, res_id)
# ignore ligand residues # ignore ligand residues
if res_name not in EXPECTED_ATOM_NUMBERS: if res_name not in EXPECTED_ATOM_NUMBERS:
continue continue
# check for c-terminal # check for c-terminal
if 'C-' in [a.terminal for a in res_atoms]: if 'C-' in [a.terminal for a in res_atoms]:
if len(res_atoms) != EXPECTED_ATOM_NUMBERS[res_name]+1: if len(res_atoms) != EXPECTED_ATOM_NUMBERS[res_name]+1:
str_ = ("Unexpected number (%d) of atoms in residue %s " str_ = ("Unexpected number ({num:d}) of atoms in residue "
"in conformation %s" % (len(res_atoms), "{res:s} in conformation {conf:s}".format(
residue_label, name)) num=len(res_atoms), res=residue_label,
conf=name))
warning(str_) warning(str_)
continue continue
# check number of atoms in residue # check number of atoms in residue
if len(res_atoms) != EXPECTED_ATOM_NUMBERS[res_name]: if len(res_atoms) != EXPECTED_ATOM_NUMBERS[res_name]:
str_ = ('Unexpected number (%d) of atoms in residue %s ' str_ = ("Unexpected number ({num:d}) of atoms in residue "
'in conformation %s' % (len(res_atoms), "{res:s} in conformation {conf:s}".format(
residue_label, name)) num=len(res_atoms), res=residue_label,
conf=name))
warning(str_) warning(str_)
@@ -86,7 +88,8 @@ def resid_from_atom(atom):
Returns Returns
string string
""" """
return '%4d %s %s' % (atom.res_num, atom.chain_id, atom.icode) return '{0:>4d} {1:s} {2:s}'.format(
atom.res_num, atom.chain_id, atom.icode)
def get_atom_lines_from_pdb(pdb_file, ignore_residues=[], keep_protons=False, def get_atom_lines_from_pdb(pdb_file, ignore_residues=[], keep_protons=False,
@@ -136,7 +139,7 @@ def get_atom_lines_from_pdb(pdb_file, ignore_residues=[], keep_protons=False,
alt_conf_tag = chr(ord(alt_conf_tag)+16) alt_conf_tag = chr(ord(alt_conf_tag)+16)
if alt_conf_tag == ' ': if alt_conf_tag == ' ':
alt_conf_tag = 'A' alt_conf_tag = 'A'
conformation = '%d%s'%(model, alt_conf_tag) conformation = '{0:d}{1:s}'.format(model, alt_conf_tag)
# set the terminal # set the terminal
if tag == 'ATOM ': if tag == 'ATOM ':
if (residue_name.strip() == 'N' if (residue_name.strip() == 'N'
@@ -190,7 +193,7 @@ def write_mol2_for_atoms(atoms, filename):
filename: name of file filename: name of file
""" """
# TODO - header needs to be converted to format string # TODO - header needs to be converted to format string
header = '@<TRIPOS>MOLECULE\n\n%d %d\nSMALL\nUSER_CHARGES\n' header = '@<TRIPOS>MOLECULE\n\n{natom:d} {id:d}\nSMALL\nUSER_CHARGES\n'
atoms_section = '@<TRIPOS>ATOM\n' atoms_section = '@<TRIPOS>ATOM\n'
for i, atom in enumerate(atoms): for i, atom in enumerate(atoms):
atoms_section += atom.make_mol2_line(i+1) atoms_section += atom.make_mol2_line(i+1)
@@ -200,15 +203,16 @@ def write_mol2_for_atoms(atoms, filename):
for j, atom2 in enumerate(atoms, i+1): for j, atom2 in enumerate(atoms, i+1):
if atom1 in atom2.bonded_atoms: if atom1 in atom2.bonded_atoms:
type_ = get_bond_order(atom1, atom2) type_ = get_bond_order(atom1, atom2)
bonds_section += '%7d %7d %7d %7s\n' % (id_, i+1, j+1, type_) bonds_section += '{0:>7d} {1:>7d} {2:>7d} {3:>7s}\n'.format(
id_, i+1, j+1, type_)
id_ += 1 id_ += 1
substructure_section = '@<TRIPOS>SUBSTRUCTURE\n\n' substructure_section = '@<TRIPOS>SUBSTRUCTURE\n\n'
if len(atoms) > 0: if len(atoms) > 0:
substructure_section = ('@<TRIPOS>SUBSTRUCTURE\n%-7d %10s %7d\n' substructure_section = (
% (atoms[0].res_num, atoms[0].res_name, '@<TRIPOS>SUBSTRUCTURE\n{0:<7d} {1:>10s} {2:>7d}\n'.format(
atoms[0].numb)) atoms[0].res_num, atoms[0].res_name, atoms[0].numb))
out = propka.lib.open_file_for_writing(filename) out = propka.lib.open_file_for_writing(filename)
out.write(header % (len(atoms), id_-1)) out.write(header.format(natom=len(atoms), id=id_-1))
out.write(atoms_section) out.write(atoms_section)
out.write(bonds_section) out.write(bonds_section)
out.write(substructure_section) out.write(substructure_section)
@@ -232,7 +236,7 @@ def get_bond_order(atom1, atom2):
if '.ar' in atom2.sybyl_type: if '.ar' in atom2.sybyl_type:
pi_electrons2 -= 1 pi_electrons2 -= 1
if pi_electrons1 > 0 and pi_electrons2 > 0: if pi_electrons1 > 0 and pi_electrons2 > 0:
type_ = '%d' % (min(pi_electrons1, pi_electrons2)+1) type_ = '{0:d}'.format(min(pi_electrons1, pi_electrons2)+1)
if '.ar' in atom1.sybyl_type and '.ar' in atom2.sybyl_type: if '.ar' in atom1.sybyl_type and '.ar' in atom2.sybyl_type:
type_ = 'ar' type_ = 'ar'
return type_ return type_
@@ -247,7 +251,7 @@ def write_input(molecular_container, filename):
""" """
out = propka.lib.open_file_for_writing(filename) out = propka.lib.open_file_for_writing(filename)
for conformation_name in molecular_container.conformation_names: for conformation_name in molecular_container.conformation_names:
out.write('MODEL %s\n' % conformation_name) out.write('MODEL {0:s}\n'.format(conformation_name))
# write atoms # write atoms
for atom in molecular_container.conformations[conformation_name].atoms: for atom in molecular_container.conformations[conformation_name].atoms:
out.write(atom.make_input_line()) out.write(atom.make_input_line())

2
propka/protonate.py
View File

@@ -71,7 +71,7 @@ class Protonate:
""" """
# atom is a protein atom # atom is a protein atom
if atom.type == 'atom': if atom.type == 'atom':
key = '%3s-%s' % (atom.res_name, atom.name) key = '{0:3s}-{1:s}'.format(atom.res_name, atom.name)
if atom.terminal: if atom.terminal:
debug(atom.terminal) debug(atom.terminal)
key = atom.terminal key = atom.terminal