/usr/lib/python2.7/dist-packages/csb/apps/precision.py is in python-csb 1.2.2+dfsg-2ubuntu1.
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The actual contents of the file can be viewed below.
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Measure the precision and coverage of a fragment library stored in Rosetta
NNmake format.
"""
import os
import multiprocessing
import matplotlib
import csb.apps
import csb.bio.io.wwpdb as wwpdb
import csb.bio.structure as structure
import csb.bio.fragments
import csb.bio.fragments.rosetta as rosetta
import csb.core
import csb.io.plots
class ExitCodes(csb.apps.ExitCodes):
IO_ERROR = 2
INVALID_DATA = 3
class AppRunner(csb.apps.AppRunner):
@property
def target(self):
return PrecisionApp
def command_line(self):
cpu = multiprocessing.cpu_count()
cmd = csb.apps.ArgHandler(self.program, __doc__)
cmd.add_scalar_option('pdb', 'p', str, 'the PDB database (a directory containing all PDB files)', required=True)
cmd.add_scalar_option('native', 'n', str, 'native structure of the target (PDB file)', required=True)
cmd.add_scalar_option('chain', 'c', str, 'chain identifier (if not specified, the first chain)', default=None)
cmd.add_scalar_option('top', 't', int, 'read top N fragments per position', default=25)
cmd.add_scalar_option('cpu', 'C', int, 'maximum degree of parallelism', default=cpu)
cmd.add_scalar_option('rmsd', 'r', float, 'RMSD cutoff for precision and coverage', default=1.5)
cmd.add_scalar_option('output', 'o', str, 'output directory', default='.')
cmd.add_boolean_option('save-structures', 's', 'create a PDB file for each fragment, superimposed over the native', default=False)
cmd.add_positional_argument('library', str, 'Fragment library file in Rosetta NNmake format')
return cmd
class PrecisionApp(csb.apps.Application):
def main(self):
if not os.path.isdir(self.args.output):
PrecisionApp.exit('Output directory does not exist', code=ExitCodes.INVALID_DATA, usage=True)
for file in [self.args.native, self.args.library]:
if not os.path.isfile(file):
PrecisionApp.exit('File not found: {0}'.format(file), code=ExitCodes.INVALID_DATA, usage=True)
self.log('\nLoading {0.library} (top {0.top} per position)... '.format(self.args), ending='')
try:
library = rosetta.RosettaFragmentMap.read(self.args.library, top=self.args.top)
self.log('{0} fragments'.format(len(library)))
try:
native = wwpdb.RegularStructureParser(self.args.native).parse_structure()
native.accession = native.accession[:4]
if self.args.chain:
native = native.chains[self.args.chain]
else:
native = native.first_chain
except (structure.Broken3DStructureError, wwpdb.PDBParseError) as se:
raise ArgumentError("Can't parse native structure: " + str(se))
except (csb.core.ItemNotFoundError) as ce:
raise ArgumentError("Chain {0!s} not found in native structure".format(ce))
self.log('Superimposing fragments...\n')
si = LibrarySuperimposer(native, library, self.args.pdb, self.args.output,
save=self.args.save_structures, cutoff=self.args.rmsd)
matches = si.run(self.args.cpu)
info = si.plot(matches)
self.log(' RMSD Cutoff {0:>6.2f} A'.format(self.args.rmsd))
self.log(' AVG Precision {0.precision:>6.2f} %'.format(info))
self.log(' Coverage {0.coverage:>6.2f} %'.format(info))
self.log(' RW Precision {0.figure}'.format(si))
except ArgumentIOError as ioe:
PrecisionApp.exit(str(ioe), code=ExitCodes.INVALID_DATA)
except ArgumentError as ae:
PrecisionApp.exit(str(ae), code=ExitCodes.INVALID_DATA)
self.log('\nDone.')
class ArgumentError(ValueError):
pass
class ArgumentIOError(ArgumentError):
pass
class GlobalInfo(object):
def __init__(self, precision, coverage):
self.precision = precision
self.coverage = coverage
def __str__(self):
return '{0.precision:6.2f} {0.coverage:6.2f}'.format(self)
def __sub__(self, rhs):
return GlobalInfo(self.precision - rhs.precision, self.coverage - rhs.coverage)
class LibrarySuperimposer(object):
def __init__(self, native, library, pdb, output, save=False, cutoff=1.5):
if not isinstance(native, structure.Chain):
raise TypeError(native)
elif native.length < 1:
raise ArgumentError('The native chain has no residues')
if not isinstance(library, rosetta.RosettaFragmentMap):
raise TypeError(library)
for i in [pdb, output]:
if not os.path.isdir(i):
raise ArgumentIOError("{0} is not a valid directory".format(i))
self._pdb = pdb
self._native = native
self._library = library
self._output = os.path.abspath(output)
self._tab = os.path.join(self._output, native.entry_id + '.fragments.tab')
self._figure = os.path.join(self._output, native.entry_id + '.precision.pdf')
self._out = open(self._tab, 'w')
self._save = bool(save)
self._cutoff = float(cutoff)
def __del__(self):
try:
if self._out and not self._out.closed:
self._out.close()
except:
pass
@property
def table(self):
return self._tab
@property
def figure(self):
return self._figure
def run(self, cpu=1):
tasks = []
matches = []
save = None
if self._save:
save = self._output
pool = multiprocessing.Pool(cpu)
for source in self._library.sources:
fragments = self._library.fromsource(source)
task = pool.apply_async(rmsd, [self._native, source, fragments, self._pdb, save])
tasks.append(task)
for task in tasks:
for match in task.get():
if isinstance(match, csb.core.string): # error
self._out.write(' [E] ')
self._out.write(match.rstrip())
self._out.write('\n')
else:
line = '{0.id}\t{0.qstart}\t{0.qend}\t{0.length}\t{0.rmsd}\n'.format(match)
self._out.write(line)
matches.append(match)
pool.terminate()
return matches
def plot(self, matches):
residues = range(1, self._native.length + 1)
precision = []
precision2 = []
background = []
covered = set()
all = {}
positive = {}
for rank in residues:
all[rank] = 0
positive[rank] = 0
for match in matches:
for rank in range(match.qstart, match.qend + 1):
all[rank] += 1
if match.rmsd <= self._cutoff:
positive[rank] += 1
covered.add(rank)
assert sorted(all.keys()) == sorted(positive.keys()) == residues
for rank in residues:
if all[rank] == 0:
precision2.append(0)
background.append(0)
else:
p = positive[rank] * 100.0 / all[rank]
precision.append(p)
precision2.append(p)
background.append(100)
coverage = len(covered) * 100.0 / len(residues)
if len(precision) > 0:
avg_precision = sum(precision) / len(precision)
else:
avg_precision = 0
with csb.io.plots.Chart() as chart:
chart.plot.bar(residues, background, color='#f5f5f5', linewidth=None, edgecolor='#f5f5f5')
chart.plot.bar(residues, precision2, color='#5ba9da', linewidth=None, edgecolor='#5ba9da')
chart.plot.set_title(self._native.entry_id)
chart.plot.set_xlabel('Residue')
chart.plot.set_xlim(1, len(residues))
chart.plot.set_ylabel('Precision, %')
chart.plot.set_ylim(0, 100)
xaxis = chart.plot.axes.xaxis
yaxis = chart.plot.axes.yaxis
#xaxis.set_minor_locator(matplotlib.ticker.IndexLocator(1, 0))
xaxis.set_major_locator(matplotlib.ticker.IndexLocator(10, 0))
xaxis.tick_bottom()
yaxis.tick_left()
for t in xaxis.get_major_ticks():
t.tick1On = False
t.tick2On = False
for t in xaxis.get_ticklabels():
t.set_fontsize(16)
for t in yaxis.get_ticklabels():
t.set_fontsize(16)
chart.plot.spines["right"].set_visible(False)
chart.plot.spines["top"].set_visible(False)
try:
chart.width = 15
chart.height = 5.5
chart.save(self._figure, chart.formats.PDF)
except IOError as io:
raise ArgumentIOError("Can't save figure: " + str(io))
return GlobalInfo(avg_precision, coverage)
def rmsd(target, source, fragments, pdb, save=None):
matches = []
try:
src_file = wwpdb.find(source, [pdb])
if src_file is None:
raise IOError("Can't find structure {0} in {1}".format(source, pdb))
src_structure = wwpdb.RegularStructureParser(src_file).parse_structure()
except (IOError, structure.Broken3DStructureError, wwpdb.PDBParseError) as ex:
matches.append('Error parsing {0:5}: {1!s}'.format(source, ex))
return matches
for fn, fragment in enumerate(fragments):
try:
if fragment.chain not in ('_', '', None):
src_chain = src_structure.chains[fragment.chain]
else:
src_chain = src_structure.first_chain
try:
query = target.subregion(fragment.qstart, fragment.qend)
subject = src_chain.subregion(fragment.start, fragment.end, clone=True)
except IndexError:
matches.append('Fragment {1.source_id:>5} {0.start:>4}-{0.end:>4} is out of range'.format(fragment))
continue
si = query.align(subject)
match = csb.bio.fragments.FragmentMatch(fragment.id, qstart=fragment.qstart, qend=fragment.qend,
probability=None, rmsd=si.rmsd, tm_score=None, qlength=target.length)
matches.append(match)
if save:
dummy = structure.Structure(subject.entry_id)
dummy.chains.append(subject)
filename = '{0.qstart:}-{0.qend}-{0.source_id}.{1.entry_id}{2}.frag'.format(fragment, query, fn or '')
dummy.to_pdb(os.path.join(save, filename))
except (structure.Broken3DStructureError, IOError) as ex:
matches.append("Can't superimpose fragment {0}: {1!s}".format(fragment.id, ex))
continue
return matches
if __name__ == '__main__':
AppRunner().run()
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