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"""Helper classes to provide a summary report of an :class:`ihm.System`"""
import ihm
import sys
import warnings
import collections
class MissingDataWarning(UserWarning):
pass
class LocalFilesWarning(UserWarning):
pass
class MissingFileWarning(UserWarning):
pass
def _get_name(name):
if name:
return repr(name)
else:
return "(unnamed)"
class _SectionReporter:
def __init__(self, title, fh):
self.fh = fh
print("\n\n# " + title, file=self.fh)
def report(self, txt):
print(" " + str(txt), file=self.fh)
class Reporter:
def __init__(self, system, fh=sys.stdout):
self.system = system
self.fh = fh
def report(self):
print("Title: %s" % self.system.title, file=self.fh)
self.report_entities()
self.report_asyms()
self.report_representations()
self.report_databases()
self.report_files()
self.report_citations()
self.report_software()
self.report_protocols()
self.report_restraints()
self.report_models()
self.report_ensembles()
def _section(self, title):
return _SectionReporter(title, self.fh)
def report_entities(self):
r = self._section("Entities (unique sequences)")
asyms_for_entity = collections.defaultdict(list)
for a in self.system.asym_units:
asyms_for_entity[a.entity].append(a)
for e in self.system.entities:
asyms = asyms_for_entity[e]
r.report("- %s (length %d, %d instances, chain IDs %s)"
% (e.description, len(e.sequence), len(asyms),
", ".join(a.id for a in asyms)))
if len(e.references) == 0:
warnings.warn(
"No reference sequence (e.g. from UniProt) provided "
"for %s" % e, MissingDataWarning)
for ref in e.references:
r.report(" - from %s" % str(ref))
def report_asyms(self):
r = self._section("Asyms/chains")
for a in self.system.asym_units:
r.report("- %s (chain ID %s)" % (a.details, a.id))
def report_citations(self):
r = self._section("Publications cited")
for c in self.system._all_citations():
r.report('- "%s", %s, %s' % (c.title, c.journal, c.year))
def report_software(self):
r = self._section("Software used")
for s in ihm._remove_identical(self.system._all_software()):
if s.version is None:
r.report("- %s (no version given)" % s.name)
else:
r.report("- %s (version %s)" % (s.name, s.version))
if not s.citation:
warnings.warn(
"No citation provided for %s" % s, MissingDataWarning)
def report_databases(self):
r = self._section("External databases referenced")
for loc in ihm._remove_identical(self.system._all_locations()):
if isinstance(loc, ihm.location.DatabaseLocation):
r.report(" - %s accession %s"
% (loc.db_name, loc.access_code))
def report_files(self):
r = self._section("Additional files referenced")
locs_by_repo = collections.defaultdict(list)
for loc in ihm._remove_identical(self.system._all_locations()):
if not isinstance(loc, ihm.location.DatabaseLocation):
locs_by_repo[loc.repo].append(loc)
for repo, locs in locs_by_repo.items():
r.report("- %s" % ("DOI: " + repo.doi if repo else "Local files"))
for loc in locs:
r.report(" - %r, %s" % (loc.path, loc.details))
if None in locs_by_repo:
warnings.warn(
"The following local files are referenced (they will need to "
"be deposited in a database or with a DOI): %s"
% [loc.path for loc in locs_by_repo[None]], LocalFilesWarning)
def report_representations(self):
r = self._section("Model representation")
for rep in self.system._all_representations():
if hasattr(rep, '_id'):
r.report("- Representation %s" % rep._id)
else:
r.report("- Representation")
for segment in rep:
r.report(" - " + segment._get_report())
def report_protocols(self):
r = self._section("Modeling protocols")
for prot in self.system._all_protocols():
r.report("- " + (prot.name if prot.name else "Unnamed protocol"))
for step in prot.steps:
r.report(" - " + step._get_report())
for analysis in prot.analyses:
r.report(" - Analysis")
for step in analysis.steps:
r.report(" - " + step._get_report())
def report_restraints(self):
r = self._section("Restraints")
for rsr in ihm._remove_identical(self.system._all_restraints()):
r.report("- " + rsr._get_report())
def report_models(self):
r = self._section("Models")
for sg in self.system.state_groups:
r.report("- State group")
for state in sg:
r.report(" - State %s" % _get_name(state.name))
for mg in state:
r.report(" - Model group %s containing %d models"
% (_get_name(mg.name), len(mg)))
def report_ensembles(self):
r = self._section("Ensembles")
for e in self.system.ensembles:
r.report("- Ensemble %s containing %d models"
% (_get_name(e.name), e.num_models))
if e.model_group is not None:
r.report(" - From model group %s"
% _get_name(e.model_group.name))
if e.precision is not None:
r.report(" - Precision %.1f" % e.precision)
if e.file:
r.report(" - In external file %s" % e.file)
if (e.model_group is not None and not e.file
and e.num_models > len(e.model_group)):
warnings.warn(
"%s references more models (%d) than are deposited in "
"its model group, but does not reference an external file"
% (e, e.num_models), MissingFileWarning)
for d in e.densities:
asym = d.asym_unit
r.report(" - Localization density for %s %d-%d"
% (asym.details, asym.seq_id_range[0],
asym.seq_id_range[1]))
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