emdbva 0.0.1.dev151__tar.gz → 0.0.1.dev152__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (56) hide show
  1. {emdbva-0.0.1.dev151/emdbva.egg-info → emdbva-0.0.1.dev152}/PKG-INFO +1 -1
  2. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152/emdbva.egg-info}/PKG-INFO +1 -1
  3. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/preparation.py +2 -1
  4. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/prepareandrun_codon_airflow.py +2 -1
  5. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/schemas/emdb_entry_full.schema.json +1 -1
  6. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/validationanalysis.py +5 -9
  7. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/version.py +1 -1
  8. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/LICENSE +0 -0
  9. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/MANIFEST.in +0 -0
  10. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/README.rst +0 -0
  11. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/emdbva.egg-info/SOURCES.txt +0 -0
  12. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/emdbva.egg-info/dependency_links.txt +0 -0
  13. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/emdbva.egg-info/entry_points.txt +0 -0
  14. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/emdbva.egg-info/requires.txt +0 -0
  15. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/emdbva.egg-info/top_level.txt +0 -0
  16. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/setup.cfg +0 -0
  17. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/setup.py +0 -0
  18. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/PATHS_codon_airflow.py +0 -0
  19. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/__init__.py +0 -0
  20. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/audit/__init__.py +0 -0
  21. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/audit/cif_revision.py +0 -0
  22. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/mainva.py +0 -0
  23. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/__init__.py +0 -0
  24. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/bars.py +0 -0
  25. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/connected_percentage.py +0 -0
  26. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/contour_level_predicator.py +0 -0
  27. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/emda_mmcc.py +0 -0
  28. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/emringer.py +0 -0
  29. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/inclusion.py +0 -0
  30. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/map_data_validation.py +0 -0
  31. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/map_map_cc.py +0 -0
  32. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/overlap_percentage.py +0 -0
  33. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/phaserandomization.py +0 -0
  34. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/phenix_cc.py +0 -0
  35. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/phenix_mm.py +0 -0
  36. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/projections.py +0 -0
  37. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/qscore.py +0 -0
  38. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/residue_locres.py +0 -0
  39. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/resmap.py +0 -0
  40. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/smoc.py +0 -0
  41. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/strudel.py +0 -0
  42. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/surfaces.py +0 -0
  43. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/metrics/threedfsc.py +0 -0
  44. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/qscores.csv +0 -0
  45. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/schemas/__init__.py +0 -0
  46. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/schemas/loader.py +0 -0
  47. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/utils/Checker.py +0 -0
  48. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/utils/ChimeraxViews.py +0 -0
  49. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/utils/MapProcessor.py +0 -0
  50. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/utils/Model.py +0 -0
  51. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/utils/__init__.py +0 -0
  52. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/utils/cl_weights.pth +0 -0
  53. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/utils/log_utils.py +0 -0
  54. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/utils/misc.py +0 -0
  55. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/utils/rescolor.py +0 -0
  56. {emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/utils/stars.py +0 -0
{emdbva-0.0.1.dev151/emdbva.egg-info → emdbva-0.0.1.dev152}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: emdbva
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- Version: 0.0.1.dev151
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+ Version: 0.0.1.dev152
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  Summary: CryoEM validation toolkit
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  Home-page: https://test.pypi.org/project/va/
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  Author: Zhe Wang
{emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152/emdbva.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: emdbva
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- Version: 0.0.1.dev151
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+ Version: 0.0.1.dev152
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  Summary: CryoEM validation toolkit
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  Home-page: https://test.pypi.org/project/va/
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  Author: Zhe Wang
{emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/preparation.py RENAMED
@@ -961,7 +961,8 @@ class PreParation:
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  breakdigits = 2
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  emdbidmin = 4
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- if len(emdid) >= emdbidmin and isinstance(emdid, str):
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+ emdbidmax = 7
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+ if isinstance(emdid, str) and emdid.isdigit() and emdbidmin <= len(emdid) <= emdbidmax:
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  topsubpath = emdid[:breakdigits]
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  middlesubpath = emdid[breakdigits:-breakdigits]
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  subpath = os.path.join(topsubpath, middlesubpath, emdid)
{emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/prepareandrun_codon_airflow.py RENAMED
@@ -149,8 +149,9 @@ class prepareandrun():
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  idsubdirs = collections.OrderedDict()
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  breakdigits = 2
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  emdbidmin = 4
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+ emdbidmax = 7
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  for id in emdids:
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- if len(id) >= emdbidmin and isinstance(id, str):
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+ if isinstance(id, str) and id.isdigit() and emdbidmin <= len(id) <= emdbidmax:
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  topsubpath = id[:breakdigits]
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  middlesubpath = id[breakdigits:-breakdigits]
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  subpath = os.path.join(topsubpath, middlesubpath, id)
{emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/schemas/emdb_entry_full.schema.json RENAMED
@@ -4,7 +4,7 @@
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  "type": "object",
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  "description": "Root object keyed by EMDB id(s), e.g. \"8117\", or map output keys, e.g. \"emd_8117.map\".",
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  "patternProperties": {
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- "^\\d{4,5}$": {
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+ "^\\d{4,7}$": {
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  "$ref": "#/definitions/EmdbEntry"
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  },
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  "^[A-Za-z0-9._-]+\\.map$": {
{emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/validationanalysis.py RENAMED
@@ -211,15 +211,11 @@ class ValidationAnalysis:
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  else:
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  self.cl = contourlevel
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  if self.emdid:
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- digits = [i for i in str(self.emdid)]
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- if len(digits) == 4:
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- subdir = '{}/{}/'.format(digits[0] + digits[1], self.emdid)
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- self.workdir = MAP_SERVER_PATH + subdir + 'va/'
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- elif len(digits) == 5:
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- subdir = '{}/{}/{}/'.format(digits[0] + digits[1], digits[2], self.emdid)
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- self.workdir = MAP_SERVER_PATH + subdir + 'va/'
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- else:
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- pass
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+ emdid_text = str(self.emdid)
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+ if not emdid_text.isdigit() or not 4 <= len(emdid_text) <= 7:
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+ raise ValueError('EMDB IDs must contain 4 to 7 digits.')
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+ subdir = os.path.join(emdid_text[:2], emdid_text[2:-2], emdid_text)
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+ self.workdir = os.path.join(MAP_SERVER_PATH, subdir, 'va') + '/'
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  self.queue = queue
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  else:
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  self.workdir = workdir
{emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/va/version.py RENAMED
@@ -18,5 +18,5 @@ under the License.
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  """
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- __version__ = '0.0.1.dev151'
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+ __version__ = '0.0.1.dev152'
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  __em_statistics_version__ = '202505.v01'
{emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/LICENSE RENAMED
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{emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/MANIFEST.in RENAMED
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{emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/README.rst RENAMED
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{emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/setup.cfg RENAMED
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{emdbva-0.0.1.dev151 → emdbva-0.0.1.dev152}/setup.py RENAMED
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