masster 0.4.3__py3-none-any.whl → 0.4.5__py3-none-any.whl

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Files changed (54) hide show
  1. masster/__init__.py +8 -8
  2. masster/_version.py +1 -1
  3. masster/chromatogram.py +1 -1
  4. masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil2_01_20250602151849.sample5 +0 -0
  5. masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil3_01_20250602150634.sample5 +0 -0
  6. masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008_v6_r38_01.sample5 +0 -0
  7. masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008_v7_r37_01.sample5 +0 -0
  8. masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C017_v5_r99_01.sample5 +0 -0
  9. masster/data/libs/__pycache__/ccm.cpython-312.pyc +0 -0
  10. masster/data/libs/__pycache__/urine.cpython-312.pyc +0 -0
  11. masster/data/libs/ccm.csv +120 -0
  12. masster/data/libs/urine.csv +4693 -0
  13. masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.timeseries.data +0 -0
  14. masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff +0 -0
  15. masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff.scan +0 -0
  16. masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff2 +0 -0
  17. masster/logger.py +11 -11
  18. masster/sample/__init__.py +1 -1
  19. masster/sample/adducts.py +338 -264
  20. masster/sample/defaults/find_adducts_def.py +21 -8
  21. masster/sample/h5.py +561 -282
  22. masster/sample/helpers.py +131 -75
  23. masster/sample/lib.py +4 -4
  24. masster/sample/load.py +31 -17
  25. masster/sample/parameters.py +1 -1
  26. masster/sample/plot.py +7 -7
  27. masster/sample/processing.py +117 -87
  28. masster/sample/sample.py +103 -90
  29. masster/sample/sample5_schema.json +196 -0
  30. masster/sample/save.py +35 -12
  31. masster/spectrum.py +1 -1
  32. masster/study/__init__.py +1 -1
  33. masster/study/defaults/align_def.py +5 -1
  34. masster/study/defaults/identify_def.py +3 -1
  35. masster/study/defaults/study_def.py +58 -25
  36. masster/study/export.py +360 -210
  37. masster/study/h5.py +560 -158
  38. masster/study/helpers.py +496 -203
  39. masster/study/helpers_optimized.py +1 -1
  40. masster/study/id.py +538 -349
  41. masster/study/load.py +233 -143
  42. masster/study/plot.py +71 -71
  43. masster/study/processing.py +456 -254
  44. masster/study/save.py +15 -5
  45. masster/study/study.py +213 -131
  46. masster/study/study5_schema.json +360 -0
  47. masster-0.4.5.dist-info/METADATA +131 -0
  48. masster-0.4.5.dist-info/RECORD +71 -0
  49. masster-0.4.3.dist-info/METADATA +0 -791
  50. masster-0.4.3.dist-info/RECORD +0 -56
  51. {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/WHEEL +0 -0
  52. {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/entry_points.txt +0 -0
  53. {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/licenses/LICENSE +0 -0
  54. {masster-0.4.3.dist-info → masster-0.4.5.dist-info}/top_level.txt +0 -0
masster/sample/defaults/find_adducts_def.py CHANGED
@@ -54,13 +54,15 @@ class find_adducts_defaults:
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  charge_span_max: int = 2
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  # Retention time constraints (in seconds - final confirmed unit)
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- retention_max_diff: float = 1.0 # 1 second - precise RT grouping
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+ retention_max_diff: float = 1.0 # 1 second - precise RT grouping
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  retention_max_diff_local: float = 1.0 # 1 second - precise RT grouping
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-
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+
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  # Mass tolerance constraints
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- mass_max_diff: float = 0.01 # 0.01 Da - strict mass tolerance for chemical specificity
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+ mass_max_diff: float = (
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+ 0.01 # 0.01 Da - strict mass tolerance for chemical specificity
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+ )
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  unit: str = "Da" # Mass tolerance unit: "Da" or "ppm"
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-
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+
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  # Probability filtering
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  min_probability: float = 0.03 # Minimum probability to consider adducts (filters low-probability adducts)
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@@ -181,7 +183,7 @@ class find_adducts_defaults:
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  return all(isinstance(item, str) for item in value)
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  else:
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  return False
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-
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+
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  # Handle unit parameter
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  if param_name == "unit":
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  if isinstance(value, str):
@@ -348,16 +350,27 @@ class find_adducts_defaults:
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  if adducts is None or adducts in ["pos", "positive"]:
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  return [
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- "+H:1:0.65", "+Na:1:0.15", "+NH4:1:0.15", "+K:1:0.05", "-H2O:0:0.15"
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+ "+H:1:0.65",
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+ "+Na:1:0.15",
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+ "+NH4:1:0.15",
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+ "+K:1:0.05",
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+ "-H2O:0:0.15",
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  ]
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  elif adducts in ["neg", "negative"]:
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  return [
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- "-H:-1:0.9", "+Cl:-1:0.1", "+CH2O2:0:0.15", "-H2O:0:0.15"
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+ "-H:-1:0.9",
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+ "+Cl:-1:0.1",
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+ "+CH2O2:0:0.15",
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+ "-H2O:0:0.15",
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  ]
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  elif isinstance(adducts, list):
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  return adducts
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  else:
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  # Fallback to positive mode if unexpected format
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  return [
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- "+H:1:0.65", "+Na:1:0.15", "+NH4:1:0.15", "+K:1:0.05", "-H2O:0:0.2"
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+ "+H:1:0.65",
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+ "+Na:1:0.15",
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+ "+NH4:1:0.15",
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+ "+K:1:0.05",
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+ "-H2O:0:0.2",
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  ]