gatewizard 1.0.0__py3-none-any.whl

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Files changed (106) hide show
  1. gatewizard/__init__.py +48 -0
  2. gatewizard/core/__init__.py +29 -0
  3. gatewizard/core/builder.py +1369 -0
  4. gatewizard/core/file_manager.py +396 -0
  5. gatewizard/core/job_monitor.py +546 -0
  6. gatewizard/core/preparation.py +998 -0
  7. gatewizard/gui/__init__.py +18 -0
  8. gatewizard/gui/app.py +2006 -0
  9. gatewizard/gui/base/__init__.py +5 -0
  10. gatewizard/gui/base/callback_manager.py +94 -0
  11. gatewizard/gui/constants.py +285 -0
  12. gatewizard/gui/frames/__init__.py +19 -0
  13. gatewizard/gui/frames/analysis.py +7332 -0
  14. gatewizard/gui/frames/builder_frame.py +1258 -0
  15. gatewizard/gui/frames/equilibration.py +3636 -0
  16. gatewizard/gui/frames/preparation_frame.py +2110 -0
  17. gatewizard/gui/frames/visualize.py +1198 -0
  18. gatewizard/gui/widgets/__init__.py +17 -0
  19. gatewizard/gui/widgets/leaflet_frame.py +350 -0
  20. gatewizard/gui/widgets/progress_tracker.py +1092 -0
  21. gatewizard/gui/widgets/propka_workflow_helper.py +1129 -0
  22. gatewizard/gui/widgets/searchable_combobox.py +367 -0
  23. gatewizard/gui/widgets/stage_tabs.py +352 -0
  24. gatewizard/main.py +155 -0
  25. gatewizard/tools/__init__.py +16 -0
  26. gatewizard/tools/equilibration.py +2515 -0
  27. gatewizard/tools/force_fields.py +408 -0
  28. gatewizard/tools/molecular_viewer.py +198 -0
  29. gatewizard/tools/validators.py +657 -0
  30. gatewizard/utils/__init__.py +47 -0
  31. gatewizard/utils/bilayer_utils.py +314 -0
  32. gatewizard/utils/config.py +407 -0
  33. gatewizard/utils/helpers.py +483 -0
  34. gatewizard/utils/logger.py +297 -0
  35. gatewizard/utils/namd_analysis.py +2463 -0
  36. gatewizard/utils/optional_deps.py +112 -0
  37. gatewizard/utils/protein_capping.py +583 -0
  38. gatewizard-1.0.0.dist-info/METADATA +256 -0
  39. gatewizard-1.0.0.dist-info/RECORD +106 -0
  40. gatewizard-1.0.0.dist-info/WHEEL +5 -0
  41. gatewizard-1.0.0.dist-info/entry_points.txt +2 -0
  42. gatewizard-1.0.0.dist-info/licenses/LICENSE +21 -0
  43. gatewizard-1.0.0.dist-info/top_level.txt +2 -0
  44. tests/__init__.py +10 -0
  45. tests/analysis_examples/analysis_example_01.py +33 -0
  46. tests/analysis_examples/analysis_example_02.py +14 -0
  47. tests/analysis_examples/analysis_example_03.py +45 -0
  48. tests/analysis_examples/analysis_example_04.py +31 -0
  49. tests/analysis_examples/analysis_example_05.py +47 -0
  50. tests/analysis_examples/analysis_example_06.py +33 -0
  51. tests/analysis_examples/analysis_example_07.py +55 -0
  52. tests/analysis_examples/analysis_example_08.py +50 -0
  53. tests/analysis_examples/analysis_example_09.py +45 -0
  54. tests/analysis_examples/analysis_example_10.py +140 -0
  55. tests/builder_examples/builder_example_01.py +6 -0
  56. tests/builder_examples/builder_example_02.py +15 -0
  57. tests/builder_examples/builder_example_03.py +12 -0
  58. tests/builder_examples/builder_example_04.py +12 -0
  59. tests/builder_examples/builder_example_05.py +12 -0
  60. tests/builder_examples/builder_example_06.py +21 -0
  61. tests/builder_examples/builder_example_07.py +9 -0
  62. tests/builder_examples/builder_example_08.py +34 -0
  63. tests/builder_examples/builder_example_09.py +36 -0
  64. tests/builder_examples/builder_example_10.py +39 -0
  65. tests/builder_examples/builder_example_11.py +27 -0
  66. tests/builder_examples/builder_example_12.py +24 -0
  67. tests/builder_examples/builder_example_13.py +25 -0
  68. tests/builder_examples/builder_example_14.py +24 -0
  69. tests/builder_examples/builder_example_15.py +4 -0
  70. tests/builder_examples/builder_example_16.py +43 -0
  71. tests/builder_examples/builder_example_17.py +34 -0
  72. tests/equilibration_examples/equilibration_example_01.py +40 -0
  73. tests/equilibration_examples/equilibration_example_02.py +47 -0
  74. tests/equilibration_examples/equilibration_example_03.py +18 -0
  75. tests/equilibration_examples/equilibration_example_04.py +75 -0
  76. tests/equilibration_examples/equilibration_example_05.py +105 -0
  77. tests/equilibration_examples/equilibration_example_06.py +151 -0
  78. tests/equilibration_examples/equilibration_example_07.py +86 -0
  79. tests/equilibration_examples/popc_membrane/status_utils.py +95 -0
  80. tests/preparation_examples/preparation_example_01.py +4 -0
  81. tests/preparation_examples/preparation_example_02.py +4 -0
  82. tests/preparation_examples/preparation_example_03.py +10 -0
  83. tests/preparation_examples/preparation_example_04.py +34 -0
  84. tests/preparation_examples/preparation_example_05.py +30 -0
  85. tests/preparation_examples/preparation_example_06.py +11 -0
  86. tests/preparation_examples/preparation_example_07.py +5 -0
  87. tests/preparation_examples/preparation_example_08.py +17 -0
  88. tests/preparation_examples/preparation_example_09.py +18 -0
  89. tests/preparation_examples/preparation_example_10.py +19 -0
  90. tests/preparation_examples/preparation_example_11.py +10 -0
  91. tests/preparation_examples/preparation_example_12.py +13 -0
  92. tests/preparation_examples/preparation_example_13.py +51 -0
  93. tests/preparation_examples/preparation_example_14.py +146 -0
  94. tests/preparation_examples/preparation_example_15.py +23 -0
  95. tests/preparation_examples/preparation_example_16.py +6 -0
  96. tests/preparation_examples/preparation_example_17.py +32 -0
  97. tests/preparation_examples/preparation_example_18.py +48 -0
  98. tests/preparation_examples/preparation_example_19.py +30 -0
  99. tests/preparation_examples/preparation_example_20.py +66 -0
  100. tests/preparation_examples/preparation_example_21.py +30 -0
  101. tests/preparation_examples/preparation_example_22.py +54 -0
  102. tests/test_analysis.py +389 -0
  103. tests/test_builder.py +570 -0
  104. tests/test_equilibration.py +721 -0
  105. tests/test_new_api.py +448 -0
  106. tests/test_preparation.py +997 -0
gatewizard/__init__.py ADDED
@@ -0,0 +1,48 @@
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+ # SPDX-License-Identifier: MIT
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+ # Copyright (c) 2025 Constanza González and Mauricio Bedoya
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+
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+ """
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+ Gatewizard - A tool for membrane protein preparation and analysis.
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+ """
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+
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+ __version__ = "1.0.0"
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+ __author__ = "Constanza González, Mauricio Bedoya"
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+ __email__ = ""
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+ __license__ = "MIT"
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+
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+ # Import main classes for easier access
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+ from gatewizard.core.preparation import (
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+ run_propka,
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+ extract_summary_section,
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+ parse_summary_section,
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+ modify_pdb_based_on_summary,
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+ )
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+
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+ from gatewizard.core.builder import Builder
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+ from gatewizard.core.job_monitor import JobMonitor
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+
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+ # GUI imports (optional, only if GUI dependencies are available)
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+ try:
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+ from gatewizard.gui.app import ProteinViewerApp
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+ GUI_AVAILABLE = True
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+ except ImportError:
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+ GUI_AVAILABLE = False
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+ ProteinViewerApp = None
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+
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+ __all__ = [
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+ "__version__",
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+ "__author__",
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+ "__email__",
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+ "__license__",
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+ "run_propka",
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+ "extract_summary_section",
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+ "parse_summary_section",
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+ "modify_pdb_based_on_summary",
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+ "Builder",
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+ "JobMonitor",
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+ "GUI_AVAILABLE",
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+ ]
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+
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+ # Add ProteinViewerApp to __all__ if GUI is available
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+ if GUI_AVAILABLE:
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+ __all__.append("ProteinViewerApp")
gatewizard/core/__init__.py ADDED
@@ -0,0 +1,29 @@
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+ """
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+ Core functionality module for Gatewizard.
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+
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+ This module contains the core business logic for protein preparation,
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+ system building, and job monitoring. It is independent of the GUI
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+ and can be used programmatically.
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+ """
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+
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+ from gatewizard.core.preparation import (
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+ run_propka,
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+ extract_summary_section,
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+ parse_summary_section,
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+ modify_pdb_based_on_summary,
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+ )
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+
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+ from gatewizard.core.builder import Builder
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+ from gatewizard.core.job_monitor import JobMonitor, JobStatus
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+ from gatewizard.core.file_manager import FileManager
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+
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+ __all__ = [
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+ "run_propka",
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+ "extract_summary_section",
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+ "parse_summary_section",
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+ "modify_pdb_based_on_summary",
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+ "Builder",
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+ "JobMonitor",
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+ "JobStatus",
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+ "FileManager",
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+ ]