├── .editorconfig ├── .github └── workflows │ └── pre-commit.yml ├── .gitignore ├── .gitlab-ci.yml ├── .markdownlint.yaml ├── .pre-commit-config.yaml ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── doc ├── Makefile ├── algorithm.rst ├── calculation.rst ├── conf.py ├── control.rst ├── data.rst ├── domains.tex ├── file.rst ├── generate_rdf_kernel_plots.py ├── index.rst ├── master.tex ├── packages.tex ├── refactor │ ├── Makefile │ ├── calculation.tex │ ├── checklist.tex │ ├── control.tex │ ├── data.tex │ ├── file.tex │ ├── hdf5file.tex │ ├── master.tex │ ├── sequence.tex │ └── visualization.tex ├── visualization.rst ├── volumes.rst └── volumes.tex ├── example_data ├── AgGeS-BOX.xyz ├── GST_111_128_bulk.xyz ├── GST_111_168_Te_surf.xyz ├── GST_111_196_bulk.xyz ├── calc_angels.py ├── hexagonal.xyz ├── snap_1000.xyz ├── snap_1100.xyz ├── snap_1300.xyz ├── snap_900.xyz ├── structure_c.xyz ├── test.batch └── xyz_generate.py ├── pymoldyn ├── __init__.py ├── __main__.py ├── _version.py ├── cli │ ├── __init__.py │ └── cli.py ├── computation │ ├── __init__.py │ └── split_and_merge │ │ ├── __init__.py │ │ ├── algorithm.py │ │ ├── domain_centers │ │ ├── __init__.py │ │ └── calculate_domain_centers.c │ │ ├── pipeline.py │ │ └── util │ │ ├── __init__.py │ │ ├── graph.py │ │ ├── node_border_iterator.py │ │ ├── numpy_extension │ │ ├── __init__.py │ │ └── find_index_of_first_element_not_equivalent.c │ │ ├── pos_bool_type.py │ │ └── prohibited.py ├── config │ ├── __init__.py │ ├── configobj.py │ ├── configuration.py │ ├── cutoff_history.py │ ├── cutoff_presets.py │ └── validate.py ├── core │ ├── __init__.py │ ├── bonds.py │ ├── calculation │ │ ├── __init__.py │ │ ├── algorithm.py │ │ ├── calculation.py │ │ ├── discretization.py │ │ ├── extension │ │ │ ├── __init__.py │ │ │ ├── algorithm.c │ │ │ ├── extension_ctypes.py │ │ │ └── extension_python.py │ │ └── gyrationtensor.py │ ├── control.py │ ├── data.py │ ├── elements.py │ ├── file.py │ └── volumes.py ├── gui │ ├── __init__.py │ ├── cutoff_history_table.py │ ├── cutoff_preset_combobox.py │ ├── cutoff_preset_table.py │ ├── cutoff_table_widget.py │ ├── dialogs │ │ ├── __init__.py │ │ ├── about_dialog.py │ │ ├── calc_settings_dialog.py │ │ ├── cutoff_history_dialog.py │ │ ├── progress_dialog.py │ │ ├── settings_dialog.py │ │ └── util │ │ │ ├── __init__.py │ │ │ ├── calc_table.py │ │ │ └── framechooser.py │ ├── gl_stack.py │ ├── gl_widget.py │ ├── histogram_widget.py │ ├── main_window.py │ ├── myApplication.py │ ├── object_select_widget.py │ ├── pdf_widget.py │ ├── tabs │ │ ├── __init__.py │ │ ├── file_tab.py │ │ ├── image_video_tab.py │ │ ├── log_tab.py │ │ ├── statistics │ │ │ ├── __init__.py │ │ │ ├── html_view.py │ │ │ ├── templates │ │ │ │ ├── __init__.py │ │ │ │ ├── atom.html │ │ │ │ ├── atoms.html │ │ │ │ ├── cavities_center.html │ │ │ │ ├── cavities_center_unknown.html │ │ │ │ ├── cavities_surface.html │ │ │ │ ├── cavities_surface_unknown.html │ │ │ │ ├── cavity_center.html │ │ │ │ ├── cavity_surface.html │ │ │ │ ├── domain.html │ │ │ │ ├── domains.html │ │ │ │ ├── domains_unknown.html │ │ │ │ └── style.css │ │ │ └── tree_list.py │ │ ├── statistics_tab.py │ │ └── view_tab.py │ └── util │ │ ├── __init__.py │ │ ├── cutoff_preview_table.py │ │ ├── labeled_combobox.py │ │ ├── table_fit.py │ │ ├── table_with_removeable_items.py │ │ └── webview.py ├── icon.png ├── statistics │ ├── __init__.py │ └── pdf.py ├── util │ ├── __init__.py │ ├── colored_exceptions.py │ ├── gl_util.py │ ├── logger.py │ ├── message.py │ └── video_output.py └── visualization │ ├── __init__.py │ └── visualization.py ├── pyproject.toml ├── requirements.txt └── setup.py /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/.editorconfig -------------------------------------------------------------------------------- /.github/workflows/pre-commit.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/.github/workflows/pre-commit.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitlab-ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/.gitlab-ci.yml -------------------------------------------------------------------------------- /.markdownlint.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/.markdownlint.yaml -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/Makefile -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/README.rst -------------------------------------------------------------------------------- /doc/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/Makefile -------------------------------------------------------------------------------- /doc/algorithm.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/algorithm.rst -------------------------------------------------------------------------------- /doc/calculation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/calculation.rst -------------------------------------------------------------------------------- /doc/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/conf.py -------------------------------------------------------------------------------- /doc/control.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/control.rst -------------------------------------------------------------------------------- /doc/data.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/data.rst -------------------------------------------------------------------------------- /doc/domains.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/domains.tex -------------------------------------------------------------------------------- /doc/file.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/file.rst -------------------------------------------------------------------------------- /doc/generate_rdf_kernel_plots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/generate_rdf_kernel_plots.py -------------------------------------------------------------------------------- /doc/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/index.rst -------------------------------------------------------------------------------- /doc/master.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/master.tex -------------------------------------------------------------------------------- /doc/packages.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/packages.tex -------------------------------------------------------------------------------- /doc/refactor/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/refactor/Makefile -------------------------------------------------------------------------------- /doc/refactor/calculation.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/refactor/calculation.tex -------------------------------------------------------------------------------- /doc/refactor/checklist.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/refactor/checklist.tex -------------------------------------------------------------------------------- /doc/refactor/control.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/refactor/control.tex -------------------------------------------------------------------------------- /doc/refactor/data.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/refactor/data.tex -------------------------------------------------------------------------------- /doc/refactor/file.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/refactor/file.tex -------------------------------------------------------------------------------- /doc/refactor/hdf5file.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/refactor/hdf5file.tex -------------------------------------------------------------------------------- /doc/refactor/master.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/refactor/master.tex -------------------------------------------------------------------------------- /doc/refactor/sequence.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/refactor/sequence.tex -------------------------------------------------------------------------------- /doc/refactor/visualization.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/refactor/visualization.tex -------------------------------------------------------------------------------- /doc/visualization.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/visualization.rst -------------------------------------------------------------------------------- /doc/volumes.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/volumes.rst -------------------------------------------------------------------------------- /doc/volumes.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/doc/volumes.tex -------------------------------------------------------------------------------- /example_data/AgGeS-BOX.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/AgGeS-BOX.xyz -------------------------------------------------------------------------------- /example_data/GST_111_128_bulk.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/GST_111_128_bulk.xyz -------------------------------------------------------------------------------- /example_data/GST_111_168_Te_surf.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/GST_111_168_Te_surf.xyz -------------------------------------------------------------------------------- /example_data/GST_111_196_bulk.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/GST_111_196_bulk.xyz -------------------------------------------------------------------------------- /example_data/calc_angels.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/calc_angels.py -------------------------------------------------------------------------------- /example_data/hexagonal.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/hexagonal.xyz -------------------------------------------------------------------------------- /example_data/snap_1000.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/snap_1000.xyz -------------------------------------------------------------------------------- /example_data/snap_1100.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/snap_1100.xyz -------------------------------------------------------------------------------- /example_data/snap_1300.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/snap_1300.xyz -------------------------------------------------------------------------------- /example_data/snap_900.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/snap_900.xyz -------------------------------------------------------------------------------- /example_data/structure_c.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/structure_c.xyz -------------------------------------------------------------------------------- /example_data/test.batch: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/test.batch -------------------------------------------------------------------------------- /example_data/xyz_generate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/example_data/xyz_generate.py -------------------------------------------------------------------------------- /pymoldyn/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/__main__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/__main__.py -------------------------------------------------------------------------------- /pymoldyn/_version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/_version.py -------------------------------------------------------------------------------- /pymoldyn/cli/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/cli/__init__.py -------------------------------------------------------------------------------- /pymoldyn/cli/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/cli/cli.py -------------------------------------------------------------------------------- /pymoldyn/computation/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/algorithm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/computation/split_and_merge/algorithm.py -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/domain_centers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/computation/split_and_merge/domain_centers/__init__.py -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/domain_centers/calculate_domain_centers.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/computation/split_and_merge/domain_centers/calculate_domain_centers.c -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/computation/split_and_merge/pipeline.py -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/util/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/util/graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/computation/split_and_merge/util/graph.py -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/util/node_border_iterator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/computation/split_and_merge/util/node_border_iterator.py -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/util/numpy_extension/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/util/numpy_extension/find_index_of_first_element_not_equivalent.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/computation/split_and_merge/util/numpy_extension/find_index_of_first_element_not_equivalent.c -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/util/pos_bool_type.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/computation/split_and_merge/util/pos_bool_type.py -------------------------------------------------------------------------------- /pymoldyn/computation/split_and_merge/util/prohibited.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/computation/split_and_merge/util/prohibited.py -------------------------------------------------------------------------------- /pymoldyn/config/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/config/configobj.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/config/configobj.py -------------------------------------------------------------------------------- /pymoldyn/config/configuration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/config/configuration.py -------------------------------------------------------------------------------- /pymoldyn/config/cutoff_history.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/config/cutoff_history.py -------------------------------------------------------------------------------- /pymoldyn/config/cutoff_presets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/config/cutoff_presets.py -------------------------------------------------------------------------------- /pymoldyn/config/validate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/config/validate.py -------------------------------------------------------------------------------- /pymoldyn/core/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/core/bonds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/bonds.py -------------------------------------------------------------------------------- /pymoldyn/core/calculation/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/calculation/__init__.py -------------------------------------------------------------------------------- /pymoldyn/core/calculation/algorithm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/calculation/algorithm.py -------------------------------------------------------------------------------- /pymoldyn/core/calculation/calculation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/calculation/calculation.py -------------------------------------------------------------------------------- /pymoldyn/core/calculation/discretization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/calculation/discretization.py -------------------------------------------------------------------------------- /pymoldyn/core/calculation/extension/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/calculation/extension/__init__.py -------------------------------------------------------------------------------- /pymoldyn/core/calculation/extension/algorithm.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/calculation/extension/algorithm.c -------------------------------------------------------------------------------- /pymoldyn/core/calculation/extension/extension_ctypes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/calculation/extension/extension_ctypes.py -------------------------------------------------------------------------------- /pymoldyn/core/calculation/extension/extension_python.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/calculation/extension/extension_python.py -------------------------------------------------------------------------------- /pymoldyn/core/calculation/gyrationtensor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/calculation/gyrationtensor.py -------------------------------------------------------------------------------- /pymoldyn/core/control.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/control.py -------------------------------------------------------------------------------- /pymoldyn/core/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/data.py -------------------------------------------------------------------------------- /pymoldyn/core/elements.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/elements.py -------------------------------------------------------------------------------- /pymoldyn/core/file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/file.py -------------------------------------------------------------------------------- /pymoldyn/core/volumes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/core/volumes.py -------------------------------------------------------------------------------- /pymoldyn/gui/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/__init__.py -------------------------------------------------------------------------------- /pymoldyn/gui/cutoff_history_table.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/cutoff_history_table.py -------------------------------------------------------------------------------- /pymoldyn/gui/cutoff_preset_combobox.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/cutoff_preset_combobox.py -------------------------------------------------------------------------------- /pymoldyn/gui/cutoff_preset_table.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/cutoff_preset_table.py -------------------------------------------------------------------------------- /pymoldyn/gui/cutoff_table_widget.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/cutoff_table_widget.py -------------------------------------------------------------------------------- /pymoldyn/gui/dialogs/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/gui/dialogs/about_dialog.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/dialogs/about_dialog.py -------------------------------------------------------------------------------- /pymoldyn/gui/dialogs/calc_settings_dialog.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/dialogs/calc_settings_dialog.py -------------------------------------------------------------------------------- /pymoldyn/gui/dialogs/cutoff_history_dialog.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/dialogs/cutoff_history_dialog.py -------------------------------------------------------------------------------- /pymoldyn/gui/dialogs/progress_dialog.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/dialogs/progress_dialog.py -------------------------------------------------------------------------------- /pymoldyn/gui/dialogs/settings_dialog.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/dialogs/settings_dialog.py -------------------------------------------------------------------------------- /pymoldyn/gui/dialogs/util/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/gui/dialogs/util/calc_table.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/dialogs/util/calc_table.py -------------------------------------------------------------------------------- /pymoldyn/gui/dialogs/util/framechooser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/dialogs/util/framechooser.py -------------------------------------------------------------------------------- /pymoldyn/gui/gl_stack.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/gl_stack.py -------------------------------------------------------------------------------- /pymoldyn/gui/gl_widget.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/gl_widget.py -------------------------------------------------------------------------------- /pymoldyn/gui/histogram_widget.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/histogram_widget.py -------------------------------------------------------------------------------- /pymoldyn/gui/main_window.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/main_window.py -------------------------------------------------------------------------------- /pymoldyn/gui/myApplication.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/myApplication.py -------------------------------------------------------------------------------- /pymoldyn/gui/object_select_widget.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/object_select_widget.py -------------------------------------------------------------------------------- /pymoldyn/gui/pdf_widget.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/pdf_widget.py -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/file_tab.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/file_tab.py -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/image_video_tab.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/image_video_tab.py -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/log_tab.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/log_tab.py -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/html_view.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/html_view.py -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/atom.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/atom.html -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/atoms.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/atoms.html -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/cavities_center.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/cavities_center.html -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/cavities_center_unknown.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/cavities_center_unknown.html -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/cavities_surface.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/cavities_surface.html -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/cavities_surface_unknown.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/cavities_surface_unknown.html -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/cavity_center.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/cavity_center.html -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/cavity_surface.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/cavity_surface.html -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/domain.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/domain.html -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/domains.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/domains.html -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/domains_unknown.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/domains_unknown.html -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/templates/style.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/templates/style.css -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics/tree_list.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics/tree_list.py -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/statistics_tab.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/statistics_tab.py -------------------------------------------------------------------------------- /pymoldyn/gui/tabs/view_tab.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/tabs/view_tab.py -------------------------------------------------------------------------------- /pymoldyn/gui/util/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/gui/util/cutoff_preview_table.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/util/cutoff_preview_table.py -------------------------------------------------------------------------------- /pymoldyn/gui/util/labeled_combobox.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/util/labeled_combobox.py -------------------------------------------------------------------------------- /pymoldyn/gui/util/table_fit.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/util/table_fit.py -------------------------------------------------------------------------------- /pymoldyn/gui/util/table_with_removeable_items.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/util/table_with_removeable_items.py -------------------------------------------------------------------------------- /pymoldyn/gui/util/webview.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/gui/util/webview.py -------------------------------------------------------------------------------- /pymoldyn/icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/icon.png -------------------------------------------------------------------------------- /pymoldyn/statistics/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymoldyn/statistics/pdf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/statistics/pdf.py -------------------------------------------------------------------------------- /pymoldyn/util/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/util/__init__.py -------------------------------------------------------------------------------- /pymoldyn/util/colored_exceptions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/util/colored_exceptions.py -------------------------------------------------------------------------------- /pymoldyn/util/gl_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/util/gl_util.py -------------------------------------------------------------------------------- /pymoldyn/util/logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/util/logger.py -------------------------------------------------------------------------------- /pymoldyn/util/message.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/util/message.py -------------------------------------------------------------------------------- /pymoldyn/util/video_output.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/util/video_output.py -------------------------------------------------------------------------------- /pymoldyn/visualization/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/visualization/__init__.py -------------------------------------------------------------------------------- /pymoldyn/visualization/visualization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pymoldyn/visualization/visualization.py -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/pyproject.toml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sciapp/pyMolDyn/HEAD/setup.py --------------------------------------------------------------------------------