pykingenie 0.1__tar.gz

pykingenie-0.1/LICENSE

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+MIT License
+
+Copyright (c) [2025] [Osvaldo Burastero]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pykingenie-0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: pykingenie
+Version: 0.1
+Author-email: Osvaldo Burastero <oburastero@gmail.com>
+License: MIT
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: plotly>=6.2.0
+Requires-Dist: kaleido>=1.0.0
+Requires-Dist: numpy>=2.2.5
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: scipy>=1.15.2
+Requires-Dist: matplotlib>=3.10.1
+Provides-Extra: dev
+Requires-Dist: black>=25.1.0; extra == "dev"
+Requires-Dist: coverage-badge>=1.1.2; extra == "dev"
+Requires-Dist: flake8>=7.3.0; extra == "dev"
+Requires-Dist: ipykernel>=6.30.0; extra == "dev"
+Requires-Dist: jupyter>=1.1.1; extra == "dev"
+Requires-Dist: notebook>=7.4.4; extra == "dev"
+Requires-Dist: numpydoc>=1.9.0; extra == "dev"
+Requires-Dist: pydata-sphinx-theme>=0.16.1; extra == "dev"
+Requires-Dist: pytest>=8.4.1; extra == "dev"
+Requires-Dist: pytest-cov>=6.2.1; extra == "dev"
+Requires-Dist: sphinx>=8.1.3; extra == "dev"
+Requires-Dist: sphinx-copybutton>=0.5.2; extra == "dev"
+Requires-Dist: sphinx-design>=0.6.1; extra == "dev"
+Requires-Dist: sphinx-tabs>=3.4.7; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: numpydoc>=1.9.0; extra == "docs"
+Requires-Dist: pydata-sphinx-theme>=0.16.1; extra == "docs"
+Requires-Dist: sphinx>=8.1.3; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5.2; extra == "docs"
+Requires-Dist: sphinx-design>=0.6.1; extra == "docs"
+Requires-Dist: sphinx-tabs>=3.4.7; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest>=8.4.1; extra == "test"
+Requires-Dist: pytest-cov>=6.2.1; extra == "test"
+Dynamic: license-file
+
+[![Test and build](https://github.com/osvalB/pykingenie/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/osvalB/pykingenie/actions/workflows/ci-cd.yml)
+[![codecov](https://codecov.io/gh/osvalB/pykingenie/graph/badge.svg)](https://codecov.io/gh/osvalB/pykingenie)
+[![Docs](https://img.shields.io/badge/docs-online-blue)](https://osvalb.github.io/pykingenie)
+
+Welcome to **pyKinGenie**!, a python package for analysing binding kinetics data 
+
+This project is under development, and breaking changes may occur at any moment!
+
+## Features
+
+- Import Octet files (.frd)
+- Import Gator files (Assay_#_Channel#.csv, Setting.ini and ExperimentStep.ini)
+- Import custom CSV files 
+- Processs the traces (alignment, baseline correction)
+- Calculate binding kinetics (*k*<sub>on</sub>, *k*<sub>off</sub>, *K*<sub>D</sub>)
+- Global fitting of multiple traces
+- One-to-one, one-to-one with mass transport limitation, and one-to-one with induced fit models
+
+## Contributing
+
+Contributions are welcome! Please contact me at oburastero@embl-hamburg.de
+
+## License
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

pykingenie-0.1/README.md

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+[![Test and build](https://github.com/osvalB/pykingenie/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/osvalB/pykingenie/actions/workflows/ci-cd.yml)
+[![codecov](https://codecov.io/gh/osvalB/pykingenie/graph/badge.svg)](https://codecov.io/gh/osvalB/pykingenie)
+[![Docs](https://img.shields.io/badge/docs-online-blue)](https://osvalb.github.io/pykingenie)
+
+Welcome to **pyKinGenie**!, a python package for analysing binding kinetics data 
+
+This project is under development, and breaking changes may occur at any moment!
+
+## Features
+
+- Import Octet files (.frd)
+- Import Gator files (Assay_#_Channel#.csv, Setting.ini and ExperimentStep.ini)
+- Import custom CSV files 
+- Processs the traces (alignment, baseline correction)
+- Calculate binding kinetics (*k*<sub>on</sub>, *k*<sub>off</sub>, *K*<sub>D</sub>)
+- Global fitting of multiple traces
+- One-to-one, one-to-one with mass transport limitation, and one-to-one with induced fit models
+
+## Contributing
+
+Contributions are welcome! Please contact me at oburastero@embl-hamburg.de
+
+## License
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

pykingenie-0.1/pyproject.toml

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+[project]
+name = "pykingenie"
+version = "0.1"
+readme = "README.md"
+license = {text = "MIT"}
+authors = [
+  { name = "Osvaldo Burastero", email = "oburastero@gmail.com" }
+]
+requires-python = ">=3.10"
+dependencies = [
+  "plotly>=6.2.0",
+  "kaleido>=1.0.0",
+  "numpy>=2.2.5",
+  "pandas>=2.2.3",
+  "scipy>=1.15.2",
+  "matplotlib>=3.10.1",
+]
+
+[build-system]
+requires = ["setuptools >= 77.0.3"]
+build-backend = "setuptools.build_meta"
+
+[project.optional-dependencies]
+dev = [
+    "black>=25.1.0",
+    "coverage-badge>=1.1.2",
+    "flake8>=7.3.0",
+    "ipykernel>=6.30.0",
+    "jupyter>=1.1.1",
+    "notebook>=7.4.4",
+    "numpydoc>=1.9.0",
+    "pydata-sphinx-theme>=0.16.1",
+    "pytest>=8.4.1",
+    "pytest-cov>=6.2.1",
+    "sphinx>=8.1.3",
+    "sphinx-copybutton>=0.5.2",
+    "sphinx-design>=0.6.1",
+    "sphinx-tabs>=3.4.7",
+]
+docs = [
+    "numpydoc>=1.9.0",
+    "pydata-sphinx-theme>=0.16.1",
+    "sphinx>=8.1.3",
+    "sphinx-copybutton>=0.5.2",
+    "sphinx-design>=0.6.1",
+    "sphinx-tabs>=3.4.7",
+]
+test = [
+    "pytest>=8.4.1",
+    "pytest-cov>=6.2.1",
+]
+
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py", "*_test.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "--cov=src/pykingenie",
+    "--cov-report=html",
+    "--cov-report=xml",
+    "--cov-report=term-missing",
+    "--verbose"
+]
+
+[tool.coverage.run]
+source = ["src/pykingenie"]
+omit = ["*/tests/*", "*/test_*"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "raise AssertionError",
+    "raise NotImplementedError",
+]
+
+[tool.sphinx]
+source-dir = "docs"
+build-dir = "docs/_build"

pykingenie-0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

pykingenie-0.1/src/__init__.py

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+#Empty file to indicate that this is a package

pykingenie-0.1/src/pykingenie/__init__.py

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+from .main              import KineticsAnalyzer
+from .octet             import OctetExperiment
+from .gator             import GatorExperiment
+from .kingenie_solution import KinGenieCsvSolution
+from .kingenie_surface  import KinGenieCsv
+
+from .utils.processing import (
+    guess_experiment_name,
+    guess_experiment_type,
+    concat_signal_lst,
+    get_palette,
+    get_plotting_df,
+    subset_data,
+    sample_type_to_letter,
+    get_colors_from_numeric_values
+)
+
+from .utils.math import (
+    single_exponential,
+    double_exponential,
+    median_filter,
+    rss_p,
+    get_rss,
+    get_desired_rss
+)
+
+from .utils.signal_surface import (
+    steady_state_one_site,
+    one_site_association_analytical,
+    one_site_dissociation_analytical,
+    ode_one_site_mass_transport_association,
+    ode_one_site_mass_transport_dissociation,
+    solve_ode_one_site_mass_transport_association,
+    solve_ode_one_site_mass_transport_dissociation,
+    differential_matrix_association_induced_fit,
+    differential_matrix_association_conformational_selection,
+    differential_matrix_dissociation_induced_fit,
+    differential_matrix_dissociation_conformational_selection,
+    constant_vector_induced_fit,
+    constant_vector_conformational_selection,
+    solve_all_states_fast,
+    solve_steady_state,
+    solve_induced_fit_association,
+    solve_conformational_selection_association,
+    solve_induced_fit_dissociation,
+    solve_conformational_selection_dissociation,
+    ode_mixture_analyte_association,
+    solve_ode_mixture_analyte_association,
+    ode_mixture_analyte_dissociation,
+    solve_ode_mixture_analyte_dissociation
+)
+
+from .utils.signal_solution  import (
+    ode_one_site_insolution,
+    solve_ode_one_site_insolution,
+    signal_ode_one_site_insolution,
+    ode_induced_fit_insolution,
+    solve_ode_induced_fit_insolution,
+    signal_ode_induced_fit_insolution,
+    ode_conformational_selection_insolution,
+    solve_ode_conformational_selection_insolution,
+    signal_ode_conformational_selection_insolution,
+    get_initial_concentration_conformational_selection,
+    get_kobs_induced_fit,
+    get_kobs_conformational_selection
+)
+
+from .utils.fitting_surface  import (
+    guess_initial_signal,
+    fit_steady_state_one_site,
+    steady_state_one_site_asymmetric_ci95,
+    fit_one_site_association,
+    fit_one_site_dissociation,
+    fit_one_site_assoc_and_disso,
+    fit_induced_fit_sites_assoc_and_disso,
+    fit_one_site_assoc_and_disso_ktr,
+    one_site_assoc_and_disso_asymmetric_ci95,
+    one_site_assoc_and_disso_asymmetric_ci95_koff
+)
+
+from .utils.fitting_general  import (
+    fit_single_exponential,
+    fit_double_exponential
+)
+
+from .utils.fitting_solution import (
+    fit_one_site_solution,
+    fit_induced_fit_solution,
+    find_initial_parameters_induced_fit_solution
+)
+
+from .utils.plotting import (
+    config_fig,
+    plot_plate_info,
+    plot_traces,
+    plot_traces_all,
+    plot_steady_state,
+    plot_association_dissociation
+)
+
+# Package metadata
+__version__ = '0.1.0'
+__author__ = 'osvalB'
+__email__ = 'oburastero@gmail.com'
+__description__ = 'A Python package for kinetics data analysis'