rxnfit 0.2.0__tar.gz

rxnfit-0.2.0/.gitignore

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+src/rxnfit/__pycache__/
+.ipynb_checkpoints/
+.DS_Store
+src/.DS_Store
+src/rxnfit/.DS_Store
+venv*
+build/
+*.egg-info/
+dist/
+docs/build/*
+!docs/build/

rxnfit-0.2.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2023, PEJpOhn
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

rxnfit-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: rxnfit
+Version: 0.2.0
+Summary: set up theoretical reaction kinetics equations
+Project-URL: Homepage, https://github.com/PEJpOhno/rxnfit
+Project-URL: Issues, https://github.com/PEJpOhno/rxnfit/issues
+Author-email: Mitsuru Ohno <pejpohn@gmail.com>
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.12
+Requires-Dist: matplotlib>=3.9.0
+Requires-Dist: numpy>=2.0.2; python_version < '3.13'
+Requires-Dist: numpy>=2.1.0; python_version >= '3.13'
+Requires-Dist: optuna>=4.7.0
+Requires-Dist: pandas>=2.2.2; python_version < '3.13'
+Requires-Dist: pandas>=2.2.3; python_version >= '3.13'
+Requires-Dist: scipy>=1.14.1
+Requires-Dist: sympy>=1.12
+Description-Content-Type: text/markdown
+
+
+## Overviews
+"rxnfit" is a Python module that builds ordinary differential equations (ODEs) for reaction kinetics from elementary reaction formulas and rate constants given in CSV format, and computes concentration time courses numerically.
+
+- When all rate constants are known, the time evolution of each species’ concentration is obtained by **numerical integration** of the ODEs (e.g. with `scipy.integrate.solve_ivp`).
+- When some rate constants are unknown, they can be **estimated by fitting** the ODE solution to experimental concentration time-course data (e.g. with `scipy.optimize.minimize`).
+- A rate constant may be given as an **expression** in other rate constants (e.g. k₂ = 2·k₁), or as a **function of time** *t* via an override CSV.
+
+**Documentation :** https://pejpohno.github.io/rxnfit/  
+**Tutorial :** in preparation  
+**How to cite :** Ohno, M. rxnfit. GitHub. https://github.com/PEJpOhno/rxnfit (2026).  
+
+## Current version and requirements
+- current version = 0.2.0
+- pyhon >=3.12
+
+[dependencies]
+- NumPy
+- pandas
+- SciPy
+- SymPy
+- Matplotlib  
+- Optuna
+
+## Copyright and license
+Copyright (c) 2025 Mitsuru Ohno
+Released under the BSD-3 license, license that can be found in the LICENSE file.
+
+## Installation
+Create and activate a Python virtual environment, then  
+
+```sh
+pip install rxnfit
+```
+
+If you want to give it a quick try, just copy or move the example directory from the cloned repo to wherever it's convenient. Then, activate your virtual environment, start Jupyter Notebook, and open one of the sample scripts inside "examples" directry to test it out.
+
+## Usage
+### Prepare csv file
+1. Describe reaction formula in csv format. THe first row shoud be header. The first column and the second column should be reaction ID (named RID) and the rate constant (named k). Other column names can be omitted.
+2. The reactants are putted in alternately with the coeficient and the chemical species. Each reaction should be described in one row.
+3. To separate the reactants and the products, two ">" are setted with two columns. As with reaction SMARTS, you may write reaction conditions between the two ">"; in the current version of rxnfit these are unused.
+4. The products are putted in alternately with the coeficient and the chemical species.
+Note the reaction formula should be inputted by the left filling. To describe chemical species, it is better to avoid to use arithmetic symbols such as "+", "-" and "*" (e.g. use "**a**"(nion) in place of "-"). The coefficient '1' can be substituted for blank.  
+5. Each elementary reaction’s rate constant must be specified in the format ‘k + RID’. If left empty, the system will automatically assign ‘k + RID’.  
+
+The rate constant k_m can also be defined as a function of another elementary reaction rate constant k_n, or as a function of time t.  
+The example of a csv format is as follows.  Attached "examples/sample_data/sample_rxn_ref1.csv" and "examples/sample_data/refX/sample_rxn_refX.csv" are also available for demonstration.
+
+example of a csv format
+
+    RID, k,,,,,,,,,,
+    1,0.054,,AcOEt,,OHa1,>,>,,AcOa1,,EtOH
+    2,1.4,,AcOiPr,,OHa1,>,>,,AcOa1,,iPrOH
+    3,0.031,,EGOAc2,2,OHa1,>,>,2,AcOa1,,EG
+
+## Modules and classes
+
+The following items are those prominently used in the example notebooks.
+
+### rxn_reader
+Reads reaction CSV and builds symbolic ODE system.
+
+| item | name | description |
+|------|------|-------------|
+| class | RxnToODE | Builds differential-type rate equations (strings) from reaction CSV, then ODE system expressions (SymPy). Attributes: rate_consts_dict, sympy_symbol_dict, sys_odes_dict, function_names. |
+| function | get_reactions | Parse reaction CSV into list of reaction data (RID, k, reactants, products, conditions). |
+| function | get_unique_species | Extract unique species names from reaction list. |
+| function | rate_constants | Extract rate constant key and value (float or expression string) per reaction. |
+
+### build_ode
+Builds numerical ODE RHS from symbolic system; supports rate-constant overrides and time-dependent k(t).
+
+| item | name | description |
+|------|------|-------------|
+| class | RxnODEbuild | Extends RxnToODE. Builds callable ODE RHS for scipy.integrate.solve_ivp. Optional rate_const_overrides (dict or CSV path) and rate_const_overrides_encoding. Methods: create_ode_system(), create_ode_system_with_rate_consts(), get_ode_system(), get_ode_info(). |
+| function | create_system_rhs | Build (t, y) RHS for solve_ivp from ODE functions dict. Optional rate_const_values (dict or callable(t)) and symbolic_rate_const_keys for variable or time-dependent rate constants. |
+
+### expdata_reader
+Loads and aligns experimental time-course data.
+
+| item | name | description |
+|------|------|-------------|
+| function | expdata_read | Read list of DataFrames into list of (t_list, C_exp_list) per dataset. |
+| function | get_y0_from_expdata | Initial concentrations per dataset in function_names order. |
+
+### expdata_fit_sci
+Fits symbolic rate constants to experimental data (scipy.optimize.minimize).
+
+| item | name | description |
+|------|------|-------------|
+| class | ExpDataFitSci | Multi-dataset fitting. run_fit(p0, ...) returns (result, param_info, fit_metrics). result has .fun (RSS), .tss, .r2; fit_metrics is dict with keys 'rss', 'tss', 'r2'. get_solver_config_args(dataset_index), get_fitted_rate_const_dict(result). plot_fitted_solution(expdata_df, ...) plots per-dataset y0 curves after run_fit. to_dataframe_list() returns list of DataFrames (one per dataset). When model has k(t), get_solver_config_args() adds rate_const_values (callable) and symbolic_rate_const_keys after run_fit(). |
+
+### solv_ode
+Numerical integration and plotting of ODE solutions.
+
+| item | name | description |
+|------|------|-------------|
+| class | SolverConfig | Dataclass: y0, t_span, t_eval, method, rtol. Optional: rate_const_values (dict or callable(t)), symbolic_rate_const_keys (both or neither). |
+| class | RxnODEsolver | Integrates ODE with builder and config. solve_system(), to_dataframe_list() returning list of DataFrames, eval_fit_metrics(expdata_df, ...) returning dict with 'rss', 'tss', 'r2', solution_plot(). When config has rate_const_values and symbolic_rate_const_keys, uses rate-constants ODE path. |
+
+### p0_opt_fit
+Optimizes initial parameter values (p0) for rate constants using Optuna, then fits with ExpDataFitSci.
+
+| item | name | description |
+|------|------|-------------|
+| class | P0OptFit | Optimizes p0 via Optuna (e.g. suggest_float with log=True) and runs ExpDataFitSci.run_fit with the best p0. optimize(n_trials, show_progress_bar, ...) returns (dict of variable → (initial, fitted), fit_metrics). fit_metrics is a dict with keys 'rss', 'tss', 'r2'. optuna_log() returns per-trial log. |
+
+## References  
+
+- **Python**: Python Software Foundation. (2024). *Python* (Version 3.13) [Computer software]. https://www.python.org/  
+- **NumPy**: Harris, C. R., Millman, K. J., van der Walt, S. J., et al. (2020). Array programming with NumPy. *Nature*, 585(7825), 357–362. https://doi.org/10.1038/s41586-020-2649-2
+- **pandas**: McKinney, W. (2010). Data Structures for Statistical Computing in Python. *Proceedings of the 9th Python in Science Conference*, 56–61. https://doi.org/10.25080/Majora-92bf1922-00a
+- **SciPy**: Virtanen, P., Gommers, R., Oliphant, T. E., et al. (2020). SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python. *Nature Methods*, 17(3), 261–272. https://doi.org/10.1038/s41592-019-0686-2
+- **SymPy**: Meurer, A., Smith, C. P., Paprocki, M., et al. (2017). SymPy: symbolic computing in Python. *PeerJ Computer Science*, 3, e103. https://doi.org/10.7717/peerj-cs.103
+- **Matplotlib**: Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. *Computing in Science & Engineering*, 9(3), 90–95. https://doi.org/10.1109/MCSE.2007.55
+- **Optuna**: Akiba, T., Sano, S., Yanase, T., Ohta, T., & Koyama, M. (2019). Optuna: A next-generation hyperparameter optimization framework. *Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (KDD '19)*, 2623–2631. https://doi.org/10.1145/3292500.3330701
+
+## Acknowledgements
+This module and its accompanying documentation were developed with the support of Cursor’s AI-assisted tools.  

rxnfit-0.2.0/README.md

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+
+## Overviews
+"rxnfit" is a Python module that builds ordinary differential equations (ODEs) for reaction kinetics from elementary reaction formulas and rate constants given in CSV format, and computes concentration time courses numerically.
+
+- When all rate constants are known, the time evolution of each species’ concentration is obtained by **numerical integration** of the ODEs (e.g. with `scipy.integrate.solve_ivp`).
+- When some rate constants are unknown, they can be **estimated by fitting** the ODE solution to experimental concentration time-course data (e.g. with `scipy.optimize.minimize`).
+- A rate constant may be given as an **expression** in other rate constants (e.g. k₂ = 2·k₁), or as a **function of time** *t* via an override CSV.
+
+**Documentation :** https://pejpohno.github.io/rxnfit/  
+**Tutorial :** in preparation  
+**How to cite :** Ohno, M. rxnfit. GitHub. https://github.com/PEJpOhno/rxnfit (2026).  
+
+## Current version and requirements
+- current version = 0.2.0
+- pyhon >=3.12
+
+[dependencies]
+- NumPy
+- pandas
+- SciPy
+- SymPy
+- Matplotlib  
+- Optuna
+
+## Copyright and license
+Copyright (c) 2025 Mitsuru Ohno
+Released under the BSD-3 license, license that can be found in the LICENSE file.
+
+## Installation
+Create and activate a Python virtual environment, then  
+
+```sh
+pip install rxnfit
+```
+
+If you want to give it a quick try, just copy or move the example directory from the cloned repo to wherever it's convenient. Then, activate your virtual environment, start Jupyter Notebook, and open one of the sample scripts inside "examples" directry to test it out.
+
+## Usage
+### Prepare csv file
+1. Describe reaction formula in csv format. THe first row shoud be header. The first column and the second column should be reaction ID (named RID) and the rate constant (named k). Other column names can be omitted.
+2. The reactants are putted in alternately with the coeficient and the chemical species. Each reaction should be described in one row.
+3. To separate the reactants and the products, two ">" are setted with two columns. As with reaction SMARTS, you may write reaction conditions between the two ">"; in the current version of rxnfit these are unused.
+4. The products are putted in alternately with the coeficient and the chemical species.
+Note the reaction formula should be inputted by the left filling. To describe chemical species, it is better to avoid to use arithmetic symbols such as "+", "-" and "*" (e.g. use "**a**"(nion) in place of "-"). The coefficient '1' can be substituted for blank.  
+5. Each elementary reaction’s rate constant must be specified in the format ‘k + RID’. If left empty, the system will automatically assign ‘k + RID’.  
+
+The rate constant k_m can also be defined as a function of another elementary reaction rate constant k_n, or as a function of time t.  
+The example of a csv format is as follows.  Attached "examples/sample_data/sample_rxn_ref1.csv" and "examples/sample_data/refX/sample_rxn_refX.csv" are also available for demonstration.
+
+example of a csv format
+
+    RID, k,,,,,,,,,,
+    1,0.054,,AcOEt,,OHa1,>,>,,AcOa1,,EtOH
+    2,1.4,,AcOiPr,,OHa1,>,>,,AcOa1,,iPrOH
+    3,0.031,,EGOAc2,2,OHa1,>,>,2,AcOa1,,EG
+
+## Modules and classes
+
+The following items are those prominently used in the example notebooks.
+
+### rxn_reader
+Reads reaction CSV and builds symbolic ODE system.
+
+| item | name | description |
+|------|------|-------------|
+| class | RxnToODE | Builds differential-type rate equations (strings) from reaction CSV, then ODE system expressions (SymPy). Attributes: rate_consts_dict, sympy_symbol_dict, sys_odes_dict, function_names. |
+| function | get_reactions | Parse reaction CSV into list of reaction data (RID, k, reactants, products, conditions). |
+| function | get_unique_species | Extract unique species names from reaction list. |
+| function | rate_constants | Extract rate constant key and value (float or expression string) per reaction. |
+
+### build_ode
+Builds numerical ODE RHS from symbolic system; supports rate-constant overrides and time-dependent k(t).
+
+| item | name | description |
+|------|------|-------------|
+| class | RxnODEbuild | Extends RxnToODE. Builds callable ODE RHS for scipy.integrate.solve_ivp. Optional rate_const_overrides (dict or CSV path) and rate_const_overrides_encoding. Methods: create_ode_system(), create_ode_system_with_rate_consts(), get_ode_system(), get_ode_info(). |
+| function | create_system_rhs | Build (t, y) RHS for solve_ivp from ODE functions dict. Optional rate_const_values (dict or callable(t)) and symbolic_rate_const_keys for variable or time-dependent rate constants. |
+
+### expdata_reader
+Loads and aligns experimental time-course data.
+
+| item | name | description |
+|------|------|-------------|
+| function | expdata_read | Read list of DataFrames into list of (t_list, C_exp_list) per dataset. |
+| function | get_y0_from_expdata | Initial concentrations per dataset in function_names order. |
+
+### expdata_fit_sci
+Fits symbolic rate constants to experimental data (scipy.optimize.minimize).
+
+| item | name | description |
+|------|------|-------------|
+| class | ExpDataFitSci | Multi-dataset fitting. run_fit(p0, ...) returns (result, param_info, fit_metrics). result has .fun (RSS), .tss, .r2; fit_metrics is dict with keys 'rss', 'tss', 'r2'. get_solver_config_args(dataset_index), get_fitted_rate_const_dict(result). plot_fitted_solution(expdata_df, ...) plots per-dataset y0 curves after run_fit. to_dataframe_list() returns list of DataFrames (one per dataset). When model has k(t), get_solver_config_args() adds rate_const_values (callable) and symbolic_rate_const_keys after run_fit(). |
+
+### solv_ode
+Numerical integration and plotting of ODE solutions.
+
+| item | name | description |
+|------|------|-------------|
+| class | SolverConfig | Dataclass: y0, t_span, t_eval, method, rtol. Optional: rate_const_values (dict or callable(t)), symbolic_rate_const_keys (both or neither). |
+| class | RxnODEsolver | Integrates ODE with builder and config. solve_system(), to_dataframe_list() returning list of DataFrames, eval_fit_metrics(expdata_df, ...) returning dict with 'rss', 'tss', 'r2', solution_plot(). When config has rate_const_values and symbolic_rate_const_keys, uses rate-constants ODE path. |
+
+### p0_opt_fit
+Optimizes initial parameter values (p0) for rate constants using Optuna, then fits with ExpDataFitSci.
+
+| item | name | description |
+|------|------|-------------|
+| class | P0OptFit | Optimizes p0 via Optuna (e.g. suggest_float with log=True) and runs ExpDataFitSci.run_fit with the best p0. optimize(n_trials, show_progress_bar, ...) returns (dict of variable → (initial, fitted), fit_metrics). fit_metrics is a dict with keys 'rss', 'tss', 'r2'. optuna_log() returns per-trial log. |
+
+## References  
+
+- **Python**: Python Software Foundation. (2024). *Python* (Version 3.13) [Computer software]. https://www.python.org/  
+- **NumPy**: Harris, C. R., Millman, K. J., van der Walt, S. J., et al. (2020). Array programming with NumPy. *Nature*, 585(7825), 357–362. https://doi.org/10.1038/s41586-020-2649-2
+- **pandas**: McKinney, W. (2010). Data Structures for Statistical Computing in Python. *Proceedings of the 9th Python in Science Conference*, 56–61. https://doi.org/10.25080/Majora-92bf1922-00a
+- **SciPy**: Virtanen, P., Gommers, R., Oliphant, T. E., et al. (2020). SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python. *Nature Methods*, 17(3), 261–272. https://doi.org/10.1038/s41592-019-0686-2
+- **SymPy**: Meurer, A., Smith, C. P., Paprocki, M., et al. (2017). SymPy: symbolic computing in Python. *PeerJ Computer Science*, 3, e103. https://doi.org/10.7717/peerj-cs.103
+- **Matplotlib**: Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. *Computing in Science & Engineering*, 9(3), 90–95. https://doi.org/10.1109/MCSE.2007.55
+- **Optuna**: Akiba, T., Sano, S., Yanase, T., Ohta, T., & Koyama, M. (2019). Optuna: A next-generation hyperparameter optimization framework. *Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (KDD '19)*, 2623–2631. https://doi.org/10.1145/3292500.3330701
+
+## Acknowledgements
+This module and its accompanying documentation were developed with the support of Cursor’s AI-assisted tools.  

rxnfit-0.2.0/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

rxnfit-0.2.0/docs/build/html/.buildinfo

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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 0355388f80fdeb1052349417a7b5bd78
+tags: 645f666f9bcd5a90fca523b33c5a78b7

rxnfit-0.2.0/docs/build/html/_sources/index.rst.txt

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+.. rxnfit documentation master file, created by
+   sphinx-quickstart on Tue Mar 10 20:22:10 2026.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+rxnfit documentation
+====================
+
+Current version: |version|, release: |release|
+
+Overviews
+--------------------------------
+"rxnfit" is a Python module that builds ordinary differential equations (ODEs) for reaction kinetics from elementary reaction formulas and rate constants given in CSV format, and computes concentration time courses numerically.
+
+- When all rate constants are known, the time evolution of each species’ concentration is obtained by **numerical integration** of the ODEs (e.g. with `scipy.integrate.solve_ivp`).
+- When some rate constants are unknown, they can be **estimated by fitting** the ODE solution to experimental concentration time-course data (e.g. with `scipy.optimize.minimize`).
+- A rate constant may be given as an **expression** in other rate constants (e.g. k₂ = 2·k₁), or as a **function of time** *t* via an override CSV.
+
+**Project Link :** https://github.com/PEJpOhno/rxnfit\
+
+**Tutorial :** in preparation
+
+**How to cite :** Ohno, M. rxnfit. GitHub. https://github.com/PEJpOhno/rxnfit (2026).  
+
+This module and its accompanying documentation were developed with the support of Cursor’s AI-assisted tools.  
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+   :hidden:
+
+   rxnfit.rxn_reader
+   rxnfit.build_ode
+   rxnfit.rate_const_ft_eval
+   rxnfit.solv_ode
+   rxnfit.expdata_reader
+   rxnfit.expdata_fit_sci
+   rxnfit.p0_opt_fit
+   rxnfit.fit_metrics
+
+   
+   
+

rxnfit-0.2.0/docs/build/html/_sources/modules.rst.txt

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+src
+===
+
+.. toctree::
+   :maxdepth: 4
+
+   rxnfit

rxnfit-0.2.0/docs/build/html/_sources/rxnfit.build_ode.rst.txt

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+rxnfit.build\_ode module
+========================
+
+.. automodule:: rxnfit.build_ode
+   :members:
+   :show-inheritance:
+   :undoc-members:

rxnfit-0.2.0/docs/build/html/_sources/rxnfit.expdata_fit_sci.rst.txt

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+rxnfit.expdata\_fit\_sci module
+===============================
+
+.. automodule:: rxnfit.expdata_fit_sci
+   :members:
+   :show-inheritance:
+   :undoc-members:

rxnfit-0.2.0/docs/build/html/_sources/rxnfit.expdata_reader.rst.txt

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+rxnfit.expdata\_reader module
+=============================
+
+.. automodule:: rxnfit.expdata_reader
+   :members:
+   :show-inheritance:
+   :undoc-members:

rxnfit-0.2.0/docs/build/html/_sources/rxnfit.fit_metrics.rst.txt

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+rxnfit.fit\_metrics module
+==========================
+
+.. automodule:: rxnfit.fit_metrics
+   :members:
+   :show-inheritance:
+   :undoc-members:

rxnfit-0.2.0/docs/build/html/_sources/rxnfit.p0_opt_fit.rst.txt

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+rxnfit.p0\_opt\_fit module
+==========================
+
+.. automodule:: rxnfit.p0_opt_fit
+   :members:
+   :show-inheritance:
+   :undoc-members:

rxnfit-0.2.0/docs/build/html/_sources/rxnfit.rate_const_ft_eval.rst.txt

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+rxnfit.rate\_const\_ft\_eval module
+===================================
+
+.. automodule:: rxnfit.rate_const_ft_eval
+   :members:
+   :show-inheritance:
+   :undoc-members:

rxnfit-0.2.0/docs/build/html/_sources/rxnfit.rst.txt

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+rxnfit package
+==============
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   rxnfit.build_ode
+   rxnfit.expdata_fit_sci
+   rxnfit.expdata_reader
+   rxnfit.fit_metrics
+   rxnfit.p0_opt_fit
+   rxnfit.rate_const_ft_eval
+   rxnfit.rxn_reader
+   rxnfit.solv_ode
+
+Module contents
+---------------
+
+.. automodule:: rxnfit
+   :members:
+   :show-inheritance:
+   :undoc-members:

rxnfit-0.2.0/docs/build/html/_sources/rxnfit.rxn_reader.rst.txt

@@ -0,0 +1,7 @@
+rxnfit.rxn\_reader module
+=========================
+
+.. automodule:: rxnfit.rxn_reader
+   :members:
+   :show-inheritance:
+   :undoc-members:

rxnfit-0.2.0/docs/build/html/_sources/rxnfit.solv_ode.rst.txt

@@ -0,0 +1,7 @@
+rxnfit.solv\_ode module
+=======================
+
+.. automodule:: rxnfit.solv_ode
+   :members:
+   :show-inheritance:
+   :undoc-members:

rxnfit-0.2.0/docs/build/html/_static/_sphinx_javascript_frameworks_compat.js

@@ -0,0 +1,123 @@
+/* Compatability shim for jQuery and underscores.js.
+ *
+ * Copyright Sphinx contributors
+ * Released under the two clause BSD licence
+ */
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}