Metadata-Version: 1.2
Name: transformapy
Version: 0.0.5
Summary: A Toolkit for Identifying Transformation Product Structures of Emerging Contaminants Using HRMS Data
Home-page: https://github.com/WangRui5/TransformaPy
Author: Wang Rui
Author-email: wtrt7009@gmail.com
License: UNKNOWN
Description: transformapy: A Toolkit for Identifying Transformation Product Structures of Emerging Contaminants Using HRMS Data
        ==================================================================================================================
        
        transformapy is a Python toolkit engineered to process molecular structures, pinpointing potential transformation products of specified compounds by leveraging observed monoisotopic masses.
        
        Contributor: Rui Wang
        =====================
        
        First release date: Feb.28.2024
        
        Update
        ======
        
        April.09.2024: transformapy 0.0.5
        
        1. **Updated `remove_2H` Function**: Modifications have been made to improve the performance and accuracy of the `remove_2H` function.
        2. **New Helper Functions**: Added `check_bad_valance_Hidx` and `remove_additional_H` functions, which are now utilized internally by `remove_2H` to enhance its functionality.
        3. **Added `add_missing_H` Function**: Introduced a new function to automatically add missing hydrogen atoms to molecules to correct their valency.
        4. **Enhanced `reaction_type` Checks**: Integrated the `add_missing_H` and `remove_additional_H` functions into the `reaction_type` function to ensure molecule structures are correctly adjusted during reactions.
        5. **Introduced `stepwise_reaction` Function**: A new function to facilitate the stepwise application of reaction steps on a target molecule, allowing more detailed control over complex reaction pathways.
        6. **Improvements to `generate_possible_TP_structures`**: Significant updates have been made to this function to optimize the generation of possible transformation product structures based on modified chemical reaction processes.
        
        
        Dependencies
        ============
        
        transformapy requires the following major dependencies:
        
        - rdkit
        - pyhrms
        
        Features
        ========
        
        transformapy provides the following functions:
        
        - Identifying Transformation Product Structures of Emerging Contaminants Using HRMS Data
        
        Paper Published Utilizing transformapy
        =======================================
        
        - Preparing
        
        Licensing
        =========
        
        The package is open source and can be utilized under the MIT license. Please find the detail in the license file.
        
        transformapy Documentation
        ===========================
        
        **Getting Started with transformapy**
        
        .. code-block:: python
        
            from transformapy.transformapy import *
        
        **Project Structure:**
        
        .. code-block:: none
        
            transformapy/
            Step 1:
            |- from_mass_to_formula
               |- get_formula_elements_range
        
            Step 2:
            ｜- unfold_formula_result
        
            Step 3:
            |- generate_possible_TP_structures_to_df
               |- generate_possible_TP_structures
                  |- modify_chemical_formula
                  |- generate_fragments
                  |- calculate_formula_differences
                  |- combine_two_frags
                  |- calculate_changed_num
                     |- parse_formula
                  |- stepwise_reaction_single_tp
                     |- one_step_reaction_based_on_fp
                        |- reaction_type
                           |- combine_fragments_and_generate_smiles
                           |- replace_dummies_with_hydrogens
                           |- replace_hydrogen_with_substituent
                           |- split_molecule_at_bond
                           |- Remove_2H
                              |- is_atom_in_double_bond
                              |- add_or_modify_bond
                              |- has_hydrogen_count
                           |- Add_2H
                           |- remove_additional_H
                              |- check_bad_valance_Hidx
                           |- add_missing_H
           
            |- remove_explicit_hydrogens
            |- draw_molecule_with_atom_indices
            |- GetIdxOfDummy
            |- adjust_valence_by_removing_hydrogen
        
        Acknowledgment
        ==============
        
        During the development of this package, Liu Huangrui from the South China Institute of Environmental Science offered essential support by conducting comprehensive tests on its functionality.
        
        Note
        ====
        
        Please note that the documentation is currently a work in progress, and there is more content that is being written. I apologize for any inconvenience this may cause, but rest assured that I am continually updating the documentation to provide you with the most comprehensive guide to using transformapy.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
