transformapy 0.0.4

A Toolkit for Identifying Transformation Product Structures of Emerging Contaminants Using HRMS Data

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 0.0.4

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

from transformapy.transformapy import *

Project Structure:

transformapy/
|- from_mass_to_formula
|- generate_possible_TP_structures
   |- modify_chemical_formula
   |- generate_fragments
   |- calculate_formula_differences
   |- combine_two_frags
   |- calculate_changed_num
      |- parse_formula
   |- stepwise_reaction
      |- 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.