transformapy 0.0.6

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

May.25.2024: transformapy 0.0.6

1. Updated the is_valid_formula function to account for cases without carbon (C).

2. Included a requirement to update pyhrms to the latest version.

3. Enhanced generate_possible_TP_structures to generate the most similar molecules based on molecular fingerprint similarity and to return intermediate steps.

4. Added the one_step_reaction_based_on_fp function.

5. Added the stepwise_reaction_single_tp function.

6. Added the unfold_formula_result function.

7. Added the get_formula_elements_range function.

8. Updated the combine_fragments_and_generate_smiles function.

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/
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.