Metadata-Version: 2.4
Name: diptox
Version: 1.0.3
Summary: Data Integration and Processing for Computational Toxicology
Author-email: Guijia Bi <gjbi@mail.dlut.edu.cn>
License: 
                                         Apache License
                                   Version 2.0, January 2004
                                http://www.apache.org/licenses/
        
           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
        
           1. Definitions.
        
              "License" shall mean the terms and conditions for use, reproduction,
              and distribution as defined by Sections 1 through 9 of this document.
        
              "Licensor" shall mean the copyright owner or entity authorized by
              the copyright owner that is granting the License.
        
              "Legal Entity" shall mean the union of the acting entity and all
              other entities that control, are controlled by, or are under common
              control with that entity. For the purposes of this definition,
              "control" means (i) the power, direct or indirect, to cause the
              direction or management of such entity, whether by contract or
              otherwise, or (ii) ownership of fifty percent (50%) or more of the
              outstanding shares, or (iii) beneficial ownership of such entity.
        
              "You" (or "Your") shall mean an individual or Legal Entity
              exercising permissions granted by this License.
        
              "Source" form shall mean the preferred form for making modifications,
              including but not limited to software source code, documentation
              source, and configuration files.
        
              "Object" form shall mean any form resulting from mechanical
              transformation or translation of a Source form, including but
              not limited to compiled object code, generated documentation,
              and conversions to other media types.
        
              "Work" shall mean the work of authorship, whether in Source or
              Object form, made available under the License, as indicated by a
              copyright notice that is included in or attached to the work
              (an example is provided in the Appendix below).
        
              "Derivative Works" shall mean any work, whether in Source or Object
              form, that is based on (or derived from) the Work and for which the
              editorial revisions, annotations, elaborations, or other modifications
              represent, as a whole, an original work of authorship. For the purposes
              of this License, Derivative Works shall not include works that remain
              separable from, or merely link (or bind by name) to the interfaces of,
              the Work and Derivative Works thereof.
        
              "Contribution" shall mean any work of authorship, including
              the original version of the Work and any modifications or additions
              to that Work or Derivative Works thereof, that is intentionally
              submitted to Licensor for inclusion in the Work by the copyright owner
              or by an individual or Legal Entity authorized to submit on behalf of
              the copyright owner. For the purposes of this definition, "submitted"
              means any form of electronic, verbal, or written communication sent
              to the Licensor or its representatives, including but not limited to
              communication on electronic mailing lists, source code control systems,
              and issue tracking systems that are managed by, or on behalf of, the
              Licensor for the purpose of discussing and improving the Work, but
              excluding communication that is conspicuously marked or otherwise
              designated in writing by the copyright owner as "Not a Contribution."
        
              "Contributor" shall mean Licensor and any individual or Legal Entity
              on behalf of whom a Contribution has been received by Licensor and
              subsequently incorporated within the Work.
        
           2. Grant of Copyright License. Subject to the terms and conditions of
              this License, each Contributor hereby grants to You a perpetual,
              worldwide, non-exclusive, no-charge, royalty-free, irrevocable
              copyright license to reproduce, prepare Derivative Works of,
              publicly display, publicly perform, sublicense, and distribute the
              Work and such Derivative Works in Source or Object form.
        
           3. Grant of Patent License. Subject to the terms and conditions of
              this License, each Contributor hereby grants to You a perpetual,
              worldwide, non-exclusive, no-charge, royalty-free, irrevocable
              (except as stated in this section) patent license to make, have made,
              use, offer to sell, sell, import, and otherwise transfer the Work,
              where such license applies only to those patent claims licensable
              by such Contributor that are necessarily infringed by their
              Contribution(s) alone or by combination of their Contribution(s)
              with the Work to which such Contribution(s) was submitted. If You
              institute patent litigation against any entity (including a
              cross-claim or counterclaim in a lawsuit) alleging that the Work
              or a Contribution incorporated within the Work constitutes direct
              or contributory patent infringement, then any patent licenses
              granted to You under this License for that Work shall terminate
              as of the date such litigation is filed.
        
           4. Redistribution. You may reproduce and distribute copies of the
              Work or Derivative Works thereof in any medium, with or without
              modifications, and in Source or Object form, provided that You
              meet the following conditions:
        
              (a) You must give any other recipients of the Work or
                  Derivative Works a copy of this License; and
        
              (b) You must cause any modified files to carry prominent notices
                  stating that You changed the files; and
        
              (c) You must retain, in the Source form of any Derivative Works
                  that You distribute, all copyright, patent, trademark, and
                  attribution notices from the Source form of the Work,
                  excluding those notices that do not pertain to any part of
                  the Derivative Works; and
        
              (d) If the Work includes a "NOTICE" text file as part of its
                  distribution, then any Derivative Works that You distribute must
                  include a readable copy of the attribution notices contained
                  within such NOTICE file, excluding those notices that do not
                  pertain to any part of the Derivative Works, in at least one
                  of the following places: within a NOTICE text file distributed
                  as part of the Derivative Works; within the Source form or
                  documentation, if provided along with the Derivative Works; or,
                  within a display generated by the Derivative Works, if and
                  wherever such third-party notices normally appear. The contents
                  of the NOTICE file are for informational purposes only and
                  do not modify the License. You may add Your own attribution
                  notices within Derivative Works that You distribute, alongside
                  or as an addendum to the NOTICE text from the Work, provided
                  that such additional attribution notices cannot be construed
                  as modifying the License.
        
              You may add Your own copyright statement to Your modifications and
              may provide additional or different license terms and conditions
              for use, reproduction, or distribution of Your modifications, or
              for any such Derivative Works as a whole, provided Your use,
              reproduction, and distribution of the Work otherwise complies with
              the conditions stated in this License.
        
           5. Submission of Contributions. Unless You explicitly state otherwise,
              any Contribution intentionally submitted for inclusion in the Work
              by You to the Licensor shall be under the terms and conditions of
              this License, without any additional terms or conditions.
              Notwithstanding the above, nothing herein shall supersede or modify
              the terms of any separate license agreement you may have executed
              with Licensor regarding such Contributions.
        
           6. Trademarks. This License does not grant permission to use the trade
              names, trademarks, service marks, or product names of the Licensor,
              except as required for reasonable and customary use in describing the
              origin of the Work and reproducing the content of the NOTICE file.
        
           7. Disclaimer of Warranty. Unless required by applicable law or
              agreed to in writing, Licensor provides the Work (and each
              Contributor provides its Contributions) on an "AS IS" BASIS,
              WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
              implied, including, without limitation, any warranties or conditions
              of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
              PARTICULAR PURPOSE. You are solely responsible for determining the
              appropriateness of using or redistributing the Work and assume any
              risks associated with Your exercise of permissions under this License.
        
           8. Limitation of Liability. In no event and under no legal theory,
              whether in tort (including negligence), contract, or otherwise,
              unless required by applicable law (such as deliberate and grossly
              negligent acts) or agreed to in writing, shall any Contributor be
              liable to You for damages, including any direct, indirect, special,
              incidental, or consequential damages of any character arising as a
              result of this License or out of the use or inability to use the
              Work (including but not limited to damages for loss of goodwill,
              work stoppage, computer failure or malfunction, or any and all
              other commercial damages or losses), even if such Contributor
              has been advised of the possibility of such damages.
        
           9. Accepting Warranty or Additional Liability. While redistributing
              the Work or Derivative Works thereof, You may choose to offer,
              and charge a fee for, acceptance of support, warranty, indemnity,
              or other liability obligations and/or rights consistent with this
              License. However, in accepting such obligations, You may act only
              on Your own behalf and on Your sole responsibility, not on behalf
              of any other Contributor, and only if You agree to indemnify,
              defend, and hold each Contributor harmless for any liability
              incurred by, or claims asserted against, such Contributor by reason
              of your accepting any such warranty or additional liability.
        
           END OF TERMS AND CONDITIONS
        
           APPENDIX: How to apply the Apache License to your work.
        
              To apply the Apache License to your work, attach the following
              boilerplate notice, with the fields enclosed by brackets "[]"
              replaced with your own identifying information. (Don't include
              the brackets!)  The text should be enclosed in the appropriate
              comment syntax for the file format. We also recommend that a
              file or class name and description of purpose be included on the
              same "printed page" as the copyright notice for easier
              identification within third-party archives.
        
           Copyright [2025] [Guijia Bi]
        
           Licensed under the Apache License, Version 2.0 (the "License");
           you may not use this file except in compliance with the License.
           You may obtain a copy of the License at
        
               http://www.apache.org/licenses/LICENSE-2.0
        
           Unless required by applicable law or agreed to in writing, software
           distributed under the License is distributed on an "AS IS" BASIS,
           WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
           See the License for the specific language governing permissions and
           limitations under the License.
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: requests
Requires-Dist: pandas
Requires-Dist: rdkit>=2023.3
Requires-Dist: tqdm
Requires-Dist: scipy
Requires-Dist: openpyxl
Requires-Dist: streamlit>=1.0.0
Dynamic: license-file

# DiPTox - Data Integration and Processing for Computational Toxicology

**DiPTox** is a Python toolkit designed for the robust preprocessing, standardization, and multi-source data integration of molecular datasets, with a focus on computational toxicology workflows.

## Official Release v1.0
We are excited to announce the first official stable release of DiPTox on PyPI! This milestone brings production-ready stability and performance enhancements:

* **Multi-Process Acceleration**:
    * Accelerate chemical preprocessing tasks by **10x or more** using the `n_jobs` parameter.
    * Intelligent task distribution across CPU cores for heavy datasets.
* **Cross-Platform Robustness**:
    * Implemented a specialized **"Guard Mechanism"** for Windows multiprocessing to prevent memory explosion and recursive process spawning issues.
    * Verified stability across Windows, Linux, and macOS environments.
* **Enhanced Data Loading**:
    * Switched to binary stream parsing for `.sdf` and `.mol` files to resolve encoding crashes (e.g., `utf-8` vs `latin-1`).
    * Auto-parsing of molecular structures to generate SMILES even when properties are missing.
### Version Update Log (1.0.3)
* **Enhanced Unit Standardization**: Custom conversion formulas now fully support molecular weight (`mw`). You can seamlessly convert between molarity and mass concentrations (e.g., using formulas like `x * mw * 1000`).
* **GUI Interface Optimization**: The Streamlit graphical interface has been beautifully redesigned for a more professional, clean, and logical scientific layout. We've reduced visual clutter, grouped configuration panels intuitively, and improved component alignment.
* **Comprehensive Audit Log (History)**: The processing history has been heavily upgraded. It now records granular parameters for every operation—including exactly which preprocessing rules were triggered, active deduplication conditions, web query statuses, and substructure search match counts.

## DiPTox Community Check-in (Optional)
To help us understand our user base and improve the software, DiPTox includes a one-time, optional survey on first use. 
-   **Completely Optional**: You can skip it with a single click.
-   **Privacy-Focused**: The information helps us with academic impact assessment. It will not be shared.

## Core Features

#### 1. Graphical User Interface (GUI)
Powered by Streamlit, the GUI allows users to perform all workflows visually without writing code.
-   **Visual Operation**: Complete workflow control via a web browser.
-   **Real-time Preview**: Instantly view data changes after applying rules.
-   **Rule Management**: Add/Remove valid atoms, salts, solvents, and **unit conversion formulas** interactively.
-   **Smart Column Mapping**: Intelligent detection of headers and binary file structures.

#### 2. Chemical Preprocessing & Standardization
A configurable pipeline to clean and normalize chemical structures.
-   **Strict Inorganic Filtering**: Updated SMARTS matching to accurately identify complex inorganic species (e.g., ionic cyanides) without misclassifying organic nitriles.
-   **Pipeline Steps**:
    -   Remove salts & solvents
    -   Handle mixtures (keep largest fragment)
    -   Remove inorganic molecules
    -   Neutralize charges & Validate atomic composition
    -   Remove explicit hydrogens, stereochemistry, and isotopes
    -   **Reject Radical Species**: Automatically discard molecules containing free radical atoms.
    -   Standardize to canonical SMILES
    -   Filter by atom count

#### 3. Unit Standardization
Normalize heterogeneous target data into a single unit effortlessly.
-   **Automatic Conversion**: Built-in rules for **Concentration**, **Time**, **Pressure**, and **Temperature**.
-   **Custom Formulas**: Define mathematical rules (e.g., `x * 1000` or `10**(-x)`) interactively via GUI or script.
-   **Unified Output**: Standardize diverse units (e.g., `ug/mL`, `g/L`, `M`) to a single target (e.g., `mg/L`).

#### 4. Data Deduplication
Flexible strategies for handling duplicate entries with advanced controls.
-   **Data Types**: Supports `continuous` (e.g., IC50) and `discrete` (e.g., Active/Inactive) targets.
-   **Methods**: `auto`, `IQR`, `3sigma`, `vote`, or custom priority rules.
-   **Log Transformation**: Optional `-log10` transformation (e.g., IC50 $\to$ pIC50) applied *before* deduplication logic to handle bioactivity data correctly.
-   **Flexible NaN Handling**: Option to retain rows with missing conditions (treating *NaN* as a valid group) instead of dropping them.

#### 5. Comprehensive History Tracking (Audit Log)
-   Records every operation (Loading, Preprocessing, Filtering, etc.) in an **Audit Log**.
-   Tracks **timestamps**, **operation details**, and row count changes (**Delta**) step-by-step.
-   Available via API (`get_history()`) and visualized in the GUI.

#### 6. Identifier & Property Integration
-   Fetch and interconvert identifiers (**CAS, SMILES, IUPAC, MW**) from multiple sources (**PubChem, ChemSpider, CompTox, Cactus, CAS Common Chemistry, ChEMBL**).
-   High-performance **concurrent requests** with automatic rate limiting and retries.

#### 7. Utility Tools
-   Perform **substructure searches** using SMILES or SMARTS patterns.
-   **Customize chemical processing rules** for neutralization reactions, salt/solvent lists, and valid atoms.
-   **Display a summary** of all currently active processing rules.

## Installation
Install the official stable version from PyPI:
```bash
pip install diptox
```

## GUI
After installation, you can launch the graphical interface directly from your terminal:

```bash
diptox-gui
```

This command will automatically open the DiPTox interface in your default web browser.

## Quick Start
```python
from diptox import DiptoxPipeline

def main():
    # Initialize processor
    DP = DiptoxPipeline()

    # Load data
    DP.load_data(input_data='file_path/list/dataframe', smiles_col, target_col, cas_col, unit_col)

    # Customize Processing Rules (Optional)
    print("--- Default Rules ---")
    DP.display_processing_rules()

    DP.manage_atom_rules(atoms=['Si'], add=True)         # Add 'Si' to the list of valid atoms
    DP.manage_default_salt(salts=['[Na+]'], add=False)   # Example: remove sodium from the salt list
    DP.manage_default_solvent(solvents='Cl', add=False)  # Example: remove chlorine from the solvent list
    DP.add_neutralization_rule('[$([N-]C=O)]', 'N')      # Add a custom neutralization rule

    print("\n--- Customized Rules ---")
    DP.display_processing_rules()

    # Configure preprocessing
    DP.preprocess(
        remove_salts=True,              # Remove salt fragments. Default: True.
        remove_solvents=True,           # Remove solvent fragments. Default: True.
        remove_mixtures=True,           # Handle mixtures based on fragment size. Default: False.
        hac_threshold=3,                # Heavy atom count threshold for fragment removal. Default: 3.
        keep_largest_fragment=True,     # Keep the largest fragment in a mixture. Default: True.
        remove_inorganic=False,         # Remove common inorganic molecules. Default: True.
        neutralize=True,                # Neutralize charges on the molecule. Default: True.
        reject_non_neutral=False,       # Only retain the molecules whose formal charge is zero. Default: False.
        check_valid_atoms=True,         # Check if all atoms are in the valid list. Default: False.
        strict_atom_check=False,        # If True, discard molecules with invalid atoms. If False, try to remove them. Default: False.
        remove_stereo=False,            # Remove stereochemistry information. Default: False.
        remove_isotopes=True,           # Remove isotopic information. Default: True.
        remove_hs=True,                 # Remove explicit hydrogen atoms. Default: True.
        reject_radical_species=True,    # Molecules containing free radical atoms are directly rejected. Default: True.
        n_jobs=4                        # Accelerate using 4 CPU cores. Default: 1 
    )

    # Configure deduplication and unit standardization
    conversion_rules = {('g/L', 'mg/L'): 'x * 1000', 
                        ('ug/L', 'mg/L'): 'x / 1000',}
    DP.config_deduplicator(condition_cols, data_type, method, custom_method, priority, standard_unit, conversion_rules, log_transform, dropna_conditions)
    DP.dataset_deduplicate()

    # Configure web queries
    DP.config_web_request(sources=['pubchem/chemspider/comptox/cactus/cas'], max_workers, ...)
    DP.web_request(send='cas', request=['smiles', 'iupac'])

    # Substructure search
    DP.substructure_search(query_pattern, is_smarts=True)

    # Save results
    DP.save_results(output_path='file_path')

    # View Processing History (Audit Log)
    print(DP.get_history())
    # Output Example:
    #               Step Timestamp  Rows Before  Rows After   Delta                               Details
    # 0     Data Loading  10:00:01            0        1000   +1000                   Source: dataset.csv
    # 1    Preprocessing  10:00:05         1000         950     -50  Valid: 950, Invalid: 50. Order: ...
    # 2    Deduplication  10:00:08          950         800    -150       Method: auto (Log10 Transformed)

# CRITICAL: This protection block is REQUIRED for Windows multiprocessing!
# It prevents infinite recursive loops and memory explosion when n_jobs > 1.
if __name__ == '__main__':
    main()
```

## Advanced Configuration

### Web Service Integration
DiPTox supports the following chemical databases:
-   `PubChem`: https://pubchem.ncbi.nlm.nih.gov/
-   `ChemSpider`: https://www.chemspider.com/
-   `CompTox`: https://comptox.epa.gov/dashboard/
-   `Cactus`: https://cactus.nci.nih.gov/
-   `CAS`: https://commonchemistry.cas.org/
-   `ChEMBL`: https://www.ebi.ac.uk/chembl/

**Note:** `ChemSpider`, `CompTox` and `CAS` require API keys. Provide them during configuration:
```python
DP.config_web_request(
    sources=['chemspider/comptox/CAS'],
    chemspider_api_key='your_personal_key',
    comptox_api_key='your_personal_key',
    cas_api_key='your_personal_key'
)
```
## Requirements
- `Python>=3.8`
- Core Dependencies:
  - `requests`
  - `rdkit>=2023.3`
  - `tqdm`
  - `openpyxl`
  - `scipy`
  - `streamlit>=1.0.0` (Required for GUI)
- Optional Dependencies (install as needed, if not installed, then send the request using `requests`.):
  - `pubchempy>=1.0.5`: For PubChem integration
  - `chemspipy>=2.0.0`: For ChemSpider (requires API key)
  - `ctx-python>=0.0.1a10`: For CompTox Dashboard (requires API key)

## License
Apache License 2.0 - See [LICENSE](https://github.com/Hya0FAD/DiPTox/blob/main/LICENSE) for details

## Support
Report issues on [GitHub Issues](https://github.com/Hya0FAD/DiPTox/issues)
