debase 0.1.16__tar.gz → 0.1.18__tar.gz

debase-0.1.18/.gitignore

@@ -0,0 +1,177 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+Pipfile.lock
+
+# poetry
+poetry.lock
+
+# pdm
+.pdm.toml
+
+# PEP 582
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+.idea/
+
+# VS Code
+.vscode/
+
+# macOS
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Windows
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+*.stackdump
+[Dd]esktop.ini
+$RECYCLE.BIN/
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+*.lnk
+
+# Linux
+*~
+
+# Temporary files
+*.tmp
+*.temp
+*.log
+.temp_*/
+.cache/
+
+# DEBase specific
+enzyme_pipeline*.log
+temp_merged_input.csv
+*.egg-info/
+
+# Project data and examples
+data/
+examples/
+!examples/test.csv  # Keep test.csv as example output
+
+# Cache files
+*.pkl
+*_cache.pkl
+
+# Large database files
+*.db
+
+# PDFs and Excel files
+*.pdf
+*.xlsx
+
+# Backup files
+*_backup.py
+lineage_format_backup.py
+
+# Temporary directories
+.temp_*
+enzyme_analysis_*

debase-0.1.18/CONTRIBUTING.md

@@ -0,0 +1,61 @@
+# Contributing to DEBase
+
+Thank you for your interest in contributing to DEBase!
+
+## Development Setup
+
+1. Clone the repository:
+```bash
+git clone https://github.com/yourusername/debase.git
+cd debase
+```
+
+2. Create a virtual environment:
+```bash
+python -m venv venv
+source venv/bin/activate  # On Windows: venv\Scripts\activate
+```
+
+3. Install in development mode:
+```bash
+pip install -e ".[dev]"
+```
+
+## Running Tests
+
+```bash
+pytest tests/
+```
+
+## Code Style
+
+We use Black for code formatting:
+```bash
+black src/ tests/
+```
+
+And isort for import sorting:
+```bash
+isort src/ tests/
+```
+
+## Project Structure
+
+```
+debase/
+├── src/debase/           # Main package source code
+├── tests/               # Test suite
+├── docs/               # Documentation
+├── examples/           # Example outputs and usage
+├── data/              # Research data (PDFs)
+└── scripts/           # Utility scripts
+```
+
+## Submitting Changes
+
+1. Fork the repository
+2. Create a feature branch
+3. Make your changes
+4. Add tests if applicable
+5. Run the test suite
+6. Submit a pull request

{debase-0.1.16/src/debase.egg-info → debase-0.1.18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: debase
-Version: 0.1.16
+Version: 0.1.18
 Summary: Enzyme lineage analysis and sequence extraction package
 Home-page: https://github.com/YuemingLong/DEBase
 Author: DEBase Team

debase-0.1.18/docs/README.md

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+# DEBase Documentation
+
+This directory contains comprehensive documentation for the DEBase enzyme analysis pipeline.
+
+## Directory Structure
+
+- `api/` - API documentation and reference
+- `examples/` - Usage examples and tutorials  
+- `tutorials/` - Step-by-step guides
+
+## Quick Start
+
+See the main [README.md](../README.md) for installation and basic usage.
+
+## Contents
+
+1. [Installation Guide](tutorials/installation.md)
+2. [API Reference](api/README.md)
+3. [Usage Examples](examples/README.md)

debase-0.1.18/docs/examples/README.md

@@ -0,0 +1,24 @@
+# DEBase Examples
+
+This directory contains example outputs and usage demonstrations for the DEBase pipeline.
+
+## Example Outputs
+
+The `../../examples/` directory contains sample results from successful pipeline runs:
+
+- `trpb_complete_pipeline.csv` - Complete TrpB enzyme dataset with sequences, mutations, and reactions
+- `carbene_complete_pipeline.csv` - Carbene transfer enzyme data with SMILES and conditions  
+- `REFINED_ENZYME_SEQUENCES.csv` - Refined sequence extraction results
+
+## Data Format
+
+Each CSV contains:
+- Full-length protein sequences (200-400+ amino acids)
+- Complete mutation lineage tracking
+- Chemical reaction SMILES strings
+- Experimental conditions and metadata
+- Performance metrics (yield, TTN, enantioselectivity)
+
+## Usage
+
+These files demonstrate the expected output format and can be used as reference for pipeline validation.

debase-0.1.18/environment.yml

@@ -0,0 +1,21 @@
+name: debase
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - pandas>=1.0.0
+  - numpy>=1.19.0
+  - matplotlib>=3.3.0
+  - seaborn>=0.11.0
+  - jupyter>=1.0.0
+  - jupyterlab>=3.0.0
+  - openpyxl>=3.0.0
+  - biopython>=1.78
+  - requests>=2.25.0
+  - tqdm>=4.60.0
+  - rdkit>=2020.03.1
+  - pip
+  - pip:
+    - PyMuPDF>=1.18.0
+    - google-generativeai>=0.3.0

debase-0.1.18/src/debase/PIPELINE_FLOW.md

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+# DEBase Pipeline Flow
+
+## Overview
+The DEBase pipeline extracts enzyme engineering data from chemistry papers through a series of modular steps.
+
+## Pipeline Architecture
+
+```
+┌─────────────────────┐     ┌─────────────────────┐
+│   Manuscript PDF    │     │       SI PDF        │
+└──────────┬──────────┘     └──────────┬──────────┘
+           │                           │
+           └───────────┬───────────────┘
+                       │
+                       ▼
+         ┌─────────────────────────────┐
+         │ 1. enzyme_lineage_extractor │
+         │   - Extract enzyme variants │
+         │   - Parse mutations         │
+         │   - Get basic metadata      │
+         └─────────────┬───────────────┘
+                       │
+                       ▼
+         ┌─────────────────────────────┐
+         │    2. cleanup_sequence      │
+         │   - Validate sequences      │
+         │   - Fix formatting issues   │
+         │   - Generate full sequences │
+         └─────────────┬───────────────┘
+                       │
+           ┌───────────┴───────────────┐
+           │                           │
+           ▼                           ▼
+┌─────────────────────────┐ ┌─────────────────────────┐
+│ 3a. reaction_info       │ │ 3b. substrate_scope     │
+│     _extractor          │ │     _extractor          │
+│ - Performance metrics   │ │ - Substrate variations  │
+│ - Model reaction        │ │ - Additional variants   │
+│ - Conditions            │ │ - Scope data            │
+└───────────┬─────────────┘ └───────────┬─────────────┘
+            │                           │
+            └───────────┬───────────────┘
+                        │
+                        ▼
+          ┌─────────────────────────────┐
+          │    4. lineage_format_o3     │
+          │   - Merge all data          │
+          │   - Fill missing sequences  │
+          │   - Format final output     │
+          └─────────────┬───────────────┘
+                        │
+                        ▼
+                ┌─────────────┐
+                │ Final CSV   │
+                └─────────────┘
+```
+
+## Module Details
+
+### 1. enzyme_lineage_extractor.py
+- **Input**: Manuscript PDF, SI PDF
+- **Output**: CSV with enzyme variants and mutations
+- **Function**: Extracts enzyme identifiers, mutation lists, and basic metadata
+
+### 2. cleanup_sequence.py  
+- **Input**: Enzyme lineage CSV
+- **Output**: CSV with validated sequences
+- **Function**: Validates protein sequences, generates full sequences from mutations
+
+### 3a. reaction_info_extractor.py
+- **Input**: PDFs + cleaned enzyme CSV
+- **Output**: CSV with reaction performance data
+- **Function**: Extracts yield, TTN, selectivity, reaction conditions
+
+### 3b. substrate_scope_extractor.py
+- **Input**: PDFs + cleaned enzyme CSV  
+- **Output**: CSV with substrate scope entries
+- **Function**: Extracts substrate variations tested with different enzymes
+
+### 4. lineage_format_o3.py
+- **Input**: Reaction CSV + Substrate scope CSV
+- **Output**: Final formatted CSV
+- **Function**: Merges data, fills missing sequences, applies consistent formatting
+
+## Key Features
+
+1. **Modular Design**: Each step can be run independently
+2. **Parallel Extraction**: Steps 3a and 3b run independently 
+3. **Error Recovery**: Pipeline can resume from any step
+4. **Clean Interfaces**: Each module has well-defined inputs/outputs
+
+## Usage
+
+```bash
+# Full pipeline
+python -m debase.wrapper_clean manuscript.pdf --si si.pdf --output results.csv
+
+# With intermediate files kept for debugging  
+python -m debase.wrapper_clean manuscript.pdf --si si.pdf --keep-intermediates
+```

{debase-0.1.16 → debase-0.1.18}/src/debase/_version.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "0.1.16"
+__version__ = "0.1.18"