first commit

Author: xinwuye

.gitignore

@@ -0,0 +1,163 @@
+# 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/
+apex/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# 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/
+
+.vscode
+.idea
+
+# custom
+/data.tar.gz
+*.pkl
+*.pkl.json
+*.log.json
+*.jpg
+bash
+data
+data_set
+results/
+gaozhangyang/
+src/models/SurfPro/
+run.sh
+output/
+work_dirs/
+workspace/
+pretrains
+cache/
+cath_classes/
+gt_pdb/
+ig_results/
+lightning_logs/
+predicted_pdb/
+raw_test_data/
+test_results/
+alphafolddb/
+cath_test_82/
+figures/
+ig_biochem_results_steps50/
+ig_results_steps50/
+tools/prepare_data/
+afdb_json2pkl.py
+cath42_82.zip
+data_processing.ipynb
+process_test_datasets.ipynb
+visualization*
+train/main_eval.py
+train/ig*
+TMscore*
+
+# Pytorch
+*.pth
+
+*.swp
+.DS_Store
+*.json
+run/wandb/
+wandb/
+esm/
+figs/
+esm/*
+sampling/*
+model_zoom/*
+run/

CONTRIBUTING.md

@@ -0,0 +1,113 @@
+# Contributing to *PLACEHOLDER*
+
+We welcome contributions from everyone to help improve and expand *PLACEHOLDER*. This document outlines the process for contributing to the project.
+
+## Table of Contents
+1. [Environment Setup](#environment-setup)
+2. [Coding Standards](#coding-standards)
+3. [Pull Request Process](#pull-request-process)
+4. [Pull Request Template](#pull-request-template)
+
+## Environment Setup
+
+To contribute to *PLACEHOLDER*, follow these steps to set up your development environment:
+
+1. Clone the repository:
+   ```
+   git clone https://github.com/gersteinlab/placeholder.git
+   cd placeholder
+   ```
+2. Create a Conda environment:
+   ```
+   conda create -n placeholder python=3.10
+   conda activate placeholder
+   ```
+3. Install the project in editable mode with development dependencies:
+   ```
+   python3 -m pip install --upgrade pip
+   pip install -e .
+   ```
+
+## Coding Standards
+
+We strive to maintain clean and consistent code throughout the project. Please adhere to the following guidelines:
+
+1. Follow PEP 8 guidelines for Python code.
+2. Use meaningful variable and function names.
+3. Write docstrings for functions and classes.
+4. Keep functions small and focused on a single task.
+5. Use type hints where appropriate.
+
+### Code Formatting
+
+We use `black` for code formatting. To ensure your code is properly formatted:
+
+1. Install black:
+   ```
+   pip install black
+   ```
+2. Run black on the codebase:
+   ```
+   black .
+   ```
+
+## Pull Request Process
+
+1. Create a new branch for your feature or bugfix; feature is for new function; bugfix is for fixing a bug:
+   ```
+   git checkout -b feature/your-feature-name
+   ```
+2. Make your changes and commit them with clear, concise commit messages.
+   1. Monitor the current conditions and check which files are modified or untracked
+   ```
+   git status
+   ```
+   2. Git add your file
+   ```
+   git add schema.py 
+   ```
+   3. Submit your change and commit
+   ```
+   git commit -m "message"
+   ```
+4. Push your branch to the repository:
+   ```
+   git push origin feature/your-feature-name
+   ```
+5. Open a pull request against the `main` branch on the website.
+6. Fill out the pull request template (see below).
+7. Address any feedback or comments from reviewers.
+
+## Pull Request Template
+
+When you open a new pull request, please use the following template:
+
+```markdown
+## Description
+
+### Changes
+[Provide a detailed list of the changes made in this PR]
+
+### Design
+[Explain the design decisions and architectural changes, if any]
+
+### Example Code
+[If applicable, provide example code demonstrating the usage of new features or fixes]
+
+## Related Issue
+[Link to the issue this PR addresses, if applicable]
+
+## Type of Change
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] This change requires a documentation update
+
+## How Has This Been Tested?
+[Describe the tests you ran to verify your changes]
+
+## Additional Notes
+[Add any additional information or context about the PR here]
+```
+
+Thank you for contributing to *PLACEHOLDER*!