Updates to fake data and energy functions

.gitignore

@@ -3,6 +3,13 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# Pickled data and visualization
+*.pkl
+!fake_histories_r4_0.pkl
+*.png
+runs/
+*.pdb
+
 # C extensions
 *.so
 

README.md

@@ -1 +1,45 @@
-# nmr
+# nmr
+
+NMR Chemical Shift Assignment using Graph Neural Networks and Reinforcement Learning
+
+## Quick Start
+
+### Generating Training Data
+
+Create synthetic datasets for supervised pre-training:
+
+```bash
+# Generate a dataset
+python scripts/generate_dataset.py --num-resid 10 --output dataset_10.pkl
+
+# Generate training histories
+python scripts/generate_histories.py \
+    --dataset dataset_10.pkl \
+    --num-histories 100
+```
+
+For detailed documentation, see [docs/fake-data-guide.md](docs/fake-data-guide.md)
+
+## Documentation
+
+- **[Fake Data Generation Guide](docs/fake-data-guide.md)** - Complete guide to generating synthetic training data
+- **[Development Guide](docs/development-guide.md)** - Setup, development patterns, and testing
+- **[Architecture Documentation](docs/architecture.md)** - System architecture and design
+- **[Project Overview](docs/project-overview.md)** - Executive summary
+
+## Project Structure
+
+```
+nmr/
+├── nmr/                    # Main package
+│   ├── construct.py        # Graph construction
+│   ├── models/             # GNN architecture
+│   └── env/                # RL environment
+├── scripts/                # Executable scripts
+│   ├── generate_dataset.py       # Dataset generation
+│   ├── generate_histories.py     # History generation
+│   ├── train_gnn.py              # Training loop
+│   └── visualize_data.py         # Data visualization
+├── tests/                  # Unit tests
+└── docs/                   # Documentation
+```

nmr/__init__.py

@@ -0,0 +1,32 @@
+"""NMR chemical shift assignment package."""
+
+from nmr.construct import construct_graph
+from nmr.models import NMRNet
+from nmr.nmr_gym.fake_data import FakeDataGenerator
+from nmr.nmr_gym.energy import Energy
+from nmr.nmr_gym.assignment_order import FractionalActivation
+from nmr.nmr_gym.gym_env import GymEnv
+from nmr.nmr_gym.fake_histories import FakeHistoryGenerator
+from nmr.nmr_gym.data_structures import Connectivity, HSQCPeak, NOEPeak, Protein
+from nmr.nmr_gym.io import load_dataset, load_histories, save_dataset, save_histories
+from nmr.nmr_gym.state import create_state_dict, validate_state_dict
+
+__all__ = [
+    "construct_graph",
+    "NMRNet",
+    "FakeDataGenerator",
+    "Energy",
+    "FractionalActivation",
+    "GymEnv",
+    "FakeHistoryGenerator",
+    "Connectivity",
+    "HSQCPeak",
+    "NOEPeak",
+    "Protein",
+    "load_dataset",
+    "load_histories",
+    "save_dataset",
+    "save_histories",
+    "create_state_dict",
+    "validate_state_dict",
+]