# boltzjobs
`boltzjobs` is a Python package designed to streamline the process of creating YAML input files for [Boltz-2](https://github.com/jwohlwend/boltz).
It provides an intuitive, object-oriented interface for defining molecular sequences, constraints, and templates, and generates a correctly formatted YAML file.
## Features
- Define **protein**, **DNA**, and **RNA chains** with support for residue modifications.
- Add **ligands** using either CCD codes or SMILES strings.
- Specify geometric **constraints**, including bonds, contacts, and binding pockets.
- Define mmCIF or PDB files as **structural templates**.
- Request property calculations, such as **binding affinity**.
## Installation
```bash
pip install git+https://github.com/ugSUBMARINE/boltzjobs.git
```
## Usage
The `Job` class is the main entry point for building a Boltz-2 input file. You can create a job, add different molecular components, and then write the final configuration to a YAML file.
```python
from boltzjobs import Job
# 1. Create a new job
job = Job(name="Herceptin-HER2_complex_design")
# 2. Add molecular components
# Add a protein chain (HER2)
her2_chain = job.add_protein_chain(sequence="MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSR", ids="A")
# Add a second protein chain (Herceptin heavy chain)
herceptin_h = job.add_protein_chain(sequence="EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS", ids="H")
# Add a ligand using a SMILES string
# The library automatically handles single-quoting the SMILES string in the YAML output
job.add_ligand(smiles="CC(=O)N[C@@H](C)C(=O)O", ids="L")
# 3. Define constraints and properties
# Define a binding pocket for the ligand, specifying contact residues on chain A
pocket = job.add_pocket(binder="L", max_distance=6.0)
pocket.add_contact_token("A", 8)
pocket.add_contact_token("A", 12)
# Request an affinity calculation for the ligand
job.request_affinity(binder="L")
# 4. Add structural templates
job.add_template(cif="templates/1n8z.cif", chain_id="A")
# 5. Write the final YAML file
# The output will be correctly formatted for Boltz-2.
job.write_yaml("boltz_input.yaml")
print("Successfully generated boltz_input.yaml")
print("-" * 20)
print(job) # You can also print the job object for a summary
```
This will generate a `boltz_input.yaml` file with the following content:
```yaml
version: 1
sequences:
- protein:
id: A
sequence: MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSR
- protein:
id: H
sequence: EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS
- ligand:
id: L
smiles: 'CC(=O)N[C@@H](C)C(=O)O'
constraints:
- pocket:
binder: L
contacts: [[A, 8], [A, 12]]
max_distance: 6.0
templates:
- cif: templates/1n8z.cif
chain_id: A
properties:
- affinity:
binder: L
```
## License
This project is licensed under the MIT License.
## References
- [Boltz-2 GitHub Repository](https://github.com/jwohlwend/boltz)
- [Boltz-2 Input File Schema Documentation](https://github.com/jwohlwend/boltz/blob/main/docs/prediction.md)
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"description": "# boltzjobs\n\n`boltzjobs` is a Python package designed to streamline the process of creating YAML input files for [Boltz-2](https://github.com/jwohlwend/boltz).\n\nIt provides an intuitive, object-oriented interface for defining molecular sequences, constraints, and templates, and generates a correctly formatted YAML file.\n\n## Features\n\n- Define **protein**, **DNA**, and **RNA chains** with support for residue modifications.\n- Add **ligands** using either CCD codes or SMILES strings.\n- Specify geometric **constraints**, including bonds, contacts, and binding pockets.\n- Define mmCIF or PDB files as **structural templates**.\n- Request property calculations, such as **binding affinity**.\n\n## Installation\n\n```bash\npip install git+https://github.com/ugSUBMARINE/boltzjobs.git\n```\n\n## Usage\n\nThe `Job` class is the main entry point for building a Boltz-2 input file. You can create a job, add different molecular components, and then write the final configuration to a YAML file.\n\n```python\nfrom boltzjobs import Job\n\n# 1. Create a new job\njob = Job(name=\"Herceptin-HER2_complex_design\")\n\n# 2. Add molecular components\n# Add a protein chain (HER2)\nher2_chain = job.add_protein_chain(sequence=\"MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSR\", ids=\"A\")\n\n# Add a second protein chain (Herceptin heavy chain)\nherceptin_h = job.add_protein_chain(sequence=\"EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS\", ids=\"H\")\n\n# Add a ligand using a SMILES string\n# The library automatically handles single-quoting the SMILES string in the YAML output\njob.add_ligand(smiles=\"CC(=O)N[C@@H](C)C(=O)O\", ids=\"L\")\n\n# 3. Define constraints and properties\n# Define a binding pocket for the ligand, specifying contact residues on chain A\npocket = job.add_pocket(binder=\"L\", max_distance=6.0)\npocket.add_contact_token(\"A\", 8)\npocket.add_contact_token(\"A\", 12)\n\n# Request an affinity calculation for the ligand\njob.request_affinity(binder=\"L\")\n\n# 4. Add structural templates\njob.add_template(cif=\"templates/1n8z.cif\", chain_id=\"A\")\n\n# 5. Write the final YAML file\n# The output will be correctly formatted for Boltz-2.\njob.write_yaml(\"boltz_input.yaml\")\n\nprint(\"Successfully generated boltz_input.yaml\")\nprint(\"-\" * 20)\nprint(job) # You can also print the job object for a summary\n```\n\nThis will generate a `boltz_input.yaml` file with the following content:\n\n```yaml\nversion: 1\nsequences:\n - protein:\n id: A\n sequence: MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSR\n - protein:\n id: H\n sequence: EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS\n - ligand:\n id: L\n smiles: 'CC(=O)N[C@@H](C)C(=O)O'\nconstraints:\n - pocket:\n binder: L\n contacts: [[A, 8], [A, 12]]\n max_distance: 6.0\ntemplates:\n - cif: templates/1n8z.cif\n chain_id: A\nproperties:\n - affinity:\n binder: L\n```\n\n## License\n\nThis project is licensed under the MIT License.\n\n## References\n\n- [Boltz-2 GitHub Repository](https://github.com/jwohlwend/boltz)\n- [Boltz-2 Input File Schema Documentation](https://github.com/jwohlwend/boltz/blob/main/docs/prediction.md)\n",
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