Upload folder using huggingface_hub

.gitattributes

@@ -33,3 +33,6 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+conf/img/cover.png filter=lfs diff=lfs merge=lfs -text
+conf/img/fig1.png filter=lfs diff=lfs merge=lfs -text
+model/boltzgen/data/feature/__pycache__/featurizer._prepare_msa_arrays_inner-545.py311.1.nbc filter=lfs diff=lfs merge=lfs -text

.github/workflows/python-publish.yml

@@ -0,0 +1,59 @@
+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build release distributions
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      url: https://pypi.org/p/boltzgen
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

.gitignore

@@ -0,0 +1,217 @@
+scripts/bindcraft/utils.py
+.tmp_wandb
+# OneScience package runtime assets and generated outputs
+weight/*.ckpt
+weight/mols.zip
+weight/mols/
+output/
+*.ipynb
+!filter.ipynb
+!similarity.ipynb
+cache
+results
+workdir
+workbench
+.vscode/
+wandb
+tmp
+slurm_out
+small_data
+.idea
+*.pkl
+*.out
+.DS_Store
+
+# Development files
+.vscode
+outputs/
+workdir
+results
+notebooks/
+*.ckpt
+samples/
+workbench
+workdir_fold
+wandb
+tmp
+debug.txt
+*.pt
+
+# 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
+#  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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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
+
+# ruff
+.ruff_cache/
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Scratch dir
+scratch
+
+# pt and yaml files
+*.pt
+
+data/PepPC/
+data/PepPC*
+*.err
+*.csv
+data/test_set
+visualization_data_designed_only
+visualization_results_designed_only
+similarity.ipynb

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Hannes Stärk
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,282 @@
+---
+frameworks:
+- PyTorch
+language:
+- en
+license: mit
+tags:
+- OneScience
+- bioscience
+- protein-design
+- binder-design
+- BoltzGen
+tasks:
+- protein-design
+---
+
+<p align="center">
+  <strong>
+    <span style="font-size: 30px;">BoltzGen</span>
+  </strong>
+</p>
+
+# Model Introduction
+
+BoltzGen is a generative model for biomolecular binder design. Given a protein, peptide, nucleic acid, or small-molecule target together with design constraints, BoltzGen can generate candidate three-dimensional structures, perform inverse folding to generate amino acid sequences, and use Boltz-2 for structure refolding, confidence analysis, filtering, and ranking.
+
+Official project: https://github.com/HannesStark/boltzgen
+
+# Model Description
+
+The complete design pipeline consists of six stages:
+
+1. `design`: A diffusion model generates candidate three-dimensional backbones satisfying the target and design constraints;
+2. `inverse_folding`: An inverse-folding model generates amino acid sequences for the candidate backbones;
+3. `folding`: Boltz-2 predicts structures for the designed sequences;
+4. `design_folding`: The designs are folded again under the design conditions to evaluate adherence to the specified constraints;
+5. `analysis`: RMSD, confidence scores, sequence composition, and other quality metrics are calculated;
+6. `filtering`: Candidates are filtered and ranked according to predefined thresholds, and structure files, CSV files, and summary PDFs are generated.
+
+The model package contains the following major pretrained checkpoints:
+
+- `boltzgen1_diverse.ckpt`: diffusion design model emphasizing structural diversity;
+- `boltzgen1_adherence.ckpt`: diffusion design model emphasizing adherence to design conditions;
+- `boltzgen1_ifold.ckpt`: inverse-folding model for amino acid sequence generation;
+- `boltz2_conf_final.ckpt`: Boltz-2 structure prediction and confidence model;
+- `boltz2_aff.ckpt`: affinity model used for protein-small-molecule tasks.
+
+# Use Cases
+
+| Use Case | Description |
+| :---: | :--- |
+| Protein binder design | Generate binder backbones and amino acid sequences for a specified protein target. |
+| Peptide and cyclic peptide design | Generate linear peptides, cyclic peptides, disulfide-containing peptides, and related candidate structures. |
+| Antibody and nanobody design | Generate candidate designs using framework, CDR, or binding-site constraints. |
+| Small-molecule binder design | Design proteins targeting small molecules and optionally calculate affinity-related model scores. |
+| Inverse folding | Generate candidate amino acid sequences for a given protein backbone. |
+| Training pipeline validation | Use the official training entry point to validate data loading, forward propagation, loss computation, backward propagation, and parameter updates. |
+
+# Usage
+
+## 1. OneCode
+
+You can use the OneCode online environment for an intelligent one-click AI4S programming experience:
+
+[Try OneCode for AI4S Programming](https://web-2069360198568017922-iaaj.ksai.scnet.cn:58043/home)
+
+## 2. Manual Installation
+
+**Hardware Requirements**
+
+- Supports DCU devices in the OneScience DTK environment;
+- DTK/HIP devices are accessed through PyTorch's `torch.cuda` compatibility interface;
+- The complete design pipeline is recommended to run on DCU;
+- CPU execution is currently suitable mainly for package import, configuration validation, and lightweight data inspection.
+
+### Download the Model Package
+
+Install the Hugging Face command-line tool and download the model repository:
+
+```bash
+python -m pip install -U huggingface_hub
+
+hf download OneScience-Group/BoltzGen --local-dir ./BoltzGen
+cd BoltzGen
+```
+
+### Install the Runtime Environment
+
+**DCU Environment**
+
+```bash
+conda create -n onescience311 python=3.11 -y
+conda activate onescience311
+
+python -m pip install "onescience[bio-dcu]" \
+  -i http://mirrors.onescience.ai:3141/pypi/simple/ \
+  --trusted-host mirrors.onescience.ai
+```
+
+Install the additional BoltzGen dependencies on top of the OneScience environment.
+
+The `bf16-mixed` configuration used by BoltzGen cannot be parsed by the older `pytorch-lightning==1.8.6`, so PyTorch Lightning has been upgraded to `pytorch-lightning==2.5.6` in the adapted environment:
+
+```bash
+python -m pip install --no-deps -r requirements.txt
+```
+
+Verify that the BoltzGen command-line entry point can be imported successfully:
+
+```bash
+python scripts/boltzgen.py --help
+```
+
+### Weights and Molecular Dictionary Preparation
+
+The official checkpoints are stored under `weight/`:
+
+| Relative Path | Purpose |
+| --- | --- |
+| `weight/boltzgen1_diverse.ckpt` | Binder backbone diffusion model emphasizing structural diversity |
+| `weight/boltzgen1_adherence.ckpt` | Binder backbone diffusion model emphasizing adherence to design conditions |
+| `weight/boltzgen1_ifold.ckpt` | Inverse-folding model for sequence generation |
+| `weight/boltz2_conf_final.ckpt` | Boltz-2 structure prediction and confidence model |
+| `weight/boltz2_aff.ckpt` | Affinity model for protein-small-molecule tasks |
+| `weight/mols` | CCD molecular dictionary required for inference |
+
+### Minimal DCU Inference
+
+**Purpose:** Use the official `1g13` example and local checkpoints to run a complete protein binder design pipeline with one candidate.
+
+First, enable offline mode:
+
+```bash
+export HF_HUB_OFFLINE=1
+export TRANSFORMERS_OFFLINE=1
+export HF_DATASETS_OFFLINE=1
+```
+
+These environment variables prevent compute nodes from attempting to access external networks.
+
+Generate the pipeline configuration:
+
+```bash
+python scripts/boltzgen.py configure \
+  conf/example/vanilla_protein/1g13prot.yaml \
+  --output output/dcu_minimal \
+  --protocol protein-anything \
+  --num_designs 1 \
+  --budget 1 \
+  --devices 1 \
+  --num_workers 0 \
+  --use_kernels false \
+  --moldir weight/mols \
+  --design_checkpoints \
+    weight/boltzgen1_diverse.ckpt \
+    weight/boltzgen1_adherence.ckpt \
+  --inverse_fold_checkpoint weight/boltzgen1_ifold.ckpt \
+  --folding_checkpoint weight/boltz2_conf_final.ckpt
+```
+
+This command only generates the stage-specific configuration files under:
+
+```text
+output/dcu_minimal/config/
+```
+
+It does not execute model inference.
+
+Successful configuration indicates that the design input, checkpoint paths, molecular dictionary, and pipeline parameters can be parsed correctly.
+
+Execute the complete pipeline:
+
+```bash
+python scripts/boltzgen.py execute output/dcu_minimal
+```
+
+This command executes all six configured stages.
+
+If every stage exits with code `0`, the end-to-end engineering pipeline is operational. Whether the final candidates are useful designs must still be evaluated using the filtering CSV files, structural quality metrics, and experimental validation.
+
+For protein-small-molecule protocols, add the following option during configuration:
+
+```text
+--affinity_checkpoint weight/boltz2_aff.ckpt
+```
+
+This enables the affinity checkpoint.
+
+The resulting affinity-related values are intended for model-based evaluation and candidate comparison and should not be interpreted directly as experimentally measured binding constants.
+
+### Stage-Specific Recovery
+
+**Purpose:** Reuse existing configuration files and intermediate results when a pipeline is interrupted or only one stage needs to be rerun.
+
+For example, to rerun only the final filtering stage:
+
+```bash
+python scripts/boltzgen.py execute output/dcu_minimal --steps filtering
+```
+
+After successful execution, the command regenerates the ranking table, candidate structures, and summary PDF under:
+
+```text
+output/dcu_minimal/final_ranked_designs/
+```
+
+Successful filtering does not necessarily mean that any candidate passes the default thresholds. The number of accepted candidates and the specific failed metrics should also be inspected.
+
+### Inference Outputs
+
+The main output structure is:
+
+```text
+output/dcu_minimal/
+├── config/                         # Actual configuration for the six pipeline stages
+├── design/                         # Candidate backbones generated by the diffusion models
+├── inverse_folding/                # Sequences generated by inverse folding
+├── folding/                        # Refolded sequence structures
+├── design_folding/                 # Design-conditioned refolding results
+├── analysis/                       # Candidate quality metrics
+└── final_ranked_designs/           # Ranked candidates, structures, and summary PDF
+```
+
+Use `final_ranked_designs/` to inspect candidate rankings and quality summaries.
+
+The absence of NaN or Inf values in structural coordinates only indicates that the numerical output is valid. It does not by itself establish structural plausibility, binding activity, or experimental validity.
+
+### Minimal Training Pipeline
+
+BoltzGen provides an official PyTorch Lightning training entry point for the following model configurations:
+
+| Configuration | Trainable Model |
+| --- | --- |
+| `inverse_folding.yaml` | Inverse-folding sequence generation model |
+| `boltzgen_small.yaml` | Small BoltzGen structural diffusion model |
+| `boltzgen.yaml` | Large BoltzGen structural diffusion model |
+
+Run the prepared minimal training configuration:
+
+```bash
+python scripts/train.py conf/train_boltzgen_small_smoke.yaml
+```
+
+This command invokes the official training entry point.
+
+If one batch completes successfully and the process exits with code `0`, the following components have been validated:
+
+- DataLoader;
+- Feature construction;
+- Forward propagation;
+- Loss computation;
+- Backward propagation;
+- `optimizer.step`.
+
+This smoke test only verifies that the training pipeline is executable. It does not indicate model convergence or usable prediction quality.
+
+Formal training requires data in the official BoltzGen format, including:
+
+```text
+targets/structures/
+targets/records/
+manifest.json
+MSA
+mols
+```
+
+Legacy OpenFold structure NPZ files require field-level compatibility conversion before they can be used by the BoltzGen training pipeline.
+
+The complete training dataset must therefore be prepared according to the official BoltzGen data schema.
+
+# OneScience Official Resources
+
+| Platform | OneScience Main Repository | Skills Repository |
+| --- | --- | --- |
+| Gitee | https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills |
+| GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills |
+
+# Citation and License
+
+- Official implementation: https://github.com/HannesStark/boltzgen
+- The upstream BoltzGen source code is distributed under the MIT License. See the top-level `LICENSE` file for details.
+- Model checkpoints, RCSB PDB-derived data, OpenFold-derived data, training datasets, and other third-party assets remain subject to their respective original licenses, copyright notices, and terms of use.

conf/config.json

@@ -0,0 +1,18 @@
+{
+  "protocol": "protein-anything",
+  "design_spec": "conf/example/vanilla_protein/1g13prot.yaml",
+  "output": "output/dcu_minimal",
+  "devices": 1,
+  "num_workers": 0,
+  "num_designs": 1,
+  "budget": 1,
+  "use_kernels": false,
+  "weights": {
+    "design_diverse": "weight/boltzgen1_diverse.ckpt",
+    "design_adherence": "weight/boltzgen1_adherence.ckpt",
+    "inverse_fold": "weight/boltzgen1_ifold.ckpt",
+    "folding": "weight/boltz2_conf_final.ckpt",
+    "affinity": "weight/boltz2_aff.ckpt"
+  },
+  "moldir": "weight/mols"
+}

conf/example/README.md

@@ -0,0 +1,434 @@
+# How to make a design specification .yaml
+
+
+**IMPORTANT:** ⚠️ All residue indices are specified **starting at 1** and we use the canonical mmcif residue index `label_asym_id`, and **not** the `auth_asym_id` author residue index! 
+You can check the indexing in your mmcif file by opening it in https://molstar.org/viewer/, hovering over a residue, and checking the index on the bottom right. You will see something like this where **41 is the index we use, the auth id 22 is incorrect**:
+
+![](../assets/label_seq_id.png)
+
+After you constructed your `.yaml` file we recommend that you run the `check` command on it:
+1. Run `boltzgen check example/vanilla_peptide_with_target_binding_site/beetletert.yaml`.  
+2. Visualize the resulting mmcif file in a protein structure viewer (e.g. PyMOL, Chimera, or online: https://molstar.org/viewer/).
+3. Your viewer should show the binding site in a different color than the rest of the target. 
+
+
+# Example based explanation:
+We provide many example `.yaml` files in the `example/` directory, including:
+
+- [design_spec_showcasing_all_functionalities.yaml](design_spec_showcasing_all_functionalities.yaml)
+- [vanilla_peptide_with_target_binding_site/beetletert.yaml](vanilla_peptide_with_target_binding_site/beetletert.yaml)
+- [peptide_against_specific_site_on_ragc/rragc.yaml](peptide_against_specific_site_on_ragc/rragc.yaml)
+- [nanobody/penguinpox.yaml](nanobody/penguinpox.yaml)
+- [fab_targets/pdl1.yaml](fab_targets/pdl1.yaml)
+- [denovo_zinc_finger_against_dna/zinc_finger.yaml](denovo_zinc_finger_against_dna/zinc_finger.yaml)
+- [protein_binding_small_molecule/chorismite.yaml](protein_binding_small_molecule/chorismite.yaml)
+- [small_molecule_from_file_and_smiles/4g37.yaml](small_molecule_from_file_and_smiles/4g37.yaml)
+
+Small example of a protein design against a target protein without binding site specified:
+```yaml
+entities:
+  # Designed protein with between 80 and 140 residues 
+  # (The length is randomly sampled)
+  - protein: 
+      id: B
+      sequence: 80..140
+
+  # The target is extracted from a .cif file
+  - file:
+      path: hard_targets/6m1u.cif
+
+      # Which chain in the .cif file to use as target (uses all chains if unspecified)
+      include: 
+        - chain:
+            id: A
+```
+
+**IMPORTANT:** ⚠️ File references inside a yaml file (e.g. to cif files) are interpreted relative to the directory of the yaml file.
+
+
+Example highlighting many (not all) functionalities:
+```yaml
+entities:
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: 8r3a.cif
+      
+      # Which chain and residues in the .cif file to use as target (uses all chains if unspecified)
+      include: 
+        - chain:
+            id: A
+            res_index: 2..50,55.. # residues between 2 and 50 and anything larger than 55
+        - chain:
+            id: B
+
+      # Which regions of the target the design should or should NOT
+      # bind to (this can be left unspecified, then we just bind anywhere)
+      binding_types:
+        - chain:
+            id: A
+            binding: 5..7,13
+        - chain:
+            id: B
+            not_binding: "all" 
+      
+      # Which regions of the target should have their structure specified.
+      # By default, everything is visibility 1 which means that the structure is specified.
+      # If the visibility is 0, then the structure is not specified.
+      structure_groups:
+        - group:
+            visibility: 1
+            id: A
+            res_index: 10..13
+        - group:
+            # The relative positioning of things in structure group 2
+            # is not specified w.r.t to things in structure group 1
+            visibility: 2 
+            id: B
+        # Overwrite the previous visibility setting and set it to 0 for res_index 13
+        - group:
+            visibility: 0
+            id: A
+            res_index: 13 
+
+      # Optionally you can say that some residues in a loaded .cif file should also be redesigned.
+      design:
+        - chain:
+            id: A
+            res_index: 14..19
+
+      # For designed regions you can say what secondary structure they should have
+      secondary_structure:
+        - chain:
+            id: A
+            loop: 14
+            helix: 15..17
+            sheet: 19
+
+  # Specify a NON-designed protein chain
+  - protein: 
+      id: X
+      sequence: AAVTTTTPPP
+
+  # Specify a designed protein chain 
+  # Numbers specify what is being designed
+  - protein: 
+      id: G
+      # random number between 15 and 20 of designed residues (inclusive)
+      sequence: 15..20AAAAAAVTTTT18PPP 
+
+  # A designed helical peptides with WHL staple 
+  # (see the constraints below that connect the peptide with the WHL ligand)
+  - protein: 
+      id: R
+      # Random number of design residues between 3 and 5,
+      # then a Cysteine, then 6 design residues, then ...
+      sequence: 3..5C6C3 
+  - ligand:
+      id: Q
+      ccd: WHL
+  
+  # A designed peptide with 17 residues
+  - protein:
+      id: H
+      sequence: 17
+
+  # specification for a designed peptide with two Cys and a disulfide bond (see constraints)
+  - protein:
+      id: S
+      sequence: 10..14C6C3
+
+constraints:
+    # specify connections as if the minimum possible number of residues was sampled
+  - bond:
+      atom1: [R, 4, SG] # connection for a helical peptides with WHL staple  between small molecule and designed peptide
+      atom2: [Q, 1, CK]
+  - bond:
+      atom1: [R, 11, SG] # connection for a helical peptides with WHL staple  between small molecule and designed peptide
+      atom2: [Q, 1, CH]
+  - bond:
+      atom1: [S, 11, SG] # connection for a disulfide bond between Cys and Cys in designed peptide
+      atom2: [S, 18, SG]
+
+```
+
+
+# Detailed Explanation
+
+```yaml
+entities:
+  # Define proteins, ligands, and structure files
+  - protein: ...
+  - ligand: ...
+  - file: ...
+
+constraints:
+  # Define bonds and total length constraints
+  - bond: ...
+  - total_len: ...
+```
+
+### Entities Section
+
+The `entities` section defines all the components of your design:
+
+#### Protein Sequences
+
+Define custom protein sequences with design flexibility:
+
+```yaml
+entities:
+  - protein:
+      id: G                   # Unique identifier 
+      sequence: 15..20AAAAAAVTTTT18PPP  # Mix of fixed residues and design regions
+      binding_types: uuuuBBBuNNNuBuu    # Binding specifications (optional)
+      secondary_structure: HHHLLLEEE     # Secondary structure constraints for designed regions (optional)
+```
+
+**Sequence notation:**
+- `15..20` - Design between 15-20 residues (inclusive)
+- `AAAA` - Fixed amino acid sequence
+- `18` - Design exactly 18 residues
+- `3..5C6C3` - Variable design residues, then fixed Cys, then more design
+
+**Binding types:**
+- `B` - Binding residue
+- `N` - Non-binding residue  
+- `u` - Unspecified (default)
+- Can specify as string: `uuuuBBBuNNNuBuu`
+- Or as ranges:
+  ```yaml
+  binding_types:
+    binding: 5..7,13      # Residues 5-7 and 13 are binding
+    not_binding: 9..11    # Residues 9-11 are non-binding
+  ```
+
+#### Ligands
+
+Define small molecule ligands using CCD codes or SMILES:
+
+```yaml
+# Using Chemical Component Dictionary (CCD) code
+entities:
+  - ligand:
+      id: [E, F] # specify list of IDs to copy the entity
+      ccd: WHL
+      binding_types: B
+
+# Using SMILES string
+entities:
+  - ligand:
+      id: Q
+      smiles: 'N[C@@H](Cc1ccc(O)cc1)C(=O)O'
+      binding_types: B
+```
+
+#### Structure Files
+
+Include existing protein structures from PDB/mmCIF files:
+
+```yaml
+entities:
+  - file:
+      path: 7rpz.cif
+      
+      # Include specific chains
+      include:
+        - chain:
+            id: A
+        - chain:
+            id: B
+      
+      # Include by proximity
+      include_proximity:
+        - chain:
+            id: A
+            res_index: 10..16
+            radius: 35
+      
+      # Exclude specific regions
+      exclude:
+        - chain:
+            id: A
+            res_index: ..5    # Exclude residues 1-5
+      
+      # Reset residue numbering
+      reset_res_index:
+        - chain:
+            id: A
+```
+
+
+# Advanced Options 
+
+**Design regions:** Specify which residues to redesign
+
+```yaml
+entities:
+  ...
+  - file:
+    ...
+    design:
+      - chain:
+          id: A
+          res_index: ..4,20..27  # Redesign residues 1-4 and 20-27
+```
+
+**Secondary structure constraints:**
+```yaml
+entities:
+  ...
+  - protein:
+    ...
+    secondary_structure:
+      - chain:
+          id: A
+          loop: 1        # Residue 1 should be loop
+          helix: 2..3    # Residues 2-3 should be helix
+          sheet: 4       # Residue 4 should be sheet
+```
+
+**Structure visibility groups:**
+```yaml
+entities:
+  ...
+  - file:
+    ...
+    structure_groups:
+      - group:
+          visibility: 1    # Visibility level (0=hidden, 1=visible, 2=highlighted)
+          id: A
+          res_index: 10..16
+```
+
+**Design insertions:**
+```yaml
+entities:
+  ...
+  - file:
+    ...
+    design_insertions:
+      - insertion:
+          id: A
+          res_index: 20              # Insert after residue 20
+          num_residues: 2..9         # Insert 2-9 residues
+          secondary_structure: HELIX  # UNSPECIFIED, LOOP, HELIX, or SHEET
+```
+
+**Binding type specifications:**
+```yaml
+entities:
+  ...
+  - protein:
+    ...
+    binding_types:
+      - chain:
+          id: A
+          binding: 5..7,13
+      - chain:
+          id: B
+          not_binding: "all"
+```
+
+### Constraints Section
+
+Define structural constraints between components:
+
+#### Bond Constraints
+
+Create covalent bonds between specific atoms:
+
+```yaml
+constraints:
+  - bond:
+      atom1: [R, 4, SG]   # [chain_id, residue_number, atom_name]
+      atom2: [Q, 1, CK]   # Connect sulfur of Cys-4 in chain R to atom CK in ligand Q
+```
+
+We now support constraints specifications of small molecules from the input file and from smiles. Check `examples/small_molecule_from_file_and_smiles/4g37.yaml`. Below is brief guidelines:
+* Small molecules from the file: check `atom_name` from the CCD and specify it.
+* Small molecules from the smiles: count index of target element from the smiles and specify its element type with index (e.g. C6, for 6th carbon from the smiles).
+
+Here is a comprehensive list of all the keys from your YAML file with explanations for each.
+
+***
+
+### Top-Level Keys
+
+* `entities`: The main list containing all molecular components of the system, such as proteins, ligands, or imported files.
+* `constraints`: A list of rules or conditions to apply to the system, like specific bonds between entities or total length restrictions.
+
+---
+
+### Entity Types (Keys within the `entities` list)
+
+* `protein`: Defines a protein entity.
+* `ligand`: Defines a small molecule ligand.
+* `file`: Specifies an external structure file (e.g., a `.cif` file) to import parts of the system from.
+
+---
+
+### Keys for `protein` Entities
+
+* `id`: A unique identifier for the protein chain (e.g., 'A', 'G').
+* `sequence`: Defines the amino acid sequence of the protein. This can include numbers to specify lengths of residues to be designed.
+* `secondary_structure`: Specifies the secondary structure of the protein.
+* `binding_types`: Defines which residues are involved in binding. Can be a string or a more detailed dictionary.
+* `cyclic`: A boolean (`true` or `false`) indicating if the protein is cyclic.
+
+---
+
+### Keys for `ligand` Entities
+
+* `id`: A unique identifier for the ligand. Can be a single ID or a list of IDs.
+* `ccd`: The Chemical Component Dictionary ID for the ligand (e.g., 'SAH').
+* `smiles`: The SMILES string representing the ligand's chemical structure.
+* `binding_types`: Specifies binding information, often a simple character like 'B' for binding.
+
+---
+
+### Keys for `file` Entities
+
+* `path`: The file path to the structure file to be included (e.g., 'example/7rpz.cif').
+* `msa`: A global flag for Multiple Sequence Alignment for the chains in the file. Can be overwritten by individual chain settings.
+* `include`: Specifies which parts of the file to include. Can be the string `"all"` or a list of chains.
+* `exclude`: Specifies which parts of an included file to exclude.
+* `fuse`: Specifies a chain to which subsequent protein entities will be fused.
+* `include_proximity`: Includes residues from the file that are within a certain distance of a specified chain.
+* `binding_types`: Defines binding interactions for specific chains within the file.
+* `structure_groups`: Defines groups of residues for visualization or other purposes.
+* `design`: Specifies which residues in the included chains are designable.
+* `secondary_structure`: Defines the secondary structure for specific residues within included chains.
+* `design_insertions`: Specifies where to insert new designable residues.
+
+---
+
+### Keys for `constraints`
+
+* `bond`: Defines a covalent bond to be formed between two specified atoms in the system.
+    * `atom1`: The first atom in the bond.
+    * `atom2`: The second atom in the bond.
+* `total_len`: Constrains the total length of the polymeric system.
+    * `min`: The minimum allowed total length.
+    * `max`: The maximum allowed total length.
+
+---
+
+### Nested Keys (found within multiple entity types)
+
+* `chain`: A sub-dictionary used in `include`, `exclude`, `binding_types`, `design`, and `secondary_structure` to specify a particular protein chain.
+    * `id`: The identifier of the chain.
+    * `msa`: A specific MSA setting for this chain, overriding the global `msa` flag.
+    * `res_index`: Specifies a range or list of residue indices.
+    * `radius`: Used in `include_proximity` to define a distance in Angstroms.
+    * `binding`: Specifies residues that are part of a binding site.
+    * `not_binding`: Specifies residues that are not part of a binding site.
+    * `loop`, `helix`, `sheet`: Used in `secondary_structure` to define the structure of specific residues.
+* `group`: Used in `structure_groups` to define a residue group.
+    * `id`: The identifier of the chain or `"all"`.
+    * `visibility`: A numerical value to control how the group is displayed.
+    * `res_index`: The residues included in this group.
+* `insertion`: Used in `design_insertions`.
+    * `id`: The chain ID where the insertion occurs.
+    * `res_index`: The residue index after which the insertion is made.
+    * `num_residues`: The number or range of residues to be inserted.
+    * `secondary_structure`: The desired secondary structure for the inserted residues (e.g., `HELIX`).

conf/example/binding_disordered_peptides/tpp4.yaml

@@ -0,0 +1,11 @@
+entities:
+  # Specify a designed protein chain 
+  # random number between 120 and 140 of designed residues (inclusive)
+  - protein:
+      id: A
+      sequence: 120..140
+  # Specify a non-designed protein chain
+  # fixed 20-mer, all residues fixed
+  - protein:
+      id: B
+      sequence: GGGILPWKWPWWPWRRGGG

conf/example/binding_disordered_regions_of_proteins/hoxd13.yaml

@@ -0,0 +1,55 @@
+entities:
+  # Specify a designed protein chain 
+  - protein:
+      id: B
+      # random number between 40 and 80 of designed residues (inclusive)
+      sequence: 40..80
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      # path to the target structure
+      path: hoxd13.cif
+      # Which chain and residues in the .cif file to use as target (uses only A: 1..71 here)
+      include: 
+        - chain:
+            id: A 
+            res_index: ..71
+      # Which regions of the target should have their structure specified
+      # Here we hide the entire target fragment (no coordinates specified)
+      structure_groups:
+        - group:
+            visibility: 0 
+            id: "all"
+      # Which regions of the target the design should or should NOT bind to
+      # Here we specify that the design should bind to residues 57..71 on chain A
+      binding_types:
+        - chain:
+            id: A
+            binding: 57..71
+
+  # Specify a non-designed protein chain fused to chain A
+  - protein:
+      id: C
+      fuse: A
+      # fixed 8-mer, all residues fixed, and all residues marked as binding
+      sequence: AAAAAAAA
+      binding_types: BBBBBBBB
+
+  # Continue pulling from the rest of chain A of the same file and fuse it to chain A
+  - file:
+      path: hoxd13.cif
+      # Subsequently included residues are fused onto chain A
+      fuse: A
+      # Include the remainder of chain A (residue 72 to the end)
+      include:
+        - chain:
+            id: A
+            res_index: 72..
+      # Start with all hidden, then explicitly show structure of a tail segment (281 to the end)
+      structure_groups:
+        - group:
+            visibility: 0
+            id: "all"
+        - group:
+            visibility: 1
+            id: A
+            res_index: 281..

conf/example/binding_disordered_regions_of_proteins/npm1.yaml

@@ -0,0 +1,28 @@
+entities:
+  # Specify a designed protein chain 
+  - protein:
+      id: G
+      # random number between 40 and 80 of designed residues (inclusive)
+      sequence: 40..80
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: npm1.cif
+      # Which chain and residues in the .cif file to use as target (uses only chain A here)
+      include:
+        - chain:
+            id: A
+      # Which regions of the target the design should or should NOT bind to
+      # Here we specify that the design should bind to residues 123..240 on chain Aand not bind to residues 1..122 on chain A
+      binding_types:
+        - chain:
+            id: A
+            binding: 123..240
+            not_binding: 1..122
+      # Which regions of the target should have their structure specified
+      # Here we keep structure specified (visible) for two disjoint segments of chain A
+      structure_groups:
+        - group:
+            visibility: 1
+            id: A
+            res_index: 12..118, 243..291
+        

conf/example/binding_disordered_regions_of_proteins/nup98.yaml

@@ -0,0 +1,20 @@
+entities:
+  # Specify a designed protein chain 
+  # random number between 40 and 80 of designed residues (inclusive)
+  - protein:
+      id: G
+      sequence: 40..80
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: nup98.cif
+      # Which chain and residues in the .cif file to use as target (uses only A: 1..400 here)
+      include:
+        - chain:
+            id: A
+            res_index: 1..400
+      # Which regions of the target should have their structure specified
+      # Here we hide the entire included target fragment (no coordinates specified)
+      structure_groups:
+        - group:
+            visibility: 0
+            id: "all"

conf/example/cyclic_against_hiv_antibody_site/9d3d.yaml

@@ -0,0 +1,40 @@
+entities:
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: 9d3d.cif
+      # Which chain and residues in the .cif file to use as target
+      # Here we include chains A, B, and C (all residues on each chain)
+      include:
+        - chain:
+            id: A
+        - chain:
+            id: B
+        - chain:
+            id: C
+      # Include residues that are within a radius of a reference region
+      # Here we include residues within a radius 30 of G:106..118
+      include_proximity:
+        - chain: 
+            id: G
+            res_index: 106..118
+            radius: 30
+      # Which regions of the target the design should or should NOT bind to
+      # Here we specify that the design should bind to residues 91, 128, and 131 on chains A, B, and C
+      binding_types:
+        - chain:
+            id: A
+            binding: 91,128,131
+        - chain:
+            id: B
+            binding: 91,128,131
+        - chain:
+            id: C
+            binding: 91,128,131
+
+  # Specify a designed protein chain
+  # random number between 8 and 18 of designed residues (inclusive)
+  - protein:
+      id: E
+      sequence: 8..18
+      # Make the designed protein chain cyclic
+      cyclic: True

conf/example/cyclotide/3ivq.yaml

@@ -0,0 +1,34 @@
+entities:
+  # Specify a designed protein chain
+  - protein: 
+      id: B
+      # 3 design residues, Cystein, 8 design residues, Cystein, 
+      # 6 design residues, Cystein, 5 design residues, Cystein, 
+      # 3 design residues, Cystein, 1 design residue, Cystein, 2 design residues
+      sequence: 3C8C6C5C3C1C2
+      # Make the designed peptide cyclic
+      cyclic: true
+
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: 3ivq.cif
+      # Which chain and residues in the .cif file to use as target (here includes all residues on chain A)
+      include:
+        - chain:
+            id: A
+
+      # Which regions of the target should have their structure specified
+      # Here we specify that all included target residues should have their structure specified
+      structure_groups: "all"
+
+constraints:
+  # Specify covalent disulfide bonds between the designed residues on chain B 
+  - bond:
+      atom1: [B, 4, SG]  # connect SG of residue 4 to SG of residue 26 on chain B
+      atom2: [B, 26, SG] 
+  - bond:
+      atom1: [B, 13, SG]  # connect SG of residue 13 to SG of residue 30 on chain B
+      atom2: [B, 30, SG] 
+  - bond:
+      atom1: [B, 20, SG]  # connect SG of residue 20 to SG of residue 32 on chain B
+      atom2: [B, 32, SG] 

conf/example/cyclotide/5wrd.yaml

@@ -0,0 +1,34 @@
+entities:
+  # Specify a designed protein chain
+  # 3 design residues, Cystein, 8 design residues, Cystein, 
+  # 6 design residues, Cystein, 5 design residues, Cystein, 
+  # 3 design residues, Cystein, 1 design residue, Cystein, 2 design residues
+  - protein: 
+      id: B
+      sequence: 3C8C6C5C3C1C2
+      # Make the designed peptide cyclic
+      cyclic: true
+
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: 5wrd.cif
+      # Which chain and residues in the .cif file to use as target (here all residues on chain A)
+      include:
+        - chain:
+            id: A
+
+      # Which regions of the target should have their structure specified
+      # Here we specify that all included target residues should have their structure specified
+      structure_groups: "all"
+
+constraints:
+  # Specify covalent difulside bonds within designed chain B 
+  - bond:
+      atom1: [B, 4, SG]  # connect SG of residue 4 to SG of residue 26 on chain B
+      atom2: [B, 26, SG]
+  - bond:
+      atom1: [B, 13, SG]  # connect SG of residue 13 to SG of residue 30 on chain B
+      atom2: [B, 30, SG]
+  - bond:
+      atom1: [B, 20, SG]  # connect SG of residue 20 to SG of residue 32 on chain B
+      atom2: [B, 32, SG]

conf/example/cylcic_against_kras_with_specific_site/cyclicdesign.yaml

@@ -0,0 +1,26 @@
+entities:
+  # Specify a designed protein chain
+  # random number between 8 and 16 of designed residues (inclusive)
+  - protein: 
+      id: B
+      sequence: 8..16
+      # Make the designed peptide cyclic
+      cyclic: true
+
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: 8jjs.cif
+      # Which chain and residues in the .cif file to use as target
+      # Here we include chains A and C (all residues on each chain)
+      include: 
+        - chain:
+            id: A
+        - chain:
+            id: C
+      # Which regions of the target the design should or should NOT bind to
+      # Here we specify discrete binding residues on chain A
+      binding_types:
+        - chain:
+            id: A
+            binding: 12,14,61,63,73,76,77,83,101,104,108
+          

conf/example/denovo_zinc_finger_against_dna/vanilla_protein.yaml

@@ -0,0 +1,16 @@
+entities:
+  # Specify a designed protein chain
+  # random number between 40 and 120 of designed residues (inclusive)
+  - protein: 
+      id: G
+      sequence: 40..120
+
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: zf.cif
+      include: 
+        # Which chain and residues in the .cif file to use as target (here includes all residues on chains C1 and B1)
+        - chain:
+            id: C1
+        - chain:
+            id: B1

conf/example/denovo_zinc_finger_against_dna/zinc_finger.yaml

@@ -0,0 +1,40 @@
+entities:
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: zf.cif
+      # Which parts of the .cif file to include as target (here includes all chains/residues)
+      include: "all" 
+      # Which parts of the included content to exclude (here excludes residues 10, 63..69, and 185.. in chain A1)
+      exclude:
+        - chain:
+            id: A1
+            res_index: ..10,63..69,185..
+      # Where to insert new designable residues into existing chains
+      # Here we insert 3..8 residues after residue 63 in chain A1
+      design_insertions:
+        - insertion:
+            id: A1
+            res_index: 63 
+            num_residues: 3..8
+      # Which regions of the target should have their structure specified
+      # Here we hide everything (no structure specified)
+      structure_groups:
+        - group:
+            visibility: 0
+            id: "all"
+      # Which residues in the target should be redesigned
+      # Here we declare A1:11..184 to be redesigned
+      design:
+        - chain:
+            id: A1
+            res_index: 11..184
+      # Which residues in the target are explicitly not redesignable (override entries in design)
+      # Here we carve out fixed positions on chain A1 to not be redesigned
+      not_design:
+        - chain:
+            id: A1
+            res_index: 11..20,29,33,39..48,57,61,72..81,90,94,100..109,118,122,129..138,147,151,157..166,175,179
+      # Reset residue numbering to be contiguous for chain A1
+      reset_res_index:
+        - chain:
+            id: A1

conf/example/design_spec_showcasing_all_functionalities.yaml

@@ -0,0 +1,191 @@
+entities:
+  - protein:
+      id: G
+      sequence: 15..20AAAAAAVTTTT18PPP # range between 15 and 20 inclusive on both sides
+      residue_constraints:
+        - position: 1
+          allowed: A # Only Alanine at position 1
+        - position: 3..5
+          disallowed: CM # No Cysteine or Methionine at positions 3-5
+        - position: 8
+          allowed: AGS # Only Ala, Gly, or Ser at position 8
+  - protein: 
+      id: R
+      sequence: 3..5C6C3 # Random number of design residues between 3 and 5, then a Cystein, then 6 design residues, then ...
+  - ligand:
+      id: Q
+      ccd: WHL
+  - protein:
+      id: H
+      sequence: 17
+      secondary_structure: # No secondary structure specified, defaults 
+  - file:
+      path: 7rpz.cif
+       
+      include: 
+        - chain:
+            id: A
+        - chain:
+            id: B
+
+      include_proximity:
+        - chain: 
+            id: A
+            res_index: 10..16
+            radius: 35
+
+      binding_types:
+        - chain:
+            id: A
+            binding: 5..7,13
+        - chain:
+            id: B
+            not_binding: "all" 
+          
+
+
+      structure_groups:
+        - group:
+            visibility: 1
+            id: A
+            res_index: 10..16
+        - group:
+            visibility: 2
+            id: B
+        - group:
+            visibility: 0
+            id: A
+            res_index: 13
+
+      design:
+        - chain:
+            id: A
+            res_index: ..4,20..27
+
+      secondary_structure:
+        - chain:
+            id: A
+            loop: 1
+            helix: 2..3
+            sheet: 4
+        
+      design_insertions:
+        - insertion:
+            id: A
+            res_index: 20 # The 20th residue will be a designed one (starting to count from 1)
+            num_residues: 2..9
+            secondary_structure: HELIX # One of UNSPECIFIED (default), LOOP, HELIX, SHEET. 
+
+  - protein: 
+      id: A
+      sequence: AAAAAAAAAAAAAAAAAAAAAAAA
+      binding_types: uuuuBBBuNNNuBuu # the missing specifications will be 'u' by default
+  - file:
+      path: 7rpz.cif
+      fuse: A
+      include: 
+        - chain:
+            id: A
+            res_index: ..5
+            
+  - protein:
+      id: B
+      sequence: AAAAAAAAAAAAAAAAAAAAAAAA
+      binding_types:
+        binding: 5..7,13
+        not_binding: 9..11
+  - ligand:
+      id: [C, D]
+      ccd: SAH
+  - ligand:
+      id: [E, F]
+      smiles: 'N[C@@H](Cc1ccc(O)cc1)C(=O)O'
+      binding_types: B
+
+
+  - file:
+      path: 7rpz.cif
+      include: "all"
+      exclude: 
+        - chain:
+            id: A
+            res_index: ..5
+
+      structure_groups:
+        - group:
+            visibility: 1
+            id: "all"
+
+        - group:
+            visibility: 0
+            id: A
+            res_index: 10..16
+  - file:
+      path: 8r3a.cif
+       
+      include: 
+        - chain:
+            id: A
+        - chain:
+            id: B
+
+      binding_types:
+        - chain:
+            id: A
+            binding: 5..7,13
+        - chain:
+            id: B
+            not_binding: "all" 
+          
+
+
+      structure_groups:
+        - group:
+            visibility: 1
+            id: A
+            res_index: 10..13
+        - group:
+            visibility: 2
+            id: B
+        - group:
+            visibility: 0
+            id: A
+            res_index: 13
+
+      design:
+        - chain:
+            id: A
+            res_index: 14..19
+
+      secondary_structure:
+        - chain:
+            id: A
+            loop: 14
+            helix: 15..17
+            sheet: 19
+  - protein:
+      id: S
+      sequence: 10C6C3
+  - protein:
+      id: T
+      sequence: C10C6C3C
+      cyclic: true
+
+constraints:
+    # specify connections as if the minimum possible number of residues was sampled
+  - bond:
+      atom1: [R, 4, SG] # connection for a helical peptides with WHL staple 
+      atom2: [Q, 1, CK]
+  - bond:
+      atom1: [R, 11, SG]
+      atom2: [Q, 1, CH]
+  - bond:
+      atom1: [S, 11, SG] # connection for a disulfide bond
+      atom2: [S, 18, SG]
+  - bond:
+      atom1: [T, 12, SG]
+      atom2: [T, 19, SG]
+
+  - total_len:
+      min: 10
+      max: 20

conf/example/disulfide_peptide_with_betahairpin_conditioning/cropped_target.yaml

@@ -0,0 +1,33 @@
+entities:
+  # Specify a designed protein chain
+  # 1 design residue, Cystein, 11..16 design residues, Cystein, 1 design residue, Cystein
+  - protein:
+      id: B
+      sequence: 1C11..16C1
+      # Specify the secondary structure of the designed peptide (here we require sheet at residues 1 and 3..11)
+      secondary_structure:
+          sheet: 1,3..11
+
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: 7nre.cif
+      # Which chain and residues in the .cif file to use as target (here includes residues 24..on chain A)
+      include:
+        - chain:
+            id: A
+            res_index: 24..
+      
+      # Which regions of the target the design should or should NOT bind to
+      # Here we specify that the design should bind to residues 26..31,381,408 on chain A
+      binding_types:
+        - chain:
+            id: A
+            binding: 26..31,381,408
+  
+
+constraints:
+  # Specify covalent disulfide bonds between the designed residues on chain B 
+  - bond:
+      atom1: [B, 2, SG]  # connect SG of residue 2 to SG of residue 14 on chain B
+      atom2: [B, 14, SG]
+

conf/example/disulfide_peptide_with_betahairpin_conditioning/proximity_cropped_target.yaml

@@ -0,0 +1,43 @@
+entities:
+  # Specify a designed protein chain
+  # 1 design residue, Cystein, 11..16 design residues, Cystein, 1 design residue, Cystein
+  - protein:
+      id: B
+      sequence: 1C11..16C1
+      # Specify the secondary structure of the designed peptide (here we require sheet at residues 1 and 3..11)
+      secondary_structure:
+          sheet: 1,3..11
+
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: 7nre.cif
+      # Which chain and residues in the .cif file to use as target (here includes residues 24..on chain A)
+      include:
+        - chain:
+            id: A
+            res_index: 24..
+      
+      # Which regions of the target the design should or should NOT bind to
+      # Here we specify that the design should bind to residues 26..31,381,408 on chain A
+      binding_types:
+        - chain:
+            id: A
+            binding: 26..31,381,408
+
+      # Include residues within a radius of a reference region
+      # Here we include residues within a radius 28 of residues 26..31,381,408 on chain A
+      include_proximity:
+        - chain: 
+            id: A
+            res_index: 26..31,381,408
+            radius: 28
+
+      
+  
+
+constraints:
+  # Specify covalent disulfide bonds between the designed residues on chain B 
+  - bond:
+      atom1: [B, 2, SG]  # connect SG of residue 2 to SG of residue 14 on chain B
+      atom2: [B, 14, SG]
+

conf/example/double_disulfide_peptide_against_specific_site/norepinephrine.yaml

@@ -0,0 +1,29 @@
+entities:
+  # Specify a designed protein chain
+  # 1..3 design residues, Cystein, Cystein, 4 design residues, Cystein, 1..3 design residues, Cystein, 1..3 design residues
+  - protein:
+      id: B
+      sequence: 1..3CC4C1..3C1..3
+  # Specification of the target which is extracted from a .cif file
+  - file:
+      path: 8wtw.cif
+      # Which chain and residues in the .cif file to use as target (here includes all residues on chain A)
+      include: 
+        - chain:
+            id: A
+
+      # Which regions of the target the design should or should NOT bind to
+      # Here we specify that the design should bind to residue 24 on chain A
+      binding_types:
+        - chain:
+            id: A
+            binding: 24
+          
+constraints:
+  # Specify covalent disulfide bonds between the designed residues on chain B 
+  - bond:
+      atom1: [B, 2, SG]  # connect SG of residue 2 to SG of residue 10 on chain B 
+      atom2: [B, 10, SG]
+  - bond:
+      atom1: [B, 3, SG]  # connect SG of residue 3 to SG of residue 8 on chain B
+      atom2: [B, 8, SG]

conf/example/fab_scaffolds/adalimumab.6cr1.yaml

@@ -0,0 +1,95 @@
+# adalimumab 6cr1
+# Target: TNF/TNFA
+# Heavy chain (label not auth): B
+# Light chain (label not auth): A
+# Full heavy chain sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSAITWNSGHIDYADSVEGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCAKVSYLSTASSLDYWGQGTLVTVSSASTKGPTVKILQSICDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCAHHHHHH
+# Full light chain sequence: DIQMTQSPSSLSASVGDRVTITCRASQGIRNYLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCQRYNRAPYTFGQGTKVEIKRTVAAPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSGKKCA
+# Variable heavy region: 1 - 121
+# Variable light region: 1 - 107
+# Heavy CDRs: GFTFDDY TWNSGH VSYLSTASSLDY
+# Light CDRs: RASQGIRNYLA AASTLQS QRYNRAPYT
+#
+path: adalimumab.6cr1.cif
+include:
+  - chain:
+      id: B  # heavy
+      res_index: 1..121
+  - chain:
+      id: A  # light
+      res_index: 1..107
+design:
+  - chain:
+      id: B
+      res_index: 26..32,52..57,99..110
+  - chain:
+      id: A
+      res_index: 24..34,50..56,89..97
+
+structure_groups:
+  - group:
+      id: B
+      visibility: 2
+  - group:
+      id: A
+      visibility: 2
+  - group:
+      id: B
+      res_index: 26..32,52..57,99..110
+      visibility: 0
+  - group:
+      id: A
+      res_index: 24..34,50..56,89..97
+      visibility: 0
+
+exclude:
+  - chain:
+      id: B
+      res_index: 26..32
+  - chain:
+      id: B
+      res_index: 52..57
+  - chain:
+      id: B
+      res_index: 99..110
+  - chain:
+      id: A
+      res_index: 24..34
+  - chain:
+      id: A
+      res_index: 50..56
+  - chain:
+      id: A
+      res_index: 89..97
+
+design_insertions:
+  - insertion:
+      id: B
+      res_index: 26
+      num_residues: 7..9
+  - insertion:
+      id: B
+      res_index: 52
+      num_residues: 5..8
+  - insertion:
+      id: B
+      res_index: 99
+      num_residues: 3..21
+  - insertion:
+      id: A
+      res_index: 24
+      num_residues: 10..17
+  - insertion:
+      id: A
+      res_index: 50
+      num_residues: 7
+  - insertion:
+      id: A
+      res_index: 89
+      num_residues: 8..12
+
+# reindex the residue index which is used in the positional encoding
+reset_res_index:
+  - chain:
+      id: B
+  - chain:
+      id: A

conf/example/fab_scaffolds/belimumab.5y9k.yaml

@@ -0,0 +1,95 @@
+# belimumab 5y9k
+# Target: TNFSF13B/CD257/BAFF
+# Heavy chain (label not auth): B
+# Light chain (label not auth): A
+# Full heavy chain sequence: QVQLQQSGAEVKKPGSSVRVSCKASGGTFNNNAINWVRQAPGQGLEWMGGIIPMFGTAKYSQNFQGRVAITADESTGTASMELSSLRSEDTAVYYCARSRDLLLFPHHALSPWGRGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH
+# Full light chain sequence: SSELTQDPAVSVALGQTVRVTCQGDSLRSYYASWYQQKPGQAPVLVIYGKNNRPSGIPDRFSGSSSGNTASLTITGAQAEDEADYYCSSRDSSGNHWVFGGGTELTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
+# Variable heavy region: 1 - 123
+# Variable light region: 1 - 108
+# Heavy CDRs: GGTFNNN IPMFGT SRDLLLFPHHALSP
+# Light CDRs: QGDSLRSYYAS GKNNRPS SSRDSSGNHWV
+#
+path: belimumab.5y9k.cif
+include:
+  - chain:
+      id: B  # heavy
+      res_index: 1..123
+  - chain:
+      id: A  # light
+      res_index: 1..108
+design:
+  - chain:
+      id: B
+      res_index: 26..32,52..57,99..112
+  - chain:
+      id: A
+      res_index: 23..33,49..55,88..98
+
+structure_groups:
+  - group:
+      id: B
+      visibility: 2
+  - group:
+      id: A
+      visibility: 2
+  - group:
+      id: B
+      res_index: 26..32,52..57,99..112
+      visibility: 0
+  - group:
+      id: A
+      res_index: 23..33,49..55,88..98
+      visibility: 0
+
+exclude:
+  - chain:
+      id: B
+      res_index: 26..32
+  - chain:
+      id: B
+      res_index: 52..57
+  - chain:
+      id: B
+      res_index: 99..112
+  - chain:
+      id: A
+      res_index: 23..33
+  - chain:
+      id: A
+      res_index: 49..55
+  - chain:
+      id: A
+      res_index: 88..98
+
+design_insertions:
+  - insertion:
+      id: B
+      res_index: 26
+      num_residues: 7..9
+  - insertion:
+      id: B
+      res_index: 52
+      num_residues: 5..8
+  - insertion:
+      id: B
+      res_index: 99
+      num_residues: 3..21
+  - insertion:
+      id: A
+      res_index: 23
+      num_residues: 10..17
+  - insertion:
+      id: A
+      res_index: 49
+      num_residues: 7
+  - insertion:
+      id: A
+      res_index: 88
+      num_residues: 8..12
+
+# reindex the residue index which is used in the positional encoding
+reset_res_index:
+  - chain:
+      id: B
+  - chain:
+      id: A

conf/example/fab_scaffolds/crenezumab.5vzy.yaml

@@ -0,0 +1,95 @@
+# crenezumab 5vzy
+# Target: Abeta
+# Heavy chain (label not auth): A
+# Light chain (label not auth): B
+# Full heavy chain sequence: EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYGMSWVRQAPGKGLELVASINSNGGSTYYPDSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCASGDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
+# Full light chain sequence: DIVMTQSPLSLPVTPGEPASISCRSSQSLVYSNGDTYLHWYLQKPGQSPQLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCSQSTHVPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
+# Variable heavy region: 1 - 112
+# Variable light region: 1 - 112
+# Heavy CDRs: GFTFSSY NSNGGS GDY
+# Light CDRs: RSSQSLVYSNGDTYLH KVSNRFS SQSTHVPWT
+#
+path: crenezumab.5vzy.cif
+include:
+  - chain:
+      id: A  # heavy
+      res_index: 1..112
+  - chain:
+      id: B  # light
+      res_index: 1..112
+design:
+  - chain:
+      id: A
+      res_index: 26..32,52..57,99..101
+  - chain:
+      id: B
+      res_index: 24..39,55..61,94..102
+
+structure_groups:
+  - group:
+      id: A
+      visibility: 2
+  - group:
+      id: B
+      visibility: 2
+  - group:
+      id: A
+      res_index: 26..32,52..57,99..101
+      visibility: 0
+  - group:
+      id: B
+      res_index: 24..39,55..61,94..102
+      visibility: 0
+
+exclude:
+  - chain:
+      id: A
+      res_index: 26..32
+  - chain:
+      id: A
+      res_index: 52..57
+  - chain:
+      id: A
+      res_index: 99..101
+  - chain:
+      id: B
+      res_index: 24..39
+  - chain:
+      id: B
+      res_index: 55..61
+  - chain:
+      id: B
+      res_index: 94..102
+
+design_insertions:
+  - insertion:
+      id: A
+      res_index: 26
+      num_residues: 7..9
+  - insertion:
+      id: A
+      res_index: 52
+      num_residues: 5..8
+  - insertion:
+      id: A
+      res_index: 99
+      num_residues: 3..21
+  - insertion:
+      id: B
+      res_index: 24
+      num_residues: 10..17
+  - insertion:
+      id: B
+      res_index: 55
+      num_residues: 7
+  - insertion:
+      id: B
+      res_index: 94
+      num_residues: 8..12
+
+# reindex the residue index which is used in the positional encoding
+reset_res_index:
+  - chain:
+      id: A
+  - chain:
+      id: B

conf/example/fab_scaffolds/dupilumab.6wgb.yaml

@@ -0,0 +1,95 @@
+# dupilumab 6wgb
+# Target: IL4R/CD124
+# Heavy chain (label not auth): A
+# Light chain (label not auth): B
+# Full heavy chain sequence: EVQLVESGGGLEQPGGSLRLSCAGSGFTFRDYAMTWVRQAPGKGLEWVSSISGSGGNTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRLSITIRPRYYGLDVWGQGTTVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGHHHHHH
+# Full light chain sequence: DIVMTQSPLSLPVTPGEPASISCRSSQSLLYSIGYNYLDWYLQKSGQSPQLLIYLGSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGFYYCMQALQTPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
+# Variable heavy region: 1 - 125
+# Variable light region: 1 - 112
+# Heavy CDRs: GFTFRDY SGSGGN DRLSITIRPRYYGLDV
+# Light CDRs: RSSQSLLYSIGYNYLD LGSNRAS MQALQTPYT
+#
+path: dupilumab.6wgb.cif
+include:
+  - chain:
+      id: A  # heavy
+      res_index: 1..125
+  - chain:
+      id: B  # light
+      res_index: 1..112
+design:
+  - chain:
+      id: A
+      res_index: 26..32,52..57,99..114
+  - chain:
+      id: B
+      res_index: 24..39,55..61,94..102
+
+structure_groups:
+  - group:
+      id: A
+      visibility: 2
+  - group:
+      id: B
+      visibility: 2
+  - group:
+      id: A
+      res_index: 26..32,52..57,99..114
+      visibility: 0
+  - group:
+      id: B
+      res_index: 24..39,55..61,94..102
+      visibility: 0
+
+exclude:
+  - chain:
+      id: A
+      res_index: 26..32
+  - chain:
+      id: A
+      res_index: 52..57
+  - chain:
+      id: A
+      res_index: 99..114
+  - chain:
+      id: B
+      res_index: 24..39
+  - chain:
+      id: B
+      res_index: 55..61
+  - chain:
+      id: B
+      res_index: 94..102
+
+design_insertions:
+  - insertion:
+      id: A
+      res_index: 26
+      num_residues: 7..9
+  - insertion:
+      id: A
+      res_index: 52
+      num_residues: 5..8
+  - insertion:
+      id: A
+      res_index: 99
+      num_residues: 3..21
+  - insertion:
+      id: B
+      res_index: 24
+      num_residues: 10..17
+  - insertion:
+      id: B
+      res_index: 55
+      num_residues: 7
+  - insertion:
+      id: B
+      res_index: 94
+      num_residues: 8..12
+
+# reindex the residue index which is used in the positional encoding
+reset_res_index:
+  - chain:
+      id: A
+  - chain:
+      id: B

conf/example/fab_scaffolds/golimumab.5yoy.yaml

@@ -0,0 +1,95 @@
+# golimumab 5yoy
+# Target: TNF/TNFA
+# Heavy chain (label not auth): H
+# Light chain (label not auth): E
+# Full heavy chain sequence: SKLQVQLVESGGGVVQPGRSLRLSCAASGFIFSSYAMHWVRQAPGNGLEWVAFMSYDGSNKKYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDRGIAAGGNYYYYGMDVWGQGTTVTVSS
+# Full light chain sequence: AGSEIVLTQSPATLSLSPGERATLSCRASQSVYSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPFTFGPGTKVDIKTSENLYFQ
+# Variable heavy region: 4 - 129
+# Variable light region: 4 - 111
+# Heavy CDRs: GFIFSSY SYDGSN DRGIAAGGNYYYYGMDV
+# Light CDRs: RASQSVYSYLA DASNRAT QQRSNWPPFT
+#
+path: golimumab.5yoy.cif
+include:
+  - chain:
+      id: H  # heavy
+      res_index: 4..129
+  - chain:
+      id: E  # light
+      res_index: 4..111
+design:
+  - chain:
+      id: H
+      res_index: 29..35,55..60,102..118
+  - chain:
+      id: E
+      res_index: 27..37,53..59,92..101
+
+structure_groups:
+  - group:
+      id: H
+      visibility: 2
+  - group:
+      id: E
+      visibility: 2
+  - group:
+      id: H
+      res_index: 29..35,55..60,102..118
+      visibility: 0
+  - group:
+      id: E
+      res_index: 27..37,53..59,92..101
+      visibility: 0
+
+exclude:
+  - chain:
+      id: H
+      res_index: 29..35
+  - chain:
+      id: H
+      res_index: 55..60
+  - chain:
+      id: H
+      res_index: 102..118
+  - chain:
+      id: E
+      res_index: 27..37
+  - chain:
+      id: E
+      res_index: 53..59
+  - chain:
+      id: E
+      res_index: 92..101
+
+design_insertions:
+  - insertion:
+      id: H
+      res_index: 29
+      num_residues: 7..9
+  - insertion:
+      id: H
+      res_index: 55
+      num_residues: 5..8
+  - insertion:
+      id: H
+      res_index: 102
+      num_residues: 3..21
+  - insertion:
+      id: E
+      res_index: 27
+      num_residues: 10..17
+  - insertion:
+      id: E
+      res_index: 53
+      num_residues: 7
+  - insertion:
+      id: E
+      res_index: 92
+      num_residues: 8..12
+
+# reindex the residue index which is used in the positional encoding
+reset_res_index:
+  - chain:
+      id: H
+  - chain:
+      id: E

conf/example/fab_scaffolds/guselkumab.4m6m.yaml

@@ -0,0 +1,95 @@
+# guselkumab 4m6m
+# Target: IL23A
+# Heavy chain (label not auth): B
+# Light chain (label not auth): A
+# Full heavy chain sequence: EVQLVQSGAEVKKPGESLKISCKGSGYSFSNYWIGWVRQMPGKGLEWMGIIDPSNSYTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCARWYYKPFDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCHHHHHH
+# Full light chain sequence: QSVLTQPPSVSGAPGQRVTISCTGSSSNIGSGYDVHWYQQLPGTAPKLLIYGNSKRPSGVPDRFSGSKSGTSASLAITGLQSEDEADYYCASWTDGLSLVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
+# Variable heavy region: 1 - 117
+# Variable light region: 1 - 111
+# Heavy CDRs: GYSFSNY DPSNSY WYYKPFDV
+# Light CDRs: TGSSSNIGSGYDVH GNSKRPS ASWTDGLSLVV
+#
+path: guselkumab.4m6m.cif
+include:
+  - chain:
+      id: B  # heavy
+      res_index: 1..117
+  - chain:
+      id: A  # light
+      res_index: 1..111
+design:
+  - chain:
+      id: B
+      res_index: 26..32,52..57,99..106
+  - chain:
+      id: A
+      res_index: 23..36,52..58,91..101
+
+structure_groups:
+  - group:
+      id: B
+      visibility: 2
+  - group:
+      id: A
+      visibility: 2
+  - group:
+      id: B
+      res_index: 26..32,52..57,99..106
+      visibility: 0
+  - group:
+      id: A
+      res_index: 23..36,52..58,91..101
+      visibility: 0
+
+exclude:
+  - chain:
+      id: B
+      res_index: 26..32
+  - chain:
+      id: B
+      res_index: 52..57
+  - chain:
+      id: B
+      res_index: 99..106
+  - chain:
+      id: A
+      res_index: 23..36
+  - chain:
+      id: A
+      res_index: 52..58
+  - chain:
+      id: A
+      res_index: 91..101
+
+design_insertions:
+  - insertion:
+      id: B
+      res_index: 26
+      num_residues: 7..9
+  - insertion:
+      id: B
+      res_index: 52
+      num_residues: 5..8
+  - insertion:
+      id: B
+      res_index: 99
+      num_residues: 3..21
+  - insertion:
+      id: A
+      res_index: 23
+      num_residues: 10..17
+  - insertion:
+      id: A
+      res_index: 52
+      num_residues: 7
+  - insertion:
+      id: A
+      res_index: 91
+      num_residues: 8..12
+
+# reindex the residue index which is used in the positional encoding
+reset_res_index:
+  - chain:
+      id: B
+  - chain:
+      id: A

conf/example/fab_scaffolds/mab1.3h42.yaml

@@ -0,0 +1,95 @@
+# mab1 3h42
+# Target: PCSK9
+# Heavy chain (label not auth): D
+# Light chain (label not auth): C
+# Full heavy chain sequence: EVQLVESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAPGKGLEWVSSISSSSSYISYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYFCARDYDFWSAYYDAFDVWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAADEVDHHHHHH
+# Full light chain sequence: ESVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLISGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGSVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
+# Variable heavy region: 1 - 123
+# Variable light region: 1 - 111
+# Heavy CDRs: GFTFSSY SSSSSY DYDFWSAYYDAFDV
+# Light CDRs: TGSSSNIGAGYDVH GNSNRPS QSYDSSLSGSV
+#
+path: mab1.3h42.cif
+include:
+  - chain:
+      id: D  # heavy
+      res_index: 1..123
+  - chain:
+      id: C  # light
+      res_index: 1..111
+design:
+  - chain:
+      id: D
+      res_index: 26..32,52..57,99..112
+  - chain:
+      id: C
+      res_index: 23..36,52..58,91..101
+
+structure_groups:
+  - group:
+      id: D
+      visibility: 2
+  - group:
+      id: C
+      visibility: 2
+  - group:
+      id: D
+      res_index: 26..32,52..57,99..112
+      visibility: 0
+  - group:
+      id: C
+      res_index: 23..36,52..58,91..101
+      visibility: 0
+
+exclude:
+  - chain:
+      id: D
+      res_index: 26..32
+  - chain:
+      id: D
+      res_index: 52..57
+  - chain:
+      id: D
+      res_index: 99..112
+  - chain:
+      id: C
+      res_index: 23..36
+  - chain:
+      id: C
+      res_index: 52..58
+  - chain:
+      id: C
+      res_index: 91..101
+
+design_insertions:
+  - insertion:
+      id: D
+      res_index: 26
+      num_residues: 7..9
+  - insertion:
+      id: D
+      res_index: 52
+      num_residues: 5..8
+  - insertion:
+      id: D
+      res_index: 99
+      num_residues: 3..21
+  - insertion:
+      id: C
+      res_index: 23
+      num_residues: 10..17
+  - insertion:
+      id: C
+      res_index: 52
+      num_residues: 7
+  - insertion:
+      id: C
+      res_index: 91
+      num_residues: 8..12
+
+# reindex the residue index which is used in the positional encoding
+reset_res_index:
+  - chain:
+      id: D
+  - chain:
+      id: C

conf/example/fab_scaffolds/necitumumab.6b3s.yaml

@@ -0,0 +1,95 @@
+# necitumumab 6b3s
+# Target: EGFR
+# Heavy chain (label not auth): B
+# Light chain (label not auth): C
+# Full heavy chain sequence: QVQLQESGPGLVKPSQTLSLTCTVSGGSISSGDYYWSWIRQPPGKGLEWIGYIYYSGSTDYNPSLKSRVTMSVDTSKNQFSLKVNSVTAADTAVYYCARVSIFGVGTFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS
+# Full light chain sequence: EIVMTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCHQYGSTPLTFGGGTKAEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGA
+# Variable heavy region: 1 - 121
+# Variable light region: 1 - 107
+# Heavy CDRs: GGSISSGDY YYSGS VSIFGVGTFDY
+# Light CDRs: RASQSVSSYLA DASNRAT HQYGSTPLT
+#
+path: necitumumab.6b3s.cif
+include:
+  - chain:
+      id: B  # heavy
+      res_index: 1..121
+  - chain:
+      id: C  # light
+      res_index: 1..107
+design:
+  - chain:
+      id: B
+      res_index: 26..34,54..58,100..110
+  - chain:
+      id: C
+      res_index: 24..34,50..56,89..97
+
+structure_groups:
+  - group:
+      id: B
+      visibility: 2
+  - group:
+      id: C
+      visibility: 2
+  - group:
+      id: B
+      res_index: 26..34,54..58,100..110
+      visibility: 0
+  - group:
+      id: C
+      res_index: 24..34,50..56,89..97
+      visibility: 0
+
+exclude:
+  - chain:
+      id: B
+      res_index: 26..34
+  - chain:
+      id: B
+      res_index: 54..58
+  - chain:
+      id: B
+      res_index: 100..110
+  - chain:
+      id: C
+      res_index: 24..34
+  - chain:
+      id: C
+      res_index: 50..56
+  - chain:
+      id: C
+      res_index: 89..97
+
+design_insertions:
+  - insertion:
+      id: B
+      res_index: 26
+      num_residues: 7..9
+  - insertion:
+      id: B
+      res_index: 54
+      num_residues: 5..8
+  - insertion:
+      id: B
+      res_index: 100
+      num_residues: 3..21
+  - insertion:
+      id: C
+      res_index: 24
+      num_residues: 10..17
+  - insertion:
+      id: C
+      res_index: 50
+      num_residues: 7
+  - insertion:
+      id: C
+      res_index: 89
+      num_residues: 8..12
+
+# reindex the residue index which is used in the positional encoding
+reset_res_index:
+  - chain:
+      id: B
+  - chain:
+      id: C