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pytest-enabler>=2.2 ; extra == 'enabler' + - pytest-mypy ; extra == 'type' + - mypy==1.14.* ; extra == 'type' + - importlib-metadata>=7.0.2 ; python_full_version < '3.10' and extra == 'type' + - jaraco-develop>=7.21 ; sys_platform != 'cygwin' and extra == 'type' + requires_python: '>=3.9' - pypi: https://files.pythonhosted.org/packages/3d/ea/ac2bf868899d0d2e82ef72d350d97a846110c709bacf2d968431576ca915/setuptools_scm-9.2.2-py3-none-any.whl name: setuptools-scm version: 9.2.2 @@ -3509,6 +3754,11 @@ packages: version: 0.3.0 sha256: 073a1acb250e4add96cfd5ef84e0036605cd6e0d0782c8c15c80e42202348458 requires_python: '>=3.8' +- pypi: https://files.pythonhosted.org/packages/6d/72/da5a6f511a8267f962a08637464a70409736ac72f9f75b069e0e96d69b64/wcwidth-0.5.2-py3-none-any.whl + name: wcwidth + version: 0.5.2 + sha256: 46912178a64217749bf3426b21e36e849fbc46e05c949407b3e364d9f7ffcadf + requires_python: '>=3.8' - pypi: https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl name: webencodings version: 0.5.1 @@ -3531,6 +3781,15 @@ packages: - pytest>=6.0.0 ; extra == 'test' - setuptools>=65 ; extra == 'test' requires_python: '>=3.8' +- pypi: https://files.pythonhosted.org/packages/87/22/b76d483683216dde3d67cba61fb2444be8d5be289bf628c13fc0fd90e5f9/wheel-0.46.3-py3-none-any.whl + name: wheel + version: 0.46.3 + sha256: 4b399d56c9d9338230118d705d9737a2a468ccca63d5e813e2a4fc7815d8bc4d + requires_dist: + - packaging>=24.0 + - pytest>=6.0.0 ; extra == 'test' + - setuptools>=77 ; extra == 'test' + requires_python: '>=3.9' - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7 md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829 diff --git a/pyproject.toml b/pyproject.toml index 834c1e9..6a5632b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -57,7 +57,7 @@ dev = [ nb = [ "molviewspec", "ipykernel", - # "openprotein-python @ git+https://github.com/OpenProteinAI/openprotein-python-private.git@6e6214088bee247f20f72afe0bec4e8f686f08d9", + "openprotein-python @ git+https://github.com/OpenProteinAI/openprotein-python-private.git@f2bd23a05b917c7e6edccd86a624f2f6cbb9f2a1", "seaborn", "scipy", ] diff --git a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb index 1ae9b9c..8dcf67a 100644 --- a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb +++ b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb @@ -1312,18 +1312,14 @@ "\n", "Typically, to validate *in silico* binder designs, we predict the target-binder complex\n", "structure and check for consistency with the original designed structure and binding\n", - "interface. Because the structure of the target is known, but the binder structure is\n", + "interface. Because the structure of the target is known, but the binder structure is\n", "not, we usually run structure prediction in single sequence mode for both the binder and\n", "target sequences using only the target structure as a template. _Single sequence mode_\n", "means that no multiple sequence alignment is used for the binder. This is important to\n", "efficiently screen large numbers of binder designs where homology search is a bottleneck.\n", "\n", - "However, because we do support templates yet (coming soon!), in this tutorial we'll\n", - "use an MSA for the target instead of a template; this generally achieves the same\n", - "objective, allowing the model to accurately recapitulate the target's known structure.\n", - "\n", - "Below, we compute an MSA for the target, and use it to predict the structure of all\n", - "designed sequences; this generally takes about 50 minutes." + "Below, we apply this approach to predict the structures of all designed sequences; this\n", + "generally takes about 50 minutes." ] }, { @@ -1348,29 +1344,28 @@ } ], "source": [ - "# 1. Compute MSA for target to use for folding\n", - "target_msa = session.align.create_msa(target.sequence)\n", - "\n", - "# 2. Create the complexes to fold\n", + "# 1. Create the complexes to fold\n", "complexes_to_fold = []\n", "for i, generated_structure in enumerate(generated_structures): # for each structure\n", " for j in range(N_SEQS_PER_STRUCTURE):\n", " designed_binder_sequence = df.loc[(i, j)][\"sequence\"]\n", + " # 1a. Create the complex to fold, containing the target sequence and designed\n", + " # binder sequence\n", " complex = Complex(\n", " {\"A\": Protein(target.sequence), \"B\": Protein(designed_binder_sequence)}\n", " )\n", - " # set MSAs to use for structure prediction\n", - " # note that `binder.msa = Protein.single_sequence_mode` needs to be set\n", - " # explicitly when running structure prediction without MSAs\n", - " complex.get_protein(chain_id=\"A\").msa = target_msa\n", + " # 1b. Set both the target MSA and the binder MSA to single sequence mode\n", + " complex.get_protein(chain_id=\"A\").msa = Protein.single_sequence_mode\n", " complex.get_protein(chain_id=\"B\").msa = Protein.single_sequence_mode\n", + " # 1c. Set the known target structure as a template for the target only\n", + " complex.get_protein(chain_id=\"A\").templates = [target]\n", " complexes_to_fold.append(complex)\n", "\n", - "# 3. Create the job\n", + "# 2. Create the job\n", "fold_job = session.fold.boltz_2.fold(complexes_to_fold)\n", "print(fold_job)\n", "\n", - "# 4. Wait for the job to finish\n", + "# 3. Wait for the job to finish\n", "_ = fold_job.wait_until_done(verbose=True)" ] }, @@ -1945,7 +1940,7 @@ }, { "cell_type": "code", - "execution_count": 47, + "execution_count": null, "id": "3816751b", "metadata": {}, "outputs": [ @@ -1974,7 +1969,9 @@ ], "source": [ "# get predicted and generated structure of top design\n", - "design_idx, structure_idx = 263, 26\n", + "design_idx, structure_idx = df_selected.reset_index().iloc[0][\n", + " [\"design_idx\", \"structure_idx\"]\n", + "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", "# superimpose predicted structure on the generate structure\n", @@ -2016,7 +2013,7 @@ }, { "cell_type": "code", - "execution_count": 48, + "execution_count": null, "id": "87fde147", "metadata": {}, "outputs": [ @@ -2045,7 +2042,9 @@ ], "source": [ "# get predicted and generated structure of top sixth design\n", - "design_idx, structure_idx = 530, 53\n", + "design_idx, structure_idx = df_selected.reset_index().iloc[5][\n", + " [\"design_idx\", \"structure_idx\"]\n", + "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", "# superimpose predicted structure on the generate structure\n", From 8c77b5639ea6b765eed31fd771784130290dd267 Mon Sep 17 00:00:00 2001 From: Timothy Fei Truong Jr Date: Fri, 30 Jan 2026 10:44:57 -0500 Subject: [PATCH 2/9] update boltzgen binder design tutorial to use templates --- ...Nanobody_binder_design_with_BoltzGen.ipynb | 31 ++++++++----------- 1 file changed, 13 insertions(+), 18 deletions(-) diff --git a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb index c168d92..404fe46 100644 --- a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb +++ b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb @@ -890,23 +890,19 @@ "\n", "Typically, to validate *in silico* binder designs, we predict the target-binder complex\n", "structure and check for consistency with the original designed structure and binding\n", - "interface. Because the structure of the target is known, but the binder structure is\n", + "interface. Because the structure of the target is known, but the binder structure is\n", "not, we usually run structure prediction in single sequence mode for both the binder and\n", "target sequences using only the target structure as a template. _Single sequence mode_\n", "means that no multiple sequence alignment is used for the binder. This is important to\n", "efficiently screen large numbers of binder designs where homology search is a bottleneck.\n", "\n", - "However, because we do support templates yet (coming soon!), in this tutorial we'll\n", - "use an MSA for the target instead of a template; this generally achieves the same\n", - "objective, allowing the model to accurately recapitulate the target's known structure.\n", - "\n", - "Below, we compute an MSA for the target, and use it to predict the structure of all\n", - "designed sequences; this generally takes about 50 minutes." + "Below, we apply this approach to predict the structures of all designed sequences; this\n", + "generally takes about 50 minutes." ] }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "id": "78ea020d", "metadata": {}, "outputs": [ @@ -926,29 +922,28 @@ } ], "source": [ - "# 1. Compute MSA for target to use for folding\n", - "target_msa = session.align.create_msa(target.sequence)\n", - "\n", - "# 2. Create the complexes to fold\n", + "# 1. Create the complexes to fold\n", "complexes_to_fold = []\n", "for i, generated_structure in enumerate(generated_structures): # for each structure\n", " for j in range(N_SEQS_PER_STRUCTURE):\n", " designed_binder_sequence = df.loc[(i, j)][\"sequence\"]\n", + " # 1a. Create the complex to fold, containing the target sequence and designed\n", + " # binder sequence\n", " complex = Complex(\n", " {\"A\": Protein(target.sequence), \"B\": Protein(designed_binder_sequence)}\n", " )\n", - " # set MSAs to use for structure prediction\n", - " # note that `binder.msa = Protein.single_sequence_mode` needs to be set\n", - " # explicitly when running structure prediction without MSAs\n", - " complex.get_protein(chain_id=\"A\").msa = target_msa\n", + " # 1b. Set both the target MSA and the binder MSA to single sequence mode\n", + " complex.get_protein(chain_id=\"A\").msa = Protein.single_sequence_mode\n", " complex.get_protein(chain_id=\"B\").msa = Protein.single_sequence_mode\n", + " # 1c. Set the known target structure as a template for the target only\n", + " complex.get_protein(chain_id=\"A\").templates = [target]\n", " complexes_to_fold.append(complex)\n", "\n", - "# 3. Create the job\n", + "# 2. Create the job\n", "fold_job = session.fold.boltz_2.fold(complexes_to_fold)\n", "print(fold_job)\n", "\n", - "# 4. Wait for the job to finish\n", + "# 3. Wait for the job to finish\n", "_ = fold_job.wait_until_done(verbose=True)" ] }, From 3bac907c9fb99e976c0baa0a6d595151ea367f68 Mon Sep 17 00:00:00 2001 From: Timothy Fei Truong Jr Date: Fri, 30 Jan 2026 10:45:42 -0500 Subject: [PATCH 3/9] update minimum python version requirement in prereqs sections --- source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb | 2 +- .../Protein_protein_binder_design_with_RFdiffusion.ipynb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb index 404fe46..48a3cba 100644 --- a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb +++ b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb @@ -33,7 +33,7 @@ "To run this tutorial, you'll need a Python environment containing the following\n", "packages:\n", "\n", - "- `openprotein_python>=0.10.1`\n", + "- `openprotein_python>=0.10.2`\n", "- `molviewspec` (for structure visualization)\n", "\n", "See the Python client [installation instructions](../python-api/installation.html) for more info.\n", diff --git a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb index 8dcf67a..48297c7 100644 --- a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb +++ b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb @@ -38,7 +38,7 @@ "To run this tutorial, you'll need a Python environment containing the following\n", "packages:\n", "\n", - "- `openprotein_python>=0.10`\n", + "- `openprotein_python>=0.10.2`\n", "- `molviewspec` (for structure visualization)\n", "\n", "See the Python client [installation instructions](../python-api/installation.html) for more info.\n", From 24e74d8c1e171a9fb49bfe280d08a8aaf04adde4 Mon Sep 17 00:00:00 2001 From: Timothy Fei Truong Jr Date: Sat, 31 Jan 2026 11:18:44 -0500 Subject: [PATCH 4/9] update success rate when using template over msa --- .../Nanobody_binder_design_with_BoltzGen.ipynb | 8 ++++---- .../Protein_protein_binder_design_with_RFdiffusion.ipynb | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb index 48a3cba..8c47afa 100644 --- a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb +++ b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb @@ -1276,8 +1276,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "# designs passing filters 250\n", - "# unique structures passing filters 77\n" + "# designs passing filters 146\n", + "# unique structures passing filters 48\n" ] } ], @@ -1479,7 +1479,7 @@ "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", - "# superimpose predicted structure on the generate structure\n", + "# superimpose predicted structure on the generated structure\n", "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n", "# visualize\n", "visualize_cif(\n", @@ -1544,7 +1544,7 @@ "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", - "# superimpose predicted structure on the generate structure\n", + "# superimpose predicted structure on the generated structure\n", "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n", "# visualize\n", "visualize_cif(\n", diff --git a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb index 48297c7..feb6305 100644 --- a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb +++ b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb @@ -1715,8 +1715,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "# designs passing filters 279\n", - "# unique structures passing filters 65\n" + "# designs passing filters 253\n", + "# unique structures passing filters 58\n" ] } ], @@ -1974,7 +1974,7 @@ "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", - "# superimpose predicted structure on the generate structure\n", + "# superimpose predicted structure on the generated structure\n", "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n", "# visualize\n", "visualize_cif(\n", @@ -2047,7 +2047,7 @@ "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", - "# superimpose predicted structure on the generate structure\n", + "# superimpose predicted structure on the generated structure\n", "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n", "# visualize\n", "visualize_cif(\n", From ebf05ca02390e51bfee2b0a137173acc8155b0df Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Fri, 6 Feb 2026 01:27:25 +0000 Subject: [PATCH 5/9] Update required package version for tutorial --- source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb index 8c47afa..4a0764d 100644 --- a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb +++ b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb @@ -33,7 +33,7 @@ "To run this tutorial, you'll need a Python environment containing the following\n", "packages:\n", "\n", - "- `openprotein_python>=0.10.2`\n", + "- `openprotein_python>=0.11.0`\n", "- `molviewspec` (for structure visualization)\n", "\n", "See the Python client [installation instructions](../python-api/installation.html) for more info.\n", From 5906d37bc532b8e6397ed933fd0ac89b865ae421 Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Fri, 6 Feb 2026 01:28:28 +0000 Subject: [PATCH 6/9] Update openprotein-python version in pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 6a5632b..5980e12 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ dependencies = [ "sphinx-notfound-page>=1.1.0,<1.2.0", "sphinx-design>=0.6.1,<0.7", # autodoc - "openprotein-python>=0.10.0,<0.11.0", + "openprotein-python>=0.11.0,<0.12.0", "ipython>=9.8.0,<10", ] From 1a5754515823162ce034cce834c420d27543897b Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Fri, 6 Feb 2026 01:37:52 +0000 Subject: [PATCH 7/9] update lock --- pixi.lock | 404 ++++++++++--------------------------------------- pyproject.toml | 16 +- 2 files changed, 90 insertions(+), 330 deletions(-) diff --git a/pixi.lock b/pixi.lock index 3722b20..335ba91 100644 --- a/pixi.lock +++ b/pixi.lock @@ -39,7 +39,7 @@ environments: - 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