rowan-python 2.1.6__tar.gz → 2.1.8__tar.gz

{rowan_python-2.1.6 → rowan_python-2.1.8}/.github/workflows/test.yml

@@ -1,30 +1,30 @@
 name: Pytest Dev
 
 on:
-  pull_request:
+  pull_request: {}
   push:
-    branches:
+    branches: master
 
 jobs:
   test:
     strategy:
       matrix:
-        python-version: ["3.13"]
+        python-version: ["3.14"]
         os: [ubuntu-latest]
 
     name: Python ${{ matrix.os }} ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: prefix-dev/setup-pixi@v0.8.7
+      - uses: prefix-dev/setup-pixi@v0.9.1
         with:
-          pixi-version: v0.45.0
+          pixi-version: v0.56.0
           cache: true
           environments: dev
 

{rowan_python-2.1.6 → rowan_python-2.1.8}/PKG-INFO

@@ -1,17 +1,17 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.6
+Version: 2.1.8
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
 Author-email: Corin Wagen <corin@rowansci.com>
 License-File: LICENSE
-Requires-Python: >=3.9
+Requires-Python: >=3.11
 Requires-Dist: httpx
 Requires-Dist: nest-asyncio
 Requires-Dist: rdkit
 Requires-Dist: setuptools
-Requires-Dist: stjames>=0.0.109
+Requires-Dist: stjames>=0.0.125
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-2.1.6 → rowan_python-2.1.8}/docs/index.md

@@ -2,8 +2,8 @@
 ::: rowan.workflow
     handler: python
     options:
-      show_source: false 
-      show_root_heading: false  
+      show_source: false
+      show_root_heading: false
       show_root_toc_entry: false
       members_order: source        # show items in the order they appear in code
       group_by_category: true      # adds “Classes”, “Functions”, … headings -->
@@ -12,8 +12,8 @@
 ::: rowan.folder
     handler: python
     options:
-      show_source: false 
-      show_root_heading: false  
+      show_source: false
+      show_root_heading: false
       show_root_toc_entry: false
       members_order: source        # show items in the order they appear in code
       group_by_category: true      # adds “Classes”, “Functions”, … headings -->
@@ -22,8 +22,8 @@
 ::: rowan.user
     handler: python
     options:
-      show_source: false 
-      show_root_heading: false  
+      show_source: false
+      show_root_heading: false
       show_root_toc_entry: false
       members_order: source        # show items in the order they appear in code
       group_by_category: true      # adds “Classes”, “Functions”, … headings -->
@@ -32,8 +32,8 @@
 ::: rowan.protein
     handler: python
     options:
-      show_source: false 
-      show_root_heading: false  
+      show_source: false
+      show_root_heading: false
       show_root_toc_entry: false
       members_order: source        # show items in the order they appear in code
       group_by_category: true      # adds “Classes”, “Functions”, … headings -->
@@ -42,8 +42,8 @@
 ::: rowan.project
     handler: python
     options:
-      show_source: false 
-      show_root_heading: false  
+      show_source: false
+      show_root_heading: false
       show_root_toc_entry: false
       members_order: source        # show items in the order they appear in code
       group_by_category: true      # adds “Classes”, “Functions”, … headings -->
@@ -52,8 +52,8 @@
 ::: rowan.utils
     handler: python
     options:
-      show_source: false 
-      show_root_heading: false  
+      show_source: false
+      show_root_heading: false
       show_root_toc_entry: false
       members_order: source        # show items in the order they appear in code
       group_by_category: true      # adds “Classes”, “Functions”, … headings -->

{rowan_python-2.1.6 → rowan_python-2.1.8}/docs/rowan_rdkit.md

@@ -1,8 +1,8 @@
 ::: rowan.rowan_rdkit
     handler: python
     options:
-      show_source: false 
-      show_root_heading: false  
+      show_source: false
+      show_root_heading: false
       show_root_toc_entry: false
       members_order: source        # show items in the order they appear in code
       group_by_category: true      # adds “Classes”, “Functions”, … headings -->

{rowan_python-2.1.6 → rowan_python-2.1.8}/docs/stylesheets/colors.css

@@ -1,6 +1,6 @@
 /* Light-mode brand green */
 :root > * {
   --md-primary-fg-color:        #16a34a;
-  --md-primary-fg-color--light: #c3d3e1; 
-  --md-primary-fg-color--dark:  #74967E; 
+  --md-primary-fg-color--light: #c3d3e1;
+  --md-primary-fg-color--dark:  #74967E;
 }

{rowan_python-2.1.6 → rowan_python-2.1.8}/examples/basic_calculation_with_constraint.py

@@ -9,7 +9,6 @@ result = rowan.submit_workflow(
     workflow_type="basic_calculation",
     name="Constrained Butane",
     workflow_data={
-        "engine": "xtb",
         "settings": {
             "method": "gfn2_xtb",
             "tasks": ["optimize"],

{rowan_python-2.1.6 → rowan_python-2.1.8}/examples/basic_calculation_with_solvent.py

@@ -13,7 +13,6 @@ def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, n
         name=f"{name} {method} optimization",
         workflow_data={
             "settings": {"method": method, "tasks": ["optimize"]},
-            "engine": "omol25",
         },
     )
 
@@ -33,7 +32,6 @@ def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, n
                 "tasks": ["energy"],
                 "solvent_settings": {"solvent": "water", "model": "cpcmx"},
             },
-            "engine": "omol25",
         },
     )
 

rowan_python-2.1.8/examples/batch_docking.py

@@ -0,0 +1,130 @@
+import time
+
+import rowan
+
+ligands = [
+    "CCC(C)(C)NC1=NCC2(CCC(=O)C2C)N1",
+    "CCC(C)CN=C1NCC2(CCCOC2)CN1",
+    "CC(C)CCNC1=NCC2CC(COC2=N)O1",
+    "CCC(CC)NC1=NCC2CC(CO)CC12",
+    "CCC(C)CN=C1NC=C2CCC(O)CC2=N1",
+    "CC(C#CC#N)C1=NC=C2C=CC(=O)CN12",
+    "CCC(CCN)C1NCC2=C(CC)SC(O)=C12",
+    "CCC(CC)N=C1NC=C2C=C(F)C=C(N)N12",
+    "CC(C)(C)C(N)C1=NCC2=CC(I)=NC=C2O1",
+    "CCC(CC)NC1=NCC2CC(N1)C(C)CN2",
+    "CCCC(C)N=C1NCC2CCNC2(C)CO1",
+    "CC(C)CC(N)C1NCC2=CC(N)=C(Br)N=C12",
+    "CC(C)C(CN)C1=NC=C2C=CN(C)C2=C1Br",
+    "CC(CC#C)NC1=NCC2=C(C)N(C)C=C2O1",
+    "CCCC(C)(N)C1=NCC2=CC(N)=CC=C2O1",
+    "CCCCC(N)C1=NC=C2C=CN(C)C(C)=C12",
+    "CCC(CC)N=C1NCC2CC(N)CCCN12",
+    "CC(C)C(C)(N)C1=NC=C2C=CNC(=N)C2=N1",
+    "CC(C)(CC#N)C1=NCC2CCN=COC2O1",
+    "C#CCC(C#N)C1=NC=C2C=CNN=C12",
+    "CCCCCNC1=NCC2=C(C)NN=C2N1",
+    "CCCCC(N)C1=NC=C2C(C)=NOC2=C1Br",
+    "CCCCCNC1=NCC2(CC#N)OCC1O2",
+    "CC(C)CCNC1=NC=C2CC(=N)OCCN12",
+    "CCCC(C#N)C1N(C)C2=C(C=NS2)C1=O",
+    "CCC(CC#N)C1=NCC2=C(CO1)OC(=N)S2",
+    "CCC(CCN)C1=NCC2=C(CO1)SC=N2",
+    "CCC(C(C)N)C1NCC2CCOC1C2(C)C",
+    "CC(C)(C)CNC1=NCC2CCOC1(O2)C#C",
+    "CCCCCN=C1N(C)C2CCOC2C1(C)C",
+    "CC(C)CCN=C1NCC2(CCOC2O1)C#C",
+    "CC(C)C(C#N)C1NCC2=CC(O)=C(Br)N=C12",
+    "CCC(C(C)N)C1(N)CC2CC(OC)C1C2C",
+    "CC(C)(C)CN=C1NC=C2CC(O)CC2O1",
+    "CCC(C)(C#N)C1=NC=C2CC(=O)C(C=O)N12",
+    "CCCC(C)NC1=NCC2(CCOC=N2)CC1",
+    "CCCC(C)N=C1N=CC2=CC(=O)N=C2C1=N",
+    "CC(C)C(C#N)C1=NC=C2C=C(O)OC2=C1N",
+    "CCCC(CN=C1NCC2=C(C)SC=C12)C=O",
+    "CC(C)(C)CN=C1NCC2=CNC3=C2C1=CN3",
+    "CCCCC(N)C1=NC=C2CNCC2=C1I",
+    "CC(CC#C)NC1=NCC2=C(NC(=C2)C#C)N1",
+    "CCC#CCN=C1NCC2=CNC=C2N1",
+    "CCCC(C#N)C1N(C)C2=C(NC=C2)OC1=O",
+    "CC(C)(C)CN=C1NC=C2C=NC=C2SC1=N",
+    "CC(C)C(C#N)C1NCC2=CN=C(C=C12)C#N",
+    "CC(C)C(C#N)C1(N)CC2CN(C)CC2C1C",
+    "CCC(C)(C)N=C1NCC2=C(NC(C)=C2)C1O",
+    "CC(C)C(C)NC1=NCC2CNC(C)C(C2)C1",
+    "CCC(C)CN=C1NCC2C(N)C(C)C(C)C12",
+    "CCC(C)(C#N)C1=NC=C2CNC(C)C(C)N12",
+    "CC(C)C(C#N)C1NCC2=C(N=C(C)N2)C1C",
+    "CCC(C)(C)NC1=NCC2=C(N=C(C)N2)C1C",
+    "CCC(C)(C)N=C1N=CC2=CN(C)N=C2N1C",
+    "CC(C)CCN=C1NC=C2C=NC(=NN12)C#C",
+    "CC(C)C(CN=C1NCC2(CN=CO2)O1)C#N",
+    "CCC(CC)N=C1N(C)C2=C(NC(=O)S2)C1=O",
+    "CCCC(C#N)C1NCC2=C(N=CS2)S1(=O)=O",
+    "CCC(C)(C)NC1=NCC2=CNN=C2C(=N)N1",
+    "CC(C)CCN=C1NC=C2C(N)=NC(C)=C2S1",
+    "CCC(C)(C)NC1=NC=C2C(=N)N=CNC2=N1",
+    "CCC(CC)N=C1N(C)C2=C(NN=N2)C1=NO",
+    "CCC(C)(C)NC1=NCC2=CN=NN2CCC1",
+    "CCC(C)CN=C1N=CC2=CNN=NC2=N1",
+    "CCC(CCN)C1=NC=C2C(N)=NSC2=N1",
+    "CCC(C)(CN)C1NCC2=C(N)OC=C2C1C",
+    "CC(C)(CCN)C1=NC=C2C(=N)SN=C2C=N1",
+    "CC(C)(C)CNC1=NC=C2C(=N)SN=C2O1",
+    "CCC(C)C(N)C1=NCC2=C(O1)C=CC(=N)S2",
+    "CCCCCN=C1NCC2=C(O1)N=C(S2)C#N",
+    "CCC(C)(CNC1=NCC2=C(O1)SC=N2)C=O",
+    "CC#CC(CN)C1=NCC2=C(O1)SN=C2C",
+    "CCCC(C#N)C1NCC2COC1(C2)C(C)=O",
+    "CC(C)(C)C(N)C1(N)CC2COC1C(C)(C)C2",
+    "CCCC(C#N)C1NCC2COC1(C)CN2C",
+    "CCC(C)(C)N=C1N(C)C2COC1(C)OC2C",
+    "CC(C)CCN=C1NCC2=C(OC1=N)N=NN2",
+    "CCC(CC#N)(C1NCC2=COC=C12)N(C)C",
+    "CCCC(C)(N)C1NCC2=C(OC=C12)N(C)C",
+    "CC(C)(C)CNC1=NCC2=C(OCC1)N=CS2",
+    "CC#CCCN=C1NCC2=COC=C2C=C1",
+    "CCCCCNC1=NC=C2C(OCC2(C)O)=C1",
+    "CCC(C)(C#N)C1N(C)C2=COC=C2N=C1N",
+    "CCC(C)(C)N=C1NCC2(C)OC(CC12)=NC",
+    "CCC(C)(CN)C1NCC2C(O)CCC1C2C",
+    "CCCC(C)NC1=NCC2COCC(C1)C2C",
+    "CC(C)C(C)NC1=NCC2COCCC2(C)O1",
+    "CC(C)CC(N)C1=NC=C2COC(C)C(C)N12",
+    "CCC(C)(C)NC1=NCC2COC(C)(O1)C2N",
+    "CCCC(C)(N)C1=NC=C2COCCOC2=N1",
+    "CCCC(C)N=C1N(C)C2=COC(N)=C2C1=O",
+    "CCCCCNC1=NCC2(C)OC=NCCC12",
+    "CCC(C(C)N)C1=NC=C2COC(N)=NC2=C1",
+    "CCCC(C)NC1=NCC2(C)OC(=O)OC2O1",
+    "CCCCC(N)C1NCC2=CON=C2C1C#C",
+    "CC(C)C(C)N=C1NCC2=C(O)N(C)C=C2O1",
+    "CCCC(C)N=C1N=CC2=C(O)N(C)C=CN12",
+    "CC(C)C(C#N)C1=NC=C2C(O)=NSC2=C1O",
+    "CCC(CC)N=C1NCC2=C(O)SC(=N)N=C12",
+    "CC(C)C(CN)C1NCC2=C(SC=C2C)C1C",
+]
+
+workflows = []
+results = {}
+
+protein = rowan.create_protein_from_pdb_id(
+    "CDK2", "1HCK", project_uuid=rowan.default_project().uuid
+)
+
+protein.sanitize()
+time.sleep(60)
+protein.refresh()
+
+workflow = rowan.submit_batch_docking_workflow(
+    ligands,
+    protein.uuid,
+    pocket=[[103.55, 100.59, 82.99], [27.76, 32.67, 48.79]],
+    executable="qvina2",
+    scoring_function="vina",
+)
+
+
+workflow.wait_for_result().fetch_latest(in_place=True)
+
+print(workflow.data["best_scores"])

rowan_python-2.1.8/examples/boltz_paired_msa.py

@@ -0,0 +1,33 @@
+import tarfile
+from pathlib import Path
+
+from stjames import MSAFormat
+
+import rowan
+
+# rowan.api_key = ""
+
+msa_directory = Path("msa_directory")
+
+msa_workflow = rowan.submit_msa_workflow(
+    initial_protein_sequences=[
+        "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
+        "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
+    ],
+    output_formats=[MSAFormat.BOLTZ],
+    name="Boltz Paired MSA Example",
+)
+
+msa_workflow.wait_for_result().fetch_latest(in_place=True)
+
+msa_workflow.download_msa_files(MSAFormat.BOLTZ, path=msa_directory)
+
+tar_path = next(msa_directory.glob("*.tar.gz"))
+with tarfile.open(tar_path, "r") as tar_ref:
+    tar_ref.extractall(msa_directory)
+
+tar_path.unlink()
+
+# by default, the csv files are named seq_<index>.csv
+# to use them for boltz, you need to set the msa path in the protein section of the boltz input
+# yaml to the path of the relevant csv file

rowan_python-2.1.8/examples/boltz_single_msa.py

@@ -0,0 +1,32 @@
+import tarfile
+from pathlib import Path
+
+from stjames import MSAFormat
+
+import rowan
+
+# rowan.api_key = ""
+
+msa_directory = Path("msa_directory")
+
+msa_workflow = rowan.submit_msa_workflow(
+    initial_protein_sequences=[
+        "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
+    ],
+    output_formats=[MSAFormat.BOLTZ],
+    name="Boltz MSA Example",
+)
+
+msa_workflow.wait_for_result().fetch_latest(in_place=True)
+
+msa_workflow.download_msa_files(MSAFormat.BOLTZ, path=msa_directory)
+
+tar_path = next(msa_directory.glob("*.tar.gz"))
+with tarfile.open(tar_path, "r") as tar_ref:
+    tar_ref.extractall(msa_directory)
+
+tar_path.unlink()
+
+# by default, the csv files are named seq_<index>.csv
+# to use them for boltz, you need to set the msa path in the protein section of the boltz input
+# yaml to the path of the relevant csv file

rowan_python-2.1.8/examples/chai_paired_msa.py

@@ -0,0 +1,51 @@
+import tarfile
+from pathlib import Path
+
+# from chai_lab.chai1 import run_inference
+from stjames import MSAFormat
+
+import rowan
+
+# rowan.api_key = ""
+example_fasta = (
+    ">protein|name=example-protein\n"
+    "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR\n"
+    ">protein|name=example-protein-2\n"
+    "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH\n"
+)
+fasta_path = Path("/tmp/input.fasta")
+fasta_path.write_text(example_fasta)
+
+output_dir = Path("/tmp/outputs")
+msa_directory = Path("msa_directory")
+
+msa_workflow = rowan.submit_msa_workflow(
+    initial_protein_sequences=[
+        "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
+        "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
+    ],
+    output_formats=[MSAFormat.CHAI],
+    name="CHAI Paired MSA Example",
+)
+
+msa_workflow.wait_for_result().fetch_latest(in_place=True)
+
+msa_workflow.download_msa_files(MSAFormat.CHAI, path=msa_directory)
+
+tar_path = next(msa_directory.glob("*.tar.gz"))
+with tarfile.open(tar_path, "r") as tar_ref:
+    tar_ref.extractall(msa_directory)
+
+tar_path.unlink()
+
+
+# run_inference(fasta_file=fasta_path,
+#         output_dir=output_dir,
+#         num_trunk_recycles=3,
+#         num_diffn_timesteps=200,
+#         seed=42,
+#         device="cpu", # or "cuda:0"
+#         use_esm_embeddings=True,
+#         use_msa_server=False,
+#         use_templates_server=False,
+#         msa_directory=msa_directory)

rowan_python-2.1.8/examples/chai_single_msa.py

@@ -0,0 +1,48 @@
+import tarfile
+from pathlib import Path
+
+# from chai_lab.chai1 import run_inference
+from stjames import MSAFormat
+
+import rowan
+
+# rowan.api_key = ""
+example_fasta = (
+    ">protein|name=example-protein\n"
+    "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW\n"
+)
+fasta_path = Path("/tmp/input.fasta")
+fasta_path.write_text(example_fasta)
+
+output_dir = Path("/tmp/outputs_2")
+msa_directory = Path("msa_directory")
+
+msa_workflow = rowan.submit_msa_workflow(
+    initial_protein_sequences=[
+        "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
+    ],
+    output_formats=[MSAFormat.CHAI],
+    name="CHAI MSA Example",
+)
+
+msa_workflow.wait_for_result().fetch_latest(in_place=True)
+
+msa_workflow.download_msa_files(MSAFormat.CHAI, path=msa_directory)
+
+tar_path = next(msa_directory.glob("*.tar.gz"))
+with tarfile.open(tar_path, "r") as tar_ref:
+    tar_ref.extractall(msa_directory)
+
+tar_path.unlink()
+
+
+# run_inference(fasta_file=fasta_path,
+#         output_dir=output_dir,
+#         num_trunk_recycles=3,
+#         num_diffn_timesteps=200,
+#         seed=42,
+#         device="cpu", # or "cuda:0"
+#         use_esm_embeddings=True,
+#         use_msa_server=False,
+#         use_templates_server=False,
+#         msa_directory=msa_directory)

rowan_python-2.1.8/examples/colabfold_paired_msa.py

@@ -0,0 +1,32 @@
+import tarfile
+from pathlib import Path
+
+from stjames import MSAFormat
+
+import rowan
+
+# rowan.api_key = ""
+
+msa_directory = Path("msa_directory")
+
+msa_workflow = rowan.submit_msa_workflow(
+    initial_protein_sequences=[
+        "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
+        "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
+    ],
+    output_formats=[MSAFormat.COLABFOLD],
+    name="Colabfold Paired MSA Example",
+)
+
+msa_workflow.wait_for_result().fetch_latest(in_place=True)
+
+msa_workflow.download_msa_files(MSAFormat.COLABFOLD, path=msa_directory)
+
+tar_path = next(msa_directory.glob("*.tar.gz"))
+with tarfile.open(tar_path, "r") as tar_ref:
+    tar_ref.extractall(msa_directory)
+
+tar_path.unlink()
+
+# This produces two folders, one with unparied msas called unpaired and one with paired msas
+# called paired

rowan_python-2.1.8/examples/colabfold_single_msa.py

@@ -0,0 +1,28 @@
+import tarfile
+from pathlib import Path
+
+from stjames import MSAFormat
+
+import rowan
+
+# rowan.api_key = ""
+
+msa_directory = Path("msa_directory")
+
+msa_workflow = rowan.submit_msa_workflow(
+    initial_protein_sequences=[
+        "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
+    ],
+    output_formats=[MSAFormat.COLABFOLD],
+    name="Colabfold MSA Example",
+)
+
+msa_workflow.wait_for_result().fetch_latest(in_place=True)
+
+msa_workflow.download_msa_files(MSAFormat.COLABFOLD, path=msa_directory)
+
+tar_path = next(msa_directory.glob("*.tar.gz"))
+with tarfile.open(tar_path, "r") as tar_ref:
+    tar_ref.extractall(msa_directory)
+
+tar_path.unlink()

{rowan_python-2.1.6 → rowan_python-2.1.8}/examples/data/workflow_example.json

@@ -174,4 +174,4 @@
     "mulliken_spin_densities": null,
     "thermal_free_energy_corr": null
   }
-}
+}

rowan_python-2.1.8/examples/double_ended_ts_search.py

@@ -0,0 +1,58 @@
+"""
+Run a double-ended transition state search using Rowan.
+
+See documentation at: https://docs.rowansci.com/science/workflows/double-ended-ts-search
+"""
+
+from stjames import Method, Molecule, Settings
+from stjames.optimization.freezing_string_method import (
+    FSMInterpolation,
+    FSMOptimizationCoordinates,
+    FSMSettings,
+)
+
+import rowan
+
+# rowan.api_key = ""
+HCN = Molecule.from_xyz(
+    """\
+H 0 0 -1.1
+C 0 0 0
+N 0 0 1.2""",
+)
+CNH = Molecule.from_xyz(
+    """\
+H 0 0 2.3
+C 0 0 0
+N 0 0 1.2""",
+)
+fsm_settings = FSMSettings(
+    optimization_coordinates=FSMOptimizationCoordinates.CARTESIAN,
+    interpolation_method=FSMInterpolation.REDUNDANT_INTERNAL_COORDINATES,
+    min_num_nodes=7,
+    num_interpolation_points=5,
+    max_optimizer_iterations=3,
+    max_line_search_steps=2,
+    max_displacement=0.1,
+)
+
+
+# Run calculation remotely
+result = rowan.submit_double_ended_ts_search_workflow(
+    reactant=HCN,
+    product=CNH,
+    calculation_settings=Settings(method=Method.GFN2_XTB),
+    search_settings=fsm_settings,
+    optimize_inputs=True,
+    optimize_ts=True,
+    name="H-C≡N Isomerization",
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/workflow/{result.uuid}")
+result.wait_for_result().fetch_latest(in_place=True)
+
+assert result and result.data
+print(result.data["forward_string_distances"])
+print(result.data["backward_string_distances"])
+
+print(result)

{rowan_python-2.1.6 → rowan_python-2.1.8}/examples/pka.py

@@ -14,9 +14,18 @@ import rowan
 # rowan.api_key = ""
 
 result = rowan.submit_pka_workflow(
-    initial_molecule=Molecule.from_smiles("n1ccccc1"),
+    initial_molecule=Molecule.from_smiles("c1ccccc1O"),
+    method="aimnet2_wagen2024",
     mode="reckless",
     name="Pyridine pKa",
 )
 
 print(result.wait_for_result().fetch_latest(in_place=True))
+
+result2 = rowan.submit_pka_workflow(
+    initial_molecule="c1ccccc1O",
+    method="chemprop_nevolianis2025",
+    name="Pyridine pKa (ML)",
+)
+
+print(result2.wait_for_result().fetch_latest(in_place=True))

rowan_python-2.1.8/examples/pose_analysis_md.py

@@ -0,0 +1,28 @@
+import rowan
+
+ligand = "CCC(C)(C)NC1=NCC2(CCC(=O)C2C)N1"
+
+cofolding_workflow = rowan.submit_protein_cofolding_workflow(
+    initial_protein_sequences=[
+        "MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL"
+    ],
+    initial_smiles_list=[ligand],
+    ligand_binding_affinity_index=0,
+    name=f"Cofolding {ligand}",
+    do_pose_refinement=True,
+)
+
+cofolding_workflow.wait_for_result().fetch_latest(in_place=True)
+
+md_workflow = rowan.submit_pose_analysis_md_workflow(
+    protein=cofolding_workflow.data["predicted_refined_structure_uuid"],
+    initial_smiles=ligand,
+    num_trajectories=1,
+    simulation_time_ns=1,
+    name="Downstream molecular dynamics",
+)
+
+md_workflow.wait_for_result().fetch_latest(in_place=True)
+
+# print ligand RMSD by frame
+print(md_workflow.data["trajectories"][0]["rmsd"])

{rowan_python-2.1.6 → rowan_python-2.1.8}/mkdocs.yml

@@ -24,8 +24,8 @@ plugins:
             show_signature_annotations: false
             merge_init_into_class: true     # if you want __init__ docs on the class
             separate_signature: true          # uses Black if it’s on your PATH
-            line_length: 88 
-            unwrap_annotated: true 
+            line_length: 88
+            unwrap_annotated: true
 nav:
   - Core API: index.md
   - Rowan RDKit: rowan_rdkit.md