478 plex init not working in pip package (#479)

cmd/vectorize.go

@@ -111,8 +111,10 @@ func VectorizeOutputs(ioPath string, toolCid string, outputDir string) (map[stri
 						}
 					}
 
+					cidPath := fmt.Sprintf("%s/%s", fileOutput.IPFS, fileOutput.FilePath)
 					ov.FilePaths = append(ov.FilePaths, absoluteFilePath)
 					ov.CIDs = append(ov.CIDs, fileOutput.IPFS)
+					ov.CidPaths = append(ov.CidPaths, cidPath)
 					outputMap[key] = ov
 				}
 			}

internal/ipwl/io.go

@@ -157,4 +157,5 @@ func PrintIOGraphStatus(ioList []IO) {
 type OutputValues struct {
 	FilePaths []string `json:"filePaths"`
 	CIDs      []string `json:"cids"`
+	CidPaths  []string `json:"cidPaths"`
 }

python/README.md

@@ -23,3 +23,10 @@ export PLAT_NAME=win_amd64
 python setup.py bdist_wheel --plat-name win_amd64
 twine upload dist/*
 ```
+
+# Dev Setups
+```
+cd python/dev
+pip install -e ../
+python example.py
+```

python/dev/example.py

@@ -0,0 +1,30 @@
+import os
+
+from plex import CoreTools, ScatteringMethod, plex_init, plex_run, plex_vectorize, plex_mint
+
+plex_dir = os.path.dirname(os.path.dirname(os.getcwd()))
+plex_path = os.path.join(plex_dir, "plex")
+jobs_dir = os.path.join(plex_dir, "jobs")
+test_data_dir = os.path.join(plex_dir, "testdata")
+
+print(f"Using plex_path, {plex_path}, if this looks incorrect then make sure you are running from the python/dev directory")
+
+small_molecules = [f"{test_data_dir}/binding/abl/ZINC000003986735.sdf", f"{test_data_dir}/binding/abl/ZINC000019632618.sdf"]
+proteins = [f"{test_data_dir}/binding/abl/7n9g.pdb"]
+
+initial_io_cid = plex_init(
+    CoreTools.EQUIBIND.value,
+    ScatteringMethod.CROSS_PRODUCT.value,
+    plex_path=plex_path,
+    small_molecule=small_molecules,
+    protein=proteins)
+
+completed_io_cid, io_file_path = plex_run(initial_io_cid, output_dir=jobs_dir, plex_path=plex_path)
+
+vectors = plex_vectorize(io_file_path, CoreTools.EQUIBIND.value, plex_path=plex_path)
+
+print(vectors)
+print(vectors['best_docked_small_molecule']['filePaths'])
+print(vectors['best_docked_small_molecule']['cids'])
+
+plex_mint(completed_io_cid, plex_path=plex_path)

python/dev/rfdiffusion.py

@@ -0,0 +1,125 @@
+
+import os
+import json
+import requests
+
+from tempfile import TemporaryDirectory, NamedTemporaryFile
+
+from plex import CoreTools, ScatteringMethod, plex_init, plex_run, plex_vectorize, plex_mint, plex_upload
+
+plex_dir = os.path.dirname(os.path.dirname(os.getcwd()))
+plex_path = os.path.join(plex_dir, "plex")
+jobs_dir = os.path.join(plex_dir, "jobs")
+
+
+def move_from_file_url_to_ipfs(url: str) -> str:
+    # Create a temporary directory using the `with` statement, so it's automatically cleaned up when we're done
+    with TemporaryDirectory() as tmp_dir:
+        # Get the file name from the url
+        file_name = url.split('/')[-1]
+
+        # Create the path to save the file
+        save_path = os.path.join(tmp_dir, file_name)
+
+        # Send a HTTP request to the url
+        response = requests.get(url, stream=True)
+
+        if response.status_code == 200:
+            # If the request is successful, open the file in write mode and download the file
+            with open(save_path, 'wb') as f:
+                for chunk in response.iter_content(chunk_size=1024): 
+                    if chunk: 
+                        f.write(chunk)
+            print(f"File downloaded successfully and saved as {save_path}")
+            cid = plex_upload(save_path, plex_path=plex_path)
+        else:
+            print(f"Failed to download file. HTTP Response Code: {response.status_code}")
+            cid = ""
+        return cid, file_name
+
+url = 'https://raw.githubusercontent.com/labdao/plex/447-add-rfdiffusion-to-plex/tools/rfdiffusion/6vja_stripped.pdb'
+protein_6vja_cid, protein_6vja_file_name = move_from_file_url_to_ipfs(url)
+
+hotspot_rfdiffusion_tool = {
+    "class": "CommandLineTool",
+    "name": "rfdiffusion_hotspot",
+    "description": "design protein binders; generally useful for conditional generation of protein backbones",
+    "baseCommand": ["/bin/bash", "-c"],
+    "arguments": [
+        "source activate SE3nv && python3 /app/scripts/run_inference.py 'contigmap.contigs=[$(inputs.motif.default) $(inputs.binder_length_min.default)-$(inputs.binder_length_max.default)]' $(inputs.hotspot.default) inference.input_pdb=$(inputs.protein.filepath) inference.output_prefix=/outputs/$(inputs.protein.basename)_backbone inference.num_designs=$(inputs.number_of_designs.default) denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0;"
+      ],
+    "dockerPull": "public.ecr.aws/p7l9w5o7/rfdiffusion:latest@sha256:0a6ff53004958ee5e770b0b25cd7f270eaf9fc285f6e91f17ad4024d2cc4ea91",
+    "gpuBool": True,
+    "networkBool": False,
+    "inputs": {
+      "protein": {
+        "type": "File",
+        "item": "",
+        "glob": ["*.pdb"]
+      },
+      "motif": {
+        "type": "string",
+        "item": "",
+        "default": "D46-200/0"
+      },
+      "hotspot": {
+        "type": "string",
+        "item": "",
+        "default": "'ppi.hotspot_res=[D170, D171, D172, D173, D174, D76, D161]'"
+      },
+      "binder_length_min": {
+        "type": "int",
+        "item": "",
+        "default": "50"
+      },
+      "binder_length_max": {
+        "type": "int",
+        "item": "",
+        "default": "100"
+      },
+      "number_of_designs": {
+        "type": "int",
+        "item": "",
+        "default": "10"
+      }
+    },
+    "outputs": {
+      "designed_backbones": {
+        "type": "Array",
+        "item": "File",
+        "glob": ["*_backbone_*.pdb"]
+      },
+      "first_designed_backbone": {
+        "type": "File",
+        "item": "",
+        "glob": ["*_backbone_0.pdb"]
+      }
+    }
+}
+
+with NamedTemporaryFile(suffix=".json", delete=False, mode='w') as temp_file:
+    # Use json.dump to write the dictionary to the file
+    json.dump(hotspot_rfdiffusion_tool, temp_file)
+    print(f"Temporary file saved as {temp_file.name}")
+
+    # flush data to disk
+    temp_file.flush()
+    hotspot_rfdiffusion_tool_cid = plex_upload(temp_file.name, wrap_file=False, plex_path=plex_path)
+    print(f"Tool saved to IPFS as {hotspot_rfdiffusion_tool_cid}")
+
+initial_io_cid = plex_init(
+    hotspot_rfdiffusion_tool_cid,
+    plex_path=plex_path,
+    protein=[f'{protein_6vja_cid}/{protein_6vja_file_name}'],
+    )
+
+CACHE = True
+if CACHE:
+    completed_io_cid = 'QmbHneUZZpNh24is1uTnCpMYKRWStgEqAaYL4aDjN6tNzQ'
+    io_cid_file_path = ''
+else:
+    completed_io_cid, io_cid_file_path = plex_run(initial_io_cid, plex_path=plex_path)
+
+vectors = plex_vectorize(completed_io_cid, hotspot_rfdiffusion_tool_cid, plex_path=plex_path)
+
+print(vectors['first_designed_backbone']['cidPaths'])

python/setup.py

@@ -16,7 +16,7 @@ def run(self):
         # Retrieve platform from environment variable
         plat_name = os.environ['PLAT_NAME']
 
-        current_binary_version = "0.8.2"
+        current_binary_version = "0.8.3"
         # map plat_name to go_bin_url
         urls = {
             "darwin_x86_64": f"https://github.com/labdao/plex/releases/download/v{current_binary_version}/plex_{current_binary_version}_darwin_amd64.tar.gz",
@@ -54,7 +54,7 @@ def download_and_extract(self, go_bin_url, temp_dir):
 
 setup(
     name="PlexLabExchange",
-    version="0.8.16",
+    version="0.8.17",
     packages=find_packages(where='src'),  # tell setuptools to look in the 'src' directory for packages
     package_dir={'': 'src'},  # tell setuptools that the packages are under the 'src' directory
     cmdclass={

python/src/plex/__init__.py

@@ -7,8 +7,9 @@
 
 
 class ScatteringMethod(Enum):
-    DOT_PRODUCT = 'dotproduct'
-    CROSS_PRODUCT = 'cross_product'
+    # values are camel case to match GoLang CLI
+    DOT_PRODUCT = 'dotProduct'
+    CROSS_PRODUCT = 'crossProduct'
 
 
 class CoreTools(Enum):
@@ -35,35 +36,39 @@ def __init__(self, message):
         super().__init__(f"{self.message}\n{self.github_issue_message}")
 
 
-def plex_init(toolpath: str, scatteringMethod="dotProduct", plex_path="plex", **kwargs):
+def plex_init(tool_path: str, scattering_method=ScatteringMethod.DOT_PRODUCT.value, plex_path="plex", **kwargs):
     cwd = os.getcwd()
     plex_work_dir = os.environ.get("PLEX_WORK_DIR", os.path.dirname(os.path.dirname(cwd)))
 
     # Convert kwargs dictionary to a JSON string
     inputs = json.dumps(kwargs)
 
-    cmd = [plex_path, "init", "-t", toolpath, "-i", inputs, f"--scatteringMethod={scatteringMethod}"]
+    cmd = [plex_path, "init", "-t", tool_path, "-i", inputs, f"--scatteringMethod={scattering_method}"]
+
+    print(' '.join(cmd))
 
     io_json_cid = ""
-    with subprocess.Popen(cmd, stdout=subprocess.PIPE, bufsize=1, universal_newlines=True, cwd=plex_work_dir) as p:
+    with subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=1, universal_newlines=True, cwd=plex_work_dir) as p:
         for line in p.stdout:
             if "Pinned IO JSON CID:" in line:
                 parts = line.split()
                 io_json_cid = parts[-1]
             print(line, end='')
+        for line in p.stderr:
+            print(line, end='')
 
     if io_json_cid == "":
         raise PlexError("Failed to initialize IO JSON CID")
 
     return io_json_cid
 
 
-def plex_vectorize(io_path: str, tool_cid: str, outputDir="", plex_path="plex"):
+def plex_vectorize(io_path: str, tool_cid: str, output_dir="", plex_path="plex"):
     cwd = os.getcwd()
     plex_work_dir = os.environ.get("PLEX_WORK_DIR", os.path.dirname(os.path.dirname(cwd)))
 
-    cmd = [plex_path, "vectorize", "-i", io_path, "-t", tool_cid, "-o", outputDir]
-    with subprocess.Popen(cmd, stdout=subprocess.PIPE, bufsize=1, universal_newlines=True, cwd=plex_work_dir) as p:
+    cmd = [plex_path, "vectorize", "-i", io_path, "-t", tool_cid, "-o", output_dir]
+    with subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=1, universal_newlines=True, cwd=plex_work_dir) as p:
         outvects = ""
         for line in p.stdout:
             if "Output Vectors were saved at:" in line:
@@ -73,40 +78,44 @@ def plex_vectorize(io_path: str, tool_cid: str, outputDir="", plex_path="plex"):
                     outvects = json.load(f)
                 os.remove(io_vector_outpath)
             print(line, end='')
+        for line in p.stderr:
+            print(line, end='')
 
     if outvects == "":
         raise PlexError("Failed to vectorize IO JSON CID")
 
     return outvects
 
 
-def plex_upload(filePath: str, wrapFile=True, plex_path="plex"):
-    cmd = [plex_path, "upload", "-p", filePath]
+def plex_upload(file_path: str, wrap_file=True, plex_path="plex"):
+    cmd = [plex_path, "upload", "-p", file_path]
 
-    if not wrapFile:
+    if not wrap_file:
         cmd.append("-w=false")
 
-    with subprocess.Popen(cmd, stdout=subprocess.PIPE, bufsize=1, universal_newlines=True) as p:
+    with subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=1, universal_newlines=True) as p:
         file_cid = ""
         for line in p.stdout:
             if "Uploaded CID:" in line:
                 parts = line.split()
                 file_cid = parts[-1]
             print(line, end='')
+        for line in p.stderr:
+            print(line, end='')
 
     if file_cid == "":
         raise PlexError("Failed to upload file to IPFS")
 
     return file_cid
 
 
-def plex_create(toolpath: str, inputDir: str, layers=2, outputDir="", verbose=False, showAnimation=False, concurrency="1", annotations=[], plex_path="plex"):
+def plex_create(tool_path: str, input_dir: str, layers=2, output_dir="", verbose=False, show_animation=False, concurrency="1", annotations=[], plex_path="plex"):
     cwd = os.getcwd()
     plex_work_dir = os.environ.get("PLEX_WORK_DIR", os.path.dirname(os.path.dirname(cwd)))
-    cmd = [plex_path, "create", "-t", toolpath, "-i", inputDir, f"--layers={layers}"]
+    cmd = [plex_path, "create", "-t", tool_path, "-i", input_dir, f"--layers={layers}"]
 
-    if outputDir:
-        cmd.append(f"-o={outputDir}")
+    if output_dir:
+        cmd.append(f"-o={output_dir}")
 
     if verbose:
         cmd.append("-v=true")
@@ -117,31 +126,33 @@ def plex_create(toolpath: str, inputDir: str, layers=2, outputDir="", verbose=Fa
     if annotations:
         cmd.append(f"--annotations={annotations.join(',')}")
 
-    if not showAnimation: # default is true in the CLI
+    if not show_animation: # default is true in the CLI
         cmd.append("--showAnimation=false")
 
-    with subprocess.Popen(cmd, stdout=subprocess.PIPE, bufsize=1, universal_newlines=True, cwd=plex_work_dir) as p:
+    with subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=1, universal_newlines=True, cwd=plex_work_dir) as p:
         io_json_cid = ""
         for line in p.stdout:
             if "Initial IO JSON file CID:" in line:
                 parts = line.split()
                 io_json_cid = parts[-1]
             print(line, end='')
+        for line in p.stderr:
+            print(line, end='')
 
     if io_json_cid == "":
         raise PlexError("Failed to create IO JSON CID")
 
     return io_json_cid
 
 
-def plex_run(io_json_cid: str, outputDir="", verbose=False, showAnimation=False, concurrency="1", annotations=[], plex_path="plex"):
+def plex_run(io_json_cid: str, output_dir="", verbose=False, show_animation=False, concurrency="1", annotations=[], plex_path="plex"):
     cwd = os.getcwd()
     # plex_work_dir = os.environ.get("PLEX_WORK_DIR", os.path.dirname(os.path.dirname(cwd)))
     plex_work_dir = os.environ.get("PLEX_WORK_DIR", os.path.dirname(cwd))
     cmd = [plex_path, "run", "-i", io_json_cid]
 
-    if outputDir:
-        cmd.append(f"-o={outputDir}")
+    if output_dir:
+        cmd.append(f"-o={output_dir}")
 
     if verbose:
         cmd.append("-v=true")
@@ -152,10 +163,10 @@ def plex_run(io_json_cid: str, outputDir="", verbose=False, showAnimation=False,
     if annotations:
         cmd.append(f"--annotations={annotations.join(',')}")
 
-    if not showAnimation: # default is true in the CLI
+    if not show_animation: # default is true in the CLI
         cmd.append("--showAnimation=false")
 
-    with subprocess.Popen(cmd, stdout=subprocess.PIPE, bufsize=1, universal_newlines=True, cwd=plex_work_dir) as p:
+    with subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=1, universal_newlines=True, cwd=plex_work_dir) as p:
         io_json_cid = ""
         io_json_local_filepath = ""
         for line in p.stdout:
@@ -166,24 +177,28 @@ def plex_run(io_json_cid: str, outputDir="", verbose=False, showAnimation=False,
                 parts = line.split()
                 io_json_local_filepath = parts[-1]
             print(line, end='')
+        for line in p.stderr:
+            print(line, end='')
 
     if io_json_cid == "" or io_json_local_filepath == "":
         raise PlexError("Failed to run IO JSON CID")
 
     return io_json_cid, io_json_local_filepath
 
 
-def plex_mint(io_json_cid: str, imageCid="", plex_path="plex"):
+def plex_mint(io_json_cid: str, image_cid="", plex_path="plex"):
     cwd = os.getcwd()
     plex_work_dir = os.environ.get("PLEX_WORK_DIR", os.path.dirname(os.path.dirname(cwd)))
     cmd = [plex_path, "mint", "-i", io_json_cid]
 
-    if imageCid:
-        cmd.append(f"-imageCid={imageCid}")
+    if image_cid:
+        cmd.append(f"-imageCid={image_cid}")
 
-    with subprocess.Popen(cmd, stdout=subprocess.PIPE, bufsize=1, universal_newlines=True, cwd=plex_work_dir) as p:
+    with subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=1, universal_newlines=True, cwd=plex_work_dir) as p:
         for line in p.stdout:
             print(line, end='')
+        for line in p.stderr:
+            print(line, end='')
 
 
 def print_io_graph_status(io_graph):