add changes

.gradio/cached_examples/13/indices.csv

@@ -0,0 +1,2 @@
+4
+1

.gradio/cached_examples/13/log.csv

@@ -0,0 +1,3 @@
+Generated Molecule,timestamp
+"{""path"": "".gradio/cached_examples/13/Generated Molecule/96624d241f3ceaf7652e/MITOCHONDRIAL_9.pdb"", ""url"": ""/gradio_api/file=/tmp/gradio/dfeb6cce50c7d0cb5ab8f1fcbc0ed91e88c6f502e6abf12023254e663fafee05/MITOCHONDRIAL_9.pdb"", ""size"": 2031480, ""orig_name"": ""MITOCHONDRIAL_9.pdb"", ""mime_type"": null, ""is_stream"": false, ""meta"": {""_type"": ""gradio.FileData""}}",2024-11-20 21:18:05.776535
+"{""path"": "".gradio/cached_examples/13/Generated Molecule/4f0e0b233c39c3b226f9/Armadillo_6.pdb"", ""url"": ""/gradio_api/file=/tmp/gradio/e9e42deb7d9ea5c72c0bd60fb8f2bbed6357d48e775667232dc67eddc7886d87/Armadillo_6.pdb"", ""size"": 1271295, ""orig_name"": ""Armadillo_6.pdb"", ""mime_type"": null, ""is_stream"": false, ""meta"": {""_type"": ""gradio.FileData""}}",2024-11-20 22:28:22.665771

.gradio/cached_examples/14/indices.csv

@@ -0,0 +1,4 @@
+0
+1
+2
+3

.gradio/cached_examples/14/log.csv

@@ -0,0 +1,5 @@
+Generated Molecule,timestamp
+"{""path"": "".gradio/cached_examples/14/Generated Molecule/8ad633716dc9e78cb06f/example_0.pdb"", ""url"": ""/gradio_api/file=/tmp/gradio/2ab77757589b1fd365f7221f92918cd369c77ddd8251942bc03a023821578dcd/example_0.pdb"", ""size"": 493208, ""orig_name"": ""example_0.pdb"", ""mime_type"": null, ""is_stream"": false, ""meta"": {""_type"": ""gradio.FileData""}}",2024-11-20 20:22:56.207790
+"{""path"": "".gradio/cached_examples/14/Generated Molecule/3e37ca179b3cb7dc122b/example_1.pdb"", ""url"": ""/gradio_api/file=/tmp/gradio/2ab77757589b1fd365f7221f92918cd369c77ddd8251942bc03a023821578dcd/example_1.pdb"", ""size"": 493208, ""orig_name"": ""example_1.pdb"", ""mime_type"": null, ""is_stream"": false, ""meta"": {""_type"": ""gradio.FileData""}}",2024-11-20 20:24:50.533021
+"{""path"": "".gradio/cached_examples/14/Generated Molecule/bcd21a78404497b34489/example_2.pdb"", ""url"": ""/gradio_api/file=/tmp/gradio/e57fb46398114333f5eb1eef64451f69b2b0c82ca4af9c045f8912b4226411b6/example_2.pdb"", ""size"": 5470578, ""orig_name"": ""example_2.pdb"", ""mime_type"": null, ""is_stream"": false, ""meta"": {""_type"": ""gradio.FileData""}}",2024-11-20 20:31:32.902767
+"{""path"": "".gradio/cached_examples/14/Generated Molecule/a2260acc1f5513075a30/MITOCHONDRIAL_9.pdb"", ""url"": ""/gradio_api/file=/tmp/gradio/dfeb6cce50c7d0cb5ab8f1fcbc0ed91e88c6f502e6abf12023254e663fafee05/MITOCHONDRIAL_9.pdb"", ""size"": 2031480, ""orig_name"": ""MITOCHONDRIAL_9.pdb"", ""mime_type"": null, ""is_stream"": false, ""meta"": {""_type"": ""gradio.FileData""}}",2024-11-20 20:58:21.867631

app.py

@@ -1,73 +1,192 @@
-import gradio as gr
 import os
+import gradio as gr
 from gradio_molecule3d import Molecule3D
-import sys
-import os
-# from boltz.main_test import predict  # Import your predict function
-current_dir = os.path.dirname(os.path.abspath(__file__))
-src_path = os.path.join(current_dir, "boltz", "src")
-sys.path.append(src_path)
-from boltz.main_test import predict  # Import your predict function
-# from boltz.src.boltz.main_test import predict
-# Example Molecule3D representation settings
-reps = [
+import spaces
+import subprocess
+import glob
+
+
+# Directory to store cached outputs
+CACHE_DIR = "gradio_cached_examples"
+
+
+reps =    [
     {
-        "model": 0,
-        "chain": "",
-        "resname": "",
-        "style": "stick",
-        "color": "whiteCarbon",
-        "residue_range": "",
-        "around": 0,
-        "byres": False,
-        "visible": False
+      "model": 0,
+      "chain": "",
+      "resname": "",
+      "style": "stick",
+      "color": "whiteCarbon",
+      "residue_range": "",
+      "around": 0,
+      "byres": False,
+      "visible": False
     }
+  ]
+# Ensure the cache directory exists
+os.makedirs(CACHE_DIR, exist_ok=True)
+
+# Define example files and precomputed outputs
+example_fasta_files = [
+    f"cache_examples/boltz_0.fasta",
+    f"cache_examples/Armadillo_6.fasta",
+    f"cache_examples/Covid_3.fasta",
+    f"cache_examples/Malaria_2.fasta",
+    f"cache_examples/MITOCHONDRIAL_9.fasta",
+    f"cache_examples/Monkeypox_4.fasta",
+    f"cache_examples/Plasmodium_1.fasta",
+    f"cache_examples/PROTOCADHERIN_8.fasta",
+    f"cache_examples/Vault_5.fasta",
+    f"cache_examples/Zipper_7.fasta",
 ]
 
-# Your prediction function
-def run_prediction(input_file):
-    # Assuming `input_file` is a Gradio `File` object
-    data = input_file.name  # Get the path to the uploaded .fasta file
-    out_dir = "./predict"  # Set your output directory
-    cache = "~/.boltz"
-    accelerator = "cpu"
-    sampling_steps = 1
-    diffusion_samples = 1
-    output_format = "pdb"
-
-    # Call your original predict function
+# matching `.pdb` files in the `CACHE_DIR`
+example_outputs = [
+    os.path.join(CACHE_DIR, os.path.basename(fasta_file).replace(".fasta", ".pdb"))
+    for fasta_file in example_fasta_files
+]
+
+# must load cached outputs
+def load_cached_example_outputs(fasta_file: str) -> str:
+    # Find the corresponding `.pdb` file
+    pdb_file = os.path.basename(fasta_file).replace(".fasta", ".pdb")
+    cached_pdb_path = os.path.join(CACHE_DIR, pdb_file)
+    if os.path.exists(cached_pdb_path):
+        return cached_pdb_path
+    else:
+        raise FileNotFoundError(f"Cached output not found for {pdb_file}")
+
+# handle example click
+def on_example_click(fasta_file: str) -> str:
+    return load_cached_example_outputs(fasta_file)
+
+# run predictions
+# @spaces.GPU(duration=120)
+def predict(data, out_dir, cache="~/.boltz", checkpoint=None, devices=1,
+            accelerator="gpu", recycling_steps=3, sampling_steps=50,
+            diffusion_samples=1, output_format="pdb", num_workers=2,
+            override=False):
+
+    print("Arguments passed to `predict` function:")
+    print(f"  data: {data}")
+    print(f"  out_dir: {out_dir}")
+    print(f"  cache: {cache}")
+    print(f"  checkpoint: {checkpoint}")
+    print(f"  devices: {devices}")
+    print(f"  accelerator: {accelerator}")
+    print(f"  recycling_steps: {recycling_steps}")
+    print(f"  sampling_steps: {sampling_steps}")
+    print(f"  diffusion_samples: {diffusion_samples}")
+    print(f"  output_format: {output_format}")
+    print(f"  num_workers: {num_workers}")
+    print(f"  override: {override}")
+    # Construct the base command
+    command = [
+        "boltz", "predict",
+        "--out_dir", out_dir,
+        "--cache", cache,
+        "--devices", str(devices),
+        "--accelerator", accelerator,
+        "--recycling_steps", str(recycling_steps),
+        "--sampling_steps", str(sampling_steps),
+        "--diffusion_samples", str(diffusion_samples),
+        "--output_format", output_format,
+        "--num_workers", str(num_workers)
+    ]
+
+    
+    # Add optional arguments if provided
+    if checkpoint:
+        command.extend(["--checkpoint", checkpoint])
+    if override:
+        command.append("--override")
+    
+
+    # Add the data argument (path to the input file)
+    command.append(data)
+
+    # print("Constructed subprocess command:")
+    # print("  " + " ".join(command))
+
+
+    # Run the command using subprocess
+    result = subprocess.run(command, capture_output=True, text=True)
+    if result.returncode == 0:
+        print("Prediction completed successfully...!")
+        print(f"Output saved to: {out_dir}")
+    else:
+        print("Prediction failed :(")
+        print("Error:", result.stderr)
+
+# @spaces.GPU(duration=60)
+def run_prediction(input_file, cache, accelerator, sampling_steps,
+                   diffusion_samples, output_format, checkpoint="./ckpt/boltz1.ckpt"):
+    # Assuming `input_file` is a path to the .fasta file
+    data = input_file.name  # Path to the uploaded .fasta file
+    print("the data : ", data)
+    # Update the `reps` settings with the chosen style and color
+
+    # Call your predict function
     predict(
         data=data,
-        out_dir=out_dir,
+        out_dir="./",
+        cache=cache,
         accelerator=accelerator,
         sampling_steps=sampling_steps,
-        output_format=output_format
+        diffusion_samples=diffusion_samples,
+        output_format=output_format,
+        checkpoint=checkpoint
     )
 
-    # Fetch the generated PDB file
-    output_pdb_path = os.path.join(out_dir, "output.pdb")
-    if os.path.exists(output_pdb_path):
-        print("Generated PDB file found:", output_pdb_path)
-        return output_pdb_path  # Return the path for Molecule3D to load
-    else:
-        print("Generated PDB file not found")
+    # Search for the latest .pdb file in the predictions folder
+    search_path = os.path.join(out_dir, "boltz_results*/predictions/**/*.pdb")
+    pdb_files = glob.glob(search_path, recursive=True)  # Enable recursive search
+    
+    if not pdb_files:
+        print("No .pdb files found in the predictions folder.")
         return None
 
-# Gradio interface setup
+    # Get the latest .pdb file based on modification time
+    latest_pdb_file = max(pdb_files, key=os.path.getmtime)
+
+    
+    # Return the latest PDB file path
+    return latest_pdb_file
+
+
 with gr.Blocks() as demo:
-    gr.Markdown("# Molecule3D - Upload a .fasta File for Prediction")
+    gr.Markdown("# 🔬 Boltz-1: Democratizing Biomolecular Interaction Modeling 🧬")
 
-    # Input: File upload component for .fasta files
-    inp = gr.File(label="Upload a .fasta File", file_types=[".fasta"])
+    with gr.Row():
+        with gr.Column(scale=1):
+            inp = gr.File(label="Upload a .fasta File", file_types=[".fasta"])
 
-    # Output: Molecule3D component for rendering the generated PDB file
-    out = Molecule3D(label="Generated Molecule", reps=reps)
+            with gr.Accordion("Advanced Settings", open=False):
+                accelerator = gr.Radio(choices=["gpu", "cpu"], value="gpu", label="Accelerator")
+                sampling_steps = gr.Slider(minimum=1, maximum=500, value=50, step=1, label="Sampling Steps")
+                diffusion_samples = gr.Slider(minimum=1, maximum=10, value=1, step=1, label="Diffusion Samples")
+            btn = gr.Button("Predict")
+            
+        with gr.Column(scale=3):
+            out = Molecule3D(label="Generated Molecule", reps=reps)
+
+        
+
+    btn.click(
+        run_prediction,
+        inputs=[inp, accelerator, sampling_steps, diffusion_samples],
+        outputs=out
+    )
+    gr.Examples(
+                examples=[[fasta_file] for fasta_file in example_fasta_files],
+                inputs=[inp],
+                outputs=out, 
+                fn=lambda fasta_file: on_example_click(fasta_file),
+                cache_examples=True
+            )
 
-    btn = gr.Button("Predict")
     
-    # Connect the button click to the prediction function
-    btn.click(run_prediction, inputs=inp, outputs=out)
 
 if __name__ == "__main__":
-    demo.launch()
-
+    demo.launch(share=True, debug=True)
+    

cache_examples/Armadillo_6.fasta

@@ -0,0 +1,4 @@
+>5AEI_2|Chains D, E, F|KR5|SYNTHETIC CONSTRUCT (32630)
+KRKRKRKRKR
+>5AEI_1|Chains A, B, C|DESIGNED ARMADILLO REPEAT PROTEIN YIIIM5AII|SYNTHETIC CONSTRUCT (32630)
+GPGSELPQMVQQLNSPDQQELQSALRKLSQIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWALSNIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWALSNIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWALSNIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWALSNIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWALSNIASGGNEQKQAVKEAGALEKLEQLQSHENEKIQKEAQEALEKLQSH

cache_examples/Covid_3.fasta

@@ -0,0 +1,2 @@
+>6VXX_1|Chains A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049)
+MGILPSPGMPALLSLVSLLSVLLMGCVAETGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSGAGSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGRENLYFQGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHHHH

cache_examples/MITOCHONDRIAL_9.fasta

@@ -0,0 +1,6 @@
+>1BMF_3|Chain G|BOVINE MITOCHONDRIAL F1-ATPASE|Bos taurus (9913)
+ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTPEDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTHSDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFSLDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQAVITKELIEIISGAAAL
+>1BMF_1|Chains A, B, C|BOVINE MITOCHONDRIAL F1-ATPASE|Bos taurus (9913)
+QKTGTAEVSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALLGKIRTDGKISEESDAKLKEIVTNFLAGFEA
+>1BMF_2|Chains D, E, F|BOVINE MITOCHONDRIAL F1-ATPASE|Bos taurus (9913)
+AAQASPSPKAGATTGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHLGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHS

cache_examples/Malaria_2.fasta

@@ -0,0 +1,10 @@
+>6E11_1|Chains AA[auth i], A[auth h], BA[auth k], B[auth j], C[auth l], Y[auth m], Z[auth n]|Unknown (Claw)|Plasmodium falciparum 3D7 (36329)
+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
+>6E11_2|Chains D[auth 1], E[auth 2], F[auth 3], G[auth 4], H[auth 5], J[auth 6]|Heat shock protein 101|Plasmodium falciparum (isolate 3D7) (36329)
+MTRRYLKYYIFVTLLFFVQVINNVLCAPDNKQEQGKYLNRTINILNAGKNIAKSYGHNKLKPIHILSALAKSDYGSTLFKENNVNAANLKEYIDIALEQTRAGAPLDNKSKIVNSAEVKETLALAEAAANKYKSPKVDVEHLLSGLSNDELVNEIFNEVYLTDEAIKAILKRKFEKTKKDKDGKTGTLYIEQFGSNMNEKVRNGKLQGIYGRDEEIRAIIESLLRYNKNSPVLVGNPGTGKTTIVEGLVYRIEKGDVPKELQGYTVISLNFRKFTSGTSYRGEFETRMKNIIKELKNKKNKIILFVDEIHLLLGAGKAEGGTDAANLLKPVLSKGEIKLIGATTIAEYRKFIESCSAFERRFEKILVEPPSVDMTVKILRSLKSKYENFYGINITDKALVAAAKISDRFIKDRYLPDKAIDLLNKACSFLQVQLSGKPRIIDVTERDIERLSYEISTLEKDVDKVSKKKYNKLIKEFEEKKEQLKKYYEEYVITGERLKRKKEIEKKLNDLKELTQNYVYSNKEPPIELQNSLKEAQQKYLELYKETVAYVEAKTHNAMNVDAVYQEHVSYIYLRDSGMPLGSLSFESSKGALKLYNSLSKSIIGNEDIIKSLSDAVVKAATGMKDPEKPIGTFLFLGPTGVGKTELAKTLAIELFNSKDNLIRVNMSEFTEAHSVSKITGSPPGYVGFSDSGQLTEAVREKPHSVVLFDELEKAHADVFKVLLQILGDGYINDNHRRNIDFSNTIIIMTSNLGAELFKKKLFFDADNSGTPEYKRVMEDVRLSLIKKCKKVFKPEFVNRIDKIGVFEPLNKKNLHKIVALRFKKLEKRLEEKNIQVSVSEKAIDYIIDQSYDPELGARPTLIFIESVIMTKFAIMYLKKELVDDMDVFVDYNSKAKNLVINLSKT
+>6E11_3|Chains I[auth A], K[auth B], M[auth C], Q[auth D], S[auth E], U[auth F], W[auth G]|Exported protein 2|Plasmodium falciparum (isolate 3D7) (36329)
+MKVSYIFSFFLLFFVYKNTNTVVCDNGYGDLAATSALTTVIKDPISLTIKDIYEHGVKNPFTKIIHKLKKFIRYRKVLRWSRMWWVLLVREIVGDNTIEKKTEKALREIWDQCTIAVYNNTLNAVESKPLLFLHGILNECRNNFATKLRQDPSLIVAKIDQIIKSQIYRFWVSEPYLKIGRSHTLYTHITPDAVPQLPKECTLKHLSSYMEEKLKSMESKKNIESGKYEFDVDSSETDSTKDDGKPDDDDDDDDNFDDDDNFDDDTVEEEDASGDLFKNEKKDENKE
+>6E11_4|Chain L[auth 0]|Endogenous cargo polypeptide|Plasmodium falciparum 3D7 (36329)
+XXXXXX
+>6E11_5|Chains N[auth a], O[auth b], P[auth c], R[auth d], T[auth e], V[auth f], X[auth g]|Translocon component PTEX150|Plasmodium falciparum (isolate 3D7) (36329)
+MRIIILALLIVCTIINYYCAVQNNGNKSLNVMPTCSMPGNDSDSNDNETGDVDNDKNNELGNANDNNEMNNENAESKNMQGENSNNQEQLNENVHANDDAMYEGTPSSDNPPQENVDANNNEQEYGPPQEEPVSENNVENVEVATDDSGNDNINNNDNFNNNDNYNDNDNFNEEPPSDDGNKNEDELTEGNQSDDKPMNEEEATINEMGKITNPFEDMLKGKVDDMDIGKMMNKDNLQSFLSSLTGNKDGSGKNPLSDMMNIFGVPQTGKEGAEGGVNKENQMKQINELKDKLETMLKGAGVNVDKIKDSIKNNDLLKNKQLLKEAISKLTLDPSMMNMLNNKDGANGKPFDINPDSMMKMFNALSNENGNLDDLKMKPTDGSFDSFNDGVDNNLVPSNPKGQNNNEEDDEEGGDDDDYDDKSFVVNSKYADNSFEDKFNTFDEKDDDVKYELFGENEEAEELNNNTTTASSKGDANNSVNTQEGEGEEESFSANEENINNNNNHNNKNYNNYNTSQQEEDDNSFNENDEPLISSSQFDNNKKNKMSVSTHNKKSKNLMDSLDLESTNYGSNSSSSMSNNYNSKNKNSKKNNKKKSSQKDYIRTDGKVSFDMATLQKTIKNFGGADNEIVQNILKKYVTIDNDDDNDADEDEDEDDDDDDDLDEDEFSVKDIKKLIEEGILDYEDLTENELRKLAKPDDNFYELSPYASDEKDLSLNETSGLTNEQLKNFLGQNGTYHMSYDSKSIDYAKQKKSEKKEDQQEDDDGFYDAYKQIKNSYDGIPNNFNHEAPQLIGNNYVFTSIYDTKENLIKFLKKNSEYDLYDDDDKEGGNFKSPLYDKYGGKLQKFKRQRAFNILKQWRAKEKKLKEKKKKEEMEENKEFDFSKNYNFSSKNDGGVTMFSKDQLEDMVKNFGGKPSAHVTDSFSRKENPFVPTNTKNNSNDDDDMDNGYVTFDGKNKVSENDDDEKGNNNDDENDNDDSNDEEELDEEEDDN

cache_examples/PROTOCADHERIN_8.fasta

@@ -0,0 +1,4 @@
+>4APX_1|Chain A|CADHERIN-23|MUS MUSCULUS (10090)
+MQVNRLPFFTNHFFDTYLLISEDTPVGSSVTQLLARDMDNDPLVFGVSGEEASRFFAVEPDTGVVWLRQPLDRETKSEFTVEFSVSDHQGVITRKVNIQVGDVNDNAPTFHNQPYSVRIPENTPVGTPIFIVNATDPDLGAGGSVLYSFQPPSPFFAIDSARGIVTVIQELDYEVTQAYQLTVNATDQDKTRPLSTLANLAIIITDLEHHHHHH
+>4APX_2|Chain B|PROTOCADHERIN-15|MUS MUSCULUS (10090)
+MQYDDDWQYEDCKLARGGPPATIVAIDEESRNGTILVDNMLIKGTAGGPDPTIELSLKDNVDYWVLLDPVKQMLFLNSTGRVLDRDPPMNIHSIVVQVQCVNKKVGTVIYHEVRIVVRDRNDNSPTFKHESYYATVNELTPVGTTIFTGFSGDNGATDIDDGPNGQIEYVIQYNPEDPTSNDTFEIPLMLTGNVVLRKRLNYEDKTRYYVIIQANDRAQNLNERRTTTTTLTVDLEHHHHHH

cache_examples/Plasmodium_1.fasta

@@ -0,0 +1,2 @@
+>1NW4_1|Chains A, B, C, D, E, F|uridine phosphorylase, putative|Plasmodium falciparum (36329)
+MALDNLLRHLKISKEQITPVVLVVGDPGRVDKIKVVCDSYVDLAYNREYKSVECHYKGQKFLCVSHGVGSAGCAVCFEELCQNGAKVIIRAGSCGSLQPDLIKRGDICICNAAVREDRVSHLLIHGDFPAVGDFDVYDTLNKCAQELNVPVFNGISVSSDMYYPNKIIPSRLEDYSKANAAVVEMELATLMVIGTLRKVKTGGILIVDGCPFKWDEGDFDNNLVPHQLENMIKIALGACAKLATKYAKGEFEAYVEQKLISEEDLNSAVDHHHHHH

cache_examples/Vault_5.fasta

@@ -0,0 +1,2 @@
+>6BP7_1|Chain A|Major vault protein|Rattus norvegicus (10116)
+MTPRTLNAWVKVVEEKAFSPEVIPMFTALSEGATPSDLNTMLNTIGGHQAAMQMLKDTINEEAAEWDRGFLGLMATEEAIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPVRMVTVPPRHYCIVANPVSRDTQSSVLFDITGQVRLRHADQEIRLAQDPFPLYPGEVLEKDITPLQVVLPNTALHLKALLDFEDKNGDKVMAGDEWLFEGPGTYIPQKEVEVVEIIQATVIKQNQALRLRARKECFDREGKGRVTGEEWLVRSVGAYLPAVFEEVLDLVDAVILTEKTALHLRALQNFRDLRGVLHRTGEEWLVTVQDTEAHVPDVYEEVLGVVPITTLGPRHYCVILDPMGPDGKNQLGQKRVVKGEKSFFLQPGERLERGIQDVYVLSEQQGLLLKALQPLEEGESEEKVSHQAGDCWLIRGPLEYVPSAKVEVVEERQAIPLDQNEGIYVQDVKTGKVRAVIGSTYMLTQDEVLWEKELPSGVEELLNLGHDPLADRGQKGTAKPLQPSAPRNKTRVVSYRVPHNAAVQVYDYRAKRARVVFGPELVTLDPEEQFTVLSLSAGRPKRPHARRALCLLLGPDFFTDVITIETADHARLQLQLAYNWHFELKNRNDPAEAAKLFSVPDFVGDACKAIASRVRGAVASVTFDDFHKNSARIIRMAVFGFEMSEDTGPDGTLLPKARDQAVFPQNGLVVSSVDVQSVEPVDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEAMSMAVESTGNAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETEAELERVKKVREMELIYARAQLELEVSKAQQLANVEAKKFKEMTEALGPGTIRDLAVAGPEMQVKLLQSLGLKSTLITDGSSPINLFSTAFGLLGLGSDGQPPAQK

cache_examples/Zipper_7.fasta

@@ -0,0 +1,4 @@
+>2DGC_1|Chain A[auth B]|DNA (5'-D(*TP*GP*GP*AP*GP*AP*TP*GP*AP*CP*GP*TP*CP*AP*TP*CP*T P*CP*C)-3')|
+TGGAGATGACGTCATCTCC
+>2DGC_2|Chain B[auth A]|PROTEIN (GCN4)|Saccharomyces cerevisiae (4932)
+MIVPESSDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGER

cache_examples/boltz_0.fasta

@@ -0,0 +1,12 @@
+>A|protein|./seq1.a3m
+MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
+>B|protein|./seq1.a3m
+MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
+>C|ccd
+SAH
+>D|ccd
+SAH
+>E|smiles
+N[C@@H](Cc1ccc(O)cc1)C(=O)O
+>F|smiles
+N[C@@H](Cc1ccc(O)cc1)C(=O)O

ckpt/boltz1.ckpt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:82f6ee66aca03664351465848c3daf2a2d4d9333e02d7242575187d9d4616d5e
+size 6921224318

ckpt/ccd.pkl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2b4afb8bf458dd5079f054e7ea33dd2fdd508702b5b38d7c91c6ad02238bdfd6
+size 497