changes to app vis 12 seq only

app.py

@@ -0,0 +1,81 @@
+
+import gradio as gr
+import os
+import pandas as pd
+import tempfile
+from pathlib import Path
+from inference_wrapper import RNAFoldingPredictor
+
+MODEL_PATH = os.environ.get("MODEL_PATH", "ptope/rna-model-weights")
+STATIC_DIR = "static"
+os.makedirs(STATIC_DIR, exist_ok=True)
+
+predictor = RNAFoldingPredictor(MODEL_PATH)
+
+# Load test sequences
+test_sequences = pd.read_csv("test_sequences.csv")
+test_seq_list = test_sequences["sequence"].dropna().unique().tolist()
+
+def create_pdb_from_prediction(prediction_df):
+    pdb_lines = ["HEADER    RNA STRUCTURE PREDICTION"]
+    atom_index = 1
+    prev_c1_index = None
+    for _, row in prediction_df.iterrows():
+        resname = row['resname']
+        resid = row['resid']
+        x, y, z = row['x_1'], row['y_1'], row['z_1']
+        c1_index = atom_index
+        pdb_lines.append(f"ATOM  {atom_index:5d}  C1'  {resname} A{resid:4d}    {x:8.3f}{y:8.3f}{z:8.3f}  1.00  0.00           C")
+        atom_index += 1
+        base_offset = {'A': (1.5, 0.0, 0.5), 'C': (1.2, 0.3, 0.3), 'G': (1.7, -0.2, 0.7), 'U': (1.0, 0.5, 0.0)}.get(resname, (1.5, 0.0, 0.0))
+        base_x, base_y, base_z = x + base_offset[0], y + base_offset[1], z + base_offset[2]
+        base_index = atom_index
+        pdb_lines.append(f"ATOM  {atom_index:5d}  N9   {resname} A{resid:4d}    {base_x:8.3f}{base_y:8.3f}{base_z:8.3f}  1.00  0.00           N")
+        atom_index += 1
+        pdb_lines.append(f"CONECT{c1_index:5d}{base_index:5d}")
+        if prev_c1_index is not None:
+            pdb_lines.append(f"CONECT{prev_c1_index:5d}{c1_index:5d}")
+        prev_c1_index = c1_index
+    pdb_lines.append("END")
+    return "\n".join(pdb_lines)
+
+def predict_and_serve(sequence, description=""):
+    sequence = sequence.strip().upper()
+    if not sequence or not all(b in "ACGU" for b in sequence):
+        return "Invalid input", None, ""
+    df = predictor.predict(sequence, description)
+    pdb_text = create_pdb_from_prediction(df)
+    filename = f"{next(tempfile._get_candidate_names())}.pdb"
+    path = Path(STATIC_DIR) / filename
+    with open(path, "w") as f:
+        f.write(pdb_text)
+    
+    space_id = os.environ.get("SPACE_ID", "your-username--space-name")  # fallback if run locally
+    iframe_url = f"https://molstar.org/viewer/?loadFromUrl=https://{space_id}.hf.space/file=static/{filename}"
+    iframe_html = f'<iframe src="{iframe_url}" width="100%" height="600px" style="border:1px solid #ccc;"></iframe>'
+    return f"Predicted {len(df)} residues.", str(path), iframe_html
+
+with gr.Blocks() as demo:
+    gr.Markdown("## 🧬 RNA 3D Viewer (Hugging Face + Mol*)")
+
+    with gr.Row():
+        with gr.Column():
+            dropdown = gr.Dropdown(choices=test_seq_list, label="Select a Test Sequence")
+            seq_input = gr.Textbox(label="RNA Sequence", lines=4)
+            desc_input = gr.Textbox(label="Description (optional)", lines=1)
+            dropdown.change(fn=lambda s: s, inputs=dropdown, outputs=seq_input)
+            submit_btn = gr.Button("Submit")
+
+        with gr.Column():
+            status_output = gr.Textbox(label="Status")
+            file_output = gr.File(label="Download .pdb")
+
+    viewer_html = gr.HTML(label="Mol* Viewer")
+
+    submit_btn.click(
+        fn=predict_and_serve,
+        inputs=[seq_input, desc_input],
+        outputs=[status_output, file_output, viewer_html]
+    )
+
+demo.launch()

requirements.txt

@@ -0,0 +1,10 @@
+gradio==3.50.2
+pandas==2.0.3
+numpy==1.24.4
+torch>=2.0.0
+transformers>=4.28.0
+tqdm>=4.65.0
+biopython==1.81
+sentence-transformers>=2.2.2
+matplotlib>=3.7.1  # Useful for potential debugging or visualization
+scikit-learn>=1.2.2  # Commonly used with transformers

test_sequences.csv

@@ -0,0 +1,63 @@
+target_id,sequence,temporal_cutoff,description,all_sequences
+R1107,GGGGGCCACAGCAGAAGCGUUCACGUCGCAGCCCCUGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU,2022-05-28,"CPEB3 ribozyme
+Human
+human CPEB3 HDV-like ribozyme",">7QR4_1|Chain A|U1 small nuclear ribonucleoprotein A|Homo sapiens (9606)
+RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM
+>7QR4_2|Chain B|RNA CPEB3 ribozyme|Homo sapiens (9606)
+GGGGGCCACAGCAGAAGCGUUCACGUCGCAGCCCCUGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU"
+R1108,GGGGGCCACAGCAGAAGCGUUCACGUCGCGGCCCCUGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU,2022-05-27,"CPEB3 ribozyme
+Chimpanzee
+Chimpanzee CPEB3 HDV-like ribozyme",">7QR3_1|Chains A, B|U1 small nuclear ribonucleoprotein A|Homo sapiens (9606)
+RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM
+>7QR3_2|Chains C, D|chimpanzee CPEB3 ribozyme|Pan troglodytes (9598)
+GGGGGCCACAGCAGAAGCGUUCACGUCGCGGCCCCUGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU"
+R1116,CGCCCGGAUAGCUCAGUCGGUAGAGCAGCGGCUAAAACAGCUCUGGGGUUGUACCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUAUUGCGGUACCCUUGUACGCCUGUUUUAGCCGCGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGCCA,2022-06-04,"Cloverleaf RNA
+Poliovirus
+Crystal Structure of Poliovirus (type 1 Mahoney) cloverleaf RNA with tRNA scaffold",">8S95_1|Chain A[auth C]|Lysine tRNA scaffold,Poliovirus cloverleaf RNA|Homo sapiens (9606)
+CGCCCGGAUAGCUCAGUCGGUAGAGCAGCGGCUAAAACAGCUCUGGGGUUGUACCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUAUUGCGGUACCCUUGUACGCCUGUUUUAGCCGCGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGCCA"
+R1117v2,UUGGGUUCCCUCACCCCAAUCAUAAAAAGG,2022-06-03,"PreQ1 class I type III riboswitch
+K. pneumoniae
+Additional Information:        This is a ligand-only target (re-release of R1117 with the corrected SMILES string).
+ID  Name    SMILES  Relevant
+001 PRF NCc1c[nH]c2nc(N)[nH]c(=O)c12    Yes
+Class I type III preQ1 riboswitch from E. coli",">8FZA_1|Chains A, B|PreQ1 Riboswitch (30-MER)|Escherichia coli (562)
+UUGGGUUCCCUCACCCCAAUCAUAAAAAGG"
+R1126,GGAAUCUCGCCCGAUGUUCGCAUCGGGAUUUGCAGGUCCAUGGAUUACACCAUGCAACGCAGACCUGUAGAUGCCACGCUAGCCGUGGUGAGGGUCGGGUCCAGAUGUCAUUCGACUUUAACGCGCCUAAGCGUUGAAGGCGUGUUAGAGCAGAUAGUUCGCUAUCUGGGGAGCCUGUUCGCAGGCUCAGGAGCCUUCGGGCUCCUAGCGCUAUUACCCCGGACACCACCGGGCAGACAAGUAAUGGUGCUCCUCGAAUGACUUCUGUUGAGUAGAGUGUGGGCUCCGCGGCUAGUGUGCACCUUAGCGGUGAAUGUCUGACACCGUUAAGGUGGUUACUCUUCGGAGUAACGCCGAGAUUCC,2022-06-11,"Traptamer
+Synthetic
+Additional Information: Contains a relevant ion.
+RNA origami 3-helix tile Traptamer",">8TVZ_1|Chain A[auth C]|RNA (363-MER)|synthetic construct (32630)
+GGAAUCUCGCCCGAUGUUCGCAUCGGGAUUUGCAGGUCCAUGGAUUACACCAUGCAACGCAGACCUGUAGAUGCCACGCUAGCCGUGGUGAGGGUCGGGUCCAGAUGUCAUUCGACUUUAACGCGCCUAAGCGUUGAAGGCGUGUUAGAGCAGAUAGUUCGCUAUCUGGGGAGCCUGUUCGCAGGCUCAGGAGCCUUCGGGCUCCUAGCGCUAUUACCCCGGACACCACCGGGCAGACAAGUAAUGGUGCUCCUCGAAUGACUUCUGUUGAGUAGAGUGUGGGCUCCGCGGCUAGUGUGCACCUUAGCGGUGAAUGUCUGACACCGUUAAGGUGGUUACUCUUCGGAGUAACGCCGAGAUUCC"
+R1128,GGAAUAUCGUCAUGGUGAUUCGUCACCAUGAGGCUAGAUCUCAUAUCUAGCGCUUUCGAGCGCUAGAGUCCUUAUCUAGCCGGUUUAUACUUUCGAGUGUGAACCCGAUAUUCCGCGGAUCACUAUGAGUCGUUCGCGGCUCAUAGUCCGGCUCAAAGGACAUCAUGGCCUGUUCGCAGGUUGUGAUUAUGAGUGAGCCGGGUAAGGCAUACCGUUCGCGGUAUGUCUUACGAUCCGC,2022-06-10,"6WJ
+Single-stranded Paranemic Crossover RNA Triangle (PXT)",">8BTZ_1|Chain A|RNA Paranemic croosover triangle (PXT)|synthetic construct (32630)
+GGAAUAUCGUCAUGGUGAUUCGUCACCAUGAGGCUAGAUCUCAUAUCUAGCGCUUUCGAGCGCUAGAGUCCUUAUCUAGCCGGUUUAUACUUUCGAGUGUGAACCCGAUAUUCCGCGGAUCACUAUGAGUCGUUCGCGGCUCAUAGUCCGGCUCAAAGGACAUCAUGGCCUGUUCGCAGGUUGUGAUUAUGAGUGAGCCGGGUAAGGCAUACCGUUCGCGGUAUGUCUUACGAUCCGC"
+R1136,GGAUACGUCUACGCUCAGUGACGGACUCUCUUCGGAGAGUCUGACAUCCGAACCAUACACGGAUGUGCCUCGCCGAACAGUCUACGGCGAGCUUAAGCGCUGGGGACGCCCAACGCAUCACAAAGACUGAGUGAUGAACCAGAAGUAUGGACUGGUUGCGUUGGUGGAGACGGUCGGGUCCAGUUCGCUGUCGAGUAGAGUGUGGGCUCCAUCGACGCCGCUUUAAGGUCCCCAAUCGUGGCGUGUCGGCCUGCUUCGGCAGGCACUGGCGCCGGGACCUUGAAGAGAUGAGAUUUCGAUCUCAUCUUUGGGUGUCUCUGGUGCUUGAGGGCCCUGUGUUCGCACAGGGCCGCUCACUGGGUGUGGACGUAUCC,2022-06-18,"Apta-FRET
+Additional Information:        Information about the bound ligand is provided in SMILES section below.
+ID        Name        SMILES        Relevant
+001        1TU        Cc1nc(Cc2cc(F)c(O)c(F)c2)c(O)n1C        Yes
+002        J93        CN(CCO)c1cc2sc(/C=C(\C#N)c3ccc(C#N)cc3)cc2s1        Yes
+003        K        [K+]        Yes
+Ligand bound state of a brocolli-pepper aptamer FRET tile",">7ZJ4_1|Chain A[auth E]|brocolli-pepper aptamer|synthetic construct (32630)
+GGAUACGUCUACGCUCAGUGACGGACUCUCUUCGGAGAGUCUGACAUCCGAACCAUACACGGAUGUGCCUCGCCGAACAGUCUACGGCGAGCUUAAGCGCUGGGGACGCCCAACGCAUCACAAAGACUGAGUGAUGAACCAGAAGUAUGGACUGGUUGCGUUGGUGGAGACGGUCGGGUCCAGUUCGCUGUCGAGUAGAGUGUGGGCUCCAUCGACGCCGCUUUAAGGUCCCCAAUCGUGGCGUGUCGGCCUGCUUCGGCAGGCACUGGCGCCGGGACCUUGAAGAGAUGAGAUUUCGAUCUCAUCUUUGGGUGUCUCUGGUGCUUGAGGGCCCUGUGUUCGCACAGGGCCGCUCACUGGGUGUGGACGUAUCC"
+R1138,GGGAGAGUACUAUUCAGAUGCAGACCGCAAGUUCAGAGCGGUUUGCAUCUAGGGUACGUUUUCGAACGUAUCCUCCGACUAAGUGUAUUCGUAUACUUAGUGCCUUGUGCCUGCUUCGGCAGGCAUGACCCAAAUGUGCCUUUCGGGGCACAUUUCCGGUCAUCCAAGUUCGCUUGGGUGAUGCGGGCGUAUAGGUUCGUCUAUACGUCCGCGUUUUCCGAGAAGAGGUAACUCGGGAAACCGGUCCACGUGACAAAGGUAGAGUUACGUGGAGGGAGCAGCUGCAAAGGGAUAAUGCAGUUGCUGGCUGGAUGCCAGAACUCACGACUGGCAUCUACGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCGCCGAAUCGACCCCAACGUGAGAGGGGUCGGUUCCCCGAGCAUAGACCAAUAUCCCAGGUUUAUGCUCCCCAACGCUGGACGAACUACCUACGUCUAGCGUUCCGGCAAAUGAGUCAAUACCUCAGACUUAUUUGCGGUGCCUGAGCCUAAACUGAACAUGGGUUCAGGCAUCUUGGCUCCAGUUCGCUGGAGCCGACGGUAGCGCUGCGUUCGCGCAGUGCUAGGGAGCAUCCGUUUUCGAGCGGAUGCUGGGCGGUUGCCUGUUCGCAGGCAAUCGGGCCUACUCAUGAUUCGUCAUGAGUGGUGACAGCGUGAUGUUCGCAUUACGCUGUCGGGUAGAUGGAGAAUU,2022-06-24,"6HBC-Young
+Additional Information:        This is a co-transcriptional product. The structure observed in the cryo-EM grids immediately after the transcription and that around 8 hours later have alternative conformations. You can submit alternative conformations as separate models (we still stick to 5 models per target maximum).
+Young conformer of a 6-helix bundle of RNA with clasp",">7PTK_1|Chain A[auth B]|RNA|synthetic construct (32630)
+GGGAGAGUACUAUUCAGAUGCAGACCGCAAGUUCAGAGCGGUUUGCAUCUAGGGUACGUUUUCGAACGUAUCCUCCGACUAAGUGUAUUCGUAUACUUAGUGCCUUGUGCCUGCUUCGGCAGGCAUGACCCAAAUGUGCCUUUCGGGGCACAUUUCCGGUCAUCCAAGUUCGCUUGGGUGAUGCGGGCGUAUAGGUUCGUCUAUACGUCCGCGUUUUCCGAGAAGAGGUAACUCGGGAAACCGGUCCACGUGACAAAGGUAGAGUUACGUGGAGGGAGCAGCUGCAAAGGGAUAAUGCAGUUGCUGGCUGGAUGCCAGAACUCACGACUGGCAUCUACGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCGCCGAAUCGACCCCAACGUGAGAGGGGUCGGUUCCCCGAGCAUAGACCAAUAUCCCAGGUUUAUGCUCCCCAACGCUGGACGAACUACCUACGUCUAGCGUUCCGGCAAAUGAGUCAAUACCUCAGACUUAUUUGCGGUGCCUGAGCCUAAACUGAACAUGGGUUCAGGCAUCUUGGCUCCAGUUCGCUGGAGCCGACGGUAGCGCUGCGUUCGCGCAGUGCUAGGGAGCAUCCGUUUUCGAGCGGAUGCUGGGCGGUUGCCUGUUCGCAGGCAAUCGGGCCUACUCAUGAUUCGUCAUGAGUGGUGACAGCGUGAUGUUCGCAUUACGCUGUCGGGUAGAUGGAGAAUU"
+R1149,GGACACGAGUAACUCGUCUAUCUUCUGCAGGCUGCUUACGGUUUCGUCCGUGUUGCAGCCGAUCAUCAGCACAUCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUCCC,2022-07-02,"SARS-CoV-2 SL5
+Additional Information:        Alternative conformations present.
+SARS-CoV-2 5 proximal stem-loop 5",">8UYS_1|Chain A|SARS-CoV-2 RNA SL5 domain.|Severe acute respiratory syndrome coronavirus 2 (2697049)
+GGACACGAGUAACUCGUCUAUCUUCUGCAGGCUGCUUACGGUUUCGUCCGUGUUGCAGCCGAUCAUCAGCACAUCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGCCUUGUCCC"
+R1156,GGAGCAUCGUGUCUCAAGUGCUUCACGGUCACAAUAUACCGUUUCGUCGGGUGCGUGGCAAUUCGGUGCACAUCAUGUCUUUCGUGGCUGGUGUGGCUCCUCAAGGUGCGAGGGGCAAGUAUAGAGCAGAGCUCC,2022-07-07,"BtCoV-HKU5 SL5
+BtCoV-HKU5 5 proximal stem-loop 5, conformation 1",">8UYE_1|Chain A|BtCoV-HKU5 5' proximal stem-loop 5|Pipistrellus bat coronavirus HKU5 (694008)
+GGAGCAUCGUGUCUCAAGUGCUUCACGGUCACAAUAUACCGUUUCGUCGGGUGCGUGGCAAUUCGGUGCACAUCAUGUCUUUCGUGGCUGGUGUGGCUCCUCAAGGUGCGAGGGGCAAGUAUAGAGCAGAGCUCC"
+R1189,GCGUACAGGGAACACGCAACCCCGAAGGAUCGGGGAAGGGACGUCGCCAGGGAGGCGAUUCCAUCAGGAUGAUGACGAGGGACUGAAGAGUGGGCGGGGUAAUACCCCGCCCCUUUUU,2022-08-11,"A-6B
+Additional Information:        The T1189/R1189 and T1190/R1190 complexes represent alternative conformations corresponding to different particles in the same cryo-EM data set. The complexes contain one RNA molecule and several (4 or 6) protein molecules. The R1189/T1189 target pair represent the A1B6 complex, while the R1190/T1190 pair - A1B4 complex. Predictions for the corresponding RNA and protein targets should be submitted in the same frame of reference so that the concatenation of corresponding models, say, R1189TS000_1 and T1189TS000_1 will give a coordinate set for the full RNA-protein complex.
+Cryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex with three RsmA protein dimers",">7YR7_1|Chains A[auth B], B[auth C], C[auth D], D[auth E], F, G|Translational regulator CsrA|Pseudomonas aeruginosa (287)
+MLILTRRVGETLMVGDDVTVTVLGVKGNQVRIGVNAPKEVAVHREEIYQRIQKEK
+>7YR7_2|Chain E[auth A]|RsmZ RNA (118-MER)|Pseudomonas aeruginosa (287)
+GCGUACAGGGAACACGCAACCCCGAAGGAUCGGGGAAGGGACGUCGCCAGGGAGGCGAUUCCAUCAGGAUGAUGACGAGGGACUGAAGAGUGGGCGGGGUAAUACCCCGCCCCUUUUU"
+R1190,GCGUACAGGGAACACGCAACCCCGAAGGAUCGGGGAAGGGACGUCGCCAGGGAGGCGAUUCCAUCAGGAUGAUGACGAGGGACUGAAGAGUGGGCGGGGUAAUACCCCGCCCCUUUUU,2022-08-11,"A-4B
+Additional Information:        The T1189/R1189 and T1190/R1190 complexes represent alternative conformations corresponding to different particles in the same cryo-EM data set. The complexes contain one RNA molecule and several (4 or 6) protein molecules. The R1189/T1189 target pair represent the A1B6 complex, while the R1190/T1190 pair - A1B4 complex. Predictions for the corresponding RNA and protein targets should be submitted in the same frame of reference so that the concatenation of corresponding models, say, R1189TS000_1 and T1189TS000_1 will give a coordinate set for the full RNA-protein complex.
+Cryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex with two RsmA protein dimers",">7YR6_1|Chains A[auth B], B[auth C], C[auth D], D[auth E]|Translational regulator CsrA|Pseudomonas aeruginosa (287)
+MLILTRRVGETLMVGDDVTVTVLGVKGNQVRIGVNAPKEVAVHREEIYQRIQKEK
+>7YR6_2|Chain E[auth A]|RsmZ RNA|Pseudomonas aeruginosa (287)
+GCGUACAGGGAACACGCAACCCCGAAGGAUCGGGGAAGGGACGUCGCCAGGGAGGCGAUUCCAUCAGGAUGAUGACGAGGGACUGAAGAGUGGGCGGGGUAAUACCCCGCCCCUUUUU"