Update app.py

app.py

@@ -36,9 +36,9 @@ st.set_page_config(
     initial_sidebar_state="collapsed",
 )
 
-# Session State Initialization
-for k, v in [("seq_val", ""), ("smi_val", ""), ("bseq_val", ""),
-             ("ssel_val", ""), ("sseqs_val", ""), ("theme", "dark")]:
+# Session State Initialization (Mapped directly to widget keys now)
+for k, v in [("seq_widget", ""), ("smi_widget", ""), ("bseq_widget", ""),
+             ("ssel_widget", ""), ("sseqs_widget", ""), ("theme", "dark")]:
     if k not in st.session_state:
         st.session_state[k] = v
 
@@ -50,11 +50,13 @@ if is_dark:
 else:
     theme_css = ":root { --bg: #f8fafc; --surface: #ffffff; --border: #e2e8f0; --border-light: #cbd5e1; --text: #0f172a; --muted: #64748b; --accent: #2563eb; --accent-dim: rgba(37, 99, 235, 0.10); --success: #059669; --success-dim: rgba(5, 150, 105, 0.10); --danger: #dc2626; --danger-dim: rgba(220, 38, 38, 0.10); --font-sans: 'Inter', sans-serif; --font-mono: 'JetBrains Mono', monospace; }"
 
+# Added overflow-y: scroll to permanently show scrollbar and prevent UI vibration
 base_css = f"""
 <link rel="preconnect" href="https://fonts.googleapis.com">
 <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
 <link href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&family=JetBrains+Mono:wght@400;500&display=swap" rel="stylesheet">
 <style>
+html {{ overflow-y: scroll !important; }}
 #MainMenu, footer, header {{ visibility: hidden; }}
 .stDeployButton, [data-testid="stToolbar"] {{ display: none; }}
 [data-testid="collapsedControl"] {{ display: none !important; }}
@@ -528,10 +530,10 @@ n_loaded = len(fold_models)
 # UI Layout
 st.markdown("<div style='padding-top: 20px;'></div>", unsafe_allow_html=True)
 
-col_logo, col_title, col_togg = st.columns([1, 8, 2], gap="small")
+col_logo, col_title, col_togg = st.columns([1.5, 8, 2], gap="small")
 with col_logo:
     try:
-        st.image("static/logo.png", width=64)
+        st.image("static/logo.png", width=110)
     except Exception:
         pass
 
@@ -571,7 +573,7 @@ with tab1:
 
     with c1:
         st.markdown("""<div style="font-size:11px; font-weight:600; letter-spacing:1px; text-transform:uppercase; color:var(--muted); font-family:var(--font-sans); margin-bottom:8px;">TARGET PROTEIN</div>""", unsafe_allow_html=True)
-        seq_input = st.text_area("Sequence", value=st.session_state.seq_val, height=180, key="seq_widget", label_visibility="collapsed", placeholder=">TargetProtein\nMKTAYIAKQRQISFVK...")
+        seq_input = st.text_area("Sequence", key="seq_widget", label_visibility="collapsed", placeholder=">TargetProtein\nMKTAYIAKQRQISFVK...", height=180)
 
         st.markdown('<p style="font-size:11px; color:var(--muted); margin:8px 0 4px">Load example:</p>', unsafe_allow_html=True)
         ex_cols = st.columns(3)
@@ -579,13 +581,13 @@ with tab1:
             with ex_cols[i]:
                 st.markdown('<div class="pill-btn">', unsafe_allow_html=True)
                 if st.button(name, key=f"seq_ex_{i}"):
-                    st.session_state.seq_val = seq
+                    st.session_state.seq_widget = seq
                     st.rerun()
                 st.markdown('</div>', unsafe_allow_html=True)
 
     with c2:
         st.markdown("""<div style="font-size:11px; font-weight:600; letter-spacing:1px; text-transform:uppercase; color:var(--muted); font-family:var(--font-sans); margin-bottom:8px;">LIGAND</div>""", unsafe_allow_html=True)
-        smi_input = st.text_area("SMILES", value=st.session_state.smi_val, height=180, key="smi_widget", label_visibility="collapsed", placeholder="CCOc1cc2c(cc1OCC)ncnc2Nc1cccc(Cl)c1")
+        smi_input = st.text_area("SMILES", key="smi_widget", label_visibility="collapsed", placeholder="CCOc1cc2c(cc1OCC)ncnc2Nc1cccc(Cl)c1", height=180)
 
         st.markdown('<p style="font-size:11px; color:var(--muted); margin:8px 0 4px">Load example:</p>', unsafe_allow_html=True)
         sm_cols = st.columns(3)
@@ -593,7 +595,7 @@ with tab1:
             with sm_cols[i]:
                 st.markdown('<div class="pill-btn">', unsafe_allow_html=True)
                 if st.button(name, key=f"smi_ex_{i}"):
-                    st.session_state.smi_val = smi
+                    st.session_state.smi_widget = smi
                     st.rerun()
                 st.markdown('</div>', unsafe_allow_html=True)
 
@@ -608,68 +610,69 @@ with tab1:
             st.error("Please enter a SMILES string.")
         else:
             t0 = time.time()
-            with st.spinner("Running ESM-2 embedding..."):
+            with st.spinner("Running prediction pipeline..."):
                 esm_mean = embed_sequence(seq)
-            with st.spinner("Computing features and running ensemble..."):
                 seqfeat = seq_features(seq)
                 lig, err = ligand_features(smi)
-            if err:
-                st.error(f"Ligand error: {err}")
-            else:
-                with st.spinner("Running 45-model ensemble..."):
+                if err:
+                    st.error(f"Ligand error: {err}")
+                else:
                     X = assemble(esm_mean, seqfeat, lig, lig_scaler)
                     pkd, ci_lo, ci_hi = predict_pkd(X, fold_models, meta, iso_cal, target_mu, target_std)
-                if pkd is None:
-                    import random
-                    random.seed(hash(seq[:20] + smi[:20]) % 2 ** 31)
-                    pkd = random.uniform(5.5, 9.0)
-                    ci_lo = pkd - 0.8
-                    ci_hi = pkd + 0.8
-                in_domain, ad_dist = check_ad(esm_mean, train_embs, ad_threshold)
-                elapsed = round(time.time() - t0, 1)
-
-                st.markdown("<hr>", unsafe_allow_html=True)
-                mc1, mc2, mc3, mc4 = st.columns(4)
-                with mc1:
-                    metric_card("Predicted pKd", f"{pkd:.2f}", accent=True)
-                with mc2:
-                    metric_card("95% model interval", f"[{ci_lo:.2f}, {ci_hi:.2f}]")
-                with mc3:
-                    metric_card("Estimated Ki", pkd_to_ki(pkd))
-                with mc4:
-                    ad_badge(in_domain, ad_dist)
-
-                st.markdown("""
-                <div style="background:var(--surface); border:1px solid var(--border); border-radius:8px;
-                            padding:24px; margin:24px 0 10px; box-shadow:0 1px 3px rgba(0,0,0,0.1)">
-                  <div style="display:flex; align-items:center; justify-content:space-between; margin-bottom:16px">
-                    <div>
-                      <div style="font-size:16px; font-weight:600; color:var(--text); font-family:var(--font-sans)">Feature Attribution</div>
-                      <div style="font-size:12px; color:var(--muted); margin-top:4px">Physicochemical drivers of this prediction</div>
-                    </div>
-                    <span style="background:var(--accent-dim); color:var(--accent); border-radius:4px; padding:4px 8px; font-size:11px; font-family:var(--font-mono); font-weight:500;">SHAP | LightGBM</span>
-                  </div>
-                """, unsafe_allow_html=True)
-                fig = xai_chart(smi, pkd, is_dark)
-                if fig:
-                    st.pyplot(fig, use_container_width=True)
-                    plt.close(fig)
-                st.markdown("</div>", unsafe_allow_html=True)
-
-                st.markdown(f"""
-                <div style="font-size:11px; color:var(--muted); font-family:var(--font-mono); display:flex; gap:12px; flex-wrap:wrap">
-                  <span>Time: {elapsed}s</span><span style="color:var(--border-light)">|</span>
-                  <span>45-model ensemble</span><span style="color:var(--border-light)">|</span>
-                  <span>{n_loaded} models loaded</span><span style="color:var(--border-light)">|</span>
-                  <span>CPU</span>
-                </div>""", unsafe_allow_html=True)
+                    
+                    if pkd is None:
+                        import random
+                        random.seed(hash(seq[:20] + smi[:20]) % 2 ** 31)
+                        pkd = random.uniform(5.5, 9.0)
+                        ci_lo = pkd - 0.8
+                        ci_hi = pkd + 0.8
+                    
+                    in_domain, ad_dist = check_ad(esm_mean, train_embs, ad_threshold)
+                    elapsed = round(time.time() - t0, 1)
+
+                    st.markdown("<hr>", unsafe_allow_html=True)
+                    mc1, mc2, mc3, mc4 = st.columns(4)
+                    with mc1:
+                        metric_card("Predicted pKd", f"{pkd:.2f}", accent=True)
+                    with mc2:
+                        metric_card("95% model interval", f"[{ci_lo:.2f}, {ci_hi:.2f}]")
+                    with mc3:
+                        metric_card("Estimated Ki", pkd_to_ki(pkd))
+                    with mc4:
+                        ad_badge(in_domain, ad_dist)
+
+                    st.markdown("""
+                    <div style="background:var(--surface); border:1px solid var(--border); border-radius:8px;
+                                padding:24px; margin:24px 0 10px; box-shadow:0 1px 3px rgba(0,0,0,0.1)">
+                      <div style="display:flex; align-items:center; justify-content:space-between; margin-bottom:16px">
+                        <div>
+                          <div style="font-size:16px; font-weight:600; color:var(--text); font-family:var(--font-sans)">Feature Attribution</div>
+                          <div style="font-size:12px; color:var(--muted); margin-top:4px">Physicochemical drivers of this prediction</div>
+                        </div>
+                        <span style="background:var(--accent-dim); color:var(--accent); border-radius:4px; padding:4px 8px; font-size:11px; font-family:var(--font-mono); font-weight:500;">SHAP | LightGBM</span>
+                      </div>
+                    """, unsafe_allow_html=True)
+                    
+                    fig = xai_chart(smi, pkd, is_dark)
+                    if fig:
+                        st.pyplot(fig, use_container_width=True)
+                        plt.close(fig)
+                    st.markdown("</div>", unsafe_allow_html=True)
+
+                    st.markdown(f"""
+                    <div style="font-size:11px; color:var(--muted); font-family:var(--font-mono); display:flex; gap:12px; flex-wrap:wrap">
+                      <span>Time: {elapsed}s</span><span style="color:var(--border-light)">|</span>
+                      <span>45-model ensemble</span><span style="color:var(--border-light)">|</span>
+                      <span>{n_loaded} models loaded</span><span style="color:var(--border-light)">|</span>
+                      <span>CPU</span>
+                    </div>""", unsafe_allow_html=True)
 
 # TAB 2: BATCH
 with tab2:
     b1, b2 = st.columns(2, gap="large")
     with b1:
         st.markdown("""<div style="font-size:11px; font-weight:600; letter-spacing:1px; text-transform:uppercase; color:var(--muted); font-family:var(--font-sans); margin-bottom:8px;">TARGET PROTEIN</div>""", unsafe_allow_html=True)
-        batch_seq = st.text_area("Sequence, plain or FASTA", value=st.session_state.bseq_val, height=180, key="bseq_widget", label_visibility="collapsed", placeholder=">Target\nMKTAYIAKQRQISFVK...")
+        batch_seq = st.text_area("Sequence, plain or FASTA", key="bseq_widget", label_visibility="collapsed", placeholder=">Target\nMKTAYIAKQRQISFVK...", height=180)
 
     with b2:
         st.markdown("""<div style="font-size:11px; font-weight:600; letter-spacing:1px; text-transform:uppercase; color:var(--muted); font-family:var(--font-sans); margin-bottom:8px;">COMPOUND LIBRARY <span style="font-weight:400; font-family:var(--font-mono); text-transform:none">(CSV with smiles column)</span></div>""", unsafe_allow_html=True)
@@ -749,10 +752,10 @@ with tab3:
     s1, s2 = st.columns(2, gap="large")
     with s1:
         st.markdown("""<div style="font-size:11px; font-weight:600; letter-spacing:1px; text-transform:uppercase; color:var(--muted); font-family:var(--font-sans); margin-bottom:8px;">LIGAND</div>""", unsafe_allow_html=True)
-        sel_smi = st.text_area("SMILES string", height=140, value=st.session_state.ssel_val, key="ssel_widget", label_visibility="collapsed", placeholder="Paste SMILES...")
+        sel_smi = st.text_area("SMILES string", key="ssel_widget", label_visibility="collapsed", placeholder="Paste SMILES...", height=140)
     with s2:
         st.markdown("""<div style="font-size:11px; font-weight:600; letter-spacing:1px; text-transform:uppercase; color:var(--muted); font-family:var(--font-sans); margin-bottom:8px;">OFF-TARGET PANEL <span style="font-weight:400; font-family:var(--font-mono); text-transform:none">(one sequence per line)</span></div>""", unsafe_allow_html=True)
-        sel_seqs = st.text_area("Sequences", height=140, value=st.session_state.sseqs_val, key="sseqs_widget", label_visibility="collapsed", placeholder="Paste sequences, one per line...")
+        sel_seqs = st.text_area("Sequences", key="sseqs_widget", label_visibility="collapsed", placeholder="Paste sequences, one per line...", height=140)
 
     st.markdown("<br>", unsafe_allow_html=True)