Working readthedocs

docs/_static/smart_search.js

@@ -0,0 +1,64 @@
+document.addEventListener("DOMContentLoaded", () => {
+  const form = document.getElementById("smartSearchForm");
+  const input = document.getElementById("smartSearchInput");
+  const status = document.getElementById("smartSearchStatus");
+
+  if (!form || !input) return;
+
+  const URL_ROOT =
+    (window.DOCUMENTATION_OPTIONS && window.DOCUMENTATION_OPTIONS.URL_ROOT) || "./";
+
+  const apiIndexUrl = URL_ROOT + "_static/api_index.json";
+
+  async function loadIndex() {
+    const r = await fetch(apiIndexUrl, { cache: "no-store" });
+    if (!r.ok) throw new Error(`Failed to load api_index.json (${r.status})`);
+    return await r.json();
+  }
+
+  function goToSearch(query) {
+    window.location.href = URL_ROOT + "search.html?q=" + encodeURIComponent(query);
+  }
+
+  form.addEventListener("submit", async (e) => {
+    e.preventDefault();
+
+    const q = (input.value || "").trim();
+    if (!q) return;
+
+    if (status) status.textContent = "Searching...";
+
+    try {
+      const idx = await loadIndex();
+
+      const key = q.toLowerCase();
+
+      // 1) Exact match by simple name (parsepdb -> parsePDB)
+      if (idx.exact_simple && idx.exact_simple[key]) {
+        window.location.href = URL_ROOT + idx.exact_simple[key];
+        return;
+      }
+
+      // 2) Exact match by full name if user pasted it
+      if (idx.exact_full && idx.exact_full[key]) {
+        window.location.href = URL_ROOT + idx.exact_full[key];
+        return;
+      }
+
+      // 3) No exact match -> normal Sphinx search (prefix search)
+      goToSearch(q);
+    } catch (err) {
+      console.error(err);
+      if (status) status.textContent = "Index not loaded; using normal search.";
+      goToSearch(q);
+    }
+  });
+
+  // Optional: make Enter always submit even if browser is weird
+  input.addEventListener("keydown", (e) => {
+    if (e.key === "Enter") {
+      e.preventDefault();
+      form.requestSubmit();
+    }
+  });
+});

docs/conf.py

@@ -73,6 +73,9 @@
 
 # Ensure this is set so Sphinx looks in the _static folder
 html_static_path = ['_static']
+html_js_files = [
+    "smart_search.js",
+]
 
 # -- Extension Configuration -------------------------------------------------
 
@@ -100,3 +103,59 @@
     'scipy': ('https://docs.scipy.org/doc/scipy/', None),
     'matplotlib': ('https://matplotlib.org/stable/', None),
 }
+import os
+import sys
+import json
+import os
+from sphinx.util.inventory import InventoryFile
+
+def build_api_index(app, exception):
+    # If build failed, don't do anything
+    if exception is not None:
+        return
+
+    inv_path = os.path.join(app.outdir, "objects.inv")
+    if not os.path.isfile(inv_path):
+        print("WARNING: objects.inv not found, skipping api_index.json generation")
+        return
+
+    with open(inv_path, "rb") as f:
+        inv = InventoryFile.load(f, "", lambda base, uri: uri)
+
+    # Map lowercase simple name -> URL
+    # Also keep full names in case you want them later
+    exact_simple = {}
+    exact_full = {}
+
+    # Prefer functions over methods if there's a collision
+    role_priority = ["py:function", "py:method"]
+
+    for role in role_priority:
+        if role not in inv:
+            continue
+        for fullname, data in inv[role].items():
+            # data = (project, version, uri, dispname)
+            uri = data[2]
+            # Sphinx inventory sometimes uses "$" as placeholder for fullname
+            uri = uri.replace("$", fullname)
+
+            simple = fullname.split(".")[-1].lower()
+            full_lower = fullname.lower()
+
+            # fill full map always
+            exact_full[full_lower] = uri
+
+            # fill simple map only if empty (function wins because we iterate functions first)
+            if simple not in exact_simple:
+                exact_simple[simple] = uri
+
+    out_path = os.path.join(app.outdir, "_static", "api_index.json")
+    os.makedirs(os.path.dirname(out_path), exist_ok=True)
+
+    with open(out_path, "w", encoding="utf-8") as f:
+        json.dump({"exact_simple": exact_simple, "exact_full": exact_full}, f)
+
+    print(f"Wrote {out_path} with {len(exact_simple)} simple entries")
+
+def setup(app):
+    app.connect("build-finished", build_api_index)

docs/index.rst

@@ -17,8 +17,8 @@ ProDy Manual
 
 .. toctree::
    :maxdepth: 2
-   :glob:
 
+   smart_search
    getprody
    apps/index
    reference/index

docs/smart_search.rst

@@ -0,0 +1,19 @@
+Smart Search
+============
+
+Type a ProDy function name.
+
+- If it's an exact match (case-insensitive), you go directly to that function page.
+- Otherwise, it falls back to normal search.
+
+.. raw:: html
+
+   <div style="max-width: 700px;">
+     <form id="smartSearchForm">
+       <input id="smartSearchInput"
+              placeholder="Enter function name (e.g. parsePDB)"
+              style="width:100%; padding:10px; font-size:16px;" />
+       <button type="submit" style="margin-top:10px; padding:8px 12px;">Search</button>
+     </form>
+     <p id="smartSearchStatus" style="margin-top:10px; opacity:0.8;"></p>
+   </div>

docs/tools/build_api_index.py

@@ -0,0 +1,76 @@
+# -*- coding: utf-8 -*-
+import json
+import os
+import sys
+import importlib
+from pathlib import Path
+
+
+def iter_module_names(pkg_name: str, pkg_root: Path):
+    """
+    Walk the package directory on disk WITHOUT importing subpackages.
+    This avoids importing prody.tests.* which breaks on RTD.
+    """
+    for py in pkg_root.rglob("*.py"):
+        # Skip caches / hidden
+        if "__pycache__" in py.parts:
+            continue
+
+        rel = py.relative_to(pkg_root)
+
+        # Skip tests entirely (this fixes your NRAS_BRAF_GDP_model_0.cif crash)
+        if "tests" in rel.parts:
+            continue
+
+        # Build module name
+        parts = list(rel.parts)
+        if parts[-1] == "__init__.py":
+            parts = parts[:-1]
+        else:
+            parts[-1] = parts[-1].replace(".py", "")
+
+        if not parts:
+            yield pkg_name
+        else:
+            yield pkg_name + "." + ".".join(parts)
+
+
+def main():
+    import prody
+
+    pkg_name = "prody"
+    pkg_root = Path(prody.__file__).resolve().parent
+
+    here = Path(__file__).resolve().parent.parent  # docs/
+    out_dir = here / "_static"
+    out_dir.mkdir(parents=True, exist_ok=True)
+    out_file = out_dir / "api_index.json"
+
+    results = []
+
+    for modname in sorted(set(iter_module_names(pkg_name, pkg_root))):
+        try:
+            mod = importlib.import_module(modname)
+        except Exception:
+            # Some modules may require optional deps or side effects.
+            # We skip them so docs build doesn't fail.
+            continue
+
+        for name, obj in vars(mod).items():
+            if callable(obj) and getattr(obj, "__module__", "") == modname:
+                qual = f"{modname}.{name}"
+                results.append(
+                    {
+                        "name": name,          # parsePDB
+                        "qualname": qual,      # prody.proteins.pdbfile.parsePDB
+                    }
+                )
+
+    with out_file.open("w", encoding="utf-8") as f:
+        json.dump(results, f, indent=2)
+
+    print(f"[smart_search] wrote {len(results)} entries to {out_file}")
+
+
+if __name__ == "__main__":
+    main()