Deploy 01b0d87

The agent can read the vector catalogue instead of remembering one

Source: https://github.com/WINTER4000/turingDNA/commit/01b0d87657c7fa96b312320edd6058984492315f

dee/core/agent_tools.py

@@ -838,6 +838,55 @@ _REGION_RE = re.compile(r"^\s*(\d{1,9})\s*(?:\.\.|-|\u2013|:)\s*(\d{1,9})\s*$")
 _PLASMID_MAX_FEATURES = 40
 
 
+def _tool_lookup_vector(args: Dict[str, Any]) -> Dict[str, Any]:
+    """What the catalogue says about a cloning backbone — and nothing else.
+
+    Exists because of a real transcript (2026-08-04): asked to build in
+    pCAMBIA1300, fetch_sequence correctly refused (it resolves genes, not
+    vectors), and the agent then recited the MCS from memory — inventing SbfI
+    and SmaI, dropping XhoI — and began designing a Golden Gate strategy on
+    it. The verified entry was in the app the whole time; the agent just had
+    no way to read it.
+
+    Reports the record verbatim. A vector that is not in the catalogue comes
+    back ok=False with the near matches, which is a fact to act on rather than
+    a gap to fill from recall.
+    """
+    from dee.core import vectors as _vec
+
+    name = str(args.get("name") or "").strip()
+    if not name:
+        return {"ok": False, "error": "Which vector? Give its name, e.g. pET-28a(+)."}
+
+    entry = _vec.find(name)
+    if entry:
+        return {"ok": True, "vector": entry, "source": "curated catalogue",
+                # Said out loud so the agent passes it on: this is a curated
+                # map, not the user's actual plasmid, and the two differ the
+                # moment anyone has modified their copy.
+                "caveat": ("Curated reference data (Addgene / NEB REBASE / "
+                           "supplier sheets), not the user's own plasmid. If "
+                           "they have modified their copy, ask them to paste "
+                           "or upload it and map that instead."),
+                "note": ("These are the ONLY fields known for this vector. Do "
+                         "not add restriction sites, coordinates or features "
+                         "that are not listed here.")}
+
+    near = _vec.search(name, limit=6)
+    return {
+        "ok": False,
+        "kind": "not_in_catalogue",
+        "error": (f"“{name}” is not in the vector catalogue "
+                  f"({_vec.catalogue_size()} backbones)."),
+        "did_you_mean": [e.get("name") for e in near],
+        # The whole point. A refusal here must not become a memory prompt.
+        "next": ("Do NOT describe this vector from memory — no MCS order, no "
+                 "sizes, no feature coordinates. Either offer one of the "
+                 "catalogue vectors above, or ask the user to paste/upload "
+                 "their backbone so map_plasmid can read the real one."),
+    }
+
+
 def _tool_edit_sequence(args: Dict[str, Any]) -> Dict[str, Any]:
     """Change the construct this conversation is working on.
 
@@ -1465,6 +1514,10 @@ _TOOLS: Dict[str, Dict[str, Any]] = {
     # Pure UI direction — no compute, no storage, no account needed.
     "focus_on":        {"fn": _tool_focus_on,        "requires_signin": False},
     "map_plasmid":     {"fn": _tool_map_plasmid,     "requires_signin": False},
+    # Reads curated reference data. No auth: knowing what pET-28a is should
+    # not require an account, and gating it would push an anonymous user back
+    # toward the recalled answer this tool exists to replace.
+    "lookup_vector":   {"fn": _tool_lookup_vector,   "requires_signin": False},
     # The only tool that changes the construct. Three flags, each earning its
     # place: signed-in because it writes; confirm because the user must agree
     # to their own DNA being altered; needs_target because the sequence comes
@@ -1545,6 +1598,33 @@ TOOL_SPECS: List[Dict[str, Any]] = [
             },
         },
     },
+    {
+        "type": "function",
+        "function": {
+            "name": "lookup_vector",
+            "description": (
+                "Look up a cloning / expression BACKBONE (pET-28a, pUC19, "
+                "pCAMBIA1300, pBI121, …) in the curated catalogue: size, "
+                "promoter, selection markers, MCS enzymes, fusion tags, "
+                "supplier. "
+                "USE THIS whenever a vector is named — fetch_sequence resolves "
+                "GENES and will refuse a vector, and a refusal is NOT "
+                "permission to describe the vector from memory. "
+                "If it is not in the catalogue, say so and offer the near "
+                "matches, or ask the user to paste their backbone and run "
+                "map_plasmid on the real thing. Never state an MCS order, a "
+                "size or a feature coordinate that this tool did not return."
+            ),
+            "parameters": {
+                "type": "object",
+                "properties": {
+                    "name": {"type": "string",
+                             "description": "Vector name, e.g. 'pCAMBIA1300'."},
+                },
+                "required": ["name"],
+            },
+        },
+    },
     {
         "type": "function",
         "function": {

dee/core/orchestrator.py

@@ -135,6 +135,7 @@ _TOOL_UI: Dict[str, Dict[str, Any]] = {
     "design_primers":         {"view": "primers",   "verb": "Checking primers"},
     "recommend_promoter":     {"view": None,        "verb": "Selecting promoter"},
     "map_plasmid":            {"view": "plasmid",   "verb": "Mapping the construct"},
+    "lookup_vector":          {"view": None,        "verb": "Looking up the vector"},
     "edit_sequence":          {"view": "plasmid",   "verb": "Editing the construct"},
     # No painter: cut sites are an answer, not a canvas. Claiming the Map tab
     # for them would tell the user to look at a tab that never changed.
@@ -307,6 +308,12 @@ def _summarize(name: str, result: Dict[str, Any]) -> str:
             size = f"{result.get('length'):,} bp"
             return (f"{labels} · {size}" if not d
                     else f"{labels} · {size} ({d:+d})")
+        if name == "lookup_vector":
+            v = result.get("vector") or {}
+            if v:
+                return (f"{v.get('name')} · {v.get('size_bp'):,} bp · "
+                        f"{len(v.get('mcs_enzymes') or [])} MCS sites")
+            return "not in the catalogue"
         if name == "map_plasmid":
             n = result.get("feature_count") or 0
             return (f"{result.get('length'):,} bp {result.get('topology')} · "
@@ -1871,6 +1878,29 @@ SYSTEM_PROMPT = (
     "propose_round2). You can reach every phase; don't hand the user off to a "
     "tab to do something you can do here.\n\n"
 
+    "A TOOL SAYING NO IS AN ANSWER, NOT AN OBSTACLE\n"
+    "When a tool cannot find something, that is a FACT about the world and you "
+    "report it. It is never permission to supply the missing data from "
+    "memory.\n"
+    "This is not hypothetical. Asked to build in pCAMBIA1300, fetch_sequence "
+    "correctly refused — it resolves genes, and a vector backbone is not a "
+    "gene. The reply was \"since I cannot fetch it, I will use its standard, "
+    "well-characterized map\", followed by a recited MCS that invented two "
+    "restriction sites and dropped a real one, and then a cloning strategy "
+    "built on top of it. The refusal was right. Everything after it was "
+    "fabricated, and it was heading for someone's bench.\n"
+    "So, concretely — after ANY failed lookup you must not state from memory: "
+    "a sequence or any part of one; an MCS or restriction-site order; a "
+    "length, coordinate or feature position; a promoter, marker or tag; a "
+    "published value of any kind. You have tools for these. Use the right one "
+    "(lookup_vector for backbones, fetch_sequence for genes, map_plasmid for "
+    "anything the user can paste), or say plainly that you don't have it and "
+    "ask.\n"
+    "\"I know this one\" is exactly the moment to stop. The user cannot tell "
+    "your recall from your tools, and a confident wrong map is worse than no "
+    "map — it is the one failure that costs them a synthesis order and weeks "
+    "at the bench.\n\n"
+
     "MAKE THE CHANGE, THEN CHECK IT\n"
     "edit_sequence is the one tool that alters the construct. When someone "
     "asks for a mutation, make it — do not describe the edit and leave them "

dee/core/vectors.py

@@ -0,0 +1,104 @@
+"""The vector catalogue, readable by the agent.
+
+WHY THIS EXISTS (2026-08-04, from a live transcript)
+-----------------------------------------------------
+A user asked Turing to build a construct in pCAMBIA1300. `fetch_sequence`
+correctly refused — it resolves GENES via Ensembl/UniProt, and a binary vector
+backbone is not a gene. Turing then wrote:
+
+    "Since I cannot fetch the raw sequence of pCAMBIA1300 directly from the
+     database, I will design the cloning strategy using its standard,
+     well-characterized map."
+
+...and recited an MCS from memory:
+
+    HindIII - SbfI - PstI - SalI - XbaI - BamHI - SmaI - KpnI - SacI - EcoRI
+
+The curated entry in dee/static/cloning_db.js — human-verified against Addgene
+and the CAMBIA product sheet — says:
+
+    EcoRI, KpnI, XbaI, SalI, PstI, HindIII, BamHI, SacI, XhoI
+
+SbfI and SmaI were invented; XhoI was dropped. A Golden Gate strategy was
+being designed on top of that. The failure was not the refusal — the refusal
+was correct and honest. The failure is that the app HAD the right answer and
+the agent had no way to reach it, so it filled the gap from recall.
+
+SINGLE SOURCE OF TRUTH
+----------------------
+dee/data/vectors.json is EXTRACTED from cloning_db.js by executing the real
+file (scripts/extract_vectors.js), never retyped — retyping 61 curated records
+is the same transcription risk this module exists to remove. A test asserts
+the two stay in agreement, so drift fails the suite instead of reaching a
+bench.
+
+This module reports what the catalogue says and nothing more. It does not
+infer, complete or interpolate: a vector that is not in here comes back as
+"not in the catalogue", which is a fact the agent can act on, rather than an
+invitation to remember one.
+"""
+from __future__ import annotations
+
+import json
+import os
+import re
+from typing import Any, Dict, List, Optional
+
+_DATA = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
+                     "data", "vectors.json")
+
+_CACHE: Optional[Dict[str, Dict[str, Any]]] = None
+
+
+def _load() -> Dict[str, Dict[str, Any]]:
+    global _CACHE
+    if _CACHE is None:
+        with open(_DATA, encoding="utf-8") as fh:
+            _CACHE = json.load(fh)
+    return _CACHE
+
+
+def _norm(name: str) -> str:
+    """'pCAMBIA-1300' / 'pCAMBIA 1300' / 'PCAMBIA1300' -> 'pcambia1300'."""
+    return re.sub(r"[^a-z0-9]", "", str(name or "").lower())
+
+
+def find(name: str) -> Optional[Dict[str, Any]]:
+    """Exact-ish lookup by id or display name. None when absent.
+
+    Deliberately NOT fuzzy. A near-match on a vector name is how pUC19 becomes
+    pUC18 and a whole cloning design shifts by one polylinker.
+    """
+    key = _norm(name)
+    if not key:
+        return None
+    data = _load()
+    if key in data:
+        return data[key]
+    for entry in data.values():
+        if _norm(entry.get("name", "")) == key or _norm(entry.get("id", "")) == key:
+            return entry
+    return None
+
+
+def search(query: str, limit: int = 8) -> List[Dict[str, Any]]:
+    """Substring matches, for 'what pCAMBIA vectors do you have?'.
+
+    Returned so the agent can OFFER real options instead of guessing which
+    one the user meant.
+    """
+    q = _norm(query)
+    data = _load()
+    if not q:
+        return list(data.values())[:limit]
+    hits = [e for e in data.values()
+            if q in _norm(e.get("name", "")) or q in _norm(e.get("id", ""))]
+    return hits[:limit]
+
+
+def catalogue_size() -> int:
+    return len(_load())
+
+
+def all_names() -> List[str]:
+    return sorted(e.get("name", "") for e in _load().values())

dee/data/vectors.json

@@ -0,0 +1,1809 @@
+{
+  "pet28a": {
+    "id": "pet28a",
+    "name": "pET-28a(+)",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5369,
+    "promoter": "T7 lac",
+    "induction": "IPTG (0.1–1 mM)",
+    "selection": [
+      "kanamycin (50 µg/mL)"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "MGSSHHHHHHSSGLVPRGSHM (His6 + thrombin)",
+      "c_term": "LEHHHHHH (His6)"
+    },
+    "mcs_enzymes": [
+      "NcoI",
+      "NheI",
+      "NdeI",
+      "BamHI",
+      "EcoRV",
+      "EcoRI",
+      "SacI",
+      "SalI",
+      "HindIII",
+      "NotI",
+      "XhoI"
+    ],
+    "flanking_5p_max": "AAGGAGATATACCATGGCT",
+    "flanking_3p_max": "CTCGAGCACCACCACCACCACCACTGAGATCC",
+    "addgene": "69864-3",
+    "supplier": "Sigma-Aldrich / Novagen",
+    "notes": "Workhorse bacterial expression vector. T7 promoter requires DE3-lysogen host (BL21(DE3), Rosetta, etc.)."
+  },
+  "pet21a": {
+    "id": "pet21a",
+    "name": "pET-21a(+)",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5443,
+    "promoter": "T7 lac",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin (100 µg/mL)"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "T7-tag (MASMTGGQQMG)",
+      "c_term": "LEHHHHHH (His6)"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "NheI",
+      "BamHI",
+      "EcoRI",
+      "SacI",
+      "SalI",
+      "HindIII",
+      "NotI",
+      "EagI",
+      "XhoI"
+    ],
+    "flanking_5p_max": "AAGGAGATATACATATG",
+    "flanking_3p_max": "CTCGAGCACCACCACCACCACCACTGA",
+    "addgene": "69740",
+    "supplier": "Sigma / Novagen",
+    "notes": "Like pET-28a but amp-resistant and no N-term His tag."
+  },
+  "pet22b": {
+    "id": "pet22b",
+    "name": "pET-22b(+)",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5493,
+    "promoter": "T7 lac",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "pelB signal (periplasmic export)",
+      "c_term": "LEHHHHHH"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "NcoI",
+      "BamHI",
+      "EcoRI",
+      "SacI",
+      "SalI",
+      "HindIII",
+      "NotI",
+      "XhoI"
+    ],
+    "flanking_5p_max": "AAGGAGATATACATATG",
+    "flanking_3p_max": "CTCGAGCACCACCACCACCACCACTGA",
+    "notes": "pelB signal peptide directs protein to the periplasm — useful for disulfide-containing or toxic proteins."
+  },
+  "pet32a": {
+    "id": "pet32a",
+    "name": "pET-32a(+)",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5900,
+    "promoter": "T7 lac",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "Trx + His6 + S-tag + thrombin",
+      "c_term": "His6"
+    },
+    "mcs_enzymes": [
+      "KpnI",
+      "BamHI",
+      "EcoRI",
+      "EcoRV",
+      "AvaI",
+      "HindIII",
+      "SalI",
+      "XhoI",
+      "NotI"
+    ],
+    "flanking_5p_max": "GGTACC",
+    "flanking_3p_max": "CTCGAG",
+    "notes": "N-terminal thioredoxin fusion enhances solubility of difficult proteins."
+  },
+  "pgex_6p_1": {
+    "id": "pgex_6p_1",
+    "name": "pGEX-6P-1",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 4984,
+    "promoter": "tac",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "GST + PreScission protease site (LEVLFQ↓GP)",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "BamHI",
+      "EcoRI",
+      "SmaI",
+      "SalI",
+      "XhoI",
+      "NotI"
+    ],
+    "flanking_5p_max": "CTGGAAGTTCTGTTCCAGGGGCCC",
+    "flanking_3p_max": "TAATAA",
+    "supplier": "Cytiva / GE Healthcare",
+    "notes": "N-terminal GST fusion (~26 kDa). Purify on glutathione resin, cleave with PreScission to release tag."
+  },
+  "pmal_c5x": {
+    "id": "pmal_c5x",
+    "name": "pMAL-c5X",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5677,
+    "promoter": "tac",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "MBP + Factor Xa site (IEGR↓)",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "EcoRI",
+      "BamHI",
+      "XbaI",
+      "SalI",
+      "PstI",
+      "HindIII"
+    ],
+    "flanking_5p_max": "GAAGGTAGGTCATATG",
+    "flanking_3p_max": "AAGCTT",
+    "supplier": "NEB",
+    "notes": "N-terminal MBP (~42 kDa) — strong solubility enhancer for difficult proteins."
+  },
+  "puc19": {
+    "id": "puc19",
+    "name": "pUC19",
+    "host": "e_coli",
+    "category": "general_cloning",
+    "size_bp": 2686,
+    "promoter": "lac (for α-complementation)",
+    "induction": "none",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "high",
+    "fusion_tag": {
+      "n_term": "none",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "EcoRI",
+      "SacI",
+      "KpnI",
+      "SmaI",
+      "BamHI",
+      "XbaI",
+      "SalI",
+      "AccI",
+      "HincII",
+      "PstI",
+      "SphI",
+      "HindIII"
+    ],
+    "flanking_5p_max": "GAATTC",
+    "flanking_3p_max": "AAGCTT",
+    "notes": "High-copy cloning vector. Blue-white screening via lacZα. No expression machinery — for shuttling DNA only."
+  },
+  "pbluescript": {
+    "id": "pbluescript",
+    "name": "pBluescript II SK(+)",
+    "host": "e_coli",
+    "category": "general_cloning",
+    "size_bp": 2961,
+    "promoter": "T7, T3 (for in vitro RNA)",
+    "induction": "n/a",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "high",
+    "fusion_tag": {
+      "n_term": "none",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "KpnI",
+      "ApaI",
+      "XhoI",
+      "SalI",
+      "AccI",
+      "HincII",
+      "ClaI",
+      "HindIII",
+      "EcoRV",
+      "EcoRI",
+      "PstI",
+      "SmaI",
+      "BamHI",
+      "SpeI",
+      "XbaI",
+      "NotI",
+      "SacII",
+      "SacI"
+    ],
+    "flanking_5p_max": "GGTACC",
+    "flanking_3p_max": "GAGCTC",
+    "supplier": "Agilent / Stratagene",
+    "notes": "Versatile cloning vector with flanking T7 + T3 promoters for in vitro RNA transcription from either strand."
+  },
+  "pcdf_duet": {
+    "id": "pcdf_duet",
+    "name": "pCDFDuet-1",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 3781,
+    "promoter": "two T7 lac (dual MCS)",
+    "induction": "IPTG",
+    "selection": [
+      "streptomycin (50 µg/mL)"
+    ],
+    "copy": "low (CDF origin)",
+    "fusion_tag": {
+      "n_term": "optional His6 (MCS1)",
+      "c_term": "optional S-tag (MCS2)"
+    },
+    "mcs_enzymes": [
+      "NcoI",
+      "NdeI",
+      "BamHI",
+      "EcoRI",
+      "SacI",
+      "NotI",
+      "AvrII",
+      "PstI",
+      "HindIII",
+      "XhoI",
+      "BglII",
+      "KpnI",
+      "PacI"
+    ],
+    "flanking_5p_max": "AAGGAGATATACCATGG",
+    "flanking_3p_max": "CTCGAG",
+    "notes": "Dual-expression vector for co-expression with pET or pACYC partners (different antibiotics, different origins)."
+  },
+  "pcdna3_1": {
+    "id": "pcdna3_1",
+    "name": "pcDNA3.1(+)",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 5428,
+    "promoter": "CMV",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin (E. coli)",
+      "G418/neomycin (mammalian)"
+    ],
+    "copy": "episomal in mammalian",
+    "fusion_tag": {
+      "n_term": "none (optional)",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NheI",
+      "AflII",
+      "HindIII",
+      "KpnI",
+      "BamHI",
+      "BstXI",
+      "EcoRI",
+      "EcoRV",
+      "NotI",
+      "XhoI",
+      "XbaI",
+      "ApaI"
+    ],
+    "flanking_5p_max": "GCTAGC",
+    "flanking_3p_max": "CTCGAGTCTAGAGG",
+    "supplier": "Invitrogen / Thermo Fisher",
+    "notes": "Standard CMV-driven mammalian expression vector. Includes BGH polyA and SV40 ori."
+  },
+  "pcdna3_4": {
+    "id": "pcdna3_4",
+    "name": "pcDNA3.4",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 5810,
+    "promoter": "CMV",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin",
+      "G418"
+    ],
+    "copy": "episomal",
+    "mcs_enzymes": [
+      "NotI",
+      "NheI",
+      "AscI",
+      "HindIII",
+      "KpnI",
+      "EcoRI",
+      "BamHI",
+      "EcoRV",
+      "XhoI"
+    ],
+    "flanking_5p_max": "GCTAGC",
+    "flanking_3p_max": "CTCGAG",
+    "supplier": "Thermo Fisher",
+    "notes": "Optimized for CHO/HEK293 transient expression. Used for therapeutic antibody / protein production."
+  },
+  "pegfp_n1": {
+    "id": "pegfp_n1",
+    "name": "pEGFP-N1",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 4733,
+    "promoter": "CMV",
+    "induction": "constitutive",
+    "selection": [
+      "kanamycin (E. coli)",
+      "G418 (mammalian)"
+    ],
+    "fusion_tag": {
+      "n_term": "none",
+      "c_term": "EGFP"
+    },
+    "mcs_enzymes": [
+      "NheI",
+      "AgeI",
+      "EcoRI",
+      "PstI",
+      "SalI",
+      "AccI",
+      "XhoI",
+      "BamHI",
+      "HindIII",
+      "SacII",
+      "KpnI",
+      "XmaI",
+      "SmaI"
+    ],
+    "flanking_5p_max": "GCTAGC",
+    "flanking_3p_max": "GGTACCGCGGGCCCGGGATCC",
+    "supplier": "Clontech / Takara",
+    "notes": "C-terminal EGFP fusion for live-cell imaging. Insert in frame at the MCS, just before the EGFP ORF."
+  },
+  "pyes2": {
+    "id": "pyes2",
+    "name": "pYES2",
+    "host": "yeast",
+    "category": "yeast_expression",
+    "size_bp": 5856,
+    "promoter": "GAL1 (galactose-inducible)",
+    "induction": "galactose 2%",
+    "selection": [
+      "ampicillin (E. coli)",
+      "URA3 (yeast — ura3- strain required)"
+    ],
+    "mcs_enzymes": [
+      "KpnI",
+      "BamHI",
+      "BstXI",
+      "EcoRI",
+      "NotI",
+      "XhoI",
+      "SphI",
+      "XbaI"
+    ],
+    "flanking_5p_max": "GGTACC",
+    "flanking_3p_max": "TCTAGA",
+    "supplier": "Invitrogen",
+    "notes": "S. cerevisiae GAL1-driven expression. Tight off-state on glucose; strong induction on galactose."
+  },
+  "ppicz": {
+    "id": "ppicz",
+    "name": "pPICZ-α",
+    "host": "pichia",
+    "category": "yeast_expression",
+    "size_bp": 3593,
+    "promoter": "AOX1 (methanol-inducible)",
+    "induction": "methanol",
+    "selection": [
+      "Zeocin (E. coli + yeast)"
+    ],
+    "fusion_tag": {
+      "n_term": "α-factor signal (secreted)",
+      "c_term": "optional Myc + His6"
+    },
+    "mcs_enzymes": [
+      "EcoRI",
+      "PmlI",
+      "SfiI",
+      "BstBI",
+      "AvrII",
+      "PvuII",
+      "NotI",
+      "SacII",
+      "XbaI"
+    ],
+    "flanking_5p_max": "GAATTC",
+    "flanking_3p_max": "TCTAGA",
+    "supplier": "Invitrogen",
+    "notes": "Pichia pastoris methanol-inducible expression with secretion signal. High protein yields."
+  },
+  "pet15b": {
+    "id": "pet15b",
+    "name": "pET-15b",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5708,
+    "promoter": "T7 lac",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "MGSSHHHHHHSSGLVPRGSHM (His6 + thrombin)",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "XhoI",
+      "BamHI"
+    ],
+    "flanking_5p_max": "AAGGAGATATACATATG",
+    "flanking_3p_max": "GGATCCTGA",
+    "supplier": "Sigma-Aldrich / Novagen",
+    "notes": "Compact pET vector with N-terminal His6 + thrombin cleavage. Smaller MCS than pET-28a."
+  },
+  "pet30a": {
+    "id": "pet30a",
+    "name": "pET-30a(+)",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5422,
+    "promoter": "T7 lac",
+    "induction": "IPTG",
+    "selection": [
+      "kanamycin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "His6 + thrombin + S-tag + enterokinase",
+      "c_term": "His6"
+    },
+    "mcs_enzymes": [
+      "NcoI",
+      "NdeI",
+      "NheI",
+      "BamHI",
+      "EcoRI",
+      "SacI",
+      "SalI",
+      "HindIII",
+      "NotI",
+      "XhoI"
+    ],
+    "flanking_5p_max": "AAGGAGATATACATATG",
+    "flanking_3p_max": "CTCGAGCACCACCACCACCACCAC",
+    "supplier": "Sigma-Aldrich / Novagen",
+    "notes": "Like pET-28a but with N-terminal S-tag and enterokinase site for tag removal."
+  },
+  "pet3a": {
+    "id": "pet3a",
+    "name": "pET-3a",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 4640,
+    "promoter": "T7",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "T7 gene 10 leader (11 aa)",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "BamHI"
+    ],
+    "flanking_5p_max": "AAGGAGATATACATATG",
+    "flanking_3p_max": "GGATCCTGA",
+    "notes": "Minimal pET — tagless expression for downstream crystallography or activity studies."
+  },
+  "pbad_hisa": {
+    "id": "pbad_hisa",
+    "name": "pBAD/HisA",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 4102,
+    "promoter": "araBAD (arabinose-inducible)",
+    "induction": "L-arabinose (0.0002–0.2%)",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "His6 + Xpress epitope + enterokinase",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NcoI",
+      "PstI",
+      "KpnI",
+      "EcoRI",
+      "BglII",
+      "XhoI",
+      "EcoRV",
+      "NheI",
+      "HindIII"
+    ],
+    "flanking_5p_max": "CCATGG",
+    "flanking_3p_max": "AAGCTT",
+    "supplier": "Invitrogen",
+    "notes": "Tightly tunable expression via arabinose titration. Best for toxic proteins where leaky expression kills cells."
+  },
+  "pcold_i": {
+    "id": "pcold_i",
+    "name": "pCold I",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 4407,
+    "promoter": "cspA (cold-shock)",
+    "induction": "15 °C cold shock + IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "His6",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "SacI",
+      "KpnI",
+      "XhoI",
+      "BamHI",
+      "EcoRI",
+      "HindIII"
+    ],
+    "flanking_5p_max": "CATATG",
+    "flanking_3p_max": "GGATCC",
+    "supplier": "Takara Bio",
+    "notes": "Cold-shock induction at 15 °C improves folding of difficult proteins. Most host proteases inactive at this temperature."
+  },
+  "ptrc99a": {
+    "id": "ptrc99a",
+    "name": "pTrc99A",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 4176,
+    "promoter": "trc (trp/lac hybrid)",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "none",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NcoI",
+      "EcoRI",
+      "SacI",
+      "KpnI",
+      "SmaI",
+      "BamHI",
+      "XbaI",
+      "SalI",
+      "AccI",
+      "HincII",
+      "PstI",
+      "SphI",
+      "HindIII"
+    ],
+    "flanking_5p_max": "CCATGG",
+    "flanking_3p_max": "AAGCTT",
+    "supplier": "Pharmacia / Cytiva",
+    "notes": "Trc promoter is stronger than lac, weaker than T7 — does not require DE3 strain. Tagless expression."
+  },
+  "pet_duet": {
+    "id": "pet_duet",
+    "name": "pETDuet-1",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5420,
+    "promoter": "two T7 lac (dual MCS)",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium (ColE1)",
+    "fusion_tag": {
+      "n_term": "His6 (MCS1)",
+      "c_term": "S-tag (MCS2)"
+    },
+    "mcs_enzymes": [
+      "NcoI",
+      "BamHI",
+      "EcoRI",
+      "SacI",
+      "NotI",
+      "SalI",
+      "HindIII",
+      "PstI",
+      "KpnI",
+      "AvrII",
+      "XhoI"
+    ],
+    "flanking_5p_max": "CCATGG",
+    "flanking_3p_max": "CTCGAG",
+    "notes": "Dual-expression for co-expressing two proteins from one plasmid. Compatible with pCDFDuet, pACYCDuet, pRSFDuet."
+  },
+  "pacyc_duet": {
+    "id": "pacyc_duet",
+    "name": "pACYCDuet-1",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 4008,
+    "promoter": "two T7 lac (dual MCS)",
+    "induction": "IPTG",
+    "selection": [
+      "chloramphenicol (34 µg/mL)"
+    ],
+    "copy": "low (p15A ori)",
+    "fusion_tag": {
+      "n_term": "His6 (MCS1)",
+      "c_term": "S-tag (MCS2)"
+    },
+    "mcs_enzymes": [
+      "NcoI",
+      "BamHI",
+      "EcoRI",
+      "SacI",
+      "NotI",
+      "SalI",
+      "HindIII",
+      "PstI",
+      "KpnI",
+      "AvrII",
+      "XhoI"
+    ],
+    "flanking_5p_max": "CCATGG",
+    "flanking_3p_max": "CTCGAG",
+    "notes": "Compatible with pETDuet/pCDFDuet/pRSFDuet for up to 8-protein co-expression. Different antibiotic, different origin."
+  },
+  "pcoldtf": {
+    "id": "pcoldtf",
+    "name": "pCold TF",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5821,
+    "promoter": "cspA",
+    "induction": "15 °C cold shock + IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "Trigger Factor (~48 kDa) + His6 + thrombin",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "KpnI",
+      "SacI",
+      "BamHI",
+      "EcoRI",
+      "EcoRV",
+      "HindIII",
+      "SalI",
+      "PstI",
+      "XbaI",
+      "XhoI"
+    ],
+    "flanking_5p_max": "GGTACC",
+    "flanking_3p_max": "CTCGAG",
+    "supplier": "Takara Bio",
+    "notes": "Cold-shock + Trigger Factor chaperone fusion — strongest folding-rescue option for aggregation-prone proteins."
+  },
+  "psb1c3": {
+    "id": "psb1c3",
+    "name": "pSB1C3",
+    "host": "e_coli",
+    "category": "general_cloning",
+    "size_bp": 2070,
+    "promoter": "none (BioBrick assembly)",
+    "induction": "n/a",
+    "selection": [
+      "chloramphenicol"
+    ],
+    "copy": "high (pUC ori)",
+    "fusion_tag": {
+      "n_term": "none",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "EcoRI",
+      "XbaI",
+      "SpeI",
+      "PstI",
+      "NotI"
+    ],
+    "flanking_5p_max": "GAATTCGCGGCCGCTTCTAGAG",
+    "flanking_3p_max": "TACTAGTAGCGGCCGCTGCAG",
+    "notes": "iGEM standard BioBrick assembly vector (RFC 10). Part insertion between BioBrick prefix and suffix."
+  },
+  "pcdna3_1_neg": {
+    "id": "pcdna3_1_neg",
+    "name": "pcDNA3.1(-)",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 5427,
+    "promoter": "CMV",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin",
+      "G418/neomycin"
+    ],
+    "copy": "episomal",
+    "mcs_enzymes": [
+      "BamHI",
+      "EcoRI",
+      "EcoRV",
+      "BstXI",
+      "NotI",
+      "XhoI",
+      "XbaI",
+      "ApaI",
+      "KpnI",
+      "HindIII",
+      "AflII",
+      "NheI"
+    ],
+    "flanking_5p_max": "GGATCC",
+    "flanking_3p_max": "GCTAGC",
+    "supplier": "Invitrogen",
+    "notes": "Reverse MCS orientation of pcDNA3.1(+). Use when cloning in opposite reading direction is needed."
+  },
+  "pcdna4_to": {
+    "id": "pcdna4_to",
+    "name": "pcDNA4/TO",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 5078,
+    "promoter": "CMV + Tet operator (2× TetO2)",
+    "induction": "tetracycline / doxycycline",
+    "selection": [
+      "ampicillin",
+      "Zeocin"
+    ],
+    "copy": "episomal",
+    "mcs_enzymes": [
+      "HindIII",
+      "KpnI",
+      "BamHI",
+      "EcoRI",
+      "EcoRV",
+      "NotI",
+      "XhoI",
+      "XbaI",
+      "ApaI",
+      "NheI"
+    ],
+    "flanking_5p_max": "AAGCTT",
+    "flanking_3p_max": "CTCGAG",
+    "supplier": "Invitrogen",
+    "notes": "Tet-on inducible mammalian expression. Use with T-REx host cell line (stable TetR expression)."
+  },
+  "pcdh_cmv": {
+    "id": "pcdh_cmv",
+    "name": "pCDH-CMV-MCS-EF1-Puro",
+    "host": "mammalian",
+    "category": "lentiviral",
+    "size_bp": 7385,
+    "promoter": "CMV (transgene) + EF1α (Puro selection)",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin (E. coli)",
+      "puromycin (mammalian)"
+    ],
+    "copy": "integrated",
+    "mcs_enzymes": [
+      "EcoRI",
+      "BamHI",
+      "NheI",
+      "XbaI",
+      "NotI",
+      "SwaI",
+      "EcoRV",
+      "SalI"
+    ],
+    "flanking_5p_max": "GAATTC",
+    "flanking_3p_max": "GCGGCCGC",
+    "supplier": "System Biosciences (SBI)",
+    "notes": "3rd-gen lentiviral transfer vector. Co-transfect with pPAX2 + pMD2.G to produce virus. Integrates into host genome."
+  },
+  "pires2_egfp": {
+    "id": "pires2_egfp",
+    "name": "pIRES2-EGFP",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 5298,
+    "promoter": "CMV",
+    "induction": "constitutive",
+    "selection": [
+      "kanamycin (E. coli)",
+      "G418 (mammalian)"
+    ],
+    "copy": "episomal",
+    "fusion_tag": {
+      "n_term": "none (bicistronic — separate EGFP via IRES)",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NheI",
+      "EcoRI",
+      "PstI",
+      "SalI",
+      "AccI",
+      "XhoI",
+      "BamHI",
+      "BstXI",
+      "EcoRV",
+      "NotI",
+      "XbaI",
+      "SacII"
+    ],
+    "flanking_5p_max": "GCTAGC",
+    "flanking_3p_max": "TCTAGA",
+    "supplier": "Clontech / Takara",
+    "notes": "Bicistronic: gene-of-interest + IRES + EGFP. EGFP marks transfected cells without fusing to your protein."
+  },
+  "ptre3g": {
+    "id": "ptre3g",
+    "name": "pTRE3G",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 3187,
+    "promoter": "PTRE3G (Tet-On 3G inducible)",
+    "induction": "doxycycline (1–1000 ng/mL)",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "episomal",
+    "mcs_enzymes": [
+      "BamHI",
+      "MluI",
+      "SalI",
+      "NheI",
+      "EcoRI",
+      "NotI",
+      "PvuI",
+      "EcoRV",
+      "HindIII"
+    ],
+    "flanking_5p_max": "GGATCC",
+    "flanking_3p_max": "AAGCTT",
+    "supplier": "Clontech / Takara",
+    "notes": "Tightest tet-inducible system. Requires co-expression of Tet-On 3G transactivator (pCMV-Tet3G)."
+  },
+  "pcmv_ha": {
+    "id": "pcmv_ha",
+    "name": "pCMV-HA",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 3787,
+    "promoter": "CMV",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "episomal",
+    "fusion_tag": {
+      "n_term": "HA epitope (YPYDVPDYA)",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "SalI",
+      "AccI",
+      "XbaI",
+      "NotI",
+      "EcoRI",
+      "BglII",
+      "KpnI",
+      "SacI"
+    ],
+    "flanking_5p_max": "GTCGAC",
+    "flanking_3p_max": "GAGCTC",
+    "supplier": "Clontech",
+    "notes": "N-terminal HA tag for immunoprecipitation and detection. Anti-HA antibodies are well-validated."
+  },
+  "p3xflag_cmv10": {
+    "id": "p3xflag_cmv10",
+    "name": "p3xFLAG-CMV-10",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 6259,
+    "promoter": "CMV",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "episomal",
+    "fusion_tag": {
+      "n_term": "3×FLAG (DYKDHDGDYKDHDIDYKDDDDK) + preprotrypsin signal",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NotI",
+      "HindIII",
+      "BglII",
+      "EcoRI",
+      "EcoRV",
+      "BamHI",
+      "SalI",
+      "KpnI",
+      "XbaI",
+      "XhoI"
+    ],
+    "flanking_5p_max": "AAGCTT",
+    "flanking_3p_max": "CTCGAG",
+    "supplier": "Sigma-Aldrich",
+    "notes": "Secreted 3×FLAG fusion. M2 anti-FLAG resin allows highly specific purification + competitive elution with FLAG peptide."
+  },
+  "plko1": {
+    "id": "plko1",
+    "name": "pLKO.1-puro",
+    "host": "mammalian",
+    "category": "lentiviral",
+    "size_bp": 7032,
+    "promoter": "U6 (shRNA) + PGK (Puro)",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin (E. coli)",
+      "puromycin (mammalian)"
+    ],
+    "copy": "integrated",
+    "mcs_enzymes": [
+      "AgeI",
+      "EcoRI"
+    ],
+    "flanking_5p_max": "ACCGG",
+    "flanking_3p_max": "CTTTTTG",
+    "addgene": "10878",
+    "notes": "Standard lentiviral shRNA knockdown vector. Clone hairpin between AgeI and EcoRI behind U6 promoter."
+  },
+  "lenticrispr_v2": {
+    "id": "lenticrispr_v2",
+    "name": "lentiCRISPR v2",
+    "host": "mammalian",
+    "category": "lentiviral",
+    "size_bp": 13044,
+    "promoter": "EF1α-short (Cas9) + U6 (sgRNA)",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin",
+      "puromycin"
+    ],
+    "copy": "integrated",
+    "mcs_enzymes": [
+      "BsmBI"
+    ],
+    "flanking_5p_max": "CACCG",
+    "flanking_3p_max": "GTTT",
+    "addgene": "52961",
+    "notes": "Single-plasmid CRISPR/Cas9 + sgRNA + Puro. Golden Gate BsmBI sgRNA cloning. Zhang lab."
+  },
+  "px330": {
+    "id": "px330",
+    "name": "pX330-U6-Chimeric_BB-CBh-hSpCas9",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 8484,
+    "promoter": "CBh (Cas9) + U6 (sgRNA)",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "episomal",
+    "mcs_enzymes": [
+      "BbsI"
+    ],
+    "flanking_5p_max": "CACCG",
+    "flanking_3p_max": "GTTT",
+    "addgene": "42230",
+    "notes": "Non-viral all-in-one CRISPR/Cas9 + sgRNA expression. BbsI Golden Gate sgRNA cloning. Zhang lab."
+  },
+  "pgbkt7": {
+    "id": "pgbkt7",
+    "name": "pGBKT7",
+    "host": "yeast",
+    "category": "yeast_expression",
+    "size_bp": 7301,
+    "promoter": "ADH1",
+    "induction": "constitutive",
+    "selection": [
+      "kanamycin (E. coli)",
+      "TRP1 (yeast)"
+    ],
+    "copy": "low",
+    "fusion_tag": {
+      "n_term": "GAL4 DNA-binding domain (1–147) + Myc",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "NcoI",
+      "SfiI",
+      "EcoRI",
+      "SmaI",
+      "BamHI",
+      "SalI",
+      "PstI"
+    ],
+    "flanking_5p_max": "CATATG",
+    "flanking_3p_max": "AAGCTT",
+    "supplier": "Clontech / Takara",
+    "notes": "Yeast two-hybrid \"bait\" vector. Co-transform with pGADT7 prey in AH109/Y2HGold to screen interactions."
+  },
+  "pgadt7": {
+    "id": "pgadt7",
+    "name": "pGADT7",
+    "host": "yeast",
+    "category": "yeast_expression",
+    "size_bp": 8000,
+    "promoter": "ADH1",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin (E. coli)",
+      "LEU2 (yeast)"
+    ],
+    "copy": "high",
+    "fusion_tag": {
+      "n_term": "GAL4 activation domain (768–881) + HA",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "SfiI",
+      "NcoI",
+      "EcoRI",
+      "SmaI",
+      "BamHI",
+      "SacI",
+      "XhoI"
+    ],
+    "flanking_5p_max": "CATATG",
+    "flanking_3p_max": "CTCGAG",
+    "supplier": "Clontech / Takara",
+    "notes": "Yeast two-hybrid \"prey\" vector. Complements pGBKT7 — partner in Matchmaker Y2H system."
+  },
+  "pyd1": {
+    "id": "pyd1",
+    "name": "pYD1",
+    "host": "yeast",
+    "category": "yeast_expression",
+    "size_bp": 5024,
+    "promoter": "GAL1",
+    "induction": "galactose 2%",
+    "selection": [
+      "ampicillin (E. coli)",
+      "TRP1 (yeast)"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "AGA2 signal + Aga2p (surface anchor) + HA",
+      "c_term": "Myc"
+    },
+    "mcs_enzymes": [
+      "NheI",
+      "BamHI",
+      "EcoRI",
+      "NotI",
+      "XhoI"
+    ],
+    "flanking_5p_max": "GCTAGC",
+    "flanking_3p_max": "CTCGAG",
+    "supplier": "Invitrogen",
+    "notes": "Yeast surface display: protein displayed on cell wall via Aga1-Aga2 disulfide. Used for directed evolution by FACS."
+  },
+  "pcambia1300": {
+    "id": "pcambia1300",
+    "name": "pCAMBIA1300",
+    "host": "plant",
+    "category": "plant_expression",
+    "size_bp": 8958,
+    "promoter": "CaMV 35S (transgene cassette optional)",
+    "induction": "n/a",
+    "selection": [
+      "kanamycin (bacteria)",
+      "hygromycin (plant)"
+    ],
+    "copy": "low",
+    "mcs_enzymes": [
+      "EcoRI",
+      "KpnI",
+      "XbaI",
+      "SalI",
+      "PstI",
+      "HindIII",
+      "BamHI",
+      "SacI",
+      "XhoI"
+    ],
+    "flanking_5p_max": "GAATTC",
+    "flanking_3p_max": "AAGCTT",
+    "supplier": "CAMBIA",
+    "notes": "Agrobacterium-mediated plant transformation binary vector. T-DNA borders flank the MCS."
+  },
+  "pbi121": {
+    "id": "pbi121",
+    "name": "pBI121",
+    "host": "plant",
+    "category": "plant_expression",
+    "size_bp": 14758,
+    "promoter": "CaMV 35S + NOS",
+    "induction": "constitutive",
+    "selection": [
+      "kanamycin (bacteria + plant)"
+    ],
+    "copy": "low",
+    "mcs_enzymes": [
+      "HindIII",
+      "XbaI",
+      "SmaI",
+      "BamHI",
+      "SacI",
+      "EcoRI"
+    ],
+    "flanking_5p_max": "TCTAGA",
+    "flanking_3p_max": "GAGCTC",
+    "supplier": "Clontech",
+    "notes": "Classic Agrobacterium binary vector. GUS reporter in MCS — replace with your gene via XbaI + SacI."
+  },
+  "pgem_t_easy": {
+    "id": "pgem_t_easy",
+    "name": "pGEM-T Easy",
+    "host": "e_coli",
+    "category": "general_cloning",
+    "size_bp": 3015,
+    "promoter": "T7 + SP6 (in vitro RNA)",
+    "induction": "n/a",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "high",
+    "mcs_enzymes": [
+      "EcoRI",
+      "BstZI",
+      "NotI",
+      "NdeI",
+      "SacI",
+      "SacII",
+      "SpeI",
+      "NsiI"
+    ],
+    "flanking_5p_max": "GAATTC",
+    "flanking_3p_max": "GAATTC",
+    "supplier": "Promega",
+    "notes": "TA cloning vector with single 3′-T overhangs for direct ligation of Taq-amplified PCR products. Blue-white screening."
+  },
+  "pjet12": {
+    "id": "pjet12",
+    "name": "pJET1.2/blunt",
+    "host": "e_coli",
+    "category": "general_cloning",
+    "size_bp": 2974,
+    "promoter": "T7 (in vitro)",
+    "induction": "n/a",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "high",
+    "mcs_enzymes": [
+      "EcoRV (blunt)",
+      "BglII",
+      "XhoI",
+      "XbaI",
+      "BamHI",
+      "NotI",
+      "NcoI",
+      "HindIII"
+    ],
+    "flanking_5p_max": "AGATCT",
+    "flanking_3p_max": "AAGCTT",
+    "supplier": "Thermo Fisher",
+    "notes": "Blunt-end PCR cloning with positive selection (lethal eco47IR disrupted by insert). No blue-white needed."
+  },
+  "paav_mcs": {
+    "id": "paav_mcs",
+    "name": "pAAV-MCS",
+    "host": "mammalian",
+    "category": "aav",
+    "size_bp": 5311,
+    "promoter": "CMV",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "packaged into AAV particles",
+    "mcs_enzymes": [
+      "EcoRI",
+      "BamHI",
+      "SalI",
+      "PstI",
+      "HindIII",
+      "NotI",
+      "XhoI",
+      "XbaI"
+    ],
+    "flanking_5p_max": "GAATTC",
+    "flanking_3p_max": "AAGCTT",
+    "supplier": "Agilent / Stratagene",
+    "notes": "AAV transfer vector. Co-transfect with pAAV-RC (rep/cap) + pHelper into HEK293 to produce virus. Insert capacity ~4.7 kb between ITRs."
+  },
+  "pfastbac1": {
+    "id": "pfastbac1",
+    "name": "pFastBac1",
+    "host": "insect",
+    "category": "baculovirus",
+    "size_bp": 4776,
+    "promoter": "polyhedrin (PH)",
+    "induction": "baculovirus infection",
+    "selection": [
+      "ampicillin",
+      "gentamicin (bacmid)"
+    ],
+    "copy": "medium",
+    "mcs_enzymes": [
+      "BamHI",
+      "EcoRI",
+      "SacI",
+      "KpnI",
+      "SmaI",
+      "NotI",
+      "XhoI",
+      "XbaI",
+      "SphI",
+      "HindIII"
+    ],
+    "flanking_5p_max": "GGATCC",
+    "flanking_3p_max": "AAGCTT",
+    "supplier": "Invitrogen / Thermo Fisher",
+    "notes": "Bac-to-Bac baculovirus expression. Transpose into DH10Bac bacmid, transfect Sf9/Sf21 cells. Strong PH-driven late expression."
+  },
+  "pfastbac_hta": {
+    "id": "pfastbac_hta",
+    "name": "pFastBac HT A",
+    "host": "insect",
+    "category": "baculovirus",
+    "size_bp": 4856,
+    "promoter": "polyhedrin (PH)",
+    "induction": "baculovirus infection",
+    "selection": [
+      "ampicillin",
+      "gentamicin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "His6 + TEV protease site (ENLYFQ↓G)",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "BamHI",
+      "EcoRI",
+      "StuI",
+      "SalI",
+      "NotI",
+      "NcoI",
+      "PstI",
+      "HindIII",
+      "KpnI"
+    ],
+    "flanking_5p_max": "GGATCC",
+    "flanking_3p_max": "AAGCTT",
+    "supplier": "Invitrogen / Thermo Fisher",
+    "notes": "Bac-to-Bac with N-terminal His6 + TEV site for cleavable affinity purification. Three frame variants (A/B/C)."
+  },
+  "prsf_duet": {
+    "id": "prsf_duet",
+    "name": "pRSFDuet-1",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 3829,
+    "promoter": "two T7 lac (dual MCS)",
+    "induction": "IPTG",
+    "selection": [
+      "kanamycin"
+    ],
+    "copy": "high (RSF ori)",
+    "fusion_tag": {
+      "n_term": "His6 (MCS1)",
+      "c_term": "S-tag (MCS2)"
+    },
+    "mcs_enzymes": [
+      "NcoI",
+      "BamHI",
+      "EcoRI",
+      "SacI",
+      "NotI",
+      "SalI",
+      "HindIII",
+      "PstI",
+      "KpnI",
+      "AvrII",
+      "XhoI"
+    ],
+    "flanking_5p_max": "CCATGG",
+    "flanking_3p_max": "CTCGAG",
+    "notes": "Highest-copy Duet vector. Compatible with pET / pCDF / pACYC Duets for multi-protein co-expression."
+  },
+  "pet24a": {
+    "id": "pet24a",
+    "name": "pET-24a(+)",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5310,
+    "promoter": "T7 lac",
+    "induction": "IPTG",
+    "selection": [
+      "kanamycin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "T7 tag (optional)",
+      "c_term": "LEHHHHHH"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "NheI",
+      "BamHI",
+      "EcoRI",
+      "SacI",
+      "SalI",
+      "HindIII",
+      "NotI",
+      "XhoI"
+    ],
+    "flanking_5p_max": "AAGGAGATATACATATG",
+    "flanking_3p_max": "CTCGAGCACCACCACCACCACCAC",
+    "notes": "Kanamycin-resistant version of pET-21a — C-terminal His6 only, no N-tag by default."
+  },
+  "pet43_1a": {
+    "id": "pet43_1a",
+    "name": "pET-43.1a (NusA)",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 7287,
+    "promoter": "T7 lac",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "NusA (~55 kDa) + His6 + thrombin",
+      "c_term": "His6 + HSV-tag"
+    },
+    "mcs_enzymes": [
+      "BamHI",
+      "EcoRI",
+      "SacI",
+      "NotI",
+      "EagI",
+      "PstI",
+      "SalI",
+      "HindIII",
+      "XhoI"
+    ],
+    "flanking_5p_max": "GGATCC",
+    "flanking_3p_max": "CTCGAG",
+    "supplier": "Sigma / Novagen",
+    "notes": "NusA is the most effective E. coli solubility tag for aggregation-prone proteins (better than MBP/GST in many cases)."
+  },
+  "ptyb1": {
+    "id": "ptyb1",
+    "name": "pTYB1 (IMPACT)",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 7477,
+    "promoter": "T7",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "none",
+      "c_term": "intein + chitin binding domain (CBD)"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "NcoI",
+      "NotI",
+      "EcoRI",
+      "BamHI",
+      "EagI",
+      "SmaI",
+      "SapI"
+    ],
+    "flanking_5p_max": "CATATG",
+    "flanking_3p_max": "TGCTCTTCCAAC",
+    "supplier": "NEB (IMPACT system)",
+    "notes": "C-terminal intein + CBD. Self-cleaves on chitin column with DTT — releases tag-free native protein with no proteolysis step."
+  },
+  "pcold_gst": {
+    "id": "pcold_gst",
+    "name": "pCold GST",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5616,
+    "promoter": "cspA (cold-shock)",
+    "induction": "15 °C cold shock + IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "GST + His6 + thrombin",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "SacI",
+      "KpnI",
+      "XhoI",
+      "BamHI",
+      "EcoRI",
+      "HindIII"
+    ],
+    "flanking_5p_max": "CATATG",
+    "flanking_3p_max": "GGATCC",
+    "supplier": "Takara Bio",
+    "notes": "Cold-shock + GST solubility fusion — useful when both temperature control and GST tag are needed."
+  },
+  "pbr322": {
+    "id": "pbr322",
+    "name": "pBR322",
+    "host": "e_coli",
+    "category": "general_cloning",
+    "size_bp": 4361,
+    "promoter": "tet, amp (native promoters)",
+    "induction": "n/a",
+    "selection": [
+      "ampicillin",
+      "tetracycline"
+    ],
+    "copy": "medium (15–20 / cell)",
+    "mcs_enzymes": [
+      "EcoRI",
+      "HindIII",
+      "BamHI",
+      "SalI",
+      "PstI",
+      "SphI",
+      "ClaI",
+      "NruI",
+      "AvaI",
+      "PvuII",
+      "ScaI",
+      "XmaIII"
+    ],
+    "flanking_5p_max": "GAATTC",
+    "flanking_3p_max": "AAGCTT",
+    "notes": "Classic foundational cloning vector. Lower copy than pUC19 — better for unstable inserts. Two antibiotic markers."
+  },
+  "pentr_d_topo": {
+    "id": "pentr_d_topo",
+    "name": "pENTR/D-TOPO (Gateway)",
+    "host": "e_coli",
+    "category": "gateway",
+    "size_bp": 2580,
+    "promoter": "none (entry clone)",
+    "induction": "n/a",
+    "selection": [
+      "kanamycin"
+    ],
+    "copy": "high",
+    "mcs_enzymes": [
+      "(directional TOPO — CACC overhang)"
+    ],
+    "flanking_5p_max": "CACC",
+    "flanking_3p_max": "",
+    "supplier": "Invitrogen / Thermo Fisher",
+    "notes": "Gateway entry vector. Clone via directional TOPO (5′ CACC overhang), then LR-recombine into any pDEST destination vector."
+  },
+  "pdonr221": {
+    "id": "pdonr221",
+    "name": "pDONR221 (Gateway)",
+    "host": "e_coli",
+    "category": "gateway",
+    "size_bp": 4762,
+    "promoter": "none (donor)",
+    "induction": "n/a",
+    "selection": [
+      "kanamycin",
+      "ccdB counterselection"
+    ],
+    "copy": "high",
+    "mcs_enzymes": [
+      "(attP1 / attP2 — BP clonase)"
+    ],
+    "flanking_5p_max": "GGGGACAAGTTTGTACAAAAAAGCAGGCT",
+    "flanking_3p_max": "GGGGACCACTTTGTACAAGAAAGCTGGGT",
+    "supplier": "Invitrogen",
+    "notes": "Gateway donor vector. BP-recombine attB-flanked PCR product to make entry clone; then LR into destination."
+  },
+  "pbabe_puro": {
+    "id": "pbabe_puro",
+    "name": "pBABE-puro",
+    "host": "mammalian",
+    "category": "retroviral",
+    "size_bp": 5169,
+    "promoter": "5′ MoMuLV LTR (transgene) + SV40 (Puro)",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin (E. coli)",
+      "puromycin (mammalian)"
+    ],
+    "copy": "integrated",
+    "mcs_enzymes": [
+      "BamHI",
+      "SnaBI",
+      "SalI",
+      "EcoRI",
+      "NheI"
+    ],
+    "flanking_5p_max": "GGATCC",
+    "flanking_3p_max": "GTCGAC",
+    "addgene": "1764",
+    "notes": "Classic Moloney MLV retroviral transfer vector. Co-transfect with packaging plasmids in Phoenix or 293T cells."
+  },
+  "plvx_ires_puro": {
+    "id": "plvx_ires_puro",
+    "name": "pLVX-IRES-Puro",
+    "host": "mammalian",
+    "category": "lentiviral",
+    "size_bp": 8155,
+    "promoter": "CMV (transgene + IRES + Puro)",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin (E. coli)",
+      "puromycin (mammalian)"
+    ],
+    "copy": "integrated",
+    "mcs_enzymes": [
+      "EcoRI",
+      "BamHI",
+      "XhoI",
+      "NotI",
+      "MluI",
+      "XbaI",
+      "SpeI"
+    ],
+    "flanking_5p_max": "GAATTC",
+    "flanking_3p_max": "GCGGCCGC",
+    "supplier": "Clontech / Takara",
+    "notes": "3rd-gen lentivirus + IRES bicistronic Puro selection. Transgene and Puro from one transcript."
+  },
+  "pmscv_puro": {
+    "id": "pmscv_puro",
+    "name": "pMSCV-puro",
+    "host": "mammalian",
+    "category": "retroviral",
+    "size_bp": 6347,
+    "promoter": "MSCV 5′ LTR + PGK (Puro)",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin",
+      "puromycin"
+    ],
+    "copy": "integrated",
+    "mcs_enzymes": [
+      "BglII",
+      "HpaI",
+      "XhoI",
+      "EcoRI"
+    ],
+    "flanking_5p_max": "AGATCT",
+    "flanking_3p_max": "GAATTC",
+    "supplier": "Clontech",
+    "notes": "Murine stem cell virus (MSCV) LTR works well in hematopoietic / stem cells where MoMuLV LTR is silenced."
+  },
+  "pci_neo": {
+    "id": "pci_neo",
+    "name": "pCI-neo",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 5472,
+    "promoter": "CMV (+ chimeric intron)",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin",
+      "G418/neomycin"
+    ],
+    "copy": "episomal",
+    "mcs_enzymes": [
+      "NheI",
+      "EcoRI",
+      "SacI",
+      "KpnI",
+      "MluI",
+      "XhoI",
+      "NotI",
+      "XbaI",
+      "BamHI",
+      "SalI"
+    ],
+    "flanking_5p_max": "GCTAGC",
+    "flanking_3p_max": "TCTAGA",
+    "supplier": "Promega",
+    "notes": "CMV + chimeric intron boosts expression ~2-fold over pcDNA3.1 in transient transfections."
+  },
+  "pcag_gfp": {
+    "id": "pcag_gfp",
+    "name": "pCAG-GFP",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 6230,
+    "promoter": "CAG (CMV enhancer + chicken β-actin + rabbit β-globin intron)",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "episomal",
+    "fusion_tag": {
+      "n_term": "none",
+      "c_term": "EGFP"
+    },
+    "mcs_enzymes": [
+      "EcoRI",
+      "AgeI",
+      "NheI"
+    ],
+    "flanking_5p_max": "GAATTC",
+    "flanking_3p_max": "ACCGGT",
+    "addgene": "11150",
+    "notes": "CAG promoter gives very strong constitutive expression across many cell types — used in vivo (mouse) and in iPSC."
+  },
+  "pad_cmv_v5_dest": {
+    "id": "pad_cmv_v5_dest",
+    "name": "pAd/CMV/V5-DEST",
+    "host": "mammalian",
+    "category": "adenoviral",
+    "size_bp": 36702,
+    "promoter": "CMV",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin (E. coli)"
+    ],
+    "copy": "packaged into Ad5 particles",
+    "fusion_tag": {
+      "n_term": "none (optional)",
+      "c_term": "V5 + His6 (optional)"
+    },
+    "mcs_enzymes": [
+      "(attR1 / attR2 — Gateway LR)"
+    ],
+    "flanking_5p_max": "CAAGTTTGTACAAAAAAGCTGAAC",
+    "flanking_3p_max": "CAACTTTGTATAATAAAGTTG",
+    "supplier": "Invitrogen",
+    "notes": "Adenoviral expression via Gateway LR. Linearize with PacI, transfect 293A cells to produce Ad5 virus."
+  },
+  "pcdh1_mcs1": {
+    "id": "pcdh1_mcs1",
+    "name": "pCDH1-MCS1-EF1-copGFP",
+    "host": "mammalian",
+    "category": "lentiviral",
+    "size_bp": 7559,
+    "promoter": "CMV (transgene) + EF1α (copGFP)",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin (E. coli)",
+      "copGFP flow-sort (mammalian)"
+    ],
+    "copy": "integrated",
+    "mcs_enzymes": [
+      "EcoRI",
+      "BamHI",
+      "NheI",
+      "NotI",
+      "XbaI",
+      "EcoRV",
+      "SwaI",
+      "ClaI",
+      "SalI"
+    ],
+    "flanking_5p_max": "GAATTC",
+    "flanking_3p_max": "GCGGCCGC",
+    "supplier": "System Biosciences (SBI)",
+    "notes": "Lentiviral transfer with copGFP marker — use FACS instead of antibiotic selection for transduced cells."
+  },
+  "px458": {
+    "id": "px458",
+    "name": "pSpCas9(BB)-2A-GFP (PX458)",
+    "host": "mammalian",
+    "category": "mammalian_expression",
+    "size_bp": 9288,
+    "promoter": "CBh (Cas9) + U6 (sgRNA)",
+    "induction": "constitutive",
+    "selection": [
+      "ampicillin (E. coli)",
+      "GFP FACS (mammalian)"
+    ],
+    "copy": "episomal",
+    "fusion_tag": {
+      "n_term": "none",
+      "c_term": "2A-EGFP (Cas9 only)"
+    },
+    "mcs_enzymes": [
+      "BbsI"
+    ],
+    "flanking_5p_max": "CACCG",
+    "flanking_3p_max": "GTTT",
+    "addgene": "48138",
+    "notes": "Cas9 + sgRNA + 2A-GFP. Sort transfected cells by GFP+. Zhang lab."
+  },
+  "pmaltose_e": {
+    "id": "pmaltose_e",
+    "name": "pMAL-p5X (periplasmic)",
+    "host": "e_coli",
+    "category": "bacterial_expression",
+    "size_bp": 5752,
+    "promoter": "tac",
+    "induction": "IPTG",
+    "selection": [
+      "ampicillin"
+    ],
+    "copy": "medium",
+    "fusion_tag": {
+      "n_term": "malE signal + MBP + Factor Xa",
+      "c_term": "none"
+    },
+    "mcs_enzymes": [
+      "NdeI",
+      "EcoRI",
+      "BamHI",
+      "XbaI",
+      "SalI",
+      "PstI",
+      "HindIII"
+    ],
+    "flanking_5p_max": "GAAGGTAGGTCATATG",
+    "flanking_3p_max": "AAGCTT",
+    "supplier": "NEB",
+    "notes": "Periplasmic variant of pMAL — malE signal exports fusion to periplasm. Cytoplasmic MBP folding bypassed."
+  }
+}

tests/test_confirm_gate.py

@@ -302,6 +302,7 @@ _GATED = {
 _UNGATED = {
     # compute and return; nothing persists
     "fetch_sequence", "fold_structure", "map_plasmid", "find_cut_sites",
+    "lookup_vector",      # reads curated reference data; writes nothing
     "design_crispr_guides", "design_primers", "design_variant_library",
     "recommend_promoter", "check_interactions", "check_prior_art",
     "propose_round2",

tests/test_vector_lookup.py

@@ -0,0 +1,172 @@
+"""The agent must not fill a failed lookup from memory.
+
+From a live transcript, 2026-08-04. A user asked Turing to build a construct
+in pCAMBIA1300. `fetch_sequence` refused — correctly; it resolves genes via
+Ensembl/UniProt and a binary vector backbone is not a gene. Turing then wrote:
+
+    "Since I cannot fetch the raw sequence of pCAMBIA1300 directly from the
+     database, I will design the cloning strategy using its standard,
+     well-characterized map."
+
+and recited an MCS:
+
+    HindIII - SbfI - PstI - SalI - XbaI - BamHI - SmaI - KpnI - SacI - EcoRI
+
+The curated entry, human-verified against Addgene and the CAMBIA sheet, is:
+
+    EcoRI, KpnI, XbaI, SalI, PstI, HindIII, BamHI, SacI, XhoI
+
+SbfI and SmaI do not appear in it. XhoI, which does, was dropped. A Golden
+Gate strategy was then being designed on that map.
+
+The refusal was not the bug. The bug is that the app HELD the verified answer
+in a frontend-only file the agent could not read, so the only path it had left
+was recall — and recall in this product reaches a synthesis order.
+
+Two things are tested here:
+  1. the data the agent now reads is the SAME data the UI shows (no second,
+     drifting copy of 61 curated records);
+  2. a miss returns a refusal that closes the door on remembering, rather than
+     an empty result that invites it.
+"""
+import json
+import os
+import re
+
+from dee.core import agent_tools as t
+from dee.core import orchestrator as orch
+from dee.core import vectors as vec
+
+_JS = "dee/static/cloning_db.js"
+_JSON = "dee/data/vectors.json"
+
+
+def _read(p):
+    with open(p, encoding="utf-8") as fh:
+        return fh.read()
+
+
+# --------------------------------------------------------------------------- #
+# one source of truth
+# --------------------------------------------------------------------------- #
+def test_the_catalogue_is_not_a_second_hand_copy():
+    """vectors.json is EXTRACTED from cloning_db.js by executing the real file
+    (scripts/extract_vectors.js). If the two ever drift, the agent and the UI
+    are telling a scientist different things about the same plasmid — which is
+    the original bug with extra steps."""
+    js = _read(_JS)
+    data = json.loads(_read(_JSON))
+    # Scope to the VECTORS block. cloning_db.js also defines ENZYMES, METHODS,
+    # TAGS and LINKERS at the same indent, and a bare `^    (\w+): {` sweeps
+    # all of them — the first version of this test failed on `gibson` and
+    # `golden_gate`, which are cloning METHODS and correctly absent here.
+    start = js.index("window.VECTORS = Object.freeze({")
+    end = js.index("\n});", start)
+    block = js[start:end]
+    ids_in_js = set(re.findall(r"^    ([a-z0-9_]+): \{", block, re.M))
+
+    missing = set(data) - ids_in_js
+    assert not missing, f"in vectors.json but not in cloning_db.js: {sorted(missing)}"
+    dropped = ids_in_js - set(data)
+    assert not dropped, f"UI knows these vectors, the agent does not: {sorted(dropped)}"
+    assert len(data) == len(ids_in_js) > 50, (len(data), len(ids_in_js))
+
+
+def test_the_extractor_is_committed_so_the_json_can_be_rebuilt():
+    """A generated file with no generator is a hand-maintained file wearing a
+    disguise, and the next person will retype into it."""
+    assert os.path.exists("scripts/extract_vectors.js")
+    src = _read("scripts/extract_vectors.js")
+    assert "cloning_db.js" in src and "VECTORS" in src
+
+
+# --------------------------------------------------------------------------- #
+# the specific plasmid that broke
+# --------------------------------------------------------------------------- #
+def test_pcambia1300_resolves_to_the_verified_record():
+    out = t.execute_tool("lookup_vector", {"name": "pCAMBIA1300"},
+                         auth_anonymous=True)
+    assert out["ok"] is True
+    v = out["vector"]
+    assert v["name"] == "pCAMBIA1300"
+    assert v["size_bp"] == 8958
+    assert v["mcs_enzymes"] == ["EcoRI", "KpnI", "XbaI", "SalI", "PstI",
+                                "HindIII", "BamHI", "SacI", "XhoI"]
+
+
+def test_the_invented_sites_are_not_in_the_real_record():
+    """The exact fabrication. SbfI and SmaI were recited into a cloning plan
+    for this vector; neither is in its curated MCS."""
+    v = vec.find("pCAMBIA1300")
+    for invented in ("SbfI", "SmaI"):
+        assert invented not in v["mcs_enzymes"], invented
+    # ...and the one that was dropped really is there
+    assert "XhoI" in v["mcs_enzymes"]
+
+
+def test_a_vector_name_is_matched_the_way_people_type_it():
+    for spelling in ("pCAMBIA1300", "pcambia1300", "PCAMBIA-1300", "pCAMBIA 1300"):
+        assert vec.find(spelling), spelling
+
+
+def test_matching_is_not_fuzzy():
+    """A near-match is how pUC19 silently becomes pUC18 and the whole
+    polylinker shifts. Better to miss and ask."""
+    assert vec.find("pCAMBIA1301") is None or \
+        vec.find("pCAMBIA1301")["name"] == "pCAMBIA1301"
+    assert vec.find("pCAM") is None
+
+
+# --------------------------------------------------------------------------- #
+# a miss must close the door, not open it
+# --------------------------------------------------------------------------- #
+def test_an_unknown_vector_is_refused_with_an_instruction_not_to_remember():
+    out = t.execute_tool("lookup_vector", {"name": "pNOTAREALVECTOR9000"},
+                         auth_anonymous=True)
+    assert out["ok"] is False
+    assert out["kind"] == "not_in_catalogue"
+    nxt = out["next"].lower()
+    assert "memory" in nxt
+    # it must name the legitimate ways forward, or "don't guess" is a dead end
+    assert "paste" in nxt or "upload" in nxt
+    assert "map_plasmid" in out["next"]
+
+
+def test_a_hit_still_says_it_is_reference_data_not_their_plasmid():
+    """A curated map and the user's actual tube diverge the moment they have
+    modified their copy. Presenting one as the other is a quieter version of
+    the same error."""
+    out = t.execute_tool("lookup_vector", {"name": "pET-28a(+)"},
+                         auth_anonymous=True)
+    assert out["ok"] is True
+    assert "not the user's own plasmid" in out["caveat"]
+    assert "do not add" in out["note"].lower()
+
+
+def test_the_tool_is_reachable_without_an_account():
+    """Gating it would push an anonymous user straight back to the recalled
+    answer this tool exists to replace."""
+    assert t._TOOLS["lookup_vector"]["requires_signin"] is False
+
+
+# --------------------------------------------------------------------------- #
+# the general rule, not just this plasmid
+# --------------------------------------------------------------------------- #
+def test_the_prompt_forbids_filling_a_failed_lookup_from_memory():
+    """The vector tool fixes one instance. The rule has to cover the class —
+    sequences, coordinates, promoters, published values."""
+    p = orch.build_system_prompt(False, {}, "")
+    assert "A TOOL SAYING NO IS AN ANSWER" in p
+    for forbidden in ("restriction-site order", "coordinate", "promoter"):
+        assert forbidden in p, forbidden
+    assert "lookup_vector" in p
+
+
+def test_the_tool_description_points_away_from_fetch_sequence():
+    """The wrong-tool call is what started this: fetch_sequence was given a
+    vector name with organism='synthetic'."""
+    spec = next(s for s in orch.TOOL_SPECS
+                if s["function"]["name"] == "lookup_vector")
+    desc = spec["function"]["description"]
+    assert "fetch_sequence" in desc
+    assert "refusal is NOT" in desc