NMRExchangeFormat · varioustoxins · Jun 2, 2026 · Jun 2, 2026 · Jun 2, 2026 · Jun 2, 2026
diff --git a/.github/scripts/json_to_nef.py b/.github/scripts/json_to_nef.py
@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+"""Convert specification/v1_2_under_review/namespaces.json to namespaces.nef."""
+
+import json
+import pynmrstar
+from pathlib import Path
+
+REPO_ROOT = Path(__file__).resolve().parents[2]
+VERSION   = (REPO_ROOT / "specification" / "current_version").read_text().strip()
+JSON_PATH = REPO_ROOT / "specification" / VERSION / "namespaces.json"
+NEF_PATH  = REPO_ROOT / "specification" / VERSION / "namespaces.nef"
+
+
+def main():
+    entries = json.loads(JSON_PATH.read_text(encoding="utf-8"))
+
+    entry = pynmrstar.Entry.from_scratch("nef_namespaces_registry")
+
+    sf = pynmrstar.Saveframe.from_scratch("nns_namespaces", tag_prefix="nns_namespaces")
+    sf.add_tag("sf_category",  "nns_namespaces")
+    sf.add_tag("sf_framecode", "nns_namespaces")
+
+    loop = pynmrstar.Loop.from_scratch(category="nns_namespaces_namespace")
+    for col in ("id", "name", "description", "url", "dictionary_url"):
+        loop.add_tag(col)
+
+    for item in entries:
+        raw_url = item.get("url") or item.get("urls") or "."
+        url = (raw_url[0] if isinstance(raw_url, list) else raw_url) or "."
+        dict_url = item.get("dict_url") or "."
+        loop.add_data([
+            item.get("id",          "."),
+            item.get("name",        "."),
+            item.get("description", "."),
+            url,
+            dict_url,
+        ])
+
+    sf.add_loop(loop)
+    entry.add_saveframe(sf)
+
+    NEF_PATH.write_text(str(entry), encoding="utf-8")
+    print(f"Written {len(entries)} namespaces to {NEF_PATH}")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/.github/workflows/generate-namespaces-nef.yml b/.github/workflows/generate-namespaces-nef.yml
@@ -0,0 +1,34 @@
+name: Generate namespaces.nef
+
+on:
+  push:
+    paths:
+      - 'specification/*/namespaces.json'
+      - 'specification/current_version'
+  workflow_dispatch:
+
+jobs:
+  generate:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install pynmrstar
+        run: pip install pynmrstar
+
+      - name: Convert JSON to NEF
+        run: python .github/scripts/json_to_nef.py
+
+      - name: Commit if changed
+        run: |
+          git config user.name  "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add specification/v1_2_under_review/namespaces.nef
+          git diff --staged --quiet || git commit -m "chore: regenerate namespaces.nef from namespaces.json"
+          git push
diff --git a/.github/workflows/update-current-symlink.yml b/.github/workflows/update-current-symlink.yml
@@ -0,0 +1,32 @@
+name: Update current symlink
+
+on:
+  push:
+    paths:
+      - 'specification/current_version'
+  workflow_dispatch:
+
+jobs:
+  update-symlink:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Update current symlink
+        run: |
+          VERSION=$(cat specification/current_version | tr -d '[:space:]')
+          if [ ! -d "specification/$VERSION" ]; then
+            echo "Error: specification/$VERSION does not exist"
+            exit 1
+          fi
+          cd specification
+          rm -f current
+          ln -s "$VERSION" current
+          cd ..
+          git config user.name  "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add specification/current
+          git diff --staged --quiet || git commit -m "chore: update current symlink to $VERSION"
+          git push
diff --git a/namespaces.html b/namespaces.html
@@ -0,0 +1,177 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>NEF Namespaces Registry</title>
+    <style>
+        /* Base Styles */
+        body {
+            font-family: system-ui, -apple-system, sans-serif;
+            padding: 2rem;
+            background: #f9fafb;
+            color: #1f2937;
+            max-width: 1200px;
+            margin: auto;
+            line-height: 1.5;
+        }
+
+        h1 { font-size: 1.75rem; margin-bottom: 0.5rem; color: #111827; }
+
+        .source-notice {
+            margin-bottom: 2rem; padding: 14px; background: #f3f4f6;
+            border-left: 4px solid #374151; color: #374151; font-size: 0.95rem;
+        }
+
+        .raw-data-link { font-weight: 700; color: #2563eb; text-decoration: underline; }
+
+        /* Table Styling - Uniform Font Size */
+        table {
+            width: 100%; border-collapse: collapse; background: white;
+            border-radius: 8px; box-shadow: 0 4px 6px -1px rgba(0, 0, 0, 0.1);
+            table-layout: fixed;
+            font-size: 0.95rem; /* Unified base size for the whole table */
+        }
+
+        th, td {
+            padding: 14px 16px; text-align: left;
+            border-bottom: 1px solid #e5e7eb; vertical-align: top;
+            word-wrap: break-word;
+        }
+
+        th {
+            background: #f3f4f6;
+            font-size: 0.8rem;
+            text-transform: uppercase;
+            color: #6b7280;
+            font-weight: 600;
+        }
+
+        /* Standardizing Program Names and Codes */
+        code {
+            background: #e5e7eb;
+            padding: 3px 6px;
+            border-radius: 4px;
+            font-family: ui-monospace, monospace;
+            font-size: 0.9rem; /* Matches the table text size */
+            color: #1f2937;
+        }
+
+        strong { font-size: 0.95rem; color: #111827; }
+
+        /* Standardizing Links */
+        .link-container a {
+            display: block;
+            color: #2563eb;
+            text-decoration: none;
+            font-size: 0.9rem; /* Normalized with the table */
+            margin-bottom: 8px;
+            word-break: break-all;
+            line-height: 1.4;
+        }
+        .link-container a:hover { text-decoration: underline; }
+
+        /* Standardizing Comments (No Dotted Line) */
+        .comment-row td {
+            background-color: #fcfcfc;
+            padding: 8px 16px 20px 16px;
+            border-bottom: 2px solid #e5e7eb;
+        }
+
+        .comment-box {
+            font-style: italic;
+            font-size: 0.9rem; /* Consistent with the rest of the table */
+            color: #4b5563;
+            line-height: 1.5;
+        }
+
+        .error-msg { color: #dc2626; padding: 40px; text-align: center; font-weight: bold; }
+    </style>
+</head>
+<body>
+
+    <h1>NEF Namespace Registry</h1>
+
+    <div class="source-notice">
+        The raw data for this table can be found at:
+        <a id="data-link" href="#" class="raw-data-link" target="_blank"></a>.
+        To register your own namespace raise an issue at <a href="https://github.com/NMRExchangeFormat/NEF/issues" class="raw-data-link" target="_blank">this repository</a> requesting one.
+    </div>
+
+    <table id="registry-table">
+        <thead>
+            <tr>
+                <th style="width: 12%">Namespace</th>
+                <th style="width: 18%">Name</th>
+                <th style="width: 25%">Description</th>
+                <th style="width: 25%">Resources</th>
+                <th style="width: 20%">Dictionary</th>
+            </tr>
+        </thead>
+        <tbody id="table-body">
+            <tr><td colspan="5" style="text-align:center; padding: 40px;">Initializing registry...</td></tr>
+        </tbody>
+    </table>
+
+    <script>
+        async function loadRegistry() {
+            const tbody = document.getElementById('table-body');
+
+            try {
+                const version = await fetch('./specification/current_version')
+                    .then(r => { if (!r.ok) throw new Error(`HTTP ${r.status}`); return r.text(); })
+                    .then(t => t.trim());
+
+                const jsonPath = `./specification/${version}/namespaces.json`;
+                const dataLink = document.getElementById('data-link');
+                dataLink.href = jsonPath;
+                dataLink.textContent = jsonPath.replace('./', '');
+
+                const response = await fetch(jsonPath);
+                if (!response.ok) throw new Error(`HTTP ${response.status}`);
+                const data = await response.json();
+
+                tbody.innerHTML = data.map(item => {
+                    // First URL only
+                    const raw = item.url || item.urls || '';
+                    const url = Array.isArray(raw) ? raw[0] : raw;
+                    const urlHtml = url
+                        ? `<a href="${url}" target="_blank" rel="noopener">${url}</a>`
+                        : '—';
+
+                    // Dictionary URL
+                    const dictUrl = item.dict_url || '';
+                    const dictHtml = dictUrl
+                        ? `<a href="${dictUrl}" target="_blank" rel="noopener">${dictUrl}</a>`
+                        : '—';
+
+                    // Comment row spanning all columns
+                    const note = item.comment || item.comments || "";
+                    const commentRow = note ? `
+                        <tr class="comment-row">
+                            <td colspan="5">
+                                <div class="comment-box">${note}</div>
+                            </td>
+                        </tr>` : '';
+
+                    return `
+                        <tr>
+                            <td><code>${item.id || ''}</code></td>
+                            <td><strong>${item.name || ''}</strong></td>
+                            <td>${item.description || ''}</td>
+                            <td class="link-container">${urlHtml}</td>
+                            <td class="link-container">${dictHtml}</td>
+                        </tr>
+                        ${commentRow}
+                    `;
+                }).join('');
+
+            } catch (err) {
+                tbody.innerHTML = `<tr><td colspan="5" class="error-msg">Error: ${err.message}</td></tr>`;
+            }
+        }
+
+        loadRegistry();
+    </script>
+</body>
+</html>
diff --git a/specification/current b/specification/current
@@ -0,0 +1 @@
+v1_1
diff --git a/specification/current_version b/specification/current_version
@@ -0,0 +1 @@
+v1_1
diff --git a/specification/v1_1/namespaces.json b/specification/v1_1/namespaces.json
@@ -0,0 +1,21 @@
+[
+  { "id": "nef", "name": "NEF Standard", "description": "Data Exchange", "url": "https://github.com/NMRExchangeFormat/NEF",
+     "dict_url":  "https://github.com/NMRExchangeFormat/NEF/blob/master/specification/v1_1/mmcif_nef_v1_1.dic"},
+  { "id": "nefpls", "name": "NEF Pipelines", "description": "Format transcoding and NEF manipulation", "url": "https://github.com/varioustoxins/NEF-Pipelines" },
+
+  { "id": "amber", "name": "Amber", "description": "Structure modelling and refinement", "url": "https://ambermd.org" },
+  { "id": "aria", "name": "Aria", "description": "Structure calculation", "url": "https://aria.pasteur.fr" },
+  { "id": "ccpn", "name": "CcpNmr Analysis", "description": "NMR spectra processing and data analysis", "url": "https://ccpn.ac.uk" },
+  { "id": "csrosetta", "name": "CS-Rosetta", "description": "Structure calculation", "url": "https://web.archive.org/web/20240421045134/https://csrosetta.chemistry.ucsc.edu/",
+    "comment": "the original version by the Bax group is still available at https://spin.niddk.nih.gov/bax/software/CSROSETTA/, the archive on the wayback machine at \"https://web.archive.org/web/20240421045134/https://csrosetta.chemistry.ucsc.edu/most probably contains the most complete reference"
+  },
+  { "id": "cyana", "name": "Cyana", "description": "Structure calculation", "url": "http://www.cyana.org" },
+  { "id": "meld", "name": "MELD", "description": "Structure modelling and refinement", "url": "https://meldmd.org" },
+  { "id": "NMRFx", "name": "NMRFx", "description": "Structure calculation", "url": "https://nmrfx.org" },
+  { "id": "pdbstat", "name": "PDBStat", "description": "NMR data validation", "url": "https://github.rpi.edu/RPIBioinformatics/PDBStat_public" },
+  { "id": "unio", "name": "Unio NMR", "description": "Structure calculation", "url": "https://unio-nmr.fr" },
+  { "id": "unres", "name": "Unres", "description": "Structure modelling and refinement", "url": "http://www.unres.pl" },
+  { "id": "pdbx", "name": "wwPDB/BMRB", "description": "Database", "url": "https://www.wwpdb.org" },
+  { "id": "XplorNIH", "name": "Xplor-NIH", "description": "Structure calculation and refinement", "url": "https://nmr.cit.nih.gov/xplor-nih/" },
+  { "id": "yasara", "name": "Yasara", "description": "Structure refinement", "url": "http://www.yasara.org" }
+]
diff --git a/specification/v1_1/namespaces.nef b/specification/v1_1/namespaces.nef
@@ -0,0 +1,32 @@
+data_nef_namespaces_registry
+
+save_nns_namespaces
+   _nns_namespaces.sf_category   nns_namespaces
+   _nns_namespaces.sf_framecode  nns_namespaces
+
+   loop_
+      _nns_namespaces_namespace.id
+      _nns_namespaces_namespace.name
+      _nns_namespaces_namespace.description
+      _nns_namespaces_namespace.url
+      _nns_namespaces_namespace.dictionary_url
+
+     nef         'NEF Standard'      'Data Exchange'                              https://github.com/NMRExchangeFormat/NEF                                           https://github.com/NMRExchangeFormat/NEF/blob/master/specification/v1_1/mmcif_nef_v1_1.dic   
+     nefpls      'NEF Pipelines'     'Format transcoding and NEF manipulation'    https://github.com/varioustoxins/NEF-Pipelines                                     .                                                                                            
+     amber       Amber               'Structure modelling and refinement'         https://ambermd.org                                                                .                                                                                            
+     aria        Aria                'Structure calculation'                      https://aria.pasteur.fr                                                            .                                                                                            
+     ccpn        'CcpNmr Analysis'   'NMR spectra processing and data analysis'   https://ccpn.ac.uk                                                                 .                                                                                            
+     csrosetta   CS-Rosetta          'Structure calculation'                      https://web.archive.org/web/20240421045134/https://csrosetta.chemistry.ucsc.edu/   .                                                                                            
+     cyana       Cyana               'Structure calculation'                      http://www.cyana.org                                                               .                                                                                            
+     meld        MELD                'Structure modelling and refinement'         https://meldmd.org                                                                 .                                                                                            
+     NMRFx       NMRFx               'Structure calculation'                      https://nmrfx.org                                                                  .                                                                                            
+     pdbstat     PDBStat             'NMR data validation'                        https://github.rpi.edu/RPIBioinformatics/PDBStat_public                            .                                                                                            
+     unio        'Unio NMR'          'Structure calculation'                      https://unio-nmr.fr                                                                .                                                                                            
+     unres       Unres               'Structure modelling and refinement'         http://www.unres.pl                                                                .                                                                                            
+     pdbx        wwPDB/BMRB          Database                                     https://www.wwpdb.org                                                              .                                                                                            
+     XplorNIH    Xplor-NIH           'Structure calculation and refinement'       https://nmr.cit.nih.gov/xplor-nih/                                                 .                                                                                            
+     yasara      Yasara              'Structure refinement'                       http://www.yasara.org                                                              .                                                                                            
+
+   stop_
+
+save_