191 lines
7.4 KiB
HTML
191 lines
7.4 KiB
HTML
<!doctype html>
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<html lang="zh-CN">
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<head>
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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>NUPACK Design 使用笔记</title>
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<style>
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:root {
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--paper: #f7f2e8;
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--ink: #162033;
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--muted: #64708a;
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--line: #ddd4c4;
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--accent: #1f6f5f;
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--accent-2: #b65b2a;
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}
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body {
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margin: 0;
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background: linear-gradient(135deg, #fbf7ee 0%, #edf5f0 100%);
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color: var(--ink);
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font-family: "Avenir Next", "Noto Sans SC", sans-serif;
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line-height: 1.65;
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}
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main {
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max-width: 960px;
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margin: 0 auto;
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padding: 36px 20px 72px;
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}
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h1, h2, h3 {
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line-height: 1.25;
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}
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h1 {
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font-size: clamp(2rem, 5vw, 4rem);
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letter-spacing: -0.04em;
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margin: 0 0 12px;
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}
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h2 {
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margin-top: 34px;
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padding-top: 18px;
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border-top: 1px solid var(--line);
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}
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code, pre {
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font-family: "Inconsolata", "SFMono-Regular", Consolas, monospace;
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}
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pre {
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overflow: auto;
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background: #15221f;
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color: #f4ead7;
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border-radius: 18px;
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padding: 16px;
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}
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.card {
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background: rgba(255, 255, 255, 0.72);
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border: 1px solid var(--line);
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border-radius: 22px;
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padding: 20px;
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margin: 18px 0;
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box-shadow: 0 18px 50px rgba(42, 31, 20, 0.08);
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}
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.toc {
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display: flex;
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flex-wrap: wrap;
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gap: 10px;
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margin: 22px 0;
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}
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a.button {
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display: inline-block;
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border: 1px solid var(--line);
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border-radius: 999px;
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padding: 9px 14px;
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color: var(--accent);
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background: #fffaf0;
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text-decoration: none;
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font-weight: 700;
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}
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.warn {
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border-left: 4px solid var(--accent-2);
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padding-left: 14px;
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color: #5b3828;
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}
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.muted {
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color: var(--muted);
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}
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table {
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width: 100%;
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border-collapse: collapse;
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background: rgba(255,255,255,0.75);
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border-radius: 16px;
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overflow: hidden;
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}
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th, td {
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border-bottom: 1px solid var(--line);
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padding: 10px;
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text-align: left;
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vertical-align: top;
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}
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th {
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background: #efe6d6;
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}
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</style>
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</head>
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<body>
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<main>
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<p class="muted">NUPACK replica / Design workflow notes</p>
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<h1>Design 使用笔记</h1>
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<p>这份笔记只讲当前网页里已经接入的功能：Design domains、target complexes、target tubes、hard constraints、soft constraints 和 defect weights。</p>
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<nav class="toc">
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<a class="button" href="#quick-start">快速跑通</a>
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<a class="button" href="#targets">Targets 怎么填</a>
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<a class="button" href="#hard">Hard constraints</a>
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<a class="button" href="#soft">Soft constraints</a>
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<a class="button" href="#speed">为什么会慢</a>
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<a class="button" href="/#design-targets">跳到主界面 Targets</a>
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<a class="button" href="/#design-hard">跳到主界面 Hard</a>
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<a class="button" href="/#design-soft">跳到主界面 Soft</a>
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<a class="button" href="/#history">跳到历史记录</a>
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</nav>
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<section id="quick-start" class="card">
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<h2>1. 快速跑通</h2>
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<p>主界面选择 <strong>Design</strong>，点击 <strong>载入示例</strong>，会得到一个可直接运行的双链设计：</p>
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<pre><code>domain:
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a = N10
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strands:
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A = a
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B = ~a
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target complex:
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AB_target = A+B
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structure = (10+)10
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target tube:
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AB_target = 1 uM
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off-target max size = 2</code></pre>
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<p><code>~a</code> 表示 domain <code>a</code> 的反向互补，因此 <code>(10+)10</code> 这个全双链目标结构是合法的。</p>
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</section>
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<section id="targets" class="card">
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<h2>2. Targets 怎么填</h2>
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<table>
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<thead>
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<tr><th>区域</th><th>含义</th><th>示例</th></tr>
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</thead>
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<tbody>
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<tr><td>Design Domains</td><td>给每段可设计区域命名，并写 IUPAC 约束。</td><td><code>a = N10</code></td></tr>
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<tr><td>链输入</td><td>Design 模式下，序列框可以写 domain composition。</td><td><code>A = a</code>, <code>B = ~a</code></td></tr>
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<tr><td>Target Complex</td><td>指定哪些链组成目标复合物，以及目标二级结构。</td><td><code>A+B</code>, <code>(10+)10</code></td></tr>
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<tr><td>Target Tube</td><td>Tube design 才需要。指定 on-target 浓度，off-target 由 max size 自动补全。</td><td><code>AB_target = 1 uM</code></td></tr>
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</tbody>
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</table>
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</section>
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<section id="hard" class="card">
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<h2>3. Hard constraints 怎么用</h2>
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<p>Hard constraint 是“必须满足”的约束，写错会让设计空间为空，或直接报错。</p>
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<table>
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<thead>
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<tr><th>类型</th><th>必填字段</th><th>当前推荐示例</th></tr>
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</thead>
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<tbody>
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<tr><td>Match</td><td>左侧、右侧</td><td><code>a</code> 与 <code>a</code></td></tr>
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<tr><td>Complementarity</td><td>左侧、右侧</td><td><code>A</code> 与 <code>B</code></td></tr>
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<tr><td>Similarity</td><td>scope、reference、上下限</td><td><code>scope=a</code>, <code>reference=R10</code></td></tr>
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<tr><td>Window</td><td>scope、source sequences</td><td><code>scope=a</code>, 每行一个 10 nt source</td></tr>
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<tr><td>Pattern</td><td>patterns；scope 可空表示全局</td><td><code>AAAA, UUUU</code></td></tr>
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</tbody>
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</table>
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<p class="warn">如果看到 “Constraint scope cannot be empty”，就是当前 constraint 类型需要填写 scope，但该字段为空。新版界面会在提交前拦截这类错误。</p>
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</section>
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<section id="soft" class="card">
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<h2>4. Soft constraints 和 weights</h2>
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<p>Soft constraint 不会替代 ensemble defect，只是给优化目标增加加权惩罚。权重越大，设计器越偏向满足它，但也可能变慢。</p>
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<p>Defect weights 用来告诉设计器哪些 domain、strand、complex 或 tube 更重要。初学时建议先不填，确认 target 能跑通后再逐步添加。</p>
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</section>
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<section id="speed" class="card">
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<h2>5. 为什么 Design 会慢</h2>
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<p>NUPACK design 是优化问题，不是一次性的结构分析。影响耗时的主要因素：</p>
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<ul>
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<li><strong>off-target max size</strong> 越大，需要考虑的非目标复合物越多。</li>
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<li><strong>f_stop</strong> 越小，停止条件越严格，通常越慢。</li>
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<li><strong>trials</strong> 大于 1 时会跑多个随机种子，NUPACK 源码里会并行提交多个 trial。</li>
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<li><strong>hard constraints</strong> 太多或互相矛盾，会反复搜索甚至失败。</li>
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</ul>
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<p>当前服务已显式设置 NUPACK 的 <code>config.threads</code>，不再只依赖 <code>OMP_NUM_THREADS</code>。本地 NUPACK 源码里有 <code>NUPACK_CUDA</code> 编译选项，但当前 wheel/镜像不是 CUDA 构建；直接“打开 GPU”不能生效，除非重新编译 NUPACK 的 CUDA 版本并替换镜像里的 wheel。</p>
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</section>
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</main>
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</body>
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</html>
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