Optimize nupack service startup and compute
This commit is contained in:
Lihatoo
commit
e1b3156754
25 changed files with 9435 additions and 0 deletions
191
service/design-guide.html
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191
service/design-guide.html
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<!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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4
service/favicon.svg
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service/favicon.svg
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 64 64">
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<rect width="64" height="64" rx="16" fill="#0f5d3c"/>
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<path d="M16 47V17h8l16 20V17h8v30h-8L24 27v20z" fill="#f7f1e6"/>
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</svg>
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After Width: | Height: | Size: 192 B |
5625
service/index.html
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service/index.html
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service/server.py
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service/server.py
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345
service/split_strand_svg.py
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service/split_strand_svg.py
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from __future__ import annotations
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import json
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import math
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from dataclasses import dataclass, field
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from html import escape
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NODE_RADIUS = 10.0
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PRIMARY_SPACE = 20.0
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PAIR_SPACE = 20.0
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PADDING = 52.0
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def _fmt(value):
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return f"{float(value):.2f}"
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def _fmt3(value):
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return f"{float(value):.3f}"
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def _pairmap_from_structure(structure):
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pair_stack = []
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dangling_stack = []
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pairs = [-1] * len(structure)
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for index, char in enumerate(structure):
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if char == "(":
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pair_stack.append(index)
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elif char == ")":
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if pair_stack:
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partner = pair_stack.pop()
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pairs[index] = partner
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pairs[partner] = index
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else:
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dangling_stack.append(index)
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if pair_stack:
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if len(pair_stack) != len(dangling_stack):
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raise ValueError("Unbalanced structure for split-strand layout.")
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for left, right in zip(pair_stack, reversed(dangling_stack)):
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pairs[left] = right
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pairs[right] = left
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return pairs
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@dataclass
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class _TreeNode:
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children: list["_TreeNode"] = field(default_factory=list)
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is_pair: bool = False
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index_a: int = -1
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index_b: int = -1
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x: float = 0.0
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y: float = 0.0
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go_x: float = 0.0
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go_y: float = 0.0
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def _add_nodes_recursive(pairmap, root, start, end):
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if start > end:
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raise ValueError(f"Invalid recursive span for split-strand layout: {start}>{end}")
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if pairmap[start] == end:
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child = _TreeNode(is_pair=True, index_a=start, index_b=end)
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_add_nodes_recursive(pairmap, child, start + 1, end - 1)
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root.children.append(child)
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return
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child = _TreeNode()
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cursor = start
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while cursor <= end:
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partner = pairmap[cursor]
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if partner > cursor:
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_add_nodes_recursive(pairmap, child, cursor, partner)
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cursor = partner + 1
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continue
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child.children.append(_TreeNode(index_a=cursor))
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cursor += 1
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root.children.append(child)
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def _setup_coords_recursive(node, parent, start_x, start_y, go_x, go_y, flipped=False):
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cross_x = -go_y
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cross_y = go_x
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node.go_x = go_x
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node.go_y = go_y
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if len(node.children) == 1:
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node.x = start_x
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node.y = start_y
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child = node.children[0]
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next_x = start_x + go_x * PRIMARY_SPACE
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next_y = start_y + (-1 if flipped else 1) * go_y * PRIMARY_SPACE
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if child.is_pair or (not child.is_pair and child.index_a >= 0):
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_setup_coords_recursive(child, node, next_x, next_y, go_x, go_y, flipped=flipped)
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else:
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_setup_coords_recursive(child, node, start_x, start_y, go_x, go_y, flipped=flipped)
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return
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if not node.children:
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node.x = start_x
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node.y = start_y
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return
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pair_count = sum(1 for child in node.children if child.is_pair)
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circle_length = (len(node.children) + 1) * PRIMARY_SPACE + (pair_count + 1) * PAIR_SPACE
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circle_radius = circle_length / (2 * math.pi)
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length_walker = PAIR_SPACE / 2.0
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if parent is None:
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node.x = go_x * circle_radius
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node.y = go_y * circle_radius
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else:
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node.x = parent.x + go_x * circle_radius
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node.y = parent.y + (-1 if flipped else 1) * go_y * circle_radius
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for child in node.children:
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length_walker += PRIMARY_SPACE
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if child.is_pair:
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length_walker += PAIR_SPACE / 2.0
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rad_angle = length_walker / circle_length * 2 * math.pi - math.pi / 2.0
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if parent is None:
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rad_angle -= math.pi / 2.0
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child_x = node.x + math.cos(rad_angle) * cross_x * circle_radius + math.sin(rad_angle) * go_x * circle_radius
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child_y = node.y + (-1 if flipped else 1) * math.cos(rad_angle) * cross_y * circle_radius + (-1 if flipped else 1) * math.sin(rad_angle) * go_y * circle_radius
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child_go_x = child_x - node.x
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||||
child_go_y = child_y - node.y
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child_go_len = math.hypot(child_go_x, child_go_y) or 1.0
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||||
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_setup_coords_recursive(
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child,
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node,
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child_x,
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||||
child_y,
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||||
child_go_x / child_go_len,
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||||
(-1 if flipped else 1) * child_go_y / child_go_len,
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||||
flipped=flipped,
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||||
)
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||||
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if child.is_pair:
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length_walker += PAIR_SPACE / 2.0
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||||
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||||
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||||
def _collect_coords_recursive(node, xs, ys, flipped=False):
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if node.is_pair:
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cross_x = -node.go_y
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cross_y = node.go_x
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||||
xs[node.index_a] = node.x + cross_x * PAIR_SPACE / 2.0
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xs[node.index_b] = node.x - cross_x * PAIR_SPACE / 2.0
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||||
ys[node.index_a] = node.y + (-1 if flipped else 1) * cross_y * PAIR_SPACE / 2.0
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ys[node.index_b] = node.y + (1 if flipped else -1) * cross_y * PAIR_SPACE / 2.0
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||||
elif node.index_a >= 0:
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xs[node.index_a] = node.x
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ys[node.index_a] = node.y
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for child in node.children:
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_collect_coords_recursive(child, xs, ys, flipped=flipped)
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def _layout_positions(display_structure):
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pairmap = _pairmap_from_structure(display_structure)
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root = _TreeNode()
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cursor = 0
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||||
while cursor < len(pairmap):
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partner = pairmap[cursor]
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if partner > cursor:
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_add_nodes_recursive(pairmap, root, cursor, partner)
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cursor = partner + 1
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continue
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root.children.append(_TreeNode(index_a=cursor))
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cursor += 1
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||||
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xs = [0.0] * len(display_structure)
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||||
ys = [0.0] * len(display_structure)
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_setup_coords_recursive(root, None, 0.0, 0.0, 0.0, 1.0, flipped=False)
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_collect_coords_recursive(root, xs, ys, flipped=False)
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||||
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min_x = min(x - NODE_RADIUS for x in xs)
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||||
min_y = min(y - NODE_RADIUS for y in ys)
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||||
xs = [x - min_x for x in xs]
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||||
ys = [y - min_y for y in ys]
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||||
return pairmap, xs, ys
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||||
|
||||
|
||||
def _strand_spans(display_sequence):
|
||||
spans = []
|
||||
start = None
|
||||
for index, char in enumerate(display_sequence):
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||||
if char == " ":
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||||
if start is not None:
|
||||
spans.append((start, index - 1))
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||||
start = None
|
||||
continue
|
||||
if start is None:
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||||
start = index
|
||||
if start is not None:
|
||||
spans.append((start, len(display_sequence) - 1))
|
||||
return spans
|
||||
|
||||
|
||||
def render_split_strands_svg(strand_sequences, structure, title=None):
|
||||
if not strand_sequences:
|
||||
raise ValueError("Split-strand layout requires at least one strand.")
|
||||
|
||||
display_sequence = " ".join(str(sequence) for sequence in strand_sequences)
|
||||
display_structure = str(structure).replace("+", " ")
|
||||
|
||||
if len(display_sequence) != len(display_structure):
|
||||
raise ValueError("Sequence and structure length mismatch for split-strand layout.")
|
||||
|
||||
pairmap, xs, ys = _layout_positions(display_structure)
|
||||
visible_indices = [index for index, char in enumerate(display_sequence) if char != " "]
|
||||
if not visible_indices:
|
||||
raise ValueError("Split-strand layout produced no visible residues.")
|
||||
|
||||
min_x = min(xs[index] for index in visible_indices) - NODE_RADIUS - PADDING
|
||||
min_y = min(ys[index] for index in visible_indices) - NODE_RADIUS - PADDING
|
||||
max_x = max(xs[index] for index in visible_indices) + NODE_RADIUS + PADDING
|
||||
max_y = max(ys[index] for index in visible_indices) + NODE_RADIUS + PADDING
|
||||
|
||||
width = max_x - min_x
|
||||
height = max_y - min_y
|
||||
|
||||
def tx(index):
|
||||
return xs[index] - min_x
|
||||
|
||||
def ty(index):
|
||||
return ys[index] - min_y
|
||||
|
||||
compact_index = {}
|
||||
compact_counter = 1
|
||||
for index in visible_indices:
|
||||
compact_index[index] = compact_counter
|
||||
compact_counter += 1
|
||||
|
||||
svg_lines = [
|
||||
'<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>',
|
||||
(
|
||||
f'<svg xmlns="http://www.w3.org/2000/svg" width="{_fmt(width)}" height="{_fmt(height)}" '
|
||||
f'viewBox="0 0 {_fmt(width)} {_fmt(height)}" preserveAspectRatio="xMidYMid meet" '
|
||||
'data-plot-engine="split-strands">'
|
||||
),
|
||||
]
|
||||
if title:
|
||||
svg_lines.append(f"<title>{escape(title)}</title>")
|
||||
svg_lines.extend(
|
||||
[
|
||||
' <script type="text/ecmascript">',
|
||||
" <![CDATA[",
|
||||
" var shown = 1;",
|
||||
" function click() {",
|
||||
' var seq = document.getElementById("seq");',
|
||||
" if (shown==1) {",
|
||||
' seq.setAttribute("style", "visibility: hidden");',
|
||||
" shown = 0;",
|
||||
" } else {",
|
||||
' seq.setAttribute("style", "visibility: visible");',
|
||||
" shown = 1;",
|
||||
" }",
|
||||
" }",
|
||||
" ]]>",
|
||||
" </script>",
|
||||
' <style type="text/css">',
|
||||
" <![CDATA[",
|
||||
" .nucleotide {",
|
||||
" font-family: SansSerif;",
|
||||
" }",
|
||||
" .backbone {",
|
||||
" stroke: grey;",
|
||||
" fill: none;",
|
||||
" stroke-width: 1.5;",
|
||||
" }",
|
||||
" .basepairs {",
|
||||
" stroke: red;",
|
||||
" fill: none;",
|
||||
" stroke-width: 2.5;",
|
||||
" }",
|
||||
" ]]>",
|
||||
" </style>",
|
||||
"",
|
||||
f' <rect style="stroke: white; fill: white" height="{_fmt(height)}" x="0" y="0" width="{_fmt(width)}" onclick="click(evt)" />',
|
||||
' <g transform="scale(1,1) translate(0,0)">',
|
||||
]
|
||||
)
|
||||
|
||||
for strand_index, (start, end) in enumerate(_strand_spans(display_sequence), start=1):
|
||||
points = " ".join(
|
||||
f"{_fmt3(tx(index))},{_fmt3(ty(index))}"
|
||||
for index in range(start, end + 1)
|
||||
)
|
||||
svg_lines.append(f' <polyline class="backbone" id="outline-{strand_index}" points=" {points} " />')
|
||||
|
||||
svg_lines.append(' <g id="pairs">')
|
||||
for left, right in enumerate(pairmap):
|
||||
if right <= left or display_sequence[left] == " " or display_sequence[right] == " ":
|
||||
continue
|
||||
svg_lines.append(
|
||||
f' <line class="basepairs" id="{compact_index[left]},{compact_index[right]}" '
|
||||
f'x1="{_fmt(tx(left))}" y1="{_fmt(ty(left))}" '
|
||||
f'x2="{_fmt(tx(right))}" y2="{_fmt(ty(right))}" />'
|
||||
)
|
||||
svg_lines.append(" </g>")
|
||||
|
||||
svg_lines.append(' <g transform="translate(-4.6, 4)" id="seq">')
|
||||
for index in visible_indices:
|
||||
base = display_sequence[index]
|
||||
svg_lines.append(
|
||||
f' <text class="nucleotide" x="{_fmt3(tx(index))}" y="{_fmt3(ty(index))}">{escape(base)}</text>'
|
||||
)
|
||||
svg_lines.append(" </g>")
|
||||
|
||||
compact_sequence = display_sequence.replace(" ", "")
|
||||
basepair_rows = [
|
||||
f' {{ i: {compact_index[left]}, j: {compact_index[right]}, type: "cWW" }}'
|
||||
for left, right in enumerate(pairmap)
|
||||
if right > left and display_sequence[left] != " " and display_sequence[right] != " "
|
||||
]
|
||||
coord_rows = [
|
||||
f' {{ x: {_fmt3(tx(index))}, y: {_fmt3(ty(index))} }}'
|
||||
for index in visible_indices
|
||||
]
|
||||
svg_lines.extend(
|
||||
[
|
||||
" </g>",
|
||||
'<script type="text/ecmascript">',
|
||||
"<![CDATA[",
|
||||
f" let sequence = {json.dumps(compact_sequence)};",
|
||||
f" let structure = {json.dumps(str(structure))};",
|
||||
" const basepairs = [",
|
||||
",\n".join(basepair_rows) + ("" if not basepair_rows else ""),
|
||||
" ];",
|
||||
" const coords = [",
|
||||
",\n".join(coord_rows) + ("" if not coord_rows else ""),
|
||||
" ];",
|
||||
"]]>",
|
||||
"</script>",
|
||||
"</svg>",
|
||||
]
|
||||
)
|
||||
return "\n".join(svg_lines)
|
||||
Loading…
Add table
Add a link
Reference in a new issue