react-cheminfo 0.15.0 → 0.17.0

package/README.md

@@ -83,6 +83,7 @@ through a wildcard subpath exactly as `react-science` serves its own.
 | **Token guard**            | `findTokenViolations`                                                                                                                                                                                                                                   | `cheminfo-check-tokens` (the bin)                                                                                                                                                       |
 | **Figures**                | `chartScale`, `chartAxisScale`, `chartAxisTitle`, `chartShare`, `chartColumnExtent`, `chartBinCounts`, `chartSeriesColor`, `rowMatrix`, `stackedMatrix`, `emptiestCorner`, `placeOverlayCard`, `overlayMetrics`                                         | `ChartFrame`, `ChartAxis`, `TrackedLineChart`, `OverlayBar`, `OverlaySelect`, `OverlaySegmented`, `OverlayToggle`, `OverlayNumber`, `OverlayLegend`, `OverlayCaption`, `OverlayReadout` |
 | **Projections**            | `pcaResult`, `embeddingResult`, `projectionTabs`, `loadingProfiles`, `explainedShares`, `confidenceEllipse`, `projectEllipse`, `pointsInPolygon`, `resolveProjectionGroups`, `PROJECTION_COPY`                                                          | `PcaViewer`, `ProjectionViewer`, `ScatterPlot`, `ScatterMatrix`                                                                                                                         |
+| **Parallel coordinates**   | `parallelAxisOf`, `parallelAxisLayouts`, `parallelIncludedMask`, `parallelKeptCount`, `parallelNearestRow`, `parallelSegmentAt`, `parallelBandAt`, `parallelRangeOf`, `parallelPalette`, `parallelColorSteps`, `paintParallelLines`                     | `ParallelCoordinates`                                                                                                                                                                   |
 | **Periodic table**         | `PERIODIC_ELEMENTS`, `elementBySymbol`, `elementByAtomicNumber`, `cellOf`, `placedElements`, `elementByArrowKey`, `categorySwatch`, `CATEGORY_LABELS`                                                                                                   | `PeriodicTable`, `ElementCell`, `CategoryLegend`                                                                                                                                        |
 
 Everything in that table is exported from `./core`, `./ui`, `./slides`,
@@ -502,6 +503,101 @@ marks itself, so the cog in the corner never lands in the middle of the scatter.
 `downloadFigure(target, options)`, `figureSvg` and `figurePng` are the same thing
 without the button, for a site saving a figure from its own menu.
 
+### `ParallelCoordinates`
+
+Many rows against many properties at once: one vertical axis per column, one
+line per row, and a brush on every axis.
+
+```tsx
+import { ParallelCoordinates } from 'react-cheminfo/ui';
+import { parallelAxisOf, parallelIncludedMask } from 'react-cheminfo/core';
+
+const axes = useMemo(
+  () => [
+    parallelAxisOf(rows, {
+      id: 'mw',
+      label: 'MW',
+      unit: 'g/mol',
+      value: (r) => r.weight,
+    }),
+    parallelAxisOf(rows, { id: 'clogp', label: 'cLogP', value: (r) => r.logP }),
+    parallelAxisOf(rows, {
+      id: 'mutagenic',
+      label: 'Mutagenic',
+      domain: [0, 2],
+      ticks: [
+        { value: 0, label: 'none' },
+        { value: 1, label: 'low' },
+        { value: 2, label: 'high' },
+      ],
+      value: (r) => r.mutagenic,
+    }),
+  ],
+  [rows],
+);
+const included = useMemo(
+  () => parallelIncludedMask(axes, ranges, rows.length),
+  [axes, ranges, rows.length],
+);
+
+<ParallelCoordinates
+  axes={axes}
+  width={width}
+  height={340}
+  colorAxis="clogp"
+  ranges={ranges}
+  onRangeChange={setRange}
+  included={included}
+  hovered={hovered}
+  onHoverChange={setHovered}
+  selected={picked}
+  onRowClick={pick}
+  renderTooltip={({ index }) => <MF mf={rows[index].mf} />}
+/>;
+<MoleculeTable included={included} />;
+```
+
+- **It is told nothing about what the rows are.** Every axis hands over one
+  `ArrayLike<number>` read in place, so a repaint costs an indexed read rather
+  than a call per value, and the same figure draws a library of molecules, a set
+  of runs and a table of measurements. `parallelAxisOf` is the one place a row
+  type is named, and it runs once per data change.
+- **The table beside it filters on the same answer.** `parallelIncludedMask` is
+  exported and is what the figure itself uses: a plot drawing one line under a
+  table showing fourteen rows is not a rounding error, it is two programs.
+- **A brush reports on release, never during the drag.** The band follows the
+  pointer live — that costs nothing, it is one component's own state — while the
+  interval reaches the caller once per gesture, so a table filtering on it is
+  asked to re-render once rather than sixty times a second. `onRangePreview` is
+  there for a caption, and for nothing else.
+- **The brush is arithmetic, not a library.** Create by dragging on a bare axis,
+  move the band, drag either edge, clear by pressing outside it: four answers to
+  one question, which part of the axis the press landed on. Written that way the
+  whole gesture is unit-tested in a runtime with no DOM, which is what a brush
+  attached to an element can never be — and it keeps 15.8 kB of `d3-brush` out
+  of every site that draws one.
+- **The axes end exactly on the data.** No nicing, because the reader is
+  comparing rows against each other and the best one has to touch the top of its
+  axis rather than float below a round number nothing reached. `nice` turns it on
+  per axis when round numbers really are the point, and a column with no spread
+  at all is opened by half a unit so that it still draws.
+- **A coded quantity writes its own graduations.** `domain: [0, 2]` with `ticks`
+  reading `none`, `low`, `high` is what a risk column needs; `2` on an axis means
+  nothing to anybody.
+- **The lines are a canvas, everything else is not.** Ten thousand polylines are
+  not ten thousand elements, so the mass is painted — the rows a brush left out
+  in one batched path underneath, the kept ones over them — while the axes, the
+  bands, the names and the card stay SVG and HTML. The consequence is worth
+  knowing before choosing it: `FigureDownload` copies SVG off the page, so a
+  saved figure keeps the axes and loses the lines.
+- **A canvas cannot read a custom property**, and the accent is the one colour a
+  site owns, so the figure asks the browser what its own `--accent`, `--text`,
+  `--text-muted` and `--surface` resolved to and paints with the answer. `ink`
+  overrides any of them.
+- **The card is a render prop**, because what belongs in it is the caller's
+  subject — a formula through `react-mf`, a structure, a name — and a readout of
+  strings cannot hold any of that.
+
 ## Carrying talks
 
 A deck is one Markdown file in the repository of the site whose subject it

package/lib/core.d.ts

@@ -12,6 +12,7 @@ export * from './error/core/index.ts';
 export * from './format/core/index.ts';
 export * from './orbital/core/index.ts';
 export * from './overlay/core/index.ts';
+export * from './parallel/core/index.ts';
 export * from './pedagogy/core/index.ts';
 export * from './periodic/core/index.ts';
 export * from './projection/core/index.ts';

package/lib/core.d.ts.map

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package/lib/core.js

@@ -12,6 +12,7 @@ export * from "./error/core/index.js";
 export * from "./format/core/index.js";
 export * from "./orbital/core/index.js";
 export * from "./overlay/core/index.js";
+export * from "./parallel/core/index.js";
 export * from "./pedagogy/core/index.js";
 export * from "./periodic/core/index.js";
 export * from "./projection/core/index.js";

package/lib/core.js.map

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package/lib/credits/core/credits.d.ts

@@ -55,6 +55,11 @@ export declare const CREDITS: readonly [{
     readonly href: "https://github.com/cheminfo/openchemlib-utils";
     readonly description: "the structure helpers built on top of OpenChemLib.";
     readonly license: "MIT";
+}, {
+    readonly id: "osiris-property-explorer";
+    readonly name: "OSIRIS Property Explorer";
+    readonly href: "https://www.organic-chemistry.org/prog/peo/";
+    readonly description: "the original toxicity and property predictions, by Thomas Sander at Actelion, now Idorsia.";
 }, {
     readonly id: "react-ocl";
     readonly name: "react-ocl";
@@ -85,6 +90,18 @@ export declare const CREDITS: readonly [{
     readonly href: "https://github.com/mljs/matrix";
     readonly description: "the linear algebra behind the numbers on the page.";
     readonly license: "MIT";
+}, {
+    readonly id: "ml-xsadd";
+    readonly name: "ml-xsadd";
+    readonly href: "https://github.com/mljs/xsadd";
+    readonly description: "the seeded generator a reproducible series is drawn from.";
+    readonly license: "MIT";
+}, {
+    readonly id: "cif-to-json";
+    readonly name: "cif-to-json";
+    readonly href: "https://github.com/cheminfo/cif-to-json";
+    readonly description: "the reader that turns a crystallographic file into data.";
+    readonly license: "MIT";
 }, {
     readonly id: "ml-spectra-processing";
     readonly name: "ml-spectra-processing";

package/lib/credits/core/credits.d.ts.map

@@ -1 +1 @@
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package/lib/credits/core/credits.js

@@ -53,6 +53,12 @@ export const CREDITS = [
         description: 'the structure helpers built on top of OpenChemLib.',
         license: 'MIT',
     },
+    {
+        id: 'osiris-property-explorer',
+        name: 'OSIRIS Property Explorer',
+        href: 'https://www.organic-chemistry.org/prog/peo/',
+        description: 'the original toxicity and property predictions, by Thomas Sander at Actelion, now Idorsia.',
+    },
     {
         id: 'react-ocl',
         name: 'react-ocl',
@@ -88,6 +94,20 @@ export const CREDITS = [
         description: 'the linear algebra behind the numbers on the page.',
         license: 'MIT',
     },
+    {
+        id: 'ml-xsadd',
+        name: 'ml-xsadd',
+        href: 'https://github.com/mljs/xsadd',
+        description: 'the seeded generator a reproducible series is drawn from.',
+        license: 'MIT',
+    },
+    {
+        id: 'cif-to-json',
+        name: 'cif-to-json',
+        href: 'https://github.com/cheminfo/cif-to-json',
+        description: 'the reader that turns a crystallographic file into data.',
+        license: 'MIT',
+    },
     {
         id: 'ml-spectra-processing',
         name: 'ml-spectra-processing',

package/lib/credits/core/credits.js.map

@@ -1 +1 @@
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+{"version":3,"file":"credits.js","sourceRoot":"","sources":["../../../src/credits/core/credits.ts"],"names":[],"mappings":"AAoBA;;;;;;;;;GASG;AACH,MAAM,UAAU,OAAO,CAAC,GAAwB;IAC9C,MAAM,MAAM,GAAkB,EAAE,CAAC;IACjC,KAAK,MAAM,EAAE,IAAI,GAAG,EAAE,CAAC;QACrB,MAAM,KAAK,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAC;QAC3B,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,mBAAmB,EAAE,EAAE,CAAC,CAAC;QAC3C,CAAC;QACD,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IACrB,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,QAAQ,CAAC,EAAU;IACjC,OAAO,OAAO,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,EAAE,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC;AAC1D,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,MAAM,OAAO,GAAG;IACrB;QACE,EAAE,EAAE,WAAW;QACf,IAAI,EAAE,YAAY;QAClB,IAAI,EAAE,wBAAwB;QAC9B,WAAW,EACT,6EAA6E;QAC/E,OAAO,EAAE,SAAS;KACnB;IACD;QACE,EAAE,EAAE,aAAa;QACjB,IAAI,EAAE,aAAa;QACnB,IAAI,EAAE,4CAA4C;QAClD,WAAW,EACT,4EAA4E;QAC9E,OAAO,EAAE,cAAc;KACxB;IACD;QACE,EAAE,EAAE,mBAAmB;QACvB,IAAI,EAAE,mBAAmB;QACzB,IAAI,EAAE,+CAA+C;QACrD,WAAW,EAAE,oDAAoD;QACjE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,0BAA0B;QAC9B,IAAI,EAAE,0BAA0B;QAChC,IAAI,EAAE,6CAA6C;QACnD,WAAW,EACT,4FAA4F;KAC/F;IACD;QACE,EAAE,EAAE,WAAW;QACf,IAAI,EAAE,WAAW;QACjB,IAAI,EAAE,2CAA2C;QACjD,WAAW,EAAE,wDAAwD;QACrE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,UAAU;QACd,IAAI,EAAE,UAAU;QAChB,IAAI,EAAE,0CAA0C;QAChD,WAAW,EACT,0EAA0E;QAC5E,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,YAAY;QAChB,IAAI,EAAE,YAAY;QAClB,IAAI,EAAE,wCAAwC;QAC9C,WAAW,EACT,2EAA2E;QAC7E,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,kBAAkB;QACtB,IAAI,EAAE,kBAAkB;QACxB,IAAI,EAAE,8CAA8C;QACpD,WAAW,EACT,kEAAkE;QACpE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,WAAW;QACf,IAAI,EAAE,WAAW;QACjB,IAAI,EAAE,gCAAgC;QACtC,WAAW,EAAE,oDAAoD;QACjE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,UAAU;QACd,IAAI,EAAE,UAAU;QAChB,IAAI,EAAE,+BAA+B;QACrC,WAAW,EAAE,2DAA2D;QACxE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,aAAa;QACjB,IAAI,EAAE,aAAa;QACnB,IAAI,EAAE,yCAAyC;QAC/C,WAAW,EAAE,0DAA0D;QACvE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,uBAAuB;QAC3B,IAAI,EAAE,uBAAuB;QAC7B,IAAI,EAAE,4CAA4C;QAClD,WAAW,EAAE,0DAA0D;QACvE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,SAAS;QACb,IAAI,EAAE,MAAM;QACZ,IAAI,EAAE,sBAAsB;QAC5B,WAAW,EAAE,sDAAsD;QACnE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,WAAW;QACf,IAAI,EAAE,WAAW;QACjB,IAAI,EAAE,0BAA0B;QAChC,WAAW,EACT,qEAAqE;QACvE,OAAO,EAAE,YAAY;KACtB;IACD;QACE,EAAE,EAAE,eAAe;QACnB,IAAI,EAAE,eAAe;QACrB,IAAI,EAAE,+CAA+C;QACrD,WAAW,EACT,+DAA+D;QACjE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,gBAAgB;QACpB,IAAI,EAAE,gBAAgB;QACtB,IAAI,EAAE,4CAA4C;QAClD,WAAW,EAAE,0DAA0D;QACvE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,eAAe;QACnB,IAAI,EAAE,eAAe;QACrB,IAAI,EAAE,kCAAkC;QACxC,WAAW,EAAE,mDAAmD;QAChE,OAAO,EAAE,WAAW;KACrB;IACD;QACE,EAAE,EAAE,MAAM;QACV,IAAI,EAAE,MAAM;QACZ,IAAI,EAAE,qBAAqB;QAC3B,WAAW,EAAE,2DAA2D;QACxE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,SAAS;QACb,IAAI,EAAE,SAAS;QACf,IAAI,EAAE,0BAA0B;QAChC,WAAW,EAAE,wDAAwD;QACrE,OAAO,EAAE,YAAY;KACtB;IACD;QACE,EAAE,EAAE,SAAS;QACb,IAAI,EAAE,SAAS;QACf,IAAI,EAAE,sBAAsB;QAC5B,WAAW,EAAE,sDAAsD;QACnE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,OAAO;QACX,IAAI,EAAE,OAAO;QACb,IAAI,EAAE,oBAAoB;QAC1B,WAAW,EAAE,iDAAiD;QAC9D,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,SAAS;QACb,IAAI,EAAE,SAAS;QACf,IAAI,EAAE,qBAAqB;QAC3B,WAAW,EAAE,kDAAkD;QAC/D,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,WAAW;QACf,IAAI,EAAE,WAAW;QACjB,IAAI,EAAE,2CAA2C;QACjD,WAAW,EAAE,6CAA6C;QAC1D,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,iBAAiB;QACrB,IAAI,EAAE,iBAAiB;QACvB,IAAI,EAAE,6CAA6C;QACnD,WAAW,EAAE,4DAA4D;QACzE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,QAAQ;QACZ,IAAI,EAAE,QAAQ;QACd,IAAI,EAAE,0CAA0C;QAChD,WAAW,EAAE,4DAA4D;QACzE,OAAO,EAAE,cAAc;KACxB;IACD;QACE,EAAE,EAAE,gBAAgB;QACpB,IAAI,EAAE,gBAAgB;QACtB,IAAI,EAAE,yCAAyC;QAC/C,WAAW,EAAE,sDAAsD;QACnE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,SAAS;QACb,IAAI,EAAE,SAAS;QACf,IAAI,EAAE,sBAAsB;QAC5B,WAAW,EAAE,sDAAsD;QACnE,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,QAAQ;QACZ,IAAI,EAAE,QAAQ;QACd,IAAI,EAAE,qBAAqB;QAC3B,WAAW,EAAE,yDAAyD;QACtE,OAAO,EAAE,eAAe;KACzB;IACD;QACE,EAAE,EAAE,aAAa;QACjB,IAAI,EAAE,aAAa;QACnB,IAAI,EAAE,0BAA0B;QAChC,WAAW,EAAE,4DAA4D;QACzE,OAAO,EAAE,eAAe;KACzB;IACD;QACE,EAAE,EAAE,SAAS;QACb,IAAI,EAAE,SAAS;QACf,IAAI,EAAE,sBAAsB;QAC5B,WAAW,EAAE,uDAAuD;QACpE,OAAO,EAAE,YAAY;KACtB;IACD;QACE,EAAE,EAAE,WAAW;QACf,IAAI,EAAE,WAAW;QACjB,IAAI,EAAE,4BAA4B;QAClC,WAAW,EAAE,0DAA0D;KACxE;IACD;QACE,EAAE,EAAE,OAAO;QACX,IAAI,EAAE,OAAO;QACb,IAAI,EAAE,oBAAoB;QAC1B,WAAW,EAAE,+CAA+C;QAC5D,OAAO,EAAE,KAAK;KACf;IACD;QACE,EAAE,EAAE,MAAM;QACV,IAAI,EAAE,MAAM;QACZ,IAAI,EAAE,mBAAmB;QACzB,WAAW,EAAE,oCAAoC;QACjD,OAAO,EAAE,KAAK;KACf;CACwC,CAAC"}

package/lib/ecosystem/core/sites.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sites.d.ts","sourceRoot":"","sources":["../../../src/ecosystem/core/sites.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,YAAY,CAAC;AAEhD,YAAY,EACV,aAAa,EACb,MAAM,EACN,cAAc,EACd,QAAQ,GACT,MAAM,YAAY,CAAC;AAEpB;;;GAGG;AACH,eAAO,MAAM,eAAe,EAAE,SAAS,aAAa,EAgOnD,CAAC;AAEF;;;;GAIG;AACH,wBAAgB,OAAO,CAAC,IAAI,EAAE,aAAa,GAAG,MAAM,CAEnD"}
+{"version":3,"file":"sites.d.ts","sourceRoot":"","sources":["../../../src/ecosystem/core/sites.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,YAAY,CAAC;AAEhD,YAAY,EACV,aAAa,EACb,MAAM,EACN,cAAc,EACd,QAAQ,GACT,MAAM,YAAY,CAAC;AAEpB;;;GAGG;AACH,eAAO,MAAM,eAAe,EAAE,SAAS,aAAa,EAwQnD,CAAC;AAEF;;;;GAIG;AACH,wBAAgB,OAAO,CAAC,IAAI,EAAE,aAAa,GAAG,MAAM,CAEnD"}

package/lib/ecosystem/core/sites.js

@@ -69,6 +69,19 @@ export const ECOSYSTEM_SITES = [
         brandAlt: '#d63384',
         mark: { plate: '#5b52e0', accent: '#ff8ac2' },
     },
+    {
+        id: 'dbe',
+        name: { lead: 'dbe', alt: 'cheminfo', dot: true },
+        host: 'dbe.cheminfo.org',
+        repository: 'https://github.com/cheminfo/dbe.cheminfo.org',
+        tagline: 'Count rings and double bonds from a formula or a structure.',
+        group: 'basics',
+        brand: '#63123f',
+        // The emerald the mark's double bond is drawn in sits at 2.5:1 on white,
+        // so the second half of the wordmark takes this darkened form instead.
+        brandAlt: '#047857',
+        mark: { plate: '#63123f', accent: '#10b981' },
+    },
     {
         id: 'nmrium',
         name: { lead: 'NMR', alt: 'ium' },
@@ -226,6 +239,33 @@ export const ECOSYSTEM_SITES = [
         brandAlt: '#0b6e85',
         mark: { plate: '#7c2d12', accent: '#06b6d4' },
     },
+    {
+        id: 'symmetry',
+        name: { lead: 'Symme', alt: 'Try' },
+        host: 'symmetry.cheminfo.org',
+        repository: 'https://github.com/cheminfo/symmetry.cheminfo.org',
+        tagline: 'Find the symmetry of a molecule, a crystal or a pattern.',
+        group: 'basics',
+        brand: '#9f1239',
+        // The gold that carries the apex of the mark sits at 2.2:1 on white, so
+        // the second half of the wordmark takes this darkened amber instead.
+        brandAlt: '#b45309',
+        mark: { plate: '#9f1239', accent: '#f59e0b' },
+    },
+    {
+        id: 'osiris',
+        name: { lead: 'osiris', alt: 'cheminfo', dot: true },
+        host: 'osiris.cheminfo.org',
+        repository: 'https://github.com/cheminfo/osiris.cheminfo.org',
+        tagline: 'Predicted toxicity risks and properties, one molecule or many.',
+        group: 'research',
+        brand: '#854d0e',
+        // The lapis and the gold are equiluminant — 1.02:1 against each other — so
+        // the mark draws the same blue lightened, and this darkened form is what
+        // the second half of the wordmark is set in.
+        brandAlt: '#1d4ed8',
+        mark: { plate: '#854d0e', accent: '#60a5fa' },
+    },
 ];
 /**
  * The address of a site, which is its host over https.

package/lib/ecosystem/core/sites.js.map

@@ -1 +1 @@
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package/lib/ecosystem/core/types.d.ts

@@ -1,6 +1,6 @@
 import type { SiteGroupId } from './groups.ts';
 /** The sites the menu links to. */
-export type SiteId = 'learn' | 'inchi' | 'vcl' | 'smiles' | 'openbabel' | 'chemcalc' | 'nmrium' | 'metabo' | 'derepflow' | 'surge' | 'tex' | 'lcao' | 'regexp' | 'pdb' | 'elucidation' | 'equilibrium' | 'polycarp' | '3d' | 'periodic-table' | 'database';
+export type SiteId = 'learn' | 'inchi' | 'vcl' | 'smiles' | 'openbabel' | 'chemcalc' | 'dbe' | 'nmrium' | 'metabo' | 'derepflow' | 'surge' | 'tex' | 'lcao' | 'regexp' | 'pdb' | 'elucidation' | 'equilibrium' | 'polycarp' | '3d' | 'periodic-table' | 'database' | 'symmetry' | 'osiris';
 /** A site's name, split the way its own wordmark splits it. */
 export interface SiteName {
     /**

package/lib/ecosystem/core/types.d.ts.map

@@ -1 +1 @@
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package/lib/ecosystem/ui/glyphs.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"glyphs.d.ts","sourceRoot":"","sources":["../../../src/ecosystem/ui/glyphs.tsx"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,OAAO,CAAC;AAEvC,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAC;AAE/C,4DAA4D;AAC5D,eAAO,MAAM,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,SAAS,CA0Y7D,CAAC"}

package/lib/ecosystem/ui/glyphs.js

@@ -15,6 +15,9 @@ export const GLYPHS = {
     openbabel: (alt) => (_jsxs("g", { fill: "none", strokeWidth: "2.6", strokeLinecap: "round", strokeLinejoin: "round", children: [_jsx("path", { d: "M6.5 12.5h19", stroke: "#ffffff" }), _jsx("path", { d: "M21 8l4.5 4.5L21 17", stroke: "#ffffff" }), _jsx("path", { d: "M25.5 21.5h-19", stroke: alt }), _jsx("path", { d: "M11 17l-4.5 4.5L11 26", stroke: alt })] })),
     // An isotopic pattern: the answer this one is asked for most.
     chemcalc: (alt) => (_jsxs("g", { strokeLinecap: "round", strokeWidth: "3.4", fill: "none", children: [_jsx("path", { d: "M9 24V15", stroke: "#ffffff" }), _jsx("path", { d: "M16 24V7", stroke: alt }), _jsx("path", { d: "M23 24V18", stroke: "#ffffff" })] })),
+    // A ring with a double bond drawn inside it: the two things a DBE adds up,
+    // and the equals sign the E of the name already is.
+    dbe: (alt) => (_jsxs("g", { fill: "none", strokeLinecap: "round", strokeLinejoin: "round", children: [_jsx("path", { d: "M16 5 25.53 10.5 25.53 21.5 16 27 6.47 21.5 6.47 10.5Z", stroke: "#ffffff", strokeWidth: "2.4" }), _jsx("path", { d: "M10.8 12.9h10.4M10.8 19.1h10.4", stroke: alt, strokeWidth: "2.9" })] })),
     // The ring and the substituent dots of the DerepFlow logo do not survive
     // 16 px, so the mark keeps the two elements that carry its meaning: the
     // compound, and the tick that says it has been identified.
@@ -56,5 +59,13 @@ export const GLYPHS = {
     // stack every database has been drawn as, and the two shapes this site asks
     // the same question in.
     database: (alt) => (_jsxs(_Fragment, { children: [_jsx("path", { d: "M5.8 9.4v5.3a10.2 3.9 0 0 0 20.4 0V9.4a10.2 3.9 0 0 1-20.4 0Z", fill: "#ffffff" }), _jsx("path", { d: "M5.8 17.4v5.3a10.2 3.9 0 0 0 20.4 0v-5.3a10.2 3.9 0 0 1-20.4 0Z", fill: "#ffffff" }), _jsx("ellipse", { cx: "16", cy: "9.4", rx: "10.2", ry: "3.9", fill: alt })] })),
+    // A tetrahedron seen from slightly above, four balls at its corners: the
+    // first shape a chemist meets symmetry in. The apex carries the answering
+    // colour, which is also the C3 axis every base triangle turns about.
+    symmetry: (alt) => (_jsxs(_Fragment, { children: [_jsxs("g", { stroke: "#ffffff", strokeWidth: "1.8", strokeLinecap: "round", fill: "none", children: [_jsx("path", { d: "M16 6.4 6.6 24.4M16 6.4 25.4 24.4M16 6.4 16 17.6" }), _jsx("path", { d: "M6.6 24.4 25.4 24.4" }), _jsx("path", { d: "M6.6 24.4 16 17.6M25.4 24.4 16 17.6", opacity: "0.5" })] }), _jsx("circle", { cx: "16", cy: "17.6", r: "2.5", fill: "#ffffff", opacity: "0.55" }), _jsx("circle", { cx: "6.6", cy: "24.4", r: "3.2", fill: "#ffffff" }), _jsx("circle", { cx: "25.4", cy: "24.4", r: "3.2", fill: "#ffffff" }), _jsx("circle", { cx: "16", cy: "6.4", r: "3.6", fill: alt })] })),
+    // Three axes with one line crossing them: a parallel-coordinates plot, which
+    // is how this site reads a set of molecules against one another. The line
+    // carries the answering colour because the line is the molecule.
+    osiris: (alt) => (_jsxs(_Fragment, { children: [_jsx("g", { stroke: "#ffffff", strokeWidth: "2.2", strokeLinecap: "round", fill: "none", children: _jsx("path", { d: "M7.4 6.8V25.2M16 6.8V25.2M24.6 6.8V25.2" }) }), _jsx("path", { d: "M7.4 21.6 16 10.4 24.6 17.2", fill: "none", stroke: alt, strokeWidth: "3.2", strokeLinecap: "round", strokeLinejoin: "round" })] })),
 };
 //# sourceMappingURL=glyphs.js.map

package/lib/ecosystem/ui/glyphs.js.map

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package/lib/parallel/core/index.d.ts

@@ -0,0 +1,29 @@
+/**
+ * What a parallel-coordinates figure has to work out before it can draw: where
+ * each axis stands, how a value on it becomes a pixel, which row the pointer
+ * is over, which rows the brushes keep, and the canvas pass that paints them.
+ *
+ * The brush is the part worth reading twice. It is a pure function of a press
+ * and a pointer rather than a behaviour attached to an element, so every one
+ * of its four gestures — create, move, resize from either edge, clear — is
+ * covered by tests in a runtime with no DOM, and the figure stays declarative.
+ */
+export type { ParallelAxisLayout, ParallelAxisPixels } from './parallelAxes.ts';
+export { PARALLEL_MARGIN, parallelAxisLayouts, parallelAxisPixels, parallelPixelAt, parallelValueToY, parallelYToValue, } from './parallelAxes.ts';
+export type { ParallelBand, ParallelBrushDrag, ParallelBrushGrip, ParallelBrushTarget, } from './parallelBrush.ts';
+export { PARALLEL_BRUSH_HALF_WIDTH, PARALLEL_BRUSH_HANDLE_REACH, PARALLEL_BRUSH_SMALLEST, parallelBandAt, parallelBandOf, parallelBrushGrip, parallelBrushTarget, parallelIsBand, parallelRangeOf, } from './parallelBrush.ts';
+export type { ParallelExtent } from './parallelExtent.ts';
+export { PARALLEL_DEGENERATE_PADDING, parallelExtent, } from './parallelExtent.ts';
+export { parallelIncludedMask, parallelKeptCount, parallelRangeKeeps, parallelSelectionKeeps, } from './parallelFilter.ts';
+export type { ParallelPoint, ParallelSegment } from './parallelHit.ts';
+export { PARALLEL_HOVER_TOLERANCE, parallelNearestRow, parallelSegmentAt, } from './parallelHit.ts';
+export { parallelAxisOrder, parallelDropIndex, parallelMoveAxis, } from './parallelOrder.ts';
+export type { ParallelHighlight, ParallelHighlightPaint, ParallelPaint, } from './parallelPaint.ts';
+export { PARALLEL_INCLUDED_ALPHA, paintParallelHighlights, paintParallelLines, preparePlotCanvas, traceParallelRow, } from './parallelPaint.ts';
+export { PARALLEL_PALETTE_STEPS, PARALLEL_PALETTE_UNKNOWN, parallelColorSteps, parallelPalette, } from './parallelPalette.ts';
+export { parallelHasRange, parallelMergeRanges, parallelRangeList, parallelWriteRange, } from './parallelSelection.ts';
+export type { ParallelGraduation } from './parallelTicks.ts';
+export { PARALLEL_TICK_COUNT, parallelTicks } from './parallelTicks.ts';
+export type { ParallelAxis, ParallelAxisScale, ParallelAxisSource, ParallelColorBy, ParallelRange, ParallelRanges, ParallelSelection, ParallelTick, } from './parallelTypes.ts';
+export { parallelAxisOf } from './parallelTypes.ts';
+//# sourceMappingURL=index.d.ts.map

package/lib/parallel/core/index.d.ts.map

@@ -0,0 +1 @@
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package/lib/parallel/core/index.js

@@ -0,0 +1,22 @@
+/**
+ * What a parallel-coordinates figure has to work out before it can draw: where
+ * each axis stands, how a value on it becomes a pixel, which row the pointer
+ * is over, which rows the brushes keep, and the canvas pass that paints them.
+ *
+ * The brush is the part worth reading twice. It is a pure function of a press
+ * and a pointer rather than a behaviour attached to an element, so every one
+ * of its four gestures — create, move, resize from either edge, clear — is
+ * covered by tests in a runtime with no DOM, and the figure stays declarative.
+ */
+export { PARALLEL_MARGIN, parallelAxisLayouts, parallelAxisPixels, parallelPixelAt, parallelValueToY, parallelYToValue, } from "./parallelAxes.js";
+export { PARALLEL_BRUSH_HALF_WIDTH, PARALLEL_BRUSH_HANDLE_REACH, PARALLEL_BRUSH_SMALLEST, parallelBandAt, parallelBandOf, parallelBrushGrip, parallelBrushTarget, parallelIsBand, parallelRangeOf, } from "./parallelBrush.js";
+export { PARALLEL_DEGENERATE_PADDING, parallelExtent, } from "./parallelExtent.js";
+export { parallelIncludedMask, parallelKeptCount, parallelRangeKeeps, parallelSelectionKeeps, } from "./parallelFilter.js";
+export { PARALLEL_HOVER_TOLERANCE, parallelNearestRow, parallelSegmentAt, } from "./parallelHit.js";
+export { parallelAxisOrder, parallelDropIndex, parallelMoveAxis, } from "./parallelOrder.js";
+export { PARALLEL_INCLUDED_ALPHA, paintParallelHighlights, paintParallelLines, preparePlotCanvas, traceParallelRow, } from "./parallelPaint.js";
+export { PARALLEL_PALETTE_STEPS, PARALLEL_PALETTE_UNKNOWN, parallelColorSteps, parallelPalette, } from "./parallelPalette.js";
+export { parallelHasRange, parallelMergeRanges, parallelRangeList, parallelWriteRange, } from "./parallelSelection.js";
+export { PARALLEL_TICK_COUNT, parallelTicks } from "./parallelTicks.js";
+export { parallelAxisOf } from "./parallelTypes.js";
+//# sourceMappingURL=index.js.map

package/lib/parallel/core/index.js.map

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package/lib/parallel/core/parallelAxes.d.ts

@@ -0,0 +1,103 @@
+/**
+ * Where each axis stands, how far it reaches, and how a value on it becomes a
+ * pixel.
+ *
+ * The first axis sits flush with the left of the drawing area and the last one
+ * flush with the right, rather than inset the way a two-axis chart insets its
+ * plot: the axes *are* the figure here, and a reader comparing the leftmost
+ * column against the rightmost must see both of them, not a margin.
+ */
+import type { ParallelAxis, ParallelAxisScale, ParallelTick } from './parallelTypes.ts';
+/** Room kept around the drawing area for the axis names and the tick labels. */
+export declare const PARALLEL_MARGIN: {
+    /** Above the drawing area, where the axis names are written. */
+    readonly top: 26;
+    /** To the right of it, so the last axis's labels are not clipped. */
+    readonly right: 54;
+    /** Below it. */
+    readonly bottom: 22;
+    /** To its left, where the first axis's tick labels are written. */
+    readonly left: 54;
+};
+/** How a value on one axis becomes a pixel, as the two numbers a multiply-add needs. */
+export interface ParallelAxisPixels {
+    /** The pixel the value zero lands on — or the value one, on a log axis. */
+    readonly offset: number;
+    /** Pixels per unit, negative because an axis grows upward. Zero when the axis is flat. */
+    readonly factor: number;
+    /** Whether a value is read through its base-10 logarithm first. */
+    readonly logarithmic: boolean;
+    /** The smallest value a log axis can place; anything at or below it is pinned there. */
+    readonly floor: number;
+}
+/** One axis, placed and measured, ready to draw. */
+export interface ParallelAxisLayout {
+    /** The axis this lays out. */
+    id: string;
+    /** Its name. */
+    label: string;
+    /** The unit written after the name, or an empty string. */
+    unit: string;
+    /** Horizontal centre, in pixels from the left of the drawing area. */
+    x: number;
+    /** The value at the bottom of the axis. */
+    min: number;
+    /** The value at its top. */
+    max: number;
+    /** How values are placed between them. */
+    scale: ParallelAxisScale;
+    /** Its graduations, already written out, from the bottom up. */
+    ticks: readonly ParallelTick[];
+    /** How a value on it becomes a pixel, worked out once here. */
+    pixels: ParallelAxisPixels;
+}
+/**
+ * Place every axis across the drawing area and work out what it reaches.
+ * @param axes - The axes, from left to right.
+ * @param count - How many rows the columns are read over.
+ * @param innerWidth - Width between the first and the last axis, in pixels.
+ * @param innerHeight - Height of the drawing area, in pixels.
+ * @returns One layout per axis, in the order they were given. A single axis is
+ * centred; two or more are spread evenly with the outer ones flush with the
+ * edges.
+ */
+export declare function parallelAxisLayouts(axes: readonly ParallelAxis[], count: number, innerWidth: number, innerHeight: number): ParallelAxisLayout[];
+/**
+ * The mapping that puts `max` at the top of the drawing area and `min` at its
+ * bottom.
+ * @param min - The value at the bottom.
+ * @param max - The value at the top.
+ * @param scale - How values are placed between them.
+ * @param innerHeight - Height of the drawing area, in pixels.
+ * @returns The mapping. An axis with no span, or one drawn in no height at
+ * all, comes back flat, which pins every value to the top rather than dividing
+ * by zero.
+ */
+export declare function parallelAxisPixels(min: number, max: number, scale: ParallelAxisScale, innerHeight: number): ParallelAxisPixels;
+/**
+ * Where one value falls on an axis, in pixels.
+ *
+ * For a single conversion — a tick, a brushed edge, a highlighted crossing.
+ * Inside a loop over rows, read `axis.pixels` and write the multiply-add out.
+ * @param pixels - The axis's mapping.
+ * @param value - The value to place.
+ * @returns The pixel, measured from the top of the drawing area. A value
+ * outside the axis lands outside the drawing area and is not clipped.
+ */
+export declare function parallelPixelAt(pixels: ParallelAxisPixels, value: number): number;
+/**
+ * Where one value falls on an axis, in pixels.
+ * @param value - The value to place.
+ * @param axis - The axis it belongs to.
+ * @returns The pixel, measured from the top of the drawing area.
+ */
+export declare function parallelValueToY(value: number, axis: ParallelAxisLayout): number;
+/**
+ * What value a pixel on an axis stands for — the brush's direction.
+ * @param y - The pixel, measured from the top of the drawing area.
+ * @param axis - The axis it belongs to.
+ * @returns The value there, or the top of a flat axis. Zero comes back
+ * unsigned, so an interval that reaches the end of an axis never reads `-0`.
+ */
+export declare function parallelYToValue(y: number, axis: ParallelAxisLayout): number;
+//# sourceMappingURL=parallelAxes.d.ts.map

package/lib/parallel/core/parallelAxes.d.ts.map

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