react-cheminfo 0.15.0 → 0.17.0

package/lib/parallel/ui/useParallelGesture.js

@@ -0,0 +1,164 @@
+/**
+ * One pointer over the whole figure, serving both the brush and the hover.
+ *
+ * A hook cannot be called inside a `map`, so a brush per axis would have to
+ * live in refs and be attached by hand; one surface that works out from the
+ * press which axis was grabbed has no such problem, and it gives the hover
+ * search the same once-a-frame coalescing the drag already pays for.
+ *
+ * The band follows the pointer live and the interval is reported on release
+ * only: a table filtering on the reported interval is asked to re-render once
+ * per gesture rather than sixty times a second.
+ */
+import { useMemo, useRef, useState } from 'react';
+import { useCapturedPointer } from "../../scatter/ui/useCapturedPointer.js";
+import { PARALLEL_MARGIN } from "../core/parallelAxes.js";
+import { parallelBandAt, parallelBandOf, parallelBrushTarget, } from "../core/parallelBrush.js";
+import { parallelNearestRow } from "../core/parallelHit.js";
+import { parallelRangeList } from "../core/parallelSelection.js";
+import { parallelAxisById, parallelAxisNear, parallelBandsOf, parallelCommitOf, parallelPointOf, } from "./parallelGestureModel.js";
+/**
+ * The brush and the hover, over one surface.
+ * @param options - See {@link ParallelGestureOptions}.
+ * @returns The gesture. See {@link ParallelGesture}.
+ */
+export function useParallelGesture(options) {
+    const { layouts, values, count, innerHeight, included, ranges } = options;
+    const { several = false } = options;
+    const { onRangeChange, onRangePreview, onHoverChange, onRowClick } = options;
+    const [draft, setDraft] = useState(null);
+    const [ownHovered, setOwnHovered] = useState(-1);
+    const [pointer, setPointer] = useState(null);
+    const hovered = options.hovered ?? ownHovered;
+    const dragRef = useRef(null);
+    const pointRef = useRef({ x: 0, y: 0 });
+    const reportedRef = useRef(-1);
+    const claimedRef = useRef(false);
+    function commit(drag, band) {
+        const layout = parallelAxisById(layouts, drag.axis);
+        if (layout === undefined)
+            return parallelRangeList(ranges[drag.axis]);
+        return parallelCommitOf({
+            list: parallelRangeList(ranges[drag.axis]),
+            index: drag.index,
+            band,
+            layout,
+            still: unmoved(drag, band),
+            several,
+        });
+    }
+    function report(index) {
+        if (index === reportedRef.current)
+            return;
+        reportedRef.current = index;
+        setOwnHovered(index);
+        onHoverChange?.(index);
+    }
+    function findRow(point) {
+        return parallelNearestRow(point, layouts, values, count, included ?? undefined);
+    }
+    function press(event) {
+        const point = parallelPointOf(event);
+        const index = parallelAxisNear(point.x, layouts);
+        const layout = layouts[index];
+        if (layout === undefined || point.y < 0 || point.y > innerHeight) {
+            claimedRef.current = false;
+            return false;
+        }
+        const list = parallelRangeList(ranges[layout.id]);
+        const bands = [];
+        for (const range of list)
+            bands.push(parallelBandOf(range, layout));
+        const target = parallelBrushTarget(point.y, bands);
+        const held = target.index === -1 ? undefined : bands[target.index];
+        const drag = {
+            axis: layout.id,
+            index: target.index,
+            grip: target.grip,
+            originY: point.y,
+            origin: held ?? { top: point.y, bottom: point.y },
+        };
+        dragRef.current = drag;
+        pointRef.current = point;
+        claimedRef.current = true;
+        setDraft({
+            axis: layout.id,
+            index: target.index,
+            band: parallelBandAt(drag, point.y, innerHeight),
+        });
+        return true;
+    }
+    function frame(claimed) {
+        const point = pointRef.current;
+        const drag = dragRef.current;
+        if (claimed && drag !== null) {
+            const band = parallelBandAt(drag, point.y, innerHeight);
+            setDraft({ axis: drag.axis, index: drag.index, band });
+            onRangePreview?.(drag.axis, commit(drag, band));
+            return;
+        }
+        setPointer({
+            x: point.x + PARALLEL_MARGIN.left,
+            y: point.y + PARALLEL_MARGIN.top,
+        });
+        report(findRow(point));
+    }
+    function release(event, keep) {
+        const drag = dragRef.current;
+        dragRef.current = null;
+        setDraft(null);
+        if (drag === null)
+            return;
+        if (event !== null)
+            pointRef.current = parallelPointOf(event);
+        if (!keep) {
+            onRangePreview?.(drag.axis, parallelRangeList(ranges[drag.axis]));
+            return;
+        }
+        const kept = commit(drag, parallelBandAt(drag, pointRef.current.y, innerHeight));
+        onRangePreview?.(drag.axis, kept);
+        onRangeChange(drag.axis, kept);
+    }
+    const { surface } = useCapturedPointer({
+        touch: false,
+        cursor: 'crosshair',
+        onPress: press,
+        onMove: (event) => {
+            pointRef.current = parallelPointOf(event);
+            return true;
+        },
+        onFrame: frame,
+        onRelease: release,
+        onLeave: () => {
+            setPointer(null);
+            report(-1);
+        },
+    });
+    const bands = useMemo(() => parallelBandsOf(layouts, ranges, draft), [layouts, ranges, draft]);
+    function handleClick(event) {
+        if (claimedRef.current || onRowClick === undefined)
+            return;
+        onRowClick(findRow(parallelPointOf(event)));
+    }
+    return {
+        surface,
+        onClick: handleClick,
+        bands,
+        hovered,
+        pointer,
+        brushing: draft !== null,
+    };
+}
+/**
+ * Whether a press took hold of an interval and let it go where it found it,
+ * which is a click on that interval rather than a move of it.
+ * @param drag - The drag, as it began.
+ * @param band - The band as the pointer left it.
+ * @returns Whether nothing moved.
+ */
+function unmoved(drag, band) {
+    return (drag.index !== -1 &&
+        band.top === drag.origin.top &&
+        band.bottom === drag.origin.bottom);
+}
+//# sourceMappingURL=useParallelGesture.js.map

package/lib/parallel/ui/useParallelGesture.js.map

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package/lib/structure/ui/useToolbarFloor.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"useToolbarFloor.d.ts","sourceRoot":"","sources":["../../../src/structure/ui/useToolbarFloor.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,OAAO,CAAC;AAKvC,0CAA0C;AAC1C,MAAM,WAAW,mBAAmB;IAClC;;;;OAIG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB;;;;OAIG;IACH,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED;;;;;;;;GAQG;AACH,wBAAgB,eAAe,CAC7B,OAAO,GAAE,mBAAwB,GAChC,SAAS,CAAC,cAAc,GAAG,IAAI,CAAC,CAiDlC"}

package/lib/structure/ui/useToolbarFloor.js

@@ -16,40 +16,47 @@ export function useToolbarFloor(options = {}) {
         const container = containerRef.current;
         if (container === null)
             return;
-        let observer = null;
-        let frame = 0;
-        let attempts = 0;
-        // The editor builds itself asynchronously, so the toolbar is usually not
-        // there yet on the first look; watching for it is what keeps a slow first
-        // paint from leaving the container at its unmeasured height for good.
+        let toolbar = null;
+        let size = null;
         const attach = () => {
-            const toolbar = findToolbar(container);
-            if (toolbar === null) {
-                attempts++;
-                if (attempts > MAX_ATTEMPTS)
-                    return;
-                frame = globalThis.requestAnimationFrame(attach);
+            const found = findToolbar(container);
+            if (found === null)
                 return;
-            }
-            observer = new ResizeObserver(() => {
+            size?.disconnect();
+            toolbar = found;
+            size = new ResizeObserver(() => {
                 // offsetHeight, because a dialog opens under a scaling transform and a
                 // measured rectangle would be that of the half drawn toolbar.
-                const floor = toolbarFloorHeight(toolbar.offsetHeight, minHeight);
-                container.style.minHeight = `${floor}px`;
+                const height = found.offsetHeight;
+                // Zero is a toolbar being torn down or not yet laid out, never a
+                // toolbar that needs no room: writing the fallback for it would undo a
+                // correct floor and leave the palette cut off.
+                if (height === 0)
+                    return;
+                container.style.minHeight = `${toolbarFloorHeight(height, minHeight)}px`;
             });
-            observer.observe(toolbar);
+            size.observe(found);
         };
+        // The editor is imported lazily and builds itself asynchronously, so it is
+        // almost never there on the first look, and how long it takes is a cold
+        // module graph and a network away from anything this code can predict. So
+        // the arrival is watched for rather than waited out: a deadline that
+        // expires leaves the toolbar cut off for the life of the page, with
+        // nothing on screen to say why.
+        const arrivals = new MutationObserver(() => {
+            if (toolbar?.isConnected === true)
+                return;
+            attach();
+        });
+        arrivals.observe(container, { childList: true, subtree: true });
         attach();
         return () => {
-            if (frame !== 0)
-                globalThis.cancelAnimationFrame(frame);
-            observer?.disconnect();
+            arrivals.disconnect();
+            size?.disconnect();
         };
     }, [minHeight, revision]);
     return containerRef;
 }
-/** Roughly two seconds of frames, after which the editor is not coming. */
-const MAX_ATTEMPTS = 120;
 /**
  * Find the toolbar canvas of the editor.
  *

package/lib/structure/ui/useToolbarFloor.js.map

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package/lib/ui.d.ts

@@ -15,6 +15,7 @@ export * from './error/ui/index.ts';
 export * from './help/ui/index.ts';
 export * from './hooks/ui/index.ts';
 export * from './overlay/ui/index.ts';
+export * from './parallel/ui/index.ts';
 export * from './pedagogy/ui/index.ts';
 export * from './periodic/ui/index.ts';
 export * from './projection/ui/index.ts';

package/lib/ui.d.ts.map

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package/lib/ui.js

@@ -15,6 +15,7 @@ export * from "./error/ui/index.js";
 export * from "./help/ui/index.js";
 export * from "./hooks/ui/index.js";
 export * from "./overlay/ui/index.js";
+export * from "./parallel/ui/index.js";
 export * from "./pedagogy/ui/index.js";
 export * from "./periodic/ui/index.js";
 export * from "./projection/ui/index.js";

package/lib/ui.js.map

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+{"version":3,"file":"ui.js","sourceRoot":"","sources":["../src/ui.ts"],"names":[],"mappings":"AAAA,cAAc,qBAAqB,CAAC;AACpC,cAAc,uBAAuB,CAAC;AACtC,cAAc,qBAAqB,CAAC;AACpC,cAAc,sBAAsB,CAAC;AACrC,cAAc,wBAAwB,CAAC;AACvC,cAAc,yBAAyB,CAAC;AACxC,cAAc,qBAAqB,CAAC;AACpC,cAAc,uBAAuB,CAAC;AACtC,cAAc,uBAAuB,CAAC;AACtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AACzC,cAAc,wBAAwB,CAAC;AACvC,cAAc,yBAAyB,CAAC;AACxC,cAAc,qBAAqB,CAAC;AACpC,cAAc,oBAAoB,CAAC;AACnC,cAAc,qBAAqB,CAAC;AACpC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,wBAAwB,CAAC;AACvC,cAAc,wBAAwB,CAAC;AACvC,cAAc,0BAA0B,CAAC;AACzC,cAAc,sBAAsB,CAAC;AACrC,cAAc,uBAAuB,CAAC;AACtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,qBAAqB,CAAC;AACpC,cAAc,sBAAsB,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "react-cheminfo",
-  "version": "0.15.0",
+  "version": "0.17.0",
   "license": "MIT",
   "description": "React components, hooks and framework-free helpers shared by the cheminfo sites: site chrome, citations, sharing, routing, pedagogy, charts, and the structure, orbital and 3D molecule viewers",
   "author": "Luc Patiny",

package/src/core.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/src/credits/core/credits.ts

@@ -77,6 +77,13 @@ 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',
@@ -115,6 +122,20 @@ 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/src/ecosystem/core/sites.ts

@@ -79,6 +79,19 @@ export const ECOSYSTEM_SITES: readonly EcosystemSite[] = [
     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' },
@@ -236,6 +249,33 @@ export const ECOSYSTEM_SITES: readonly EcosystemSite[] = [
     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' },
+  },
 ];
 
 /**

package/src/ecosystem/core/types.ts

@@ -8,6 +8,7 @@ export type SiteId =
   | 'smiles'
   | 'openbabel'
   | 'chemcalc'
+  | 'dbe'
   | 'nmrium'
   | 'metabo'
   | 'derepflow'
@@ -21,7 +22,9 @@ export type SiteId =
   | 'polycarp'
   | '3d'
   | 'periodic-table'
-  | 'database';
+  | 'database'
+  | 'symmetry'
+  | 'osiris';
 
 /** A site's name, split the way its own wordmark splits it. */
 export interface SiteName {

package/src/ecosystem/ui/glyphs.tsx

@@ -129,6 +129,18 @@ export const GLYPHS: Record<SiteId, (alt: string) => ReactNode> = {
       <path d="M23 24V18" stroke="#ffffff" />
     </g>
   ),
+  // 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) => (
+    <g fill="none" strokeLinecap="round" strokeLinejoin="round">
+      <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"
+      />
+      <path d="M10.8 12.9h10.4M10.8 19.1h10.4" stroke={alt} strokeWidth="2.9" />
+    </g>
+  ),
   // 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.
@@ -363,4 +375,38 @@ export const GLYPHS: Record<SiteId, (alt: string) => ReactNode> = {
       <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) => (
+    <>
+      <g stroke="#ffffff" strokeWidth="1.8" strokeLinecap="round" fill="none">
+        <path d="M16 6.4 6.6 24.4M16 6.4 25.4 24.4M16 6.4 16 17.6" />
+        <path d="M6.6 24.4 25.4 24.4" />
+        <path d="M6.6 24.4 16 17.6M25.4 24.4 16 17.6" opacity="0.5" />
+      </g>
+      <circle cx="16" cy="17.6" r="2.5" fill="#ffffff" opacity="0.55" />
+      <circle cx="6.6" cy="24.4" r="3.2" fill="#ffffff" />
+      <circle cx="25.4" cy="24.4" r="3.2" fill="#ffffff" />
+      <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) => (
+    <>
+      <g stroke="#ffffff" strokeWidth="2.2" strokeLinecap="round" fill="none">
+        <path d="M7.4 6.8V25.2M16 6.8V25.2M24.6 6.8V25.2" />
+      </g>
+      <path
+        d="M7.4 21.6 16 10.4 24.6 17.2"
+        fill="none"
+        stroke={alt}
+        strokeWidth="3.2"
+        strokeLinecap="round"
+        strokeLinejoin="round"
+      />
+    </>
+  ),
 };

package/src/parallel/core/index.ts

@@ -0,0 +1,96 @@
+/**
+ * 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';