@czi-sds/data-viz 2.1.1 → 2.3.0

package/dist/index.esm.d.ts

@@ -2,6 +2,7 @@
 import { DatasetComponentOption, ECharts, EChartsOption, ScatterSeriesOption } from "echarts";
 import { HTMLAttributes } from "react";
 import { DiscreteColorGeneratorOptions, TooltipProps, TooltipTableContentProps } from "@czi-sds/components";
+import { PluginUISpec } from "molstar/lib/mol-plugin-ui/spec";
 import { CustomElementProperty } from "molstar/lib/mol-model-props/common/custom-element-property";
 
 //#region src/common/colorScales.d.ts
@@ -297,14 +298,102 @@ interface ResidueRef {
   /** Insertion code, or `""` when the residue has none. */
   insCode: string;
 }
+/**
+ * A chain the viewer found in the structure it loaded, reported through
+ * `onChainsChange` so a consumer can label, color or hide chains by name
+ * without parsing the structure itself.
+ *
+ * `chainId` is the file's own name for the chain, the same one `ResidueRef`
+ * reports, and the key every chain-keyed prop takes. A chain carrying several
+ * symmetry operators appears once, under the first.
+ *
+ * Describes the chain's polymer. The ligands and ions sitting on it are drawn
+ * and are hidden and selected with it, but are not counted here or spanned by
+ * the range below - they are no part of the sequence. A chain holding nothing
+ * but heteroatoms is left out altogether, having no sequence to describe.
+ */
+interface ChainRef {
+  /** Chain as named in the file (`auth_asym_id`), e.g. `"A"`. */
+  chainId: string;
+  /** Chain as the sequence panel captions it. */
+  label: string;
+  /** Lowest 0-based residue index of the chain's polymer. */
+  startIndex: number;
+  /** Highest 0-based residue index of the chain's polymer. */
+  endIndex: number;
+  /** Polymer residues the chain holds. */
+  residueCount: number;
+}
+/**
+ * What is selected, in the two ways a caller might say it. `null` selects
+ * nothing.
+ *
+ * The two combine: `{ chains: ["A"], residues: [150] }` takes all of chain A
+ * plus one residue elsewhere. `chains` is kept as named rather than expanded
+ * into indices, so a whole-chain selection survives a round trip through a
+ * consumer's state at its original size.
+ */
+interface StructureSelection {
+  /**
+   * 0-based residue indices, counting residues in file order across the whole
+   * structure - the same index `plddt` and `residueOverlay` are keyed by.
+   */
+  residues?: number[];
+  /** Whole chains by `chainId`, each standing for every residue on it. */
+  chains?: string[];
+}
+/**
+ * How large a downloaded image is, in pixels.
+ *
+ * Named rather than given as dimensions because the aspect is Mol*'s to
+ * choose: each of these is one of its own presets, and a size picked here
+ * would have to be reconciled with the canvas the image is rendered from.
+ */
+type DownloadResolution = "low" | "medium" | "high" | "maximum";
+/** Pixel dimensions each resolution produces, for documentation and labels. */
+declare const DOWNLOAD_RESOLUTIONS: Record<DownloadResolution, string>;
+/**
+ * Turns on the capture button under the reset-camera control, and says what it
+ * should produce. Omit it and no button is drawn.
+ *
+ * The image is rendered fresh at the size asked for rather than scaled up from
+ * the canvas, so a high resolution costs time rather than sharpness - which is
+ * why the default sits in the middle rather than at the top.
+ */
+interface StructureDownload {
+  /**
+   * Size of the image. See `DOWNLOAD_RESOLUTIONS` for the pixel dimensions.
+   * @default "medium"
+   */
+  resolution?: DownloadResolution;
+  /**
+   * Background behind the structure, as `#RRGGBB`. Omit for a transparent
+   * one, which is what a figure usually wants - the viewer's own canvas color
+   * is deliberately not inherited, since a screenshot tends to outlive the
+   * theme it was taken under.
+   */
+  backgroundColor?: string;
+  /**
+   * Draw the orientation axes into the image. Independent of `showAxes`, which
+   * is about the view rather than the capture: the widget orients a reader who
+   * can turn the structure, and earns its place less in a still.
+   * @default false
+   */
+  showAxes?: boolean;
+  /**
+   * Name for the downloaded file, without an extension. Defaults to the one
+   * Mol* derives from the loaded structure.
+   */
+  filename?: string;
+}
 /** A whole-structure statistic shown along the bottom of the viewer. */
 interface StructureStat {
   value: string;
   label: string;
 }
 interface ProteinStructureViewerProps extends Omit<HTMLAttributes<HTMLDivElement>, "onSelect"> {
-  /** Structure to render, as raw PDB text. */
-  pdb: string;
+  /** Structure to render, as raw PDB or mmCIF (PDBx) text. */
+  structure: string;
   /**
    * Per-residue pLDDT confidence on a 0-1 scale, ordered by residue. When
    * supplied the structure is colored by pLDDT unless `residueOverlay` takes
@@ -326,6 +415,11 @@ interface ProteinStructureViewerProps extends Omit<HTMLAttributes<HTMLDivElement
    * @default true
    */
   showAxes?: boolean;
+  /**
+   * Adds a capture button beneath the reset-camera control, which downloads a
+   * PNG of the structure as it currently stands. Omit for no button.
+   */
+  download?: StructureDownload | null;
   /**
    * Show the sequence panel pinned along the bottom of the viewer.
    * @default true
@@ -339,11 +433,64 @@ interface ProteinStructureViewerProps extends Omit<HTMLAttributes<HTMLDivElement
   /** Per-residue values that override pLDDT coloring while set. */
   residueOverlay?: ResidueValueOverlay | null;
   /**
-   * 0-based index of the selected residue, or null when none is selected.
-   * Controlled: selecting a residue zooms the camera in on it, and clearing the
-   * selection zooms back out to the default view.
+   * What is selected, or null when nothing is. Controlled: the camera frames
+   * whatever the selection covers, and clearing it zooms back out to the
+   * default view.
+   *
+   * Residues are drawn in ball-and-stick over the cartoon; whole chains are
+   * left as they are and the chains around them dim, the same as hovering a
+   * chain's name.
+   */
+  selection?: StructureSelection | null;
+  /**
+   * Chains hidden from the 3D view, by `chainId`. Leave undefined to let the
+   * viewer own visibility itself, which is what the chain legend's toggles
+   * drive; passing it takes that over, and the toggles then only report.
    */
-  selectedResidue?: number | null;
+  hiddenChains?: string[];
+  /**
+   * Color per chain, by `chainId`, as `#RRGGBB`. Chains left out fall back to
+   * the viewer's palette. Only visible while chain coloring is what is on
+   * screen, which is when neither `plddt` nor `residueOverlay` is set.
+   */
+  chainColors?: Record<string, string>;
+  /**
+   * Show the chain legend, which lists each chain with its color and a
+   * visibility toggle. Ignored on a single-chain structure, where there is
+   * nothing to tell apart or hide.
+   * @default true
+   */
+  showChainLegend?: boolean;
+  /**
+   * Stop other chains from dimming in the 3D view while a chain's name is
+   * pointed at, in the legend or above its grid in the sequence panel.
+   *
+   * The dim is on by default, since on a complex it is how a reader finds out
+   * which chain is which. Turn it off where the movement is more distracting
+   * than the answer is useful - a grid of viewers a pointer crosses on its way
+   * somewhere else, or a page driving its own highlighting through `selection`.
+   * @default false
+   */
+  disableChainHighlightOnHover?: boolean;
+  /**
+   * Mol* plugin spec laid over the viewer's own, which is how the whole of
+   * Mol*'s configuration is reachable without a prop here for each setting.
+   * Anything named here wins, so `canvas3d.postprocessing`, a `PluginConfig`
+   * item, or `layout.initial` can all be set to something other than the
+   * default the viewer picked.
+   *
+   * List-valued keys - `behaviors`, `config`, `actions`, `animations`,
+   * `customFormats`, `customParamEditors` - are appended to rather than
+   * replaced. For `config` that is what lets an entry override the viewer's,
+   * since Mol* reads the list in order. It also means a behavior cannot be
+   * taken away: the ones the viewer drops stay dropped, and the ones it keeps
+   * cannot be removed from here.
+   *
+   * Read once, when the plugin is created, except for `canvas3d`, which is
+   * re-applied whenever it changes. Creating the plugin throws away the camera,
+   * so the rest is deliberately not reactive.
+   */
+  molstarSpec?: Partial<PluginUISpec>;
   /**
    * Up to three whole-structure stats shown along the bottom. A null entry
    * reserves its column without rendering anything, so the columns never shift
@@ -357,25 +504,74 @@ interface ProteinStructureViewerProps extends Omit<HTMLAttributes<HTMLDivElement
    * the structure.
    */
   onResidueHover?: (residue: ResidueRef | null) => void;
-  /** Called when the user clicks empty space, clearing the selection. */
-  onSelectionClear?: () => void;
+  /**
+   * Called with the new selection whenever the user makes one - clicking a
+   * residue, dragging across the sequence, clicking a chain caption - and with
+   * `null` when they click empty space to clear it.
+   *
+   * A whole-chain selection arrives as `{ chains: [id] }` rather than as every
+   * index on it, so echoing it straight back into `selection` costs nothing.
+   */
+  onSelectionChange?: (selection: StructureSelection | null) => void;
+  /**
+   * Called with the chains found in the structure, whenever a structure is
+   * loaded. Fires with `[]` when the structure holds none.
+   */
+  onChainsChange?: (chains: ChainRef[]) => void;
+  /**
+   * Called with the chains now hidden when a visibility toggle is used. Fires
+   * whether or not `hiddenChains` is controlled, so a consumer can follow the
+   * viewer's own state without owning it.
+   */
+  onChainVisibilityChange?: (hiddenChains: string[]) => void;
 }
 /**
- * Per-residue readout that replaces the whole-structure stats while a residue
- * is hovered or selected.
+ * Readout that replaces the whole-structure stats while something is hovered
+ * or selected. Covers one residue or many: a drag across the sequence and a
+ * whole-chain selection report through this too, as a mean over what they
+ * cover.
  */
 interface ResidueReadout {
-  /** e.g. "PHE 17" */
+  /** e.g. "PHE 17", "Chain A", or "24 residues". */
   label: string;
-  /** Residue pLDDT on a 0-1 scale, or null when unavailable. */
+  /**
+   * pLDDT on a 0-1 scale, or null when unavailable. The mean across the
+   * residues covered when there is more than one, ignoring those without a
+   * score.
+   */
   plddt: number | null;
   /**
-   * Residue overlay value, or null when the overlay holds none for it - which
-   * is also what a structure paints neutral - or when no overlay is set.
+   * Overlay value, or null when the overlay holds none - which is also what a
+   * structure paints neutral - or when no overlay is set. The mean across the
+   * residues covered when there is more than one, ignoring those the overlay
+   * says nothing about.
    */
   value: number | null;
+  /**
+   * Residues the readout covers, which is what makes the numbers above means
+   * rather than readings. 1 for a single residue.
+   */
+  residueCount: number;
 }
 //#endregion
+//#region src/core/ProteinStructureViewer/utils/structureFormat.d.ts
+/**
+ * Structure text formats Mol* can parse from the viewer's `structure` prop.
+ *
+ * `"mmcif"` covers both mmCIF and PDBx; they are the same text format, and
+ * that is the name Mol*'s trajectory parser uses. Binary CIF (`.bcif`) is not
+ * accepted: the prop is a string.
+ */
+type StructureFormat = "pdb" | "mmcif";
+/**
+ * Infers whether `text` is PDB or mmCIF (PDBx).
+ *
+ * mmCIF documents start with a `data_` block and name their coordinates
+ * `_atom_site.`. PDB never does either, so either marker is enough. A leading
+ * comment (`# ...`) before `data_` is still mmCIF.
+ */
+declare function detectStructureFormat(text: string): StructureFormat;
+//#endregion
 //#region src/core/ProteinStructureViewer/utils/plddt.d.ts
 /**
  * AlphaFold's pLDDT confidence bands. Thresholds are on the 0-1 scale that
@@ -394,6 +590,23 @@ declare const PLDDT_COLOR_SCALE: ColorScale;
  * them its neighbour's score.
  */
 declare function injectPlddtIntoPdb(pdbData: string, plddtValues: number[]): string;
+/**
+ * Rewrites an mmCIF (PDBx) file's `_atom_site.B_iso_or_equiv` column with
+ * pLDDT scores so Mol* can read them off the parsed model, the same way
+ * `injectPlddtIntoPdb` rewrites the PDB B-factor column. Scores arrive on a
+ * 0-1 scale and are stored on the conventional 0-100 one. Residues past the
+ * end of `plddtValues` fall back to a mid-confidence 50.
+ *
+ * If the file has no B-factor column, one is appended to the atom-site loop
+ * rather than leaving the scores behind.
+ */
+declare function injectPlddtIntoMmcif(mmcifData: string, plddtValues: number[]): string;
+/**
+ * Rewrites a structure file's B-factors with pLDDT scores. Dispatches to
+ * `injectPlddtIntoPdb` or `injectPlddtIntoMmcif` from `format`, or from
+ * detecting the format of `data` when `format` is omitted.
+ */
+declare function injectPlddt(data: string, plddtValues: number[], format?: StructureFormat): string;
 //#endregion
 //#region src/core/ProteinStructureViewer/index.d.ts
 declare const _default$1: import("react").MemoExoticComponent<import("react").ForwardRefExoticComponent<ProteinStructureViewerProps & import("react").RefAttributes<HTMLDivElement>>>;
@@ -559,4 +772,4 @@ interface StackedBarChartProps extends HTMLAttributes<HTMLDivElement> {
 //#region src/core/StackedBarChart/index.d.ts
 declare const StackedBarChart: (props: StackedBarChartProps) => JSX.Element;
 //#endregion
-export { type ColorScale, type ContinuousColorStop, _default as HeatmapChart, HeatmapChartProps, PLASMA_COLOR_SCALE, PLDDT_COLOR_SCALE, _default$1 as ProteinStructureViewer, ProteinStructureViewerProps, ResidueReadout, ResidueRef, ResidueValueOverlay, StackedBarChart, type StackedBarChartDataItem, type StackedBarChartProps, type SteppedColorStop, StructureStat, injectPlddtIntoPdb, sampleColorScale, toCssGradient };
+export { ChainRef, type ColorScale, type ContinuousColorStop, DOWNLOAD_RESOLUTIONS, DownloadResolution, _default as HeatmapChart, HeatmapChartProps, PLASMA_COLOR_SCALE, PLDDT_COLOR_SCALE, _default$1 as ProteinStructureViewer, ProteinStructureViewerProps, ResidueReadout, ResidueRef, ResidueValueOverlay, StackedBarChart, type StackedBarChartDataItem, type StackedBarChartProps, type SteppedColorStop, StructureDownload, type StructureFormat, StructureSelection, StructureStat, detectStructureFormat, injectPlddt, injectPlddtIntoMmcif, injectPlddtIntoPdb, sampleColorScale, toCssGradient };