bravais 0.1.4 → 0.2.1

package/dist/types/cif/errors.d.ts

@@ -1,3 +1,9 @@
+/** The text is not CIF the tokenizer and parser accept. */
+export declare class CifSyntaxError extends Error {
+    /** 1-based line of the problem. */
+    readonly line: number;
+    constructor(message: string, line: number);
+}
 /** The CIF parses but does not describe a structure this package can use. */
 export declare class CifStructureError extends Error {
     constructor(message: string);

package/dist/types/cif/structure.d.ts

@@ -1,15 +1,13 @@
 import type { Lattice, Site, SpaceGroupInfo, SymmetryOperation } from "../structure/types.js";
 import { type CifBlock } from "./parser.js";
-import { CifStructureError } from "./errors.js";
-export { CifStructureError };
 export interface ParsedCifStructure {
     lattice: Lattice;
     sites: Site[];
-    /** Null when the file lists no operators; see `spaceGroup` then. */
+    /** Null when the file lists no operations; see `spaceGroup` then. */
     operations: SymmetryOperation[] | null;
     spaceGroup: SpaceGroupInfo;
 }
 /** True when the block carries atom coordinates (the one a viewer wants). */
 export declare function isStructureBlock(block: CifBlock): boolean;
-/** Lattice, merged sites, operators and space-group tags of one data block. */
+/** Lattice, merged sites, operations and space-group tags of one data block. */
 export declare function parseCifStructure(block: CifBlock): ParsedCifStructure;

package/dist/types/cif/{symmetry-operators.d.ts → symmetry-operations.d.ts}

@@ -3,4 +3,4 @@ import type { SymmetryOperation } from "../structure/types.js";
  * Parse a symmetry operation as CIF files write it, such as
  * `-x+1/2, y, -z+1/2`, into a rotation matrix and translation.
  */
-export declare function parseSymmetryOperator(text: string): SymmetryOperation;
+export declare function parseSymmetryOperation(text: string): SymmetryOperation;

package/dist/types/cif/tokenizer.d.ts

@@ -4,12 +4,6 @@ export interface CifToken {
     text: string;
     line: number;
 }
-/** The text is not CIF the tokenizer and parser accept. */
-export declare class CifSyntaxError extends Error {
-    /** 1-based line of the problem. */
-    readonly line: number;
-    constructor(message: string, line: number);
-}
 /**
  * Split CIF 1.1 text into tokens. Comments are dropped; quoted strings and
  * semicolon text fields become single value tokens holding their content.

package/dist/types/index.d.ts

@@ -1,22 +1,20 @@
 import type { Structure } from "./structure/types.js";
+export { CifStructureError, CifSyntaxError } from "./cif/errors.js";
 export { parseCif, type CifBlock, type CifDocument, type CifLoop, } from "./cif/parser.js";
-export { CifSyntaxError } from "./cif/tokenizer.js";
-export { CifStructureError, parseCifStructure, type ParsedCifStructure, } from "./cif/structure.js";
-export { parseSymmetryOperator } from "./cif/symmetry-operators.js";
+export { parseCifStructure, type ParsedCifStructure } from "./cif/structure.js";
+export { parseSymmetryOperation } from "./cif/symmetry-operations.js";
 export { SpaceGroupLookupError, ensureMoyo, operationsForSpaceGroup, } from "./symmetry/moyo.js";
 export { SymmetryAnalysisError, symmetryDataset, type SymmetryDataset, type SymmetryOptions, } from "./symmetry/dataset.js";
 export { typesetSymbol } from "./symmetry/symbol.js";
 export { expandStructure } from "./structure/expand.js";
 export { latticeFromParameters, latticeFromVectors, } from "./structure/lattice.js";
-export { buildScene, structureElements } from "./scene/build.js";
+export type { Bond } from "./structure/bonds.js";
+export type { Lattice, LatticeParameters, Mat3, Site, SpaceGroupInfo, Species, Structure, SymmetryOperation, Vec3, } from "./structure/types.js";
+export { buildScene, structureElements, type BuildSceneOptions, type SceneAtom, type SceneLayer, type StructureScene, } from "./scene/build.js";
 export { createViewer, type Viewer, type ViewerOptions, } from "./render/viewer.js";
 export { createThumbnailRenderer, type ThumbnailRenderer, } from "./render/thumbnails.js";
-export type { SceneLayer } from "./scene/build.js";
 export type { ViewState } from "./render/view-state.js";
 export { elementColor, elementColorAssignments, ensureElementColors, resetElementColors, } from "./render/palette.js";
-export type { BuildSceneOptions, SceneAtom, StructureScene, } from "./scene/build.js";
-export type { Bond } from "./structure/bonds.js";
-export type { Lattice, LatticeParameters, Mat3, Site, SpaceGroupInfo, Species, Structure, SymmetryOperation, Vec3, } from "./structure/types.js";
 /**
  * Read the first structure in a CIF file. Its symmetry comes from the
  * file's list of symmetry operations or, without one, from its space-group

package/dist/types/render/camera.d.ts

@@ -1,11 +1,6 @@
-import { Box3, OrthographicCamera, Quaternion, Vector3 } from "three";
+import { Box3, OrthographicCamera, Quaternion } from "three";
 import type { Mat3 } from "../structure/types.js";
 import type { ViewState } from "./view-state.js";
-/** Camera outward direction and up vector of the standard view of a cell. */
-export declare function standardViewVectors(cell: Mat3): {
-    outward: Vector3;
-    up: Vector3;
-};
 /** Distance of the orthographic camera from its target; only the clipping depends on it. */
 export declare function cameraDistance(span: number): number;
 export declare function standardQuaternion(cell: Mat3): Quaternion;
@@ -15,11 +10,6 @@ export declare function standardView(cell: Mat3): ViewState;
 export declare function applyViewState(camera: OrthographicCamera, view: Pick<ViewState, "quaternion" | "target">, distance: number, span: number): void;
 /** The orientation of a camera as a view-state quaternion. */
 export declare function quaternionTuple(quaternion: Quaternion): [number, number, number, number];
-/** Size of `bounds` projected on the screen plane of `quaternion`. */
-export declare function projectedSize(bounds: Box3, quaternion: Quaternion): {
-    width: number;
-    height: number;
-};
 /** Orthographic zoom (pixels per ångström) that fits `bounds` in the viewport. */
 export declare function fitZoom(bounds: Box3, quaternion: Quaternion, width: number, height: number): number;
 /** Frustum of an orthographic camera in pixel units, so `zoom` is pixels per ångström. */

package/dist/types/render/gizmo.d.ts

@@ -8,7 +8,6 @@ export declare class AxesGizmo {
     /** The a, b and c arrows, built once and turned to each new cell. */
     private readonly arrows;
     private readonly headlight;
-    private readonly inverse;
     private readonly direction;
     /** `fontFamily` is the interface font the axis letters are drawn in. */
     constructor(fontFamily: string);

package/dist/types/render/materials.d.ts

@@ -1,14 +1,10 @@
 import { DataTexture, LineBasicMaterial, MeshStandardMaterial } from "three";
-export declare const METALNESS = 0.1;
-export declare const ROUGHNESS = 0.6;
 export declare const AMBIENT_LIGHT_INTENSITY = 0.8;
 export declare const HEADLIGHT_INTENSITY = 2.2;
 export declare const HEADLIGHT_OFFSET: readonly [number, number, number];
 export declare const BACKGROUND_COLOR = "#fafafa";
-export declare const CELL_FRAME_COLOR = "#444444";
 /** The part of a partially occupied site nobody occupies: a faint, see-through tint. */
 export declare const VACANCY_COLOR = "#f2f2f2";
-export declare const VACANCY_OPACITY = 0.3;
 /** Added to a vacancy texel's start fraction so the shader can tell it apart. */
 export declare const VACANCY_FLAG = 2;
 /**

package/dist/types/render/model.d.ts

@@ -1,12 +1,10 @@
 import { Box3, Group } from "three";
 import type { SceneLayer } from "../scene/build.js";
-import type { Mat3, Vec3 } from "../structure/types.js";
+import type { Mat3 } from "../structure/types.js";
 export interface SceneModel {
     group: Group;
-    /** Cell row vectors of the first layer, the frame everything is centred on. */
+    /** Cell row vectors of the first layer; `group` moves its centre to the origin. */
     cell: Mat3;
-    /** Centre of that cell, which `group` moves to the origin. */
-    center: Vec3;
     /** Bounds of every atom and cell corner of every layer, in the centred frame. */
     bounds: Box3;
     /** Largest cell edge length of any layer. */
@@ -15,10 +13,18 @@ export interface SceneModel {
     elements: string[];
     dispose(): void;
 }
-export declare function cellCenter(cell: Mat3): Vec3;
 /**
  * Build the three.js objects for the layers, centred on the first cell. A
  * layer at opacity 0 is not drawn but still counts toward the centre, the
  * bounds and the span.
  */
 export declare function createSceneModel(layers: SceneLayer[]): SceneModel;
+/**
+ * A placeholder atom, bond and cell frame in every material a structure is
+ * drawn with, opaque and see-through, so their shaders can compile before
+ * the first structure arrives. It gives no element a colour.
+ */
+export declare function createShaderWarmup(): {
+    group: Group;
+    dispose(): void;
+};

package/dist/types/render/oklab.d.ts

@@ -15,7 +15,6 @@ export interface Oklch {
     h: number;
 }
 export declare function hexToOklab(hex: string): Oklab;
-export declare function isInGamut(lab: Oklab): boolean;
 export declare function oklabToHex(lab: Oklab): string;
 export declare function oklabToOklch(lab: Oklab): Oklch;
 export declare function oklchToOklab(lch: Oklch): Oklab;

package/dist/types/render/viewer.d.ts

@@ -22,7 +22,7 @@ export interface Viewer {
     resetView(): void;
     /** Fit the canvas to the container again; the viewer does this itself when the container resizes. */
     resize(): void;
-    /** Draw a frame now. */
+    /** Draw a frame now, or as soon as the shaders finish compiling. */
     render(): void;
     /** Call `listener` when the user rotates or zooms. Returns a function that removes it. */
     onInteraction(listener: () => void): () => void;
@@ -32,6 +32,8 @@ export interface Viewer {
 /**
  * Create a viewer inside `container`. It fills the container and follows
  * its size, so give the container a height. Adds the class `bravais-viewer`
- * to the container and one small stylesheet to the page.
+ * to the container and one small stylesheet to the page. Its shaders start
+ * compiling in the background at once, and drawing waits until they are
+ * ready.
  */
 export declare function createViewer(container: HTMLElement, options?: ViewerOptions): Viewer;

package/dist/types/structure/bonds.d.ts

@@ -12,8 +12,6 @@ export interface Bond {
     /** Distance between them in ångström. */
     length: number;
 }
-/** VESTA's bond-search maximum for an element pair, or null when VESTA draws none. */
-export declare function bondCutoff(elementA: string, elementB: string): number | null;
 /**
  * Bonds between the given atoms by VESTA's cutoff table. Only pairs VESTA
  * lists get bonds, so no metal-metal or anion-anion sticks appear. The bonds

package/dist/types/structure/elements.d.ts

@@ -1,8 +1,5 @@
 /** Element symbols in atomic-number order. */
 export declare const ELEMENT_SYMBOLS: string[];
-/** Deuterium keeps its own symbol for display and counts as hydrogen. */
-export declare const DEUTERIUM = "D";
-export declare function isElementSymbol(symbol: string): boolean;
 /**
  * The element behind a CIF atom label or type symbol: `Fe3+`, `O2-`, `Co1`,
  * `OW`, `fe` and `Wat` all resolve. Null when no element symbol fits.

package/dist/types/structure/fractional.d.ts

@@ -1,12 +1,10 @@
 import type { SymmetryOperation, Vec3 } from "./types.js";
 /** Generated equivalents this close in fractional coordinates are one atom. */
 export declare const EQUIVALENT_TOLERANCE = 0.001;
-/** Fold a coordinate into [0, 1); a value within `nearOne` below 1 becomes 0. */
-export declare function wrap(value: number, nearOne?: number): number;
+/** Fold a coordinate into [0, 1); a value within `tolerance` below 1 becomes 0. */
+export declare function wrap(value: number, tolerance?: number): number;
 /** Fold a fractional position into the cell. */
 export declare function wrapVector(fractional: Vec3): Vec3;
-/** Periodic distance of two fractional positions, per axis, below `tolerance`. */
-export declare function samePosition(p: Vec3, q: Vec3, tolerance: number): boolean;
 /**
  * Fractional positions bucketed by where they fall in the cell, so finding
  * those within a tolerance of a position, across the periodic boundaries,

package/dist/types/symmetry/resolve.d.ts

@@ -1,4 +1,4 @@
-import { type ParsedCifStructure } from "../cif/structure.js";
+import type { ParsedCifStructure } from "../cif/structure.js";
 import { type SymmetryOperation } from "../structure/types.js";
 /**
  * The operations a parsed CIF's atoms are expanded with: the file's own

package/examples/CoO.cif

@@ -0,0 +1,254 @@
+#------------------------------------------------------------------------------
+#$Date: 2024-05-06 10:39:41 +0300 (Mon, 06 May 2024) $
+#$Revision: 291735 $
+#$URL: file:///home/coder/svn-repositories/_RELOADED_COD/cod-reloaded/cif/9/00/86/9008618.cif $
+#------------------------------------------------------------------------------
+#
+# This file is available in the Crystallography Open Database (COD),
+# http://www.crystallography.net/. The original data for this entry
+# were provided the American Mineralogist Crystal Structure Database,
+# http://rruff.geo.arizona.edu/AMS/amcsd.php
+#
+# The file may be used within the scientific community so long as
+# proper attribution is given to the journal article from which the
+# data were obtained.
+#
+data_9008618
+loop_
+_publ_author_name
+'Wyckoff, R. W. G.'
+_publ_section_title
+;
+ Second edition. Interscience Publishers, New York, New York
+ rocksalt structure
+;
+_journal_name_full               'Crystal Structures'
+_journal_page_first              85
+_journal_page_last               237
+_journal_volume                  1
+_journal_year                    1963
+_chemical_formula_structural     CoO
+_chemical_formula_sum            'Co O'
+_space_group_IT_number           225
+_symmetry_space_group_name_Hall  '-F 4 2 3'
+_symmetry_space_group_name_H-M   'F m -3 m'
+_cell_angle_alpha                90
+_cell_angle_beta                 90
+_cell_angle_gamma                90
+_cell_length_a                   4.2667
+_cell_length_b                   4.2667
+_cell_length_c                   4.2667
+_cell_formula_units_Z            4
+_cell_volume                     77.674
+_database_code_amcsd             0011296
+_exptl_crystal_density_diffrn    6.408
+_cod_original_sg_symbol_H-M      'F m 3 m'
+_cod_database_code               9008618
+_amcsd_formula_title             CoO
+loop_
+_space_group_symop_operation_xyz
+x,y,z
+x,1/2+y,1/2+z
+1/2+x,y,1/2+z
+1/2+x,1/2+y,z
+z,-x,y
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+-y,z,-x
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+-x,z,y
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+z,-y,-x
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+-y,x,z
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+-z,-y,-x
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+-x,-z,-y
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+-y,-z,-x
+-y,1/2-z,1/2-x
+1/2-y,-z,1/2-x
+1/2-y,1/2-z,-x
+loop_
+_atom_site_label
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+Co 0.00000 0.00000 0.00000
+O 0.50000 0.50000 0.50000
+loop_
+_cod_related_entry_id
+_cod_related_entry_database
+_cod_related_entry_code
+1 ChemSpider 8117730
+2 AMCSD 0011296

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "bravais",
-  "version": "0.1.4",
+  "version": "0.2.1",
   "description": "A minimal crystal structure viewer for the web: reads CIF files and draws them with three.js.",
   "license": "MIT",
   "author": "Jiacheng Wang",
@@ -36,6 +36,7 @@
   },
   "files": [
     "dist",
+    "examples/CoO.cif",
     "CHANGELOG.md",
     "THIRD_PARTY_NOTICES.md"
   ],