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Comparing version 2.0.3 to 2.0.4

.devcontainer/devcontainers.json
.github/workflows/dependency-review.yml
CITATION.cff
codecov.yml

2

build/3Dmol-min.js.LICENSE.txt
/*!
* 3dmol v2.0.3
* 3dmol v2.0.4
* JavaScript/TypeScript molecular visualization library
* Author: David Koes and contributors
*/

2

build/3Dmol.ui-min.js.LICENSE.txt
/*!
* 3dmol v2.0.3
* 3dmol v2.0.4
* JavaScript/TypeScript molecular visualization library

@@ -4,0 +4,0 @@ * Author: David Koes and contributors

2

build/types/autoload.d.ts

@@ -9,2 +9,2 @@ export declare var autoinit: boolean;

export declare var viewers: any;
export declare function autoload(viewer?: any, callback?: any): void;
export declare function autoload(viewer?: any, callback?: (arg0: any) => void): void;

27

build/types/GLDraw.d.ts
import { Geometry } from "./WebGL";
import { Color, Colored } from "colors";
/**

@@ -15,2 +16,7 @@ * Enum for cylinder cap styles.

}
export interface Point {
x: number;
y: number;
z: number;
}
/**

@@ -25,3 +31,3 @@ * Lower level utilities for creating WebGL shape geometries.

* @memberof GLDraw
* @param {geometry}
* @param {Geometry}
* geo

@@ -32,3 +38,3 @@ * @param {Point}

* to
* @param {float}
* @param {number}
* radius

@@ -41,6 +47,6 @@ * @param {Color}

* */
function drawCylinder(geo: Geometry, from: any, to: any, radius: number, color: any, fromCap?: CAP, toCap?: CAP): void;
function drawCylinder(geo: Geometry, from: any, to: any, radius: number, color: Color | Color[], fromCap?: CAP, toCap?: CAP): void;
/** Create a cone
* @memberof GLDraw
* @param {geometry}
* @param {Geometry}
* geo

@@ -51,3 +57,3 @@ * @param {Point}

* to
* @param {float}
* @param {number}
* radius

@@ -57,16 +63,17 @@ * @param {Color}

* */
function drawCone(geo: Geometry, from: any, to: any, radius: number, color?: any): void;
function drawCone(geo: Geometry, from: any, to: any, radius: number, color?: Color): void;
/** Create a sphere.
* @memberof GLDraw
* @param {geometry}
* @param {Geometry}
* geo
* @param {Point}
* pos
* @param {float}
* @param {number}
* radius
* @param {Color}
* color
* @param {number} quality of sphere (default 2, higher increases number of triangles)
* @param {number}
* sphereQuality - Quality of sphere (default 2, higher increases number of triangles)
*/
function drawSphere(geo: Geometry, pos: any, radius: any, color: any, sphereQuality?: any): void;
function drawSphere(geo: Geometry, pos: any, radius: number, color: Colored, sphereQuality?: number): void;
}

3

build/types/GLModel.d.ts

@@ -253,2 +253,3 @@ import { Geometry } from "./WebGL";

private static deepCopyAndCache;
private static readonly ignoredKeys;
/** given a selection specification, return true if atom is selected.

@@ -488,3 +489,3 @@ * Does not support context-aware selectors like expand/within/byres.

static parseCrd(data: any, format: string): any;
static parseMolData(data?: any, format?: string, options?: any): any;
static parseMolData(data?: string | ArrayBuffer, format?: string, options?: ParserOptionsSpec): any;
}

@@ -491,0 +492,0 @@ /** Atom style specification */

5

build/types/GLViewer.d.ts

@@ -0,1 +1,2 @@

import { Renderer } from "./WebGL";
import { Vector3, XYZ } from "./WebGL/math";

@@ -237,3 +238,3 @@ import { Mesh } from "./WebGL";

*/
getRenderer(): any;
getRenderer(): Renderer;
/**

@@ -1012,3 +1013,3 @@ * Set the duration of the hover delay

*/
hasVolumetricRender(): any;
hasVolumetricRender(): boolean;
/**

@@ -1015,0 +1016,0 @@ * Enable/disable fog for content far from the camera

16

build/types/Gradient.d.ts

@@ -26,3 +26,3 @@ import { Color } from "./colors";

range(): [number, number];
valueToHex(val: any, range: any): any;
valueToHex(val: number, range?: number[]): number;
}

@@ -37,6 +37,6 @@ /**

mult: number;
max: number;
min: number;
constructor(min: any, max: any);
valueToHex(val: any, range: any): any;
max?: number;
min?: number;
constructor(min?: number, max?: number);
valueToHex(val: number, range?: any[]): number;
range(): [number, number];

@@ -68,4 +68,4 @@ }

min: number;
constructor(min: any, max: any);
valueToHex(val: any, range: any): number;
constructor(min: number, max: number);
valueToHex(val: number, range?: any[]): number;
range(): [number, number];

@@ -98,3 +98,3 @@ }

range(): [number, number];
valueToHex(val: any, range: any): number;
valueToHex(val: number, range?: any[]): number;
}

@@ -101,0 +101,0 @@ export declare const builtinGradients: {

2

build/types/Label.d.ts

@@ -58,3 +58,3 @@ import { Vector2 } from "./WebGL";

frame: any;
constructor(text: any, parameters: any);
constructor(text: string, parameters: LabelSpec);
getStyle(): any;

@@ -61,0 +61,0 @@ setContext(): void;

5

build/types/parsers/CDJSON.d.ts

@@ -0,1 +1,2 @@

import { ParserOptionsSpec } from "./ParserOptionsSpec";
/**

@@ -10,3 +11,3 @@ * This parses the ChemDoodle json file format. Although this is registered

* @category Parsers
*/
export declare function CDJSON(str: any, options: any): any[][] & Record<string, any>;
*/
export declare function CDJSON(str: string, options: ParserOptionsSpec): any[][] & Record<string, any>;

5

build/types/parsers/CIF.d.ts
import { ParserOptionsSpec } from './ParserOptionsSpec';
/**
* Puts atoms specified in mmCIF fromat in str into atoms
*
* @param {string} str
* @param {ParserOptionsSpec} options
* @category Parsers
*/
*/
export declare function CIF(str: string, options?: ParserOptionsSpec): any[] & Record<string, any>;

12

build/types/parsers/CUBE.d.ts

@@ -0,9 +1,9 @@

import { ParserOptionsSpec } from "./ParserOptionsSpec";
/**
* @param {string}
* str
* @param {ParserOptionsSpec}
* options
* @param {string}
* str
* @param {ParserOptionsSpec}
* options
* @category Parsers
*/
export declare function CUBE(str: any, options: any): any[][] & Record<string, any>;
export declare function CUBE(str: string, options: ParserOptionsSpec): any[][] & Record<string, any>;

17

build/types/parsers/GRO.d.ts
/**
* Parse a gro file from str and create atoms
*
* @param {string}
* str
* @param {ParserOptionsSpec}
* options*
* @category Parsers
*/
export declare function GRO(str: any): any[][] & Record<string, any>;
*
* @param {string}
* str
* @param {ParserOptionsSpec}
* options*
* @category Parsers
*/
export declare function GRO(str: string): any[][] & Record<string, any>;

7

build/types/parsers/LAMMPSTRJ.d.ts

@@ -0,6 +1,7 @@

import { ParserOptionsSpec } from "./ParserOptionsSpec";
/**
* Parse a lammps trajectory file from str and create atoms
*
* @category Parsers
*/
export declare function LAMMPSTRJ(str: any, options: any): any[];
*/
export declare function LAMMPSTRJ(str: string, options: ParserOptionsSpec): any[];

10

build/types/parsers/MMTF.d.ts

@@ -1,5 +0,7 @@

/** @param bindata - binary UInt8Array buffer or a base64 encoded string
* @param ParserOptionsSpec
* @category Parsers
import { ParserOptionsSpec } from "./ParserOptionsSpec";
/**
* @param bindata - binary UInt8Array buffer or a base64 encoded string
* @param ParserOptionsSpec
* @category Parsers
*/
export declare function MMTFparser(bindata: any, options: any): any[][] & Record<string, any>;
export declare function MMTFparser(bindata: any, options: ParserOptionsSpec): any[][] & Record<string, any>;

5

build/types/parsers/MOL2.d.ts

@@ -0,1 +1,2 @@

import { ParserOptionsSpec } from "./ParserOptionsSpec";
/**

@@ -7,3 +8,3 @@ * @param {string}

* @category Parsers
*/
export declare function MOL2(str: any, options: any): any[][] & Record<string, any>;
*/
export declare function MOL2(str: string, options: ParserOptionsSpec): any[][] & Record<string, any>;

8

build/types/parsers/PDB.d.ts

@@ -0,2 +1,6 @@

import { ParserOptionsSpec } from "./ParserOptionsSpec";
/**
* Parse pdb file from str and create atoms if computeStruct is true will always perform secondary structure analysis,
* otherwise only do analysis of SHEET/HELIX comments are missing
*
* @param {string} str

@@ -8,3 +12,3 @@ * @param {ParserOptionsSpec} options - keepH (do not strip hydrogens), noSecondaryStructure,

*
*/
export declare function PDB(str: any, options: any): any[] & Record<string, any>;
*/
export declare function PDB(str: string, options: ParserOptionsSpec): any[] & Record<string, any>;

10

build/types/parsers/PQR.d.ts

@@ -0,4 +1,4 @@

import { ParserOptionsSpec } from "./ParserOptionsSpec";
/**
* Parse a pqr file from str and create atoms. A pqr file is assumed to be a
* whitespace delimited PDB with charge and radius fields.
* Parse a pqr file from str and create atoms. A pqr file is assumed to be a whitespace delimited PDB with charge and radius fields.
*

@@ -9,4 +9,4 @@ * @param {string}

* options - noSecondaryStructure (do not compute ss)
* @category Parsers
*/
export declare function PQR(str: any, options: any): any[][] & Record<string, any>;
* @category Parsers
*/
export declare function PQR(str: string, options: ParserOptionsSpec): any[][] & Record<string, any>;

14

build/types/parsers/PRMTOP.d.ts
/**
* Parse a prmtop file from str and create atoms
*
* @param {string}
* str
* @param {ParserOptionsSpec}
* options - noSecondaryStructure (do not compute ss)
*
* @param {string}
* str
* @param {ParserOptionsSpec}
* options - noSecondaryStructure (do not compute ss)
* @category Parsers
*/
export declare function PRMTOP(str: any): any[][];
*/
export declare function PRMTOP(str: string): any[][];

6

build/types/parsers/SDF.d.ts

@@ -0,1 +1,2 @@

import { ParserOptionsSpec } from "./ParserOptionsSpec";
/**

@@ -7,4 +8,3 @@ * @param {string}

* @category Parsers
*/
export declare function SDF(str: any, options: any): any[][] & Record<string, any>;
*/
export declare function SDF(str: string, options: ParserOptionsSpec): any;

120

build/types/parsers/utils/anumToSymbol.d.ts

@@ -1,119 +0,1 @@

export declare const anumToSymbol: {
1: string;
2: string;
3: string;
4: string;
5: string;
6: string;
7: string;
8: string;
9: string;
10: string;
11: string;
12: string;
13: string;
14: string;
15: string;
16: string;
17: string;
18: string;
19: string;
20: string;
21: string;
22: string;
23: string;
24: string;
25: string;
26: string;
27: string;
28: string;
29: string;
30: string;
31: string;
32: string;
33: string;
34: string;
35: string;
36: string;
37: string;
38: string;
39: string;
40: string;
41: string;
42: string;
43: string;
44: string;
45: string;
46: string;
47: string;
48: string;
49: string;
50: string;
51: string;
52: string;
53: string;
54: string;
55: string;
56: string;
71: string;
72: string;
73: string;
74: string;
75: string;
76: string;
77: string;
78: string;
79: string;
80: string;
81: string;
82: string;
83: string;
84: string;
85: string;
86: string;
87: string;
88: string;
104: string;
105: string;
106: string;
107: string;
108: string;
109: string;
110: string;
111: string;
112: string;
113: string;
114: string;
115: string;
116: string;
117: string;
118: string;
57: string;
58: string;
59: string;
60: string;
61: string;
62: string;
63: string;
64: string;
65: string;
66: string;
67: string;
68: string;
69: string;
70: string;
89: string;
90: string;
91: string;
92: string;
93: string;
94: string;
95: string;
96: string;
97: string;
98: string;
99: string;
100: string;
101: string;
102: string;
};
export declare const anumToSymbol: any;

14

build/types/parsers/utils/areConnected.d.ts

@@ -1,1 +0,13 @@

export declare function areConnected(atom1: any, atom2: any): boolean;
export declare function areConnected(atom1: {
elem: any;
x: number;
y: number;
z: number;
altLoc: string;
}, atom2: {
elem: any;
x: number;
y: number;
z: number;
altLoc: string;
}): boolean;

2

build/types/parsers/utils/assignBackboneHBonds.d.ts

@@ -1,1 +0,1 @@

export declare function assignBackboneHBonds(atomsarray: any, hbondCutoff: any): void;
export declare function assignBackboneHBonds(atomsarray: string | any[], hbondCutoff: number): void;

5

build/types/parsers/utils/assignBonds.d.ts

@@ -1,1 +0,4 @@

export declare function assignBonds(atoms: any): void;
/**
* @param {AtomSpec[]} atoms
*/
export declare function assignBonds(atoms: string | any[]): void;

6

build/types/parsers/utils/assignPDBBonds.d.ts

@@ -1,1 +0,5 @@

export declare function assignPDBBonds(atomsarray: any): void;
/**
* @param {AtomSpec[]}
* atomsarray
*/
export declare function assignPDBBonds(atomsarray: string | any[]): void;

2

build/types/parsers/utils/atomNameToElem.d.ts

@@ -1,1 +0,1 @@

export declare function atomNameToElem(name: any, nothetero: any): any;
export declare function atomNameToElem(name: string, nothetero: boolean): string;

79

build/types/parsers/utils/bondLength.d.ts

@@ -1,78 +0,3 @@

export declare let bondTable: {
H: number;
He: number;
Li: number;
Be: number;
B: number;
C: number;
N: number;
O: number;
F: number;
Ne: number;
Na: number;
Mg: number;
Al: number;
Si: number;
P: number;
S: number;
Cl: number;
Ar: number;
K: number;
Ca: number;
Sc: number;
Ti: number;
V: number;
Mn: number;
Fe: number;
Co: number;
Ni: number;
Cu: number;
Zn: number;
Ga: number;
Ge: number;
Se: number;
Br: number;
Kr: number;
Rb: number;
Sr: number;
Y: number;
Zr: number;
Nb: number;
Mo: number;
Tc: number;
Ru: number;
Rh: number;
Pd: number;
Ag: number;
Cd: number;
In: number;
Sn: number;
Sb: number;
Te: number;
I: number;
Xe: number;
Cs: number;
Ba: number;
Lu: number;
Hf: number;
Ta: number;
W: number;
Re: number;
Os: number;
Ir: number;
Pt: number;
Au: number;
Hg: number;
Tl: number;
Pb: number;
Bi: number;
Rn: number;
};
/** Get the length used for bond identification for the specified element.
*
*/
export declare function bondLength(elem: any): any;
/** Set the length used for bond identification for the specified element.
*
*/
export declare let bondTable: any;
export declare function bondLength(elem: string | number): any;
export declare function setBondLength(elem: string, radius: number): void;

2

build/types/parsers/utils/computeSecondaryStructure.d.ts

@@ -1,1 +0,1 @@

export declare function computeSecondaryStructure(atomsarray: any, hbondCutoff: any): void;
export declare function computeSecondaryStructure(atomsarray: string | any[], hbondCutoff: number | undefined): void;

8

build/types/parsers/utils/getSinglePDB.d.ts

@@ -1,1 +0,7 @@

export declare function getSinglePDB(lines: any, options: any, sslookup: any): Record<string, any>[];
import { ParserOptionsSpec } from "../ParserOptionsSpec";
export declare function getSinglePDB(lines: string[], options: ParserOptionsSpec, sslookup: {
[x: string]: {
[x: string]: any;
};
hasOwnProperty?: any;
}): Record<string, any>[];

7

build/types/parsers/utils/isEmpty.d.ts

@@ -1,1 +0,6 @@

export declare function isEmpty(obj: any): boolean;
export declare function isEmpty(obj: {
[x: string]: {
[x: string]: any;
};
hasOwnProperty?: any;
}): boolean;

10

build/types/parsers/utils/processSymmetries.d.ts

@@ -1,1 +0,9 @@

export declare function processSymmetries(copyMatrices: any, atoms: any, options: any, cryst: any): void;
import { ParserOptionsSpec } from 'parsers/ParserOptionsSpec';
export declare function processSymmetries(copyMatrices: string[] | any[], atoms: any[], options: ParserOptionsSpec, cryst: {
a: any;
b: number;
c: number;
alpha: number;
beta: number;
gamma: number;
}): void;

2

build/types/parsers/utils/validateBonds.d.ts

@@ -1,1 +0,1 @@

export declare function validateBonds(atomsarray: any, serialToIndex: any): void;
export declare function validateBonds(atomsarray: string[] | any[], serialToIndex: number[]): void;

4

build/types/parsers/VASP.d.ts

@@ -7,3 +7,3 @@ /**

* @category Parsers
*/
export declare function VASP(str: any): any[][] & Record<string, any>;
*/
export declare function VASP(str: string): any[][] & Record<string, any>;

4

build/types/parsers/XYZ.d.ts
import { ParserOptionsSpec } from './ParserOptionsSpec';
/**
* Read an XYZ file from str and return result
*
* @param {string} str
* @param {ParserOptionsSpec} options
* @category Parsers
*/
*/
export declare function XYZ(str: string, options: ParserOptionsSpec): any[][] & Record<string, any>;

2

build/types/partialCharges.d.ts

@@ -170,2 +170,2 @@ export declare const partialCharges: {

};
export declare function applyPartialCharges(atom: any, keepexisting: any): void;
export declare function applyPartialCharges(atom: Record<string, any>, keepexisting: boolean): void;

10

build/types/ProteinSurface4.d.ts

@@ -18,5 +18,9 @@ /**

* Render surface synchronously if true
* @param {boolean} [$3Dmol.SyncSurface=false]
* @param {boolean} [$3Dmol.syncSurface=false]
* @type {boolean} */
export declare var syncSurface: boolean;
/**
*
* @param {boolean} val - Whether surfaces should be rendered synchronously or in parallel.
*/
export declare function setSyncSurface(val: boolean): void;

@@ -73,2 +77,4 @@ export declare class MarchingCubeInitializer {

verts: any[];
static MarchingCube: MarchingCubeInitializer;
constructor();
readonly vdwRadii: {

@@ -109,3 +115,3 @@ H: number;

marchingcubeinit(stype: any): void;
marchingcube(stype: any): void;
marchingcube(stype: number): void;
}

2

build/types/specs.d.ts

@@ -90,2 +90,4 @@ import { AtomStyleSpec, BondStyle, GLModel } from "./GLModel";

model?: GLModel | number | GLModel[] | number[];
/** frame index of individual frame to style; will apply to all frames if not set */
frame?: number;
/** index of the atom or atoms to select */

@@ -92,0 +94,0 @@ index?: number | number[];

8

build/types/VolumeData.d.ts

@@ -54,7 +54,7 @@ import { Matrix4 } from "./WebGL/math";

};
vasp: (str: any) => void;
dx: (str: any) => void;
cube(str: any): void;
ccp4(bin: any): void;
vasp: (str: string) => void;
dx: (str: string) => void;
cube(str: string): void;
ccp4(bin: Int8Array): void;
}
export {};

34

build/types/VolumetricRender.d.ts

@@ -30,3 +30,3 @@ import { Sphere } from "./WebGL/shapes";

export declare class GLVolumetricRender {
static interpolateArray(data: any, fitCount: any): any[];
static interpolateArray(data: string | any[], fitCount: number): any[];
hidden: boolean;

@@ -47,3 +47,24 @@ boundingSphere: Sphere;

minunit: any;
constructor(data: any, spec: any);
constructor(data: {
matrix: {
elements: any;
};
size: {
x: number;
y: number;
z: number;
};
unit: {
x: number;
y: number;
z: number;
};
origin: {
x: number;
y: number;
z: number;
};
data: number[];
getIndex: (arg0: number, arg1: number, arg2: number) => number;
}, spec: VolumetricRendererSpec);
/**

@@ -54,4 +75,9 @@ * Initialize webgl objects for rendering

*/
globj(group: any): void;
removegl(group: any): void;
globj(group: {
remove: (arg0: any) => void;
add: (arg0: any) => void;
}): void;
removegl(group: {
remove: (arg0: any) => void;
}): void;
get position(): Vector3;

@@ -58,0 +84,0 @@ get x(): number;

2

build/types/WebGL/math/utils/conversionMatrix3.d.ts

@@ -12,2 +12,2 @@ import { Matrix3 } from "../math";

*/
export declare function conversionMatrix3(a: any, b: number, c: number, alpha: number, beta: number, gamma: number): Matrix3;
export declare function conversionMatrix3(a: number, b: number, c: number, alpha: number, beta: number, gamma: number): Matrix3;

6

build/types/WebGL/Renderer.d.ts

@@ -12,3 +12,3 @@ /**

devicePixelRatio: number;
domElement: Element;
domElement: HTMLCanvasElement;
autoClear: boolean;

@@ -45,3 +45,2 @@ autoClearColor: boolean;

private _oldFlipSided;
private _oldBlending;
private _oldDepthTest;

@@ -92,2 +91,3 @@ private _oldDepthWrite;

supportsImposters: boolean;
regen: boolean;
};

@@ -110,3 +110,3 @@ getContext(): WebGLRenderingContext | WebGL2RenderingContext;

renderBuffer(camera: any, lights: any, fog: any, material: any, geometryGroup: any, object: any): void;
render(scene: any, camera: any, forceClear: any): void;
render(scene: any, camera: any, forceClear?: any): void;
reinitFrameBuffer(): void;

@@ -113,0 +113,0 @@ setFrameBuffer(): void;

4

build/types/WebGL/shaders/lib/instanced/uniforms.d.ts

@@ -21,8 +21,8 @@ import { Color } from "../../../../colors";

type: string;
value: any[];
value: number[];
};
directionalLightDirection: {
type: string;
value: any[];
value: number[];
};
};

4

build/types/WebGL/shaders/lib/lambertdouble/uniforms.d.ts

@@ -21,8 +21,8 @@ import { Color } from "../../../../colors";

type: string;
value: any[];
value: number[];
};
directionalLightDirection: {
type: string;
value: any[];
value: number[];
};
};

4

build/types/WebGL/shaders/lib/sphereimposter/uniforms.d.ts

@@ -21,8 +21,8 @@ import { Color } from "../../../../colors";

type: string;
value: any[];
value: number[];
};
directionalLightDirection: {
type: string;
value: any[];
value: number[];
};
};

4

build/types/WebGL/shaders/lib/stickimposter/uniforms.d.ts

@@ -21,8 +21,8 @@ import { Color } from "../../../../colors";

type: string;
value: any[];
value: number[];
};
directionalLightDirection: {
type: string;
value: any[];
value: number[];
};
};

5

build/types/WebGL/shaders/lib/volumetric/uniforms.d.ts

@@ -0,1 +1,2 @@

import { Matrix4 } from "WebGL/math";
import { Color } from "../../../../colors";

@@ -45,7 +46,7 @@ export declare const uniforms: {

type: string;
value: any[];
value: Matrix4[];
};
projinv: {
type: string;
value: any[];
value: Matrix4[];
};

@@ -52,0 +53,0 @@ transfermin: {

77

jsdoc.conf.json

@@ -5,5 +5,8 @@ {

},
"plugins": ["plugins/markdown",
"../../node_modules/better-docs/typescript",
"../../node_modules/better-docs/category"],
"plugins": [
"plugins/markdown",
"../../node_modules/better-docs/typescript",
"../../node_modules/better-docs/category"
],
"recurseDepth": 10,
"source": {

@@ -13,35 +16,59 @@ "includePattern": "\\.(jsx|js|ts|tsx)$"

"templates": {
"search": true,
"cleverLinks": true,
"monospaceLinks": false,
"footer": "",
"copyright":"3Dmol.js © 2019-2022",
"copyright":"3Dmol.js © 2019-2023",
"linenums" : true,
"collapseSymbols" : false,
"inverseNav" : true,
"highlightTutorialCode" : true,
"better-docs": {
"name": "<a href=\"http://3dmol.org\"><b>3Dmol</b>.js</a>",
"title": "3Dmol.js Documentation",
"css": "../tutorials/style.css",
"navLinks": [
{
"label": "Github",
"href": "https://github.com/3dmol/3Dmol.js"
}
]
}
"highlightTutorialCode" : true
},
"markdown" : {
"parser" : "gfm",
"hardwrap" : true
"hardwrap": true,
"idInHeadings": true
},
"opts":{
"encoding": "utf8",
"destination": "doc/",
"recurse": true,
"encoding": "utf8",
"template": "./node_modules/better-docs",
"destination": "doc",
"tutorials": "tutorials",
"search": true
},
"tutorials": "tutorials/"
"verbose": true,
"template": "./node_modules/clean-jsdoc-theme",
"copyright": "3Dmol.js © 2019-2023",
"theme_opts": {
"default_theme": "light",
"includeFilesListInHomepage": true,
"homepageTitle": "3Dmol.js",
"displayModuleHeader": true,
"footer":"3Dmol.js © 2019-2023 | <a href='https://pitt.edu/' target='_blank'>University of Pittsburgh</a> | <a href='https://github.com/3dmol/3Dmol.js/blob/master/LICENSE' target='_blank'>License</a>",
"title": "3Dmol.js",
"create_style": "article ul li { list-style: disc}",
"menu": [
{
"title": " Documentation",
"link": "https://3dmol.org/doc/index.html"
},
{
"title": "Tutorials",
"link": "tutorial-home.html"
},
{
"title": "GitHub",
"link": "https://github.com/3dmol/3Dmol.js",
"target": "_blank"
}
],
"meta": [
{
"name": "Author",
"content": "David Koes & 3Dmoljs Contributors"
},
{
"name": "Description",
"content": "A modern, object-oriented JavaScript library for visualizing molecular data"
}
]
},
"tutorials": "tutorials/"
}
}

24

package.json
{
"name": "3dmol",
"version": "2.0.3",
"version": "2.0.4",
"description": "JavaScript/TypeScript molecular visualization library",

@@ -25,2 +25,6 @@ "repository": {

},
"engines": {
"npm": ">=8.11",
"node": ">=16.16.0"
},
"license": "BSD-3-Clause",

@@ -30,4 +34,7 @@ "main": "build/3Dmol.js",

"scripts": {
"build": "webpack --config webpack.dev.js --mode development && webpack --config webpack.prod.js --mode production && python3 tests/auto/generate_tests.py && npm run doc",
"prepare": "npm run build",
"build": "npm run build:dev && npm run build:prod && npm run generate:tests && npm run doc",
"build:dev": "webpack --config webpack.dev.js --mode development",
"build:prod": "webpack --config webpack.prod.js --mode production",
"prepare": "npm run build:dev && npm run build:prod",
"postinstall": "npm run build",
"jest": "npx jest --testPathIgnorePatterns=render.test.js",

@@ -38,14 +45,12 @@ "test": "npm run generate:jest && npm run jest && npm run glcheck",

"clean:glcheck": "rm -rf ./tests/glcheck/render-failures",
"generate:tests": "python3 tests/auto/generate_tests.py",
"generate:glcheck": "python3 ./tests/glcheck/generate_glcheck_render_tests.py -min",
"generate:jest": "python3 tests/jest/generate_jest_render_tests.py",
"cover": "npm run generate:jest && npx jest --coverage",
"doc": "npx jsdoc -c jsdoc.conf.json src doc.md"
"doc": "rm -rf doc/ && npx jsdoc -c jsdoc.conf.json src doc.md"
},
"engines": {
"npm": ">=8.11",
"node": ">=16.16.0"
},
"dependencies": {
"clean-jsdoc-theme": "^4.2.9",
"iobuffer": "^5.3.1",
"netcdfjs": "^2.0.2",
"netcdfjs": "^3.0.0",
"pako": "^2.1.0",

@@ -58,2 +63,3 @@ "upng-js": "^2.1.0"

"@babel/plugin-transform-typescript": "^7.20.7",
"@types/pako": "^2.0.0",
"better-docs": "github:3dmol/better-docs#master",

@@ -60,0 +66,0 @@ "canvas": "^2.11.0",

20

src/autoload.ts
//auto-initialization
import { createViewer } from "./GLViewer";
import { GLViewer, createViewer } from "./GLViewer";
import { SurfaceType } from "./ProteinSurface4";

@@ -20,4 +20,4 @@ import { get, specStringToObject } from "./utilities";

//viewer and callback are used by the testing harness
export function autoload(viewer?, callback?) {
var i, dataname, type;
export function autoload(viewer?: any, callback?: (arg0: any) => void) {
var i: string | number, dataname: string, type: string;
if (document.querySelector(".viewer_3Dmoljs") != null)

@@ -77,3 +77,3 @@ autoinit = true;

datauri.push(uri);
datatypes.push(uri.substr(uri.lastIndexOf('.') + 1));
datatypes.push(uri.substring(uri.lastIndexOf('.') + 1));
} else if (i.substring(0, 3) === "cid" && (i !== "cid")) {

@@ -118,3 +118,3 @@ datauri.push("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + divdata[i] + "/SDF?record_type=3d");

var m = stylere.exec(dataname);
var selname, newsel, styleobj;
var selname: string, newsel: any, styleobj: any;
if (m) {

@@ -149,3 +149,3 @@ selname = "select" + m[1];

//apply all the selections/styles parsed out above to the passed viewer
var applyStyles = function (glviewer) {
var applyStyles = function (glviewer: GLViewer) {
glviewer.setStyle(select, style);

@@ -171,3 +171,3 @@

if (UI) {
viewer.addSurface(SurfaceType.VDW, sty, sel, sel).then((surfid) => {
viewer.addSurface(SurfaceType.VDW, sty, sel, sel).then((surfid: any) => {
UI.loadSurface("VDW", sel, sty, surfid);

@@ -220,4 +220,4 @@ });

//load multiple data elements in serial
i = 0;
var process = function (moldata) {
let i = 0;
var process = function (moldata: any) {
//add moldata to viewer and load next model

@@ -231,3 +231,3 @@ uri = datauri[i]; //this is where the moldata came from

}
i += 1;
i +=1;
if (i < datauri.length) {

@@ -234,0 +234,0 @@ get(datauri[i]).then(process);

2

src/colors.ts

@@ -1,2 +0,2 @@

import { Gradient, GradientType } from "./Gradient";
import { GradientType } from "./Gradient";

@@ -3,0 +3,0 @@ /* @interface

91

src/GLDraw.ts
import { Vector3 } from "./WebGL/math";
import { Geometry } from "./WebGL";
import { Color, Colored } from "colors";

@@ -20,2 +21,7 @@

export interface Point {
x: number;
y: number;
z: number;
}

@@ -33,3 +39,3 @@ /**

function getRotationMatrix(dx: number, dy: number, dz: number) {
var dxy = Math.sqrt(dx * dx + dy * dy);
var dxy = Math.hypot(dx, dy);
var dyz;

@@ -53,3 +59,3 @@

dy = -sinA * dx + cosA * dy;
dyz = Math.sqrt(dy * dy + dz * dz);
dyz = Math.hypot(dy, dz);

@@ -130,3 +136,3 @@ // about new x axis - Theta

getVerticesForRadius(radius, cap, capType) {
getVerticesForRadius(radius: any, cap: CAP, capType: any) {
if (typeof (this.cache) !== "undefined" && this.cache[radius] !== undefined)

@@ -279,7 +285,6 @@ if (this.cache[radius][cap + capType] !== undefined)

/**
* Create a cylinder
* @memberof GLDraw
* @param {geometry}
* @param {Geometry}
* geo

@@ -290,3 +295,3 @@ * @param {Point}

* to
* @param {float}
* @param {number}
* radius

@@ -299,3 +304,3 @@ * @param {Color}

* */
export function drawCylinder(geo: Geometry, from, to, radius: number, color, fromCap:CAP = 0, toCap:CAP = 0) {
export function drawCylinder(geo: Geometry, from: any, to: any, radius: number, color: Color | Color[], fromCap:CAP = 0, toCap:CAP = 0) {
if (!from || !to)

@@ -306,3 +311,3 @@ return;

var drawcaps = toCap || fromCap;
color = color || { r: 0, g: 0, b: 0 };
color = color || ({ r: 0, g: 0, b: 0 } as Color);

@@ -366,8 +371,8 @@ var e = getRotationMatrix(to.x-from.x, to.y-from.y, to.z-from.z);

// colors
colorArray[offset] = color.r;
colorArray[offset + 3] = color.r;
colorArray[offset + 1] = color.g;
colorArray[offset + 4] = color.g;
colorArray[offset + 2] = color.b;
colorArray[offset + 5] = color.b;
colorArray[offset] = (color as Color).r;
colorArray[offset + 3] = (color as Color).r;
colorArray[offset + 1] = (color as Color).g;
colorArray[offset + 4] = (color as Color).g;
colorArray[offset + 2] = (color as Color).b;
colorArray[offset + 5] = (color as Color).b;

@@ -457,16 +462,16 @@ // faces

colorArray[v1offset] = color.r;
colorArray[v2offset] = color.r;
colorArray[v3offset] = color.r;
colorArray[v4offset] = color.r;
colorArray[v1offset] = (color as Color).r;
colorArray[v2offset] = (color as Color).r;
colorArray[v3offset] = (color as Color).r;
colorArray[v4offset] = (color as Color).r;
colorArray[v1offset + 1] = color.g;
colorArray[v2offset + 1] = color.g;
colorArray[v3offset + 1] = color.g;
colorArray[v4offset + 1] = color.g;
colorArray[v1offset + 1] = (color as Color).g;
colorArray[v2offset + 1] = (color as Color).g;
colorArray[v3offset + 1] = (color as Color).g;
colorArray[v4offset + 1] = (color as Color).g;
colorArray[v1offset + 2] = color.b;
colorArray[v2offset + 2] = color.b;
colorArray[v3offset + 2] = color.b;
colorArray[v4offset + 2] = color.b;
colorArray[v1offset + 2] = (color as Color).b;
colorArray[v2offset + 2] = (color as Color).b;
colorArray[v3offset + 2] = (color as Color).b;
colorArray[v4offset + 2] = (color as Color).b;

@@ -582,3 +587,3 @@ nx1 = e[0] * normals[v1].x + e[3] * normals[v1].y + e[6] * normals[v1].z;

* @memberof GLDraw
* @param {geometry}
* @param {Geometry}
* geo

@@ -589,3 +594,3 @@ * @param {Point}

* to
* @param {float}
* @param {number}
* radius

@@ -595,9 +600,9 @@ * @param {Color}

* */
export function drawCone (geo: Geometry, from, to, radius: number, color?) {
export function drawCone (geo: Geometry, from: any, to: any, radius: number, color?: Color) {
if (!from || !to)
return;
//TODO: check if from and to do not contain x,y,z and if so generate a center based on the passed selections
// TODO: check if from and to do not contain x,y,z and if so generate a center based on the passed selections
color = color || { r: 0, g: 0, b: 0 };
color = color || ({ r: 0, g: 0, b: 0 } as Color);

@@ -695,2 +700,7 @@ let ndir = new Vector3(to.x-from.x, to.y-from.y, to.z-from.z);

interface MyObject {
vertices: any[];
verticesRows: any[][];
normals: any[];
}

@@ -702,3 +712,3 @@ // Sphere component sphereVertexCache

getVerticesForRadius(radius, sphereQuality) {
getVerticesForRadius(radius: number, sphereQuality: any) {
sphereQuality = sphereQuality || 2;

@@ -713,3 +723,3 @@

var obj = {
var obj: MyObject = {
vertices: [],

@@ -772,13 +782,14 @@ verticesRows: [],

* @memberof GLDraw
* @param {geometry}
* @param {Geometry}
* geo
* @param {Point}
* pos
* @param {float}
* @param {number}
* radius
* @param {Color}
* color
* @param {number} quality of sphere (default 2, higher increases number of triangles)
* @param {number}
* sphereQuality - Quality of sphere (default 2, higher increases number of triangles)
*/
export function drawSphere(geo:Geometry, pos, radius, color, sphereQuality?) {
export function drawSphere(geo:Geometry, pos: any, radius: number, color: Colored, sphereQuality?: number) {

@@ -807,5 +818,5 @@ var vobj = sphereVertexCache.getVerticesForRadius(radius, sphereQuality);

colorArray[offset] = color.r;
colorArray[offset + 1] = color.g;
colorArray[offset + 2] = color.b;
colorArray[offset] = (color as Colored).r;
colorArray[offset + 1] = (color as Colored).g;
colorArray[offset + 2] = (color as Colored).b;

@@ -812,0 +823,0 @@ }

12

src/GLShape.ts

@@ -6,3 +6,3 @@ import { Geometry, Material } from "./WebGL";

import { DoubleSide } from "./WebGL";
import { Color, CC, ColorSpec } from "./colors";
import { Color, CC, ColorSpec, Colored } from "./colors";
import { MarchingCube } from "./ProteinSurface4";

@@ -14,5 +14,3 @@ import { VolumeData } from "./VolumeData";

import { adjustVolumeStyle, extend, Func, makeFunction } from "./utilities";
import { Gradient, GradientType } from "./Gradient";
import { LineStyleSpec } from "GLModel";
import { VolumetricRendererSpec } from "VolumetricRender";
import { GradientType } from "./Gradient";

@@ -755,6 +753,6 @@

this.intersectionShape.sphere.push(new Sphere(sphereSpec.center, sphereSpec.radius));
GLDraw.drawSphere(this.geo, sphereSpec.center,
sphereSpec.radius, sphereSpec.color as Colored, sphereSpec.quality);
GLDraw.drawSphere(this.geo, sphereSpec.center,
sphereSpec.radius, sphereSpec.color, sphereSpec.quality);
this.components.push({

@@ -761,0 +759,0 @@ centroid: new Vector3(sphereSpec.center.x,

49

src/Gradient.ts

@@ -28,3 +28,3 @@ import { CC, Color } from "./colors";

//return a Gradient object, even if what is specified is descriptive
export function getGradient(grad): GradientType {
export function getGradient(grad: any): GradientType {
if (grad instanceof GradientType) {

@@ -87,4 +87,4 @@ return grad;

//map value to hex color, range is provided
valueToHex(val, range) {
var lo, hi;
valueToHex(val: number, range?: number[]) {
var lo: number, hi: number;
val = this.mult * val; //reverse if necessary

@@ -111,3 +111,3 @@ if (range) {

else middle = (lo + hi) / 2;
var scale, color;
var scale: number, color: number;

@@ -139,5 +139,5 @@ //scale bottom from red to white

mult: number;
max: number;
min: number;
constructor(min, max) {
max?: number;
min?: number;
constructor(min?: number, max?: number) {
super();

@@ -157,4 +157,4 @@ this.mult = 1.0;

//map value to hex color, range is provided
valueToHex(val, range) {
var lo, hi;
valueToHex(val: number, range?: any[]) {
var lo: number, hi: number;
val = this.mult * val;

@@ -165,4 +165,4 @@ if (range) {

} else {
lo = this.min;
hi = this.max;
lo = this.min!;
hi = this.max!;
}

@@ -181,3 +181,3 @@

var scale, color;
var scale: number, color: number;
if (val < q1) {

@@ -238,3 +238,3 @@ //scale green up, red up, blue down

min: number;
constructor(min, max) {
constructor(min: number, max: number) {
super();

@@ -258,4 +258,4 @@ this.mult = 1.0;

//map value to hex color, range is provided
valueToHex(val, range) {
var lo, hi;
valueToHex(val: number, range?: any[]) {
var lo: number, hi: number;
val = this.mult * val;

@@ -359,4 +359,4 @@ if (range) {

//map value to hex color, range is provided
valueToHex(val, range) {
var lo, hi;
valueToHex(val: number, range?: any[]) {
var lo: number, hi: number;
if (range) {

@@ -394,11 +394,10 @@ lo = range[0];

//map from names to gradient constructors
export const builtinGradients = {
rwb: RWB,
RWB: RWB,
roygb: ROYGB,
ROYGB: ROYGB,
sinebow: Sinebow,
linear: CustomLinear
export const builtinGradients = {
"rwb": RWB,
"RWB": RWB,
"roygb": ROYGB,
"ROYGB": ROYGB,
"sinebow": Sinebow,
"linear": CustomLinear
};

@@ -405,0 +404,0 @@

13

src/Label.ts

@@ -6,3 +6,2 @@ import {

Sprite,
Vector3,
Vector2,

@@ -14,8 +13,8 @@ } from "./WebGL";

//Adapted from the text sprite example from http://stemkoski.github.io/Three.js/index.html
// Adapted from the text sprite example from http://stemkoski.github.io/Three.js/index.html
export let LabelCount = 0;
// function for drawing rounded rectangles - for Label drawing
function roundRect(ctx, x, y, w, h, r, drawBorder) {
// Function for drawing rounded rectangles - for Label drawing
function roundRect(ctx: CanvasRenderingContext2D, x: any, y: any, w: number, h: number, r: number, drawBorder: boolean) {
ctx.beginPath();

@@ -37,3 +36,3 @@ ctx.moveTo(x + r, y);

//do all the checks to figure out what color is desired
function getColor(style, stylealpha?: any, init?: any) {
function getColor(style: any, stylealpha?: any, init?: any) {
var ret = init;

@@ -111,3 +110,3 @@ if (typeof style != "undefined") {

frame: any;
constructor(text, parameters) {
constructor(text: string, parameters: LabelSpec) {
this.id = LabelCount++;

@@ -189,3 +188,3 @@ this.stylespec = parameters || {};

) {
spriteAlignment = SpriteAlignment[spriteAlignment];
spriteAlignment = (SpriteAlignment as any)[spriteAlignment] ;
}

@@ -192,0 +191,0 @@

11

src/parsers/CDJSON.ts

@@ -0,1 +1,3 @@

import { ParserOptionsSpec } from "./ParserOptionsSpec";
/**

@@ -10,4 +12,5 @@ * This parses the ChemDoodle json file format. Although this is registered

* @category Parsers
*/
export function CDJSON(str, options) {
*/
export function CDJSON(str: string, options: ParserOptionsSpec) {
var atoms: any[][] & Record<string, any> = [[]];

@@ -18,3 +21,3 @@ if (typeof str === "string") {

}
var molecules = str.m;
var molecules = (str as any).m;
var atomsInFile = molecules[0].a; // Assumes there is at least one

@@ -45,3 +48,3 @@ var bondsInFile = molecules[0].b; // molecule and ignores any more

var elem = currentAtom.l || "C";
atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
atom.elem = elem[0].toUpperCase() + elem.substring(1).toLowerCase();

@@ -48,0 +51,0 @@ atom.serial = atoms[atoms.length - 1].length;

33

src/parsers/CIF.ts
import { ParserOptionsSpec } from './ParserOptionsSpec';
// puts atoms specified in mmCIF fromat in str into atoms

@@ -7,10 +6,12 @@ import { assignBonds } from "./utils/assignBonds";

import { processSymmetries } from "./utils/processSymmetries";
import { conversionMatrix3, Matrix4, Vector3, } from "../WebGL"
import { conversionMatrix3, Matrix3, Matrix4, Vector3, } from "../WebGL"
/**
* Puts atoms specified in mmCIF fromat in str into atoms
*
* @param {string} str
* @param {ParserOptionsSpec} options
* @category Parsers
*/
*/
export function CIF(str: string, options: ParserOptionsSpec = {}) {

@@ -24,3 +25,3 @@ var atoms: any[] & Record<string, any> = [];

//coordinate conversion
var fractionalToCartesian = function (cmat, x, y, z) {
var fractionalToCartesian = function (cmat: Matrix3, x: number, y: number, z: number) {
return new Vector3(x, y, z).applyMatrix3(cmat);

@@ -30,3 +31,3 @@ };

// Used to handle quotes correctly
function splitRespectingQuotes(string, separator) {
function splitRespectingQuotes(string: string, separator: string | any[]) {
var sections: any[] = [];

@@ -37,3 +38,3 @@ var sectionStart = 0;

while (
string.substr(sectionEnd, separator.length) !== separator &&
string.substring(sectionEnd, sectionEnd + separator.length) !== separator &&
sectionEnd < string.length

@@ -55,3 +56,3 @@ ) {

}
sections.push(string.substr(sectionStart, sectionEnd - sectionStart));
sections.push(string.substring(sectionStart, sectionEnd));
sectionStart = sectionEnd = sectionEnd + separator.length;

@@ -96,3 +97,3 @@ }

line = lineArr.join('');
line = line.substr(0, dot) + "_" + line.substr(dot + 1);
line = line.substring(0, dot) + "_" + line.substring(dot + 1);
}

@@ -128,3 +129,3 @@ }

// if nothing left on the line go to the next one
var restOfLine = linesFiltered[lineNum].substr(
var restOfLine = linesFiltered[lineNum].substring(
linesFiltered[lineNum].indexOf(dataItemName) + dataItemName.length

@@ -135,3 +136,3 @@ );

if (linesFiltered[lineNum][0] === ";") {
var dataBlock = linesFiltered[lineNum].substr(1);
var dataBlock = linesFiltered[lineNum].substring(1);
lineNum++;

@@ -150,3 +151,3 @@ while (linesFiltered[lineNum] !== ";") {

lineNum++;
} else if (linesFiltered[lineNum].substr(0, 5) === "loop_") {
} else if (linesFiltered[lineNum].substring(0, 5) === "loop_") {
lineNum++;

@@ -198,3 +199,3 @@ var dataItems: any[] = [];

var conversionMatrix;
var conversionMatrix: Matrix3;
if (mmCIF._cell_length_a !== undefined) {

@@ -272,3 +273,3 @@ var a = parseFloat(mmCIF._cell_length_a);

}
atom.elem = elem[0].toUpperCase() + elem.substr(1, 1).toLowerCase();
atom.elem = elem[0].toUpperCase() + elem.substring(1, 2).toLowerCase();
atom.bonds = [];

@@ -332,3 +333,3 @@ atom.ss = "c";

}
var parseTerm = function (term) {
var parseTerm = function (term: string) {
var negative = term.match("-");

@@ -338,3 +339,3 @@ term = term.replace(/[-xyz]/g, "");

var numerator, denominator;
var numerator: number, denominator: number;
if (fractionParts[1] === undefined) {

@@ -358,3 +359,3 @@ denominator = 1;

);
var componentStrings = transform.split(",").map(function (val) {
var componentStrings = transform.split(",").map(function (val: string) {
return val.replace(/-/g, "+-");

@@ -361,0 +362,0 @@ });

20

src/parsers/CUBE.ts
import { Vector3, Matrix4 } from "../WebGL";
import { assignBonds } from "./utils/assignBonds";
import { anumToSymbol } from "./utils/anumToSymbol";
import { ParserOptionsSpec } from "./ParserOptionsSpec";
/**
* @param {string}
* str
* @param {ParserOptionsSpec}
* options
* @param {string}
* str
* @param {ParserOptionsSpec}
* options
* @category Parsers
*/
export function CUBE(str, options) {
export function CUBE(str: string, options: ParserOptionsSpec) {
options = options || {};

@@ -40,6 +40,6 @@ var atoms: any[][] & Record<string, any> = [[]];

// we are going to go with n<0 means angstrom - note this is just the first n
var convFactor = (lineArr[0] > 0) ? 0.529177 : 1;
var convFactor = ((lineArr[0] as any) > 0) ? 0.529177 : 1;
origin.multiplyScalar(convFactor);
var nX = Math.abs(lineArr[0]);
var nX = Math.abs((lineArr[0] as any));
var xVec = new Vector3(parseFloat(lineArr[1]),

@@ -50,3 +50,3 @@ parseFloat(lineArr[2]), parseFloat(lineArr[3]))

lineArr = lines[4].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
var nY = Math.abs(lineArr[0]);
var nY = Math.abs((lineArr[0] as any));
var yVec = new Vector3(parseFloat(lineArr[1]),

@@ -57,3 +57,3 @@ parseFloat(lineArr[2]), parseFloat(lineArr[3]))

lineArr = lines[5].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
var nZ = Math.abs(lineArr[0]);
var nZ = Math.abs((lineArr[0] as any));
var zVec = new Vector3(parseFloat(lineArr[1]),

@@ -60,0 +60,0 @@ parseFloat(lineArr[2]), parseFloat(lineArr[3]))

18

src/parsers/GRO.ts

@@ -6,11 +6,11 @@ import { assignPDBBonds } from "./utils/assignPDBBonds";

* Parse a gro file from str and create atoms
*
* @param {string}
* str
* @param {ParserOptionsSpec}
* options*
* @category Parsers
*
* @param {string}
* str
* @param {ParserOptionsSpec}
* options*
* @category Parsers
*/
*/
export function GRO(str /*, options*/) {
export function GRO(str: string /*, options*/) {
var allatoms: any[][] & Record<string, any> = [];

@@ -57,3 +57,3 @@ var lines = str.split(/\r?\n|\r/);

for (var b = 0; b < 3; b++) {
box[b] = parseFloat(box[b]) * 10.0;
(box[b] as any) = parseFloat(box[b]) * 10.0;
}

@@ -60,0 +60,0 @@ allatoms.box = box;

10

src/parsers/LAMMPSTRJ.ts

@@ -0,1 +1,2 @@

import { ParserOptionsSpec } from "./ParserOptionsSpec";
import { assignBonds } from "./utils/assignBonds";

@@ -5,8 +6,9 @@

* Parse a lammps trajectory file from str and create atoms
*
* @category Parsers
*/
*/
export function LAMMPSTRJ(str, options) {
export function LAMMPSTRJ(str: string, options: ParserOptionsSpec) {
var atoms: any[] = [];
var dic = {
var dic:any = {
id: "serial",

@@ -47,3 +49,3 @@ type: "atom",

var atom: Record<string, any> = {};
var properties = {};
var properties: any = {};
var tokens = lines[j].split(" ");

@@ -50,0 +52,0 @@ for (var k = 0; k < tokens.length; k++) {

39

src/parsers/MMTF.ts
import { base64ToArray } from "../utilities";
import { Matrix4 } from "../WebGL";
import { ParserOptionsSpec } from "./ParserOptionsSpec";
import { computeSecondaryStructure } from "./utils/computeSecondaryStructure";

@@ -11,8 +12,8 @@ import { processSymmetries } from "./utils/processSymmetries";

var fromCharCode = function (charCodeArray) {
var fromCharCode = function (charCodeArray: any) {
return String.fromCharCode.apply(null, charCodeArray).replace(/\0/g, '');
};
var convertSS = function (val) {
//convert mmtf code to 3dmol code
var convertSS = function (val: number | boolean) {
// Convert mmtf code to 3dmol code
/*

@@ -45,8 +46,10 @@ 0: pi helix

/** @param bindata - binary UInt8Array buffer or a base64 encoded string
* @param ParserOptionsSpec
* @category Parsers
/**
* @param bindata - binary UInt8Array buffer or a base64 encoded string
* @param ParserOptionsSpec
* @category Parsers
*/
export function MMTFparser(bindata, options) {
export function MMTFparser(bindata: any, options: ParserOptionsSpec) {
var noH = !options.keepH; // suppress hydrogens by default

@@ -73,3 +76,2 @@ var selAltLoc = options.altLoc ? options.altLoc : 'A'; //default alternate location to select if present

// setup index counters
var modelIndex = 0;
var chainIndex = 0;

@@ -81,4 +83,2 @@ var groupIndex = 0;

var secStructList = mmtfData.secStructList;
var insCodeList = mmtfData.insCodeList;
var sequenceIndexList = mmtfData.sequenceIndexList;
var bFactorList = mmtfData.bFactorList;

@@ -94,3 +94,3 @@ var altLocList = mmtfData.altLocList;

// hoisted loop variables
var i, j, k, kl, m, n;
var i: number, j: number, k: number, kl: number, m: number, n: number;

@@ -116,3 +116,3 @@

let chainIsPolymer: boolean[] = [];
mmtfData.entityList.forEach(entity => {
mmtfData.entityList.forEach((entity: { chainIndexList: any[]; type: string; }) => {
entity.chainIndexList.forEach(ch => {

@@ -164,11 +164,2 @@ chainIsPolymer[ch] = entity.type == "polymer";

}
var insCode = null as string | null;
if (mmtfData.insCodeList) {
insCode = String.fromCharCode(insCodeList[groupIndex]);
}
var sequenceIndex = null;
if (sequenceIndexList) {
sequenceIndex = sequenceIndexList[groupIndex];
}
var groupId = mmtfData.groupIdList[groupIndex];

@@ -178,4 +169,4 @@ var groupName = groupData.groupName;

var startAtom = atomIndex;
//note the following is not identical to respecting HETATM records
//this information isn't available in MMTF.
// Note the following is not identical to respecting HETATM records
// this information isn't available in MMTF.
let isHETATM = mmtfHETATMtypes.has(groupType) || !chainIsPolymer[chainIndex];

@@ -311,4 +302,2 @@

}
modelIndex += 1;
}

@@ -315,0 +304,0 @@

18

src/parsers/MOL2.ts

@@ -0,3 +1,4 @@

import { ParserOptionsSpec } from "./ParserOptionsSpec";
let SYBYLtoElem = {
let SYBYLtoElem:any = {
'C.1': 'C',

@@ -53,4 +54,4 @@ 'C1': 'C',

// parse SYBYL mol2 file from string - assumed to only contain one molecule
// tag
// Parse SYBYL mol2 file from string - assumed to only contain one molecule tag
/**

@@ -62,4 +63,5 @@ * @param {string}

* @category Parsers
*/
export function MOL2(str, options) {
*/
export function MOL2(str: string, options: ParserOptionsSpec) {
var atoms: any[][] & Record<string,any> = [[]];

@@ -77,3 +79,3 @@ var noH = false;

var lines = str.substr(mol_pos, str.length).split(/\r?\n|\r/);
var lines = str.substring(mol_pos).split(/\r?\n|\r/);
while (lines.length > 0) {

@@ -100,3 +102,3 @@ // serial is atom's index in file; index is atoms index in 'atoms'

var end = start + natoms;
var line;
var line: string;
// Process ATOMS

@@ -113,3 +115,3 @@ for (i = start; i < end; i++) {

elem = elem.split(".")[0];
elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
elem = elem[0].toUpperCase() + elem.substring(1).toLowerCase();
}

@@ -116,0 +118,0 @@

16

src/parsers/PDB.ts

@@ -1,9 +0,8 @@

// parse pdb file from str and create atoms
// if computeStruct is true will always perform secondary structure
// analysis,
// otherwise only do analysis of SHEET/HELIX comments are missing
import { ParserOptionsSpec } from "./ParserOptionsSpec";
import { getSinglePDB } from "./utils/getSinglePDB";
/**
* Parse pdb file from str and create atoms if computeStruct is true will always perform secondary structure analysis,
* otherwise only do analysis of SHEET/HELIX comments are missing
*
* @param {string} str

@@ -15,4 +14,5 @@ * @param {ParserOptionsSpec} options - keepH (do not strip hydrogens), noSecondaryStructure,

*
*/
export function PDB(str, options) {
*/
export function PDB(str: string, options: ParserOptionsSpec) {
options = options || {};

@@ -22,3 +22,3 @@ var atoms: any[] & Record<string, any> = []; //a separate list for each model

atoms.modelData = [];
var lines = str.split(/\r?\n|\r/);
var lines: any = str.split(/\r?\n|\r/);
while (lines.length > 0) {

@@ -25,0 +25,0 @@ var pdbinfo = getSinglePDB(lines, options, sslookup);

47

src/parsers/PQR.ts

@@ -0,16 +1,17 @@

import { ParserOptionsSpec } from "./ParserOptionsSpec";
import { assignPDBBonds } from "./utils/assignPDBBonds";
import { computeSecondaryStructure } from "./utils/computeSecondaryStructure";
/**
* Parse a pqr file from str and create atoms. A pqr file is assumed to be a
* whitespace delimited PDB with charge and radius fields.
*
* @param {string}
* str
* @param {ParserOptionsSpec}
* options - noSecondaryStructure (do not compute ss)
* @category Parsers
*/
export function PQR(str, options) {
/**
* Parse a pqr file from str and create atoms. A pqr file is assumed to be a whitespace delimited PDB with charge and radius fields.
*
* @param {string}
* str
* @param {ParserOptionsSpec}
* options - noSecondaryStructure (do not compute ss)
* @category Parsers
*/
export function PQR(str: string, options: ParserOptionsSpec) {
var atoms: any[][] & Record<string, any> = [[]];

@@ -21,6 +22,6 @@ var computeStruct = !options.noSecondaryStructure;

var lines = str.split(/\r?\n|\r/);
var line;
var line: string | string[];
for (let i = 0; i < lines.length; i++) {
line = lines[i].replace(/^\s*/, ''); // remove indent
var recordName = line.substr(0, 6);
var recordName = line.substring(0, 6);

@@ -41,12 +42,12 @@ if (recordName.indexOf("END") == 0) {

// be filled out (e.g. the chain) so this doesn't work
var hetflag;
let serial = parseInt(line.substr(6, 5));
let atom = line.substr(12, 4).replace(/ /g, "");
let resn = line.substr(17, 3).trim();
let chain = line.substr(21, 1);
let resi = parseInt(line.substr(22, 4));
var hetflag: boolean;
let serial = parseInt(line.substring(6, 11));
let atom = line.substring(12, 16).replace(/ /g, "");
let resn = line.substring(17, 20).trim();
let chain = line.substring(21, 22);
let resi = parseInt(line.substring(22, 26));
// however let's split the coordinates, charge and radius by
// whitespace
// to support extra precision
var vals = line.substr(30).trim().split(/\s+/);
var vals = line.substring(30).trim().split(/\s+/);
var x = parseFloat(vals[0]);

@@ -62,3 +63,3 @@ var y = parseFloat(vals[1]);

// second character in the atom name being lowercase
elem = atom.substr(0, 2);
elem = atom.substring(0, 2);
}

@@ -96,6 +97,6 @@

// described in CONECT. But what about 2JYT???
var from = parseInt(line.substr(6, 5));
var from = parseInt(line.substring(6, 11));
var fromAtom = atoms[atoms.length-1][serialToIndex[from]];
for (let j = 0; j < 4; j++) {
var to = parseInt(line.substr([ 11, 16, 21, 26 ][j], 5));
var to = parseInt(line.substring([ 11, 16, 21, 26 ][j], [ 11, 16, 21, 26 ][j] + 5));
var toAtom = atoms[atoms.length-1][serialToIndex[to]];

@@ -102,0 +103,0 @@ if (fromAtom !== undefined && toAtom !== undefined) {

16

src/parsers/PRMTOP.ts
// @ts-nocheck
/**
* Parse a prmtop file from str and create atoms
*
* @param {string}
* str
* @param {ParserOptionsSpec}
* options - noSecondaryStructure (do not compute ss)
*
* @param {string}
* str
* @param {ParserOptionsSpec}
* options - noSecondaryStructure (do not compute ss)
* @category Parsers
*/
*/
export function PRMTOP(str /*, options*/) {
export function PRMTOP(str: string /*, options*/) {
var atoms = [];
var atomIndex;
var atomIndex: number;
var count = 0;

@@ -17,0 +17,0 @@ var lines = str.split(/\r?\n|\r/);

79

src/parsers/SDF.ts

@@ -1,8 +0,5 @@

/*
* @param {!Array.<string>} lines
* @param {ParserOptionsSpec} options
* @returns {!Array.<Array<Object>>}
*/
var parseV2000 = function (lines, options) {
var atoms: any[][] & Record<string, any> = [[]];
import { ParserOptionsSpec } from "./ParserOptionsSpec";
var parseV2000 = function (lines: any, options: ParserOptionsSpec) {
var atoms: any & Record<string, any> = [[]];
var noH = false;

@@ -13,19 +10,19 @@ if (typeof options.keepH !== "undefined") noH = !options.keepH;

if (lines.length < 4) break;
var atomCount = parseInt(lines[3].substr(0, 3));
var atomCount = parseInt(lines[3].substring(0, 3));
if (isNaN(atomCount) || atomCount <= 0) break;
var bondCount = parseInt(lines[3].substr(3, 3));
var bondCount = parseInt(lines[3].substring(3, 6));
var offset = 4;
if (lines.length < 4 + atomCount + bondCount) break;
// serial is atom's index in file; index is atoms index in 'atoms'
// Serial is atom's index in file; index is atoms index in 'atoms'
var serialToIndex: number[] = [];
var start = atoms[atoms.length - 1].length;
var end = start + atomCount;
var i, line;
var i: number, line: string;
for (i = start; i < end; i++, offset++) {
line = lines[offset];
var atom: Record<string, any> = {};
var elem = line.substr(31, 3).replace(/ /g, "");
var elem = line.substring(31, 34).replace(/ /g, "");
atom.atom = atom.elem =
elem[0].toUpperCase() + elem.substr(1).toLowerCase();
elem[0].toUpperCase() + elem.substring(1).toLowerCase();

@@ -35,5 +32,5 @@ if (atom.elem !== "H" || !noH) {

serialToIndex[i] = atoms[atoms.length - 1].length;
atom.x = parseFloat(line.substr(0, 10));
atom.y = parseFloat(line.substr(10, 10));
atom.z = parseFloat(line.substr(20, 10));
atom.x = parseFloat(line.substring(0, 10));
atom.y = parseFloat(line.substring(10, 20));
atom.z = parseFloat(line.substring(20, 30));
atom.hetflag = true;

@@ -50,5 +47,5 @@ atom.bonds = [];

line = lines[offset];
var from = serialToIndex[parseInt(line.substr(0, 3)) - 1 + start];
var to = serialToIndex[parseInt(line.substr(3, 3)) - 1 + start];
var order = parseFloat(line.substr(6));
var from = serialToIndex[parseInt(line.substring(0, 3)) - 1 + start];
var to = serialToIndex[parseInt(line.substring(3, 6)) - 1 + start];
var order = parseFloat(line.substring(6));
if (typeof from != "undefined" && typeof to != "undefined") {

@@ -72,8 +69,9 @@ atoms[atoms.length - 1][from].bonds.push(to);

/*
/**
* @param {!Array.<string>} lines
* @param {ParserOptionsSpec} options
* @returns {!Array.<!Array<!Object>>}
*/
var parseV3000 = function (lines, options) {
*/
var parseV3000 = function (lines: any, options: ParserOptionsSpec) {
var atoms: any[][] & Record<string, any> = [[]];

@@ -89,3 +87,3 @@ var noH = false;

var counts = lines[5].substr(13).match(/\S+/g);
var counts = lines[5].substring(13).match(/\S+/g);

@@ -107,11 +105,11 @@ if (counts.length < 2) break;

var end = start + atomCount;
var i, line;
var i: number, line: string;
for (i = start; i < end; i++, offset++) {
line = lines[offset];
var atomParts = line.substr(6).match(/\S+/g);
if (atomParts.length > 4) {
var atomParts = line.substring(6).match(/\S+/g);
if (atomParts!.length > 4) {
var atom: Record<string, any> = {};
var elem = atomParts[1].replace(/ /g, "");
var elem = atomParts![1].replace(/ /g, "");
atom.atom = atom.elem =
elem[0].toUpperCase() + elem.substr(1).toLowerCase();
elem[0].toUpperCase() + elem.substring(1).toLowerCase();

@@ -121,5 +119,5 @@ if (atom.elem !== "H" || !noH) {

serialToIndex[i] = atoms[atoms.length - 1].length;
atom.x = parseFloat(atomParts[2]);
atom.y = parseFloat(atomParts[3]);
atom.z = parseFloat(atomParts[4]);
atom.x = parseFloat(atomParts![2]);
atom.y = parseFloat(atomParts![3]);
atom.z = parseFloat(atomParts![4]);
atom.hetflag = true;

@@ -143,7 +141,7 @@ atom.bonds = [];

line = lines[offset];
var bondParts = line.substr(6).match(/\S+/g);
if (bondParts.length > 3) {
var from = serialToIndex[parseInt(bondParts[2]) - 1 + start];
var to = serialToIndex[parseInt(bondParts[3]) - 1 + start];
var order = parseFloat(bondParts[1]);
var bondParts = line.substring(6).match(/\S+/g);
if (bondParts!.length > 3) {
var from = serialToIndex[parseInt(bondParts![2]) - 1 + start];
var to = serialToIndex[parseInt(bondParts![3]) - 1 + start];
var order = parseFloat(bondParts![1]);
if (typeof from != "undefined" && typeof to != "undefined") {

@@ -172,3 +170,2 @@ atoms[atoms.length - 1][from].bonds.push(to);

/**

@@ -180,9 +177,9 @@ * @param {string}

* @category Parsers
*/
*/
export function SDF(str, options) {
export function SDF(str: string, options: ParserOptionsSpec) {
var molformat = "V2000";
var lines = str.split(/\r?\n|\r/);
if (lines.length > 3 && lines[3].length > 38) {
molformat = lines[3].substr(34, 5);
molformat = lines[3].substring(34, 39);
}

@@ -194,3 +191,3 @@ if (molformat === "V2000") {

}
return [[]];
return [['']];
}

2

src/parsers/utils/anumToSymbol.ts

@@ -1,2 +0,2 @@

export const anumToSymbol = {
export const anumToSymbol:any = {
1: 'H', 2: 'He',

@@ -3,0 +3,0 @@ 3:'Li',4:'Be', 5: 'B', 6: 'C', 7:'N', 8:'O', 9:'F', 10: 'Ne',

7

src/parsers/utils/areConnected.ts
import { bondLength } from "./bondLength";
/*
* return true if atom1 and atom2 are probably bonded to each other based on distance alone
*/
export function areConnected(atom1, atom2) {
* Return true if atom1 and atom2 are probably bonded to each other based on distance alone
*/
export function areConnected(atom1: { elem: any; x: number; y: number; z: number; altLoc: string; }, atom2: { elem: any; x: number; y: number; z: number; altLoc: string; }) {
var maxsq = bondLength(atom1.elem) + bondLength(atom2.elem);

@@ -8,0 +9,0 @@ maxsq += 0.25; // fudge factor, especially important for md frames, also see 1i3d

4

src/parsers/utils/assignBackboneHBonds.ts

@@ -1,5 +0,5 @@

// this will identify all hydrogen bonds between backbone
// This will identify all hydrogen bonds between backbone
// atoms; assume atom names are correct, only identifies
// single closest hbond
export function assignBackboneHBonds(atomsarray, hbondCutoff) {
export function assignBackboneHBonds(atomsarray: string | any[], hbondCutoff: number) {
let maxlength = hbondCutoff || 3.2;

@@ -6,0 +6,0 @@ let maxlengthSq = maxlength*maxlength;

11

src/parsers/utils/assignBonds.ts
import { areConnected } from "./areConnected";
/*
/**
* @param {AtomSpec[]} atoms
*/
export function assignBonds(atoms) {
// assign bonds - yuck, can't count on connect records
*/
export function assignBonds(atoms: string | any[]) {
// Assign bonds - yuck, can't count on connect records
for (var i = 0, n = atoms.length; i < n; i++) {

@@ -35,3 +36,3 @@ // Don't reindex if atoms are already indexed

var findConnections = function (points, otherPoints) {
var findConnections = function (points: string | any[], otherPoints: string | any[]) {
for (var i = 0; i < points.length; i++) {

@@ -38,0 +39,0 @@ var atom1 = points[i];

15

src/parsers/utils/assignPDBBonds.ts

@@ -1,3 +0,2 @@

// this is optimized for proteins where it is assumed connected
// atoms are on the same or next residue
// This is optimized for proteins where it is assumed connected atoms are on the same or next residue

@@ -8,11 +7,13 @@ import { areConnected } from "./areConnected";

/*
/**
* @param {AtomSpec[]}
* atomsarray
*/
export function assignPDBBonds(atomsarray) {
*/
export function assignPDBBonds(atomsarray: string | any[]) {
// assign bonds - yuck, can't count on connect records
var protatoms: any[] = [];
var hetatoms: any[] = [];
var i, n;
var i: number, n: number;
for (i = 0, n = atomsarray.length; i < n; i++) {

@@ -36,3 +37,3 @@ var atom: any = atomsarray[i];

var reschain = -1;
var lastResConnected;
var lastResConnected: boolean;

@@ -39,0 +40,0 @@ for (i = 0, n = protatoms.length; i < n; i++) {

6

src/parsers/utils/atomNameToElem.ts
import { bondTable } from "./bondLength";
//attempts to infer atomic element from an atom name
export function atomNameToElem(name, nothetero) {
// Attempts to infer atomic element from an atom name
export function atomNameToElem(name: string, nothetero: boolean) {
var elem = name.replace(/ /g, "");

@@ -10,3 +10,3 @@ if(elem.length > 0 && elem[0] == 'H' && elem != 'Hg' && elem != 'He' && elem != 'Hf' && elem != 'Hs' && elem != 'Ho') {

if(elem.length > 1) {
elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
elem = elem[0].toUpperCase() + elem.substring(1).toLowerCase();
if(typeof(bondTable[elem]) === 'undefined') {

@@ -13,0 +13,0 @@ //not a known element, probably should just use first letter

15

src/parsers/utils/bondLength.ts
/* Covalent radii lookup table used to identify bonds in assignBonds
*/
export let bondTable = {
// Covalent radii lookup table used to identify bonds in assignBonds
export let bondTable:any = {
H :0.37, He:0.32,

@@ -16,12 +15,8 @@ Li:1.34,Be:0.90, B :0.82,C :0.77,N :0.75,O :0.73,F :0.71,Ne:0.69,

/** Get the length used for bond identification for the specified element.
*
*/
export function bondLength(elem) {
// Get the length used for bond identification for the specified element.
export function bondLength(elem: string | number) {
return bondTable[elem] || 1.6;
};
/** Set the length used for bond identification for the specified element.
*
*/
// Set the length used for bond identification for the specified element.
export function setBondLength(elem:string, radius:number) {

@@ -28,0 +23,0 @@ if(radius < 0) radius = 0;

8

src/parsers/utils/computeSecondaryStructure.ts
import { assignBackboneHBonds } from "./assignBackboneHBonds";
export function computeSecondaryStructure(atomsarray, hbondCutoff) {
assignBackboneHBonds(atomsarray, hbondCutoff);
export function computeSecondaryStructure(atomsarray: string | any[], hbondCutoff: number | undefined) {
assignBackboneHBonds(atomsarray, hbondCutoff!);
// compute, per residue, what the secondary structure is
var chres = {}; // lookup by chain and resid
var i, il, c, r; // i: used in for loop, il: length of atomsarray
var atom, val;
var i: number, il: number, c: string | number, r: number; // i: used in for loop, il: length of atomsarray
var atom: { chain: string | number; hbondDistanceSq: number; hbondOther: any; resi: number; ss: string; ssbegin: boolean; ssend: boolean; }, val: string;

@@ -11,0 +11,0 @@ //identify helices first

99

src/parsers/utils/getSinglePDB.ts

@@ -9,5 +9,6 @@ import { Matrix4 } from "../../WebGL";

import { validateBonds } from "./validateBonds";
import { ParserOptionsSpec } from "../ParserOptionsSpec";
//return one model worth of pdb, returns atoms, modelData, and remaining lines
export function getSinglePDB(lines, options, sslookup) {
// Return one model worth of pdb, returns atoms, modelData, and remaining lines
export function getSinglePDB(lines: string[], options: ParserOptionsSpec, sslookup: { [x: string]: { [x: string]: any; }; hasOwnProperty?: any; }) {
var atoms: any[] = [];

@@ -22,8 +23,7 @@ var assignbonds =

var modelData: Record<string, any> = { symmetries: [] };
var atom;
var atom: any;
var remainingLines = [];
var hasStruct = false;
var serialToIndex: number[] = []; // map from pdb serial to index in atoms
var line;
var line: string | string[];
var seenbonds: Record<any, any> = {}; //sometimes connect records are duplicated as an unofficial means of relaying bond orders

@@ -33,5 +33,6 @@

line = lines[i].replace(/^\s*/, ""); // remove indent
var recordName = line.substr(0, 6);
var startChain, startResi, endChain, endResi;
var recordName = line.substring(0, 6);
var startChain: string, startResi: number, endResi: number;
if (recordName.indexOf("END") == 0) {

@@ -50,21 +51,21 @@ remainingLines = lines.slice(i + 1);

} else if (recordName == "ATOM " || recordName == "HETATM") {
var resn, chain, resi, icode, x, y, z, hetflag, elem, serial, altLoc, b;
altLoc = line.substr(16, 1);
var resn: any, chain: any, resi: string | number, icode: string, x: number, y: number, z: number, hetflag: boolean, elem: string | string[], serial: number, altLoc: string, b: number;
altLoc = line.substring(16, 17);
if (altLoc != " " && altLoc != selAltLoc && selAltLoc != "*") continue;
serial = parseInt(line.substr(6, 5));
atom = line.substr(12, 4).replace(/ /g, "");
resn = line.substr(17, 3).replace(/ /g, "");
chain = line.substr(21, 1);
resi = parseInt(line.substr(22, 4));
icode = line.substr(26, 1);
x = parseFloat(line.substr(30, 8));
y = parseFloat(line.substr(38, 8));
z = parseFloat(line.substr(46, 8));
b = parseFloat(line.substr(60, 8));
elem = line.substr(76, 2).replace(/ /g, "");
serial = parseInt(line.substring(6, 11));
atom = line.substring(12, 16).replace(/ /g, "");
resn = line.substring(17, 20).replace(/ /g, "");
chain = line.substring(21, 22);
resi = parseInt(line.substring(22, 26));
icode = line.substring(26, 27);
x = parseFloat(line.substring(30, 38));
y = parseFloat(line.substring(38, 46));
z = parseFloat(line.substring(46, 54));
b = parseFloat(line.substring(60, 68));
elem = line.substring(76, 78).replace(/ /g, "");
if (elem === "" || typeof bondTable[elem] === "undefined") {
// for some incorrect PDB files
elem = atomNameToElem(line.substr(12, 2), line[0] == "A");
elem = atomNameToElem(line.substring(12, 14), line[0] == "A");
} else {
elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
elem = elem[0].toUpperCase() + elem.substring(1).toLowerCase();
}

@@ -101,7 +102,5 @@

} else if (recordName == "SHEET ") {
hasStruct = true;
startChain = line.substr(21, 1);
startResi = parseInt(line.substr(22, 4));
endChain = line.substr(32, 1);
endResi = parseInt(line.substr(33, 4));
startChain = line.substring(21, 22);
startResi = parseInt(line.substring(22, 26));
endResi = parseInt(line.substring(33, 37));
if (!(startChain in sslookup)) {

@@ -120,3 +119,3 @@ sslookup[startChain] = {};

// described in CONECT. But what about 2JYT???
var from = parseInt(line.substr(6, 5));
var from = parseInt(line.substring(6, 11));
var fromindex = serialToIndex[from];

@@ -126,3 +125,3 @@ var fromAtom = atoms[fromindex];

for (let j = 0; j < 4; j++) {
var to = parseInt(line.substr(coffsets[j], 5));
var to = parseInt(line.substring(coffsets[j], coffsets[j]+5));
var toindex = serialToIndex[to];

@@ -161,7 +160,5 @@ let from_to = fromindex+":"+toindex;

} else if (recordName == "HELIX ") {
hasStruct = true;
startChain = line.substr(19, 1);
startResi = parseInt(line.substr(21, 4));
endChain = line.substr(31, 1);
endResi = parseInt(line.substr(33, 4));
startChain = line.substring(19, 20);
startResi = parseInt(line.substring(21, 25));
endResi = parseInt(line.substring(33, 37));
if (!(startChain in sslookup)) {

@@ -178,9 +175,9 @@ sslookup[startChain] = {};

recordName == "REMARK" &&
line.substr(13, 5) == "BIOMT"
line.substring(13, 18) == "BIOMT"
) {
var n;
var n: number;
var matrix = new Matrix4();
for (n = 1; n <= 3; n++) {
line = lines[i].replace(/^\s*/, "");
if (parseInt(line.substr(18, 1)) == n) {
if (parseInt(line.substring(18, 19)) == n) {
// check for all

@@ -191,9 +188,9 @@ // three lines

// "BIOMT" to n
matrix.elements[n - 1] = parseFloat(line.substr(23, 10));
matrix.elements[n - 1 + 4] = parseFloat(line.substr(33, 10));
matrix.elements[n - 1 + 8] = parseFloat(line.substr(43, 10));
matrix.elements[n - 1 + 12] = parseFloat(line.substr(53));
matrix.elements[n - 1] = parseFloat(line.substring(23, 33));
matrix.elements[n - 1 + 4] = parseFloat(line.substring(33, 43));
matrix.elements[n - 1 + 8] = parseFloat(line.substring(43, 53));
matrix.elements[n - 1 + 12] = parseFloat(line.substring(53));
i++;
} else {
while (line.substr(13, 5) == "BIOMT") {
while (line.substring(13, 18) == "BIOMT") {
i++;

@@ -211,9 +208,9 @@ line = lines[i].replace(/^\s*/, "");

} else if (recordName == "CRYST1") {
let a, b, c, alpha, beta, gamma;
a = parseFloat(line.substr(7, 8));
b = parseFloat(line.substr(16, 8));
c = parseFloat(line.substr(25, 8));
alpha = parseFloat(line.substr(34, 6));
beta = parseFloat(line.substr(41, 6));
gamma = parseFloat(line.substr(48, 6));
let a: number, b: number, c: number, alpha: number, beta: number, gamma: number;
a = parseFloat(line.substring(7, 15));
b = parseFloat(line.substring(16, 24));
c = parseFloat(line.substring(25, 33));
alpha = parseFloat(line.substring(34, 40));
beta = parseFloat(line.substring(41, 47));
gamma = parseFloat(line.substring(48, 54));
modelData.cryst = {

@@ -228,7 +225,7 @@ a: a,

} else if (recordName == "ANISOU") {
let serial = parseInt(line.substr(6, 5));
let serial = parseInt(line.substring(6, 11));
var anisouAtomIndex = serialToIndex[serial];
var anisouAtom = atoms[anisouAtomIndex];
if (anisouAtom) {
var vals = line.substr(30).trim().split(/\s+/);
var vals = line.substring(30).trim().split(/\s+/);
var uMat = {

@@ -235,0 +232,0 @@ u11: parseInt(vals[0]),

4

src/parsers/utils/isEmpty.ts

@@ -1,3 +0,3 @@

export function isEmpty(obj) {
var name;
export function isEmpty(obj: { [x: string]: { [x: string]: any; }; hasOwnProperty?: any; }) {
var name: string;
for (name in obj) {

@@ -4,0 +4,0 @@ return false;

11

src/parsers/utils/processSymmetries.ts

@@ -0,9 +1,10 @@

import { ParserOptionsSpec } from 'parsers/ParserOptionsSpec';
import { Matrix3, conversionMatrix3, Vector3 } from '../../WebGL';
//adds symmetry info to either duplicate and rotate/translate biological unit later or add extra atoms now
//matrices may be modified if normalization is requested
export function processSymmetries(copyMatrices, atoms, options, cryst) {
// Adds symmetry info to either duplicate and rotate/translate biological unit later or add extra atoms now
// matrices may be modified if normalization is requested
export function processSymmetries(copyMatrices: string[] | any[], atoms: any[], options: ParserOptionsSpec, cryst: { a: any; b: number; c: number; alpha: number; beta: number; gamma: number; }) {
var dontDuplicate = !options.duplicateAssemblyAtoms;
var end = atoms.length;
var offset = end;
var t, l, n; // Used in for loops
var t: any, l: number, n: number; // Used in for loops

@@ -112,3 +113,3 @@ let modifiedIdentity = -1;

//we have explicitly duplicated the atoms, remove model symmetry information
copyMatrices.length = 0;
(copyMatrices as any).length = 0;
} else if (copyMatrices.length > 1) {

@@ -115,0 +116,0 @@ for (t = 0; t < atoms.length; t++) {

2

src/parsers/utils/standardResidues.ts

@@ -1,2 +0,2 @@

export const standardResidues = new Set([
export const standardResidues: Set<string> = new Set([
"ABU",

@@ -3,0 +3,0 @@ "ACD",

4

src/parsers/utils/validateBonds.ts

@@ -1,3 +0,3 @@

//make sure bonds are actually two way
export function validateBonds (atomsarray, serialToIndex) {
// Make sure bonds are actually two way
export function validateBonds (atomsarray: string[] | any[], serialToIndex: number[]) {
for (var i = 0, n = atomsarray.length; i < n; i++) {

@@ -4,0 +4,0 @@ var atom = atomsarray[i];

17

src/parsers/VASP.ts

@@ -9,4 +9,5 @@ import { Matrix3 } from "../WebGL";

* @category Parsers
*/
export function VASP(str /*,options*/) {
*/
export function VASP(str: string /*,options*/) {
var atoms: any[][] & Record<string, any> = [[]];

@@ -37,5 +38,5 @@ var lattice: Record<string, number | Float32Array> = {};

lattice.xVec = new Float32Array(lines[2].replace(/^\s+/, "").split(/\s+/));
lattice.yVec = new Float32Array(lines[3].replace(/^\s+/, "").split(/\s+/));
lattice.zVec = new Float32Array(lines[4].replace(/^\s+/, "").split(/\s+/));
lattice.xVec = new Float32Array((lines[2] as any).replace(/^\s+/, "").split(/\s+/));
lattice.yVec = new Float32Array((lines[3] as any).replace(/^\s+/, "").split(/\s+/));
lattice.zVec = new Float32Array((lines[4] as any).replace(/^\s+/, "").split(/\s+/));

@@ -61,3 +62,3 @@ var matrix = new Matrix3(

var atomSpeciesNumber = new Int16Array(
lines[6].replace(/^\s+/, "").split(/\s+/)
(lines[6] as any).replace(/^\s+/, "").split(/\s+/)
);

@@ -92,7 +93,7 @@ var vaspMode = lines[7].replace(/\s+/, "");

var coords = new Float32Array(
lines[atomCounter + j].replace(/^\s+/, "").split(/\s+/)
(lines[atomCounter + j] as any).replace(/^\s+/, "").split(/\s+/)
);
var atom: Record<string, number | []> = {};
atom.elem = atomSymbol;
(atom.elem as any) = atomSymbol;
if (vaspMode == "cartesian") {

@@ -99,0 +100,0 @@ atom.x = lattice.length * coords[0];

8

src/parsers/XYZ.ts
import { ParserOptionsSpec } from './ParserOptionsSpec';
// read an XYZ file from str and return result

@@ -8,6 +7,9 @@ import { Matrix3 } from "../WebGL";

/**
* Read an XYZ file from str and return result
*
* @param {string} str
* @param {ParserOptionsSpec} options
* @category Parsers
*/
*/
export function XYZ(str: string, options: ParserOptionsSpec) {

@@ -53,3 +55,3 @@ options = options || {};

atom.atom = atom.elem =
elem[0].toUpperCase() + elem.substr(1, 1).toLowerCase();
elem[0].toUpperCase() + elem.substring(1, 2).toLowerCase();
atom.x = parseFloat(tokens[1]);

@@ -56,0 +58,0 @@ atom.y = parseFloat(tokens[2]);

4

src/partialCharges.ts

@@ -174,9 +174,9 @@ //properties for mapping

//this can be supplied to mapAtomProperties
export function applyPartialCharges(atom, keepexisting) {
export function applyPartialCharges(atom: Record<string, any>, keepexisting: boolean) {
if(!keepexisting || typeof(atom.partialCharge) === "undefined") {
if(atom.resn && atom.atom) {
var key = atom.resn+":"+atom.atom;
atom.properties.partialCharge = partialCharges[key];
atom.properties.partialCharge = (partialCharges as any)[key];
}
}
};

2

src/specs.ts

@@ -98,2 +98,4 @@ // Specifications for various object types used in 3Dmol.js

model?: GLModel | number | GLModel[] | number[];
/** frame index of individual frame to style; will apply to all frames if not set */
frame?: number;
/** index of the atom or atoms to select */

@@ -100,0 +102,0 @@ index?: number | number[];

7

src/SurfaceWorker.js
//Hackish way to create webworker (independent of $3Dmol namespace) within minified file
//We need to convert actual javascript into a string, not typescript, so for the time being
//this will remain a JS file

@@ -24,3 +25,3 @@ $3Dmol.workerString = function(){

}
ps.marchingcube(type);
ps.marchingcube(type); // jshint ignore:line
var VandF = ps.getFacesAndVertices(obj.atomsToShow);

@@ -35,8 +36,8 @@ self.postMessage(VandF);

// (See: http://stackoverflow.com/questions/1661197/what-characters-are-valid-for-javascript-variable-names)
$3Dmol.workerString += ";\nfunction _classCallCheck() {};"; //hack for babel
$3Dmol.workerString += ";\n"+$3Dmol.Vector3.toString();
$3Dmol.workerString += ";\n"+$3Dmol.MarchingCubeInitializer.toString()+";\nvar MarchingCube = new MarchingCubeInitializer();";
$3Dmol.workerString += ";\n"+$3Dmol.MarchingCubeInitializer.toString()+";\n\n";
$3Dmol.workerString += ";\n"+$3Dmol.PointGrid.toString()+";\n";
$3Dmol.workerString += ";\nvar ProteinSurface = "+$3Dmol.ProteinSurface.toString()+";\n";
$3Dmol.workerString = $3Dmol.workerString.replace(/[a-zA-Z_$]{1}[0-9a-zA-Z_$]*WEBPACK_IMPORTED_MODULE_[0-9]__\./g,''); //replace webpack generated prefixes
//console.log($3Dmol.workerString);
$3Dmol.SurfaceWorker = window.URL ? window.URL.createObjectURL(new Blob([$3Dmol.workerString],{type: 'text/javascript'})) : undefined;

18

src/utilities.ts

@@ -281,3 +281,3 @@ //a collection of miscellaneous utility functions

str = str.replace(/%7E/, '~'); //copy/pasting urls sometimes does this
str = str.replace(/%7E/g, '~'); //copy/pasting urls sometimes does this
//convert things that look like numbers into numbers

@@ -423,5 +423,5 @@ var massage = function (val) {

}
if (query.substr(0, 5) === 'mmtf:') {
if (query.substring(0, 5) === 'mmtf:') {
pdbUri = options && options.pdbUri ? options.pdbUri : "https://mmtf.rcsb.org/v1.0/full/";
query = query.substr(5).toUpperCase();
query = query.substring(5).toUpperCase();
uri = pdbUri + query;

@@ -443,3 +443,3 @@ if (options && typeof options.noComputeSecondaryStructure === 'undefined') {

else {
if (query.substr(0, 4) === 'pdb:') {
if (query.substring(0, 4) === 'pdb:') {
type = 'mmtf';

@@ -454,3 +454,3 @@ if (options && options.format) {

}
query = query.substr(4).toUpperCase();
query = query.substring(4).toUpperCase();
if (!query.match(/^[1-9][A-Za-z0-9]{3}$/)) {

@@ -469,5 +469,5 @@ alert("Wrong PDB ID");

} else if (query.substr(0, 4) == 'cid:') {
} else if (query.substring(0, 4) == 'cid:') {
type = "sdf";
query = query.substr(4);
query = query.substring(4);
if (!query.match(/^[0-9]+$/)) {

@@ -478,4 +478,4 @@ alert("Wrong Compound ID"); return;

"/SDF?record_type=3d";
} else if (query.substr(0, 4) == 'url:') {
uri = query.substr(4);
} else if (query.substring(0, 4) == 'url:') {
uri = query.substring(4);
type = uri;

@@ -482,0 +482,0 @@ }

55

src/VolumeData.ts

@@ -5,3 +5,3 @@ import { base64ToArray } from "./utilities";

import { CUBE } from "./parsers/CUBE";
import {inflate} from "pako";
import { inflate } from "pako";

@@ -56,3 +56,3 @@

try {
if (this[format] && this.isbinary.has(format)) {
if ((this as any)[format] && this.isbinary.has(format)) {
if (typeof (str) == "string") {

@@ -72,7 +72,7 @@ //assume base64 encoded

if (this[format]) {
if ((this as any)[format]) {
if (this.isbinary.has(format) && typeof (str) == "string") {
str = base64ToArray(str);
}
this[format](str);
(this as any)[format](str);
}

@@ -178,3 +178,3 @@

*/
vasp = function (str) {
vasp = function (str: string) {

@@ -203,3 +203,3 @@ var lines = str.replace(/^\s+/, "").split(/[\n\r]/);

// each dimension
var v;
var v: string[];
v = lines[2].replace(/^\s+/, "").split(/\s+/);

@@ -225,6 +225,7 @@ var xVec = new Vector3(parseFloat(v[0]), parseFloat(v[1]), parseFloat(v[2])).multiplyScalar(convFactor * l_units);

var nX = Math.abs(lineArr[0]);
var nY = Math.abs(lineArr[1]);
var nZ = Math.abs(lineArr[2]);
var nX = Math.abs(parseFloat(lineArr[0]));
var nY = Math.abs(parseFloat(lineArr[1]));
var nZ = Math.abs(parseFloat(lineArr[2]));
var origin = this.origin = new Vector3(0, 0, 0);

@@ -253,10 +254,10 @@

lines.splice(0, 1); //Remove the dimension line
lines.splice(0, 1); // Remove the dimension line
var raw = lines.join(" ");
raw = raw.replace(/^\s+/, '');
raw = raw.split(/[\s\r]+/);
raw.splice(nX * nY * nZ + 1);
var rawArray = raw.split(/[\s\r]+/);
rawArray.splice(nX * nY * nZ + 1);
var preConvertedData = new Float32Array(raw); //We still have to format it to get the density
var preConvertedData = Float32Array.from(rawArray, parseFloat); //We still have to format it to get the density

@@ -280,5 +281,5 @@ for (var i = 0; i < preConvertedData.length; i++) {

// parse dx data - does not support all features of the file format
dx = function (str) {
dx = function (str: string) {
var lines = str.split(/[\n\r]+/);
var m;
var m: string[];
var recounts = /gridpositions\s+counts\s+(\d+)\s+(\d+)\s+(\d+)/;

@@ -345,8 +346,8 @@ var reorig = /^origin\s+(\S+)\s+(\S+)\s+(\S+)/;

var raw = lines.splice(i).join(" ");
raw = raw.split(/[\s\r]+/);
this.data = new Float32Array(raw);
var rawArray = raw.split(/[\s\r]+/);
this.data = Float32Array.from(rawArray, parseFloat);
};
// parse cube data
cube(str) {
cube(str: string) {
var lines = str.split(/\r?\n/);

@@ -373,4 +374,4 @@

raw = raw.replace(/^\s+/, '');
raw = raw.split(/[\s\r]+/);
this.data = new Float32Array(raw);
var rawArray = raw.split(/[\s\r]+/);
this.data = Float32Array.from(rawArray, parseFloat);

@@ -382,3 +383,3 @@ };

//parse cp4 files
ccp4(bin) {
ccp4(bin: Int8Array) {

@@ -501,3 +502,3 @@ // http://www.ccp4.ac.uk/html/maplib.html#description

var h = header;
var basisX = [
var basisX: Array<any> = [
h.xlen,

@@ -508,3 +509,3 @@ 0,

var basisY = [
var basisY: Array<any> = [
h.ylen * Math.cos(Math.PI / 180.0 * h.gamma),

@@ -515,3 +516,3 @@ h.ylen * Math.sin(Math.PI / 180.0 * h.gamma),

var basisZ = [
var basisZ: Array<any> = [
h.zlen * Math.cos(Math.PI / 180.0 * h.beta),

@@ -530,5 +531,5 @@ h.zlen * (

var basis = [0, basisX, basisY, basisZ];
var nxyz = [0, h.MX, h.MY, h.MZ];
var mapcrs = [0, h.MAPC, h.MAPR, h.MAPS];
var basis: Array<any> = [0, basisX, basisY, basisZ];
var nxyz: Array<any> = [0, h.MX, h.MY, h.MZ];
var mapcrs: Array<any> = [0, h.MAPC, h.MAPR, h.MAPS];

@@ -535,0 +536,0 @@ this.matrix = new Matrix4();

18

src/VolumetricRender.ts
import { Sphere } from "./WebGL/shapes";
import { Vector3, Matrix4 } from "./WebGL/math";
import { VolumetricMaterial, Mesh, Texture, Object3D } from "./WebGL";
import { VolumetricMaterial, Mesh, Texture, Object3D, Material } from "./WebGL";
import { CC } from "./colors";

@@ -34,4 +34,4 @@ import { GLShape } from "./GLShape";

static interpolateArray(data, fitCount) {
function linearInterpolate(before, after, atPoint) {
static interpolateArray(data: string | any[], fitCount: number) {
function linearInterpolate(before: number, after: number, atPoint: number) {
return before + (after - before) * atPoint;

@@ -69,3 +69,3 @@ }

constructor(data, spec) {
constructor(data: { matrix: { elements: any; }; size: { x: number; y: number; z: number; }; unit: { x: number; y: number; z: number; }; origin: { x: number; y: number; z: number; }; data: number[]; getIndex: (arg0: number, arg1: number, arg2: number) => number; }, spec: VolumetricRendererSpec) {
spec = spec || {};

@@ -78,4 +78,4 @@ var transferfn = Object.assign([], spec.transferfn);

// arrange points based on position property
transferfn.forEach(function (a) { a.value = parseFloat(a.value); });
transferfn.sort(function (a, b) { return a.value - b.value; });
transferfn.forEach(function (a: { value: any; }) { a.value = parseFloat(a.value); });
transferfn.sort(function (a: { value: number; }, b: { value: number; }) { return a.value - b.value; });
this.min = transferfn[0].value;

@@ -235,3 +235,3 @@ if (transferfn.length == 0) transferfn.push(transferfn[0]); //need at least two

*/
globj(group) {
globj(group: { remove: (arg0: any) => void; add: (arg0: any) => void; }) {

@@ -267,3 +267,3 @@ if (this.renderedShapeObj) {

var mesh = new Mesh(this.geo, material);
var mesh = new Mesh(this.geo, (material as Material));
this.shapeObj.add(mesh);

@@ -275,3 +275,3 @@

removegl(group) {
removegl(group: { remove: (arg0: any) => void; }) {
if (this.renderedShapeObj) {

@@ -278,0 +278,0 @@ // dispose of geos and materials

1

src/WebGL/Camera.ts

@@ -1,2 +0,1 @@

import type { Quaternion } from "./math";
import { Object3D } from "./core";

@@ -3,0 +2,0 @@ import { Matrix4, Vector3 } from "./math";

22

src/WebGL/core/Geometry.ts

@@ -5,3 +5,3 @@ import type { Material } from './../materials/Material';

import { Vector3 } from "../math";
import { CC, Color, Colored } from "../../colors";
import { CC, Color } from "../../colors";
const BUFFERSIZE = 65535; //limited to 16bit indices

@@ -58,3 +58,3 @@ export class GeometryGroup {

var centroid = new Vector3();
var offset, x, y, z;
var offset: number, x: number, y: number, z: number;

@@ -91,10 +91,10 @@ for (var i = 0; i < this.vertices; ++i) {

//vertex indices
var a,
b,
c,
var a: number,
b: number,
c: number,
//and actual vertices
vA,
vB,
vC,
norm;
vA: Vector3,
vB: Vector3,
vC: Vector3,
norm: { normalize: () => void; x: number; y: number; z: number; };

@@ -202,3 +202,3 @@ for (var i = 0; i < faces.length / 3; ++i) {

" point [\n";
let x, y, z;
let x: string | number, y: string | number, z: string | number;
for (let i = 0; i < this.vertices; ++i) {

@@ -247,3 +247,3 @@ let offset = i * 3;

ret += indent + " coord Coordinate {\n" + indent + " point [\n";
let x, y, z;
let x: string | number, y: string | number, z: string | number;
for (let i = 0; i < this.vertices; ++i) {

@@ -250,0 +250,0 @@ let offset = i * 3;

2

src/WebGL/core/Object3D.ts

@@ -257,3 +257,3 @@ import type { Material } from './../materials/Material';

__removeObject<T extends Object3D>(object: T) {
var idx;
var idx: number;
if (object instanceof Light) {

@@ -260,0 +260,0 @@ idx = this.__lights.indexOf(object as unknown as Light);

10

src/WebGL/core/Projector.ts

@@ -10,7 +10,4 @@ import type { Vector3 } from '../math';

static unprojectVector(vector: Vector3, camera: Camera) {
camera.projectionMatrixInverse.getInverse(camera.projectionMatrix);
viewProjectionMatrix.multiplyMatrices(camera.matrixWorld, camera.projectionMatrixInverse);
return vector.applyProjection(viewProjectionMatrix);

@@ -21,7 +18,4 @@

static projectVector(vector: Vector3, camera: Camera) {
camera.matrixWorldInverse.getInverse(camera.matrixWorld);
viewProjectionMatrix.multiplyMatrices(camera.projectionMatrix, camera.matrixWorldInverse);
return vector.applyProjection(viewProjectionMatrix);

@@ -31,12 +25,8 @@ };

projectVector(vector: Vector3, camera: Camera) {
return Projector.projectVector(vector, camera);
}
unprojectVector(vector: Vector3, camera: Camera) {
return Projector.unprojectVector(vector, camera);
}
}

30

src/WebGL/core/Raycaster.ts

@@ -9,4 +9,2 @@ import type { Camera } from '../Camera';

const viewProjectionMatrix = new Matrix4();

@@ -106,16 +104,16 @@

//Iterate through intersection objects
var i,
il,
norm,
normProj,
cylProj,
rayProj,
distance,
closestDistSq,
denom,
discriminant,
s,
t,
s_c,
t_c;
var i: number,
il: number,
norm: Vector3,
normProj: number,
cylProj: number,
rayProj: number,
distance: number,
closestDistSq: number,
denom: number,
discriminant: number,
s: number,
t: number,
s_c: number,
t_c: number;
//triangle faces

@@ -122,0 +120,0 @@ for (i = 0, il = intersectionShape.triangle.length; i < il; i++) {

2

src/WebGL/materials/Material.ts

@@ -64,3 +64,3 @@ import {FrontSide} from "../constants/Sides";

} else {
this[key] = newValue;
(this as any)[key] = newValue;
}

@@ -67,0 +67,0 @@ }

8

src/WebGL/math/utils/conversionMatrix3.ts

@@ -16,3 +16,3 @@ // return conversion matrix given crystal unit cell parameters

export function conversionMatrix3(
a: any,
a: number,
b: number,

@@ -24,7 +24,9 @@ c: number,

) {
// convert to radians
// Convert to radians
alpha = (alpha * Math.PI) / 180;
beta = (beta * Math.PI) / 180;
gamma = (gamma * Math.PI) / 180;
const sqr = (x) => x*x;
const sqr = (x: number) => {
return x*x
};
const cosAlpha = Math.cos(alpha);

@@ -31,0 +33,0 @@ const cosBeta = Math.cos(beta);

27

src/WebGL/Renderer.ts

@@ -31,3 +31,3 @@ /**

devicePixelRatio = 1.0; //set in setSize
domElement: Element;
domElement: HTMLCanvasElement;
autoClear = true;

@@ -73,3 +73,2 @@ autoClearColor = true;

private _oldFlipSided = -1 as number | boolean;
private _oldBlending = -1;
private _oldDepthTest = -1;

@@ -220,2 +219,3 @@ private _oldDepthWrite = -1;

supportsImposters: Boolean(this._extFragDepth) || !this.isWebGL1(),
regen: false
};

@@ -332,3 +332,3 @@ }

if (!material.imposter)
//ignore reflection with imposters
// Ignore reflection with imposters
flipSided = reflected ? !flipSided : flipSided;

@@ -391,3 +391,2 @@

}
this._oldBlending = blending;
}

@@ -437,2 +436,3 @@

program = this.setProgram(camera, lights, fog, material, object, this);
if(!program) return;

@@ -578,3 +578,3 @@ attributes = program.attributes;

render(scene, camera, forceClear) {
render(scene, camera, forceClear?) {
if (camera instanceof Camera === false) {

@@ -1206,2 +1206,4 @@ console.error("Renderer.render: camera is not an instance of Camera.");

if (shader == null) return null;
this._gl.shaderSource(shader, str);

@@ -1258,2 +1260,3 @@ this._gl.compileShader(shader);

program = this._gl.createProgram();
if(program == null) return null;

@@ -1284,4 +1287,4 @@ // set up precision

this._gl.attachShader(program, glVertexShader);
this._gl.attachShader(program, glFragmentShader);
if(glVertexShader != null) this._gl.attachShader(program, glVertexShader);
if(glFragmentShader != null) this._gl.attachShader(program, glFragmentShader);

@@ -1359,2 +1362,3 @@ this._gl.linkProgram(program);

}
if( material.program == null) return null;

@@ -1516,3 +1520,3 @@ var refreshMaterial = false;

private addObject(object, scene) {
var g, gl, geometry, material, geometryGroup;
var g, gl, geometry, geometryGroup;

@@ -1535,3 +1539,2 @@ if (!object.__webglInit) {

geometry = object.geometry;
material = object.material;

@@ -1807,7 +1810,5 @@ for (g = 0, gl = geometry.geometryGroups.length; g < gl; g++) {

intensity,
distance,
zlights = this._lights,
dirColors = zlights.directional.colors,
dirPositions = zlights.directional.positions,
dirCount = 0,
dirLength = 0,

@@ -1821,6 +1822,4 @@ dirOffset = 0;

intensity = light.intensity;
distance = light.distance;
if (light instanceof Light) {
dirCount++;

@@ -2017,3 +2016,2 @@ this._direction.getPositionFromMatrix(light.matrixWorld);

this._currentCamera = null;
this._oldBlending = -1;
this._oldDepthWrite = -1;

@@ -2032,3 +2030,2 @@ this._oldDepthTest = -1;

this._currentCamera = null;
this._oldBlending = -1;
this._oldDepthWrite = -1;

@@ -2035,0 +2032,0 @@ this._oldDepthTest = -1;

6

src/WebGL/shaders/lib/instanced/uniforms.ts

@@ -8,4 +8,4 @@ import { Color } from "../../../../colors";

fogFar: { type: 'f', value: 2000},
directionalLightColor: { type: 'fv', value: [] },
directionalLightDirection: { type: 'fv', value: [] }
}
directionalLightColor: { type: 'fv', value: [] as number[] },
directionalLightDirection: { type: 'fv', value: [] as number[] }
}

6

src/WebGL/shaders/lib/lambertdouble/uniforms.ts

@@ -8,4 +8,4 @@ import { Color } from "../../../../colors";

fogFar: { type: 'f', value: 2000},
directionalLightColor: { type: 'fv', value: [] },
directionalLightDirection: { type: 'fv', value: [] }
}
directionalLightColor: { type: 'fv', value: [] as number[] },
directionalLightDirection: { type: 'fv', value: [] as number[] }
}

6

src/WebGL/shaders/lib/sphereimposter/uniforms.ts

@@ -8,4 +8,4 @@ import { Color } from "../../../../colors";

fogFar: { type: 'f', value: 2000},
directionalLightColor: { type: 'fv', value: [] },
directionalLightDirection: { type: 'fv', value: [] }
}
directionalLightColor: { type: 'fv', value: [] as number[] },
directionalLightDirection: { type: 'fv', value: [] as number[] }
}

6

src/WebGL/shaders/lib/stickimposter/uniforms.ts

@@ -8,4 +8,4 @@ import { Color } from "../../../../colors";

fogFar: { type: 'f', value: 2000},
directionalLightColor: { type: 'fv', value: [] },
directionalLightDirection: { type: 'fv', value: [] }
}
directionalLightColor: { type: 'fv', value: [] as number[] },
directionalLightDirection: { type: 'fv', value: [] as number[] }
}

8

src/WebGL/shaders/lib/volumetric/uniforms.ts

@@ -0,1 +1,2 @@

import { Matrix4 } from "WebGL/math";
import { Color } from "../../../../colors";

@@ -14,7 +15,6 @@

subsamples: { type: 'f', value: 5.0}, //how many substeps to take
textmat: { type: 'mat4', value: []},
projinv: { type: 'mat4', value: []},
textmat: { type: 'mat4', value: [] as Matrix4[] },
projinv: { type: 'mat4', value: [] as Matrix4[] },
transfermin: {type: 'f', value: -0.2 },
transfermax: {type: 'f', value: 0.2},
}
}

3

tsconfig.json

@@ -11,4 +11,3 @@ {

"declaration": true,
"suppressImplicitAnyIndexErrors": true,
"noUnusedLocals": false,
"noUnusedLocals": true,
"moduleResolution": "node",

@@ -15,0 +14,0 @@ "lib": [

44

webpack.common.js

@@ -11,39 +11,45 @@ /* eslint-disable no-undef*/

module.exports = {
module.exports = {
target: "web",
entry: {'3Dmol':["./src/index.ts",
"./src/SurfaceWorker.js",
"./src/exporter.js"
],
'3Dmol.ui': [ "./src/ui/ui.js",
entry: {
'3Dmol': [
"./src/index.ts",
"./src/SurfaceWorker.js",
"./src/exporter.js"
],
'3Dmol.ui': [
"./src/ui/ui.js",
"./src/ui/state.js",
"./src/ui/icon.js",
"./src/ui/form.js",
"./src/ui/defaultValues.js"]},
"./src/ui/form.js",
"./src/ui/defaultValues.js"
]
},
output: {
path: path.resolve(__dirname, "build"),
globalObject: "this",
library: '[name]',
libraryTarget: "umd",
globalObject: "this"
},
resolve: {
extensions: [".ts", ".tsx", ".js", ".json"],
},
module: {
rules: [
{ test: /\.tsx?$/, loader: "ts-loader"},
{ test: /\.frag/, loader: "raw-loader" },
{ test: /\.vert/, loader: "raw-loader" }
{ test: /\.tsx?$/, loader: "ts-loader" },
{ test: /\.frag$/, loader: "raw-loader" },
{ test: /\.vert$/, loader: "raw-loader" }
],
},
plugins: [
new webpack.ProvidePlugin({
MMTF: path.resolve(__dirname, "./src/vendor/mmtf.js"),
$: "jquery"
MMTF: path.resolve(__dirname, "./src/vendor/mmtf.js"),
$: "jquery"
}),
new webpack.BannerPlugin({ banner }),
new ESLintPlugin()],
new webpack.BannerPlugin({ banner }),
new ESLintPlugin()
],
stats: {
errorDetails: true,
}
};

9

webpack.dev.js
/* eslint-disable no-undef*/
const { merge } = require('webpack-merge');

@@ -7,7 +6,7 @@ const common = require('./webpack.common.js');

module.exports = merge(common, {
mode: 'development',
devtool: 'inline-source-map',
mode: 'development',
devtool: 'inline-source-map',
output: {
filename: `[name].js`,
}
filename: '[name].js',
},
});

12

webpack.prod.js
/* eslint-disable no-undef*/
const { merge } = require('webpack-merge');

@@ -8,5 +7,5 @@ const common = require('./webpack.common.js');

module.exports = merge(common, {
mode: 'production',
mode: "production",
optimization: {
usedExports: false, //essential for pulling in $3Dmol namespace
usedExports: false,
minimizer: [

@@ -18,6 +17,5 @@ new TerserPlugin({

compress: true,
mangle:
{
mangle: {
reserved: ["MarchingCube"],
}
},
},

@@ -29,3 +27,3 @@ }),

filename: `[name]-min.js`,
}
},
});
doc/$3Dmol.Label.html
doc/$3Dmol.UI.html
doc/ArrowSpec.html
doc/AtomSelectionSpec.html
doc/AtomSpec.html
doc/AtomStyleSpec.html
doc/autoload.ts.html
doc/BondStyle.html
doc/BoxSpec.html
doc/CartoonStyleSpec.html
doc/ClickSphereStyleSpec.html
doc/Color.html
doc/colors.ts.html
doc/CrossStyleSpec.html
doc/CurveSpec.html
doc/CustomLinear.html
doc/CustomShapeSpec.html
doc/Cylinder.html
doc/CylinderSpec.html
doc/glcartoon.ts.html
doc/GLDraw.html
doc/GLDraw.ts.html
doc/GLModel.html
doc/GLModel.ts.html
doc/global.html
doc/global.html#XYZ
doc/GLShape_GLShape.html
doc/GLShape.html
doc/GLShape.ts.html
doc/GLViewer.html
doc/GLViewer.ts.html
doc/GLVolumetricRender.html
doc/Gradient.ts.html
doc/IsoSurfaceSpec.html
doc/Label.ts.html
doc/LabelSpec.html
doc/LineSpec.html
doc/LineStyleSpec.html
doc/Matrix3.html
doc/Matrix4.html
doc/ParserOptionsSpec.html
doc/parsers_CDJSON.ts.html
doc/parsers_CIF.ts.html
doc/parsers_CUBE.ts.html
doc/parsers_GRO.ts.html
doc/parsers_LAMMPSTRJ.ts.html
doc/parsers_MMTF.ts.html
doc/parsers_MOL2.ts.html
doc/parsers_ParserOptionsSpec.ts.html
doc/parsers_PDB.ts.html
doc/parsers_PQR.ts.html
doc/parsers_PRMTOP.ts.html
doc/parsers_SDF.ts.html
doc/parsers_utils_bondLength.ts.html
doc/parsers_VASP.ts.html
doc/parsers_XYZ.ts.html
doc/ProteinSurface4.ts.html
doc/Quaternion.html
doc/Ray.html
doc/ROYGB.html
doc/RWB.html
doc/scripts/app.min.js
doc/scripts/linenumber.js
doc/scripts/search.js
doc/ShapeSpec.html
doc/Sinebow.html
doc/specs.ts.html
doc/Sphere.html
doc/SphereSpec.html
doc/SphereStyleSpec.html
doc/StickStyleSpec.html
doc/styles/app.min.css
doc/styles/iframe.css
doc/styles/prettify-jsdoc.css
doc/styles/prettify-tomorrow.css
doc/styles/reset.css
doc/SurfaceStyleSpec.html
doc/Triangle.html
doc/tutorial-code.html
doc/tutorial-embeddable.html
doc/tutorial-learning_environment.html
doc/tutorial-url.html
doc/ui_form.js.html
doc/ui_icon.js.html
doc/ui_state.js.html
doc/ui_ui.js.html
doc/UnitCellStyleSpec.html
doc/utilities.ts.html
doc/Vector2.html
doc/Vector3.html
doc/ViewerGridSpec.html
doc/ViewerSpec.html
doc/VolumeData.html
doc/VolumeData.ts.html
doc/VolumetricRender.ts.html
doc/VolumetricRendererSpec.html
doc/WebGL_math_math.ts.html
doc/WebGL_math_Quaternion.ts.html
doc/WebGL_math_utils_conversionMatrix3.ts.html
doc/WebGL_math_Vector2.ts.html
doc/WebGL_shapes_Cylinder.ts.html
doc/WebGL_shapes_Sphere.ts.html
doc/WebGL_shapes_Triangle.ts.html
doc/WithinSelectionSpec.html
.github/workflows/CI.yml

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.github/workflows/CodeQL-Analysis.yml

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.github/workflows/npm-publish.yml

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build/3Dmol-min.js

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build/3Dmol.js

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build/3Dmol.ui.js

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src/GLModel.ts

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src/GLViewer.ts

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src/ProteinSurface4.ts

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