@chemistry/molecule 2.7.0 → 3.0.1

package/README.md

@@ -1,12 +1,71 @@
-# @chemistry/molecule
-
-[![npm version](https://badge.fury.io/js/%40chemistry%2Fmolecule.svg)](https://badge.fury.io/js/%40chemistry%2molecule)
-[![Build Status](https://travis-ci.com/chemistry/chem-js-lib.svg?branch=master)](https://travis-ci.org/chemistry/chem-js-lib)
-[![codecov](https://codecov.io/gh/chemistry/chem-js-lib/branch/master/graph/badge.svg)](https://codecov.io/gh/chemistry/chem-js-lib)
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-
-## Molecule
-Simple library that allows working with molecule (add atom, bonds, etc.) & preforming substructure search;
-
-## Commands:
-  * Build project: `npm run build`
+# @chemistry/molecule
+
+[![npm version](https://badge.fury.io/js/%40chemistry%2Fmolecule.svg)](https://badge.fury.io/js/%40chemistry%2Fmolecule)
+[![License: MIT](https://img.shields.io/badge/License-MIT-gren.svg)](https://opensource.org/licenses/MIT)
+
+Library for working with molecular structures — add atoms, bonds, and export to SVG.
+
+## Install
+
+```bash
+npm install @chemistry/molecule
+```
+
+## Usage
+
+```typescript
+import { Molecule } from '@chemistry/molecule';
+
+// Load molecule from JNMol format
+const mol = new Molecule();
+mol.load({
+  id: 'acetone',
+  title: 'Acetone',
+  atoms: {
+    a1: { x: 0, y: 0, z: 0, type: 'C' },
+    a2: { x: 1.2, y: 0, z: 0, type: 'C' },
+    a3: { x: 2.4, y: 0, z: 0, type: 'O' },
+  },
+  bonds: {
+    b1: { atom1: 'a1', atom2: 'a2', order: 1 },
+    b2: { atom1: 'a2', atom2: 'a3', order: 2 },
+  },
+});
+
+// Query molecule properties
+console.log(mol.getAtomCount()); // 3
+console.log(mol.getBondCount()); // 2
+
+// Export to SVG string
+const svg = mol.toSVG();
+```
+
+## API
+
+### `new Molecule()`
+
+Creates an empty molecule instance.
+
+### `mol.load(data: unknown)`
+
+Loads molecular data in JNMol format (atoms with x/y/z coordinates and type, bonds with atom references and order).
+
+### `mol.getAtomCount(): number`
+
+Returns the number of atoms in the molecule.
+
+### `mol.getBondCount(): number`
+
+Returns the number of bonds in the molecule.
+
+### `mol.toSVG(options?: SvgExportOptions): string`
+
+Renders the molecule as an SVG string. Accepts optional display options for bond length, colors, labels, etc.
+
+## Peer Dependencies
+
+- `react` (optional) — required only for SVG export functionality
+
+## License
+
+MIT

package/dist/index.d.ts

@@ -1,2 +1,3 @@
-export * from "./molecule";
-export * from "./models";
+export * from './molecule';
+export * from './models';
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,UAAU,CAAC"}

package/dist/index.js

@@ -0,0 +1,3 @@
+export * from './molecule';
+export * from './models';
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,UAAU,CAAC"}

package/dist/models.d.ts

@@ -1,21 +1,22 @@
-export declare enum MoleculeDataFormat {
-    jmol = "jmol",
-    jnmol = "jnmol"
-}
-export declare enum displayLabelsType {
-    dispalyAllLabels = "dispalyAllLabels",
-    hideAllCarbonLabels = "hideAllCarbonLabels",
-    hideNonTerminalCarbonLabels = "hideNonTerminalCarbonLabels"
-}
-export interface SvgExportOptions {
-    colorElements?: boolean;
-    bondLength?: number;
-    bondWidth?: number;
-    bondSpacing?: number;
-    bondShorerning?: number;
-    fontFamily?: string;
-    fontSize?: number;
-    displayHydrogens?: boolean;
-    displayLabels?: displayLabelsType;
-}
-export declare const defaultSvgOptions: SvgExportOptions;
+export declare enum MoleculeDataFormat {
+    jmol = "jmol",
+    jnmol = "jnmol"
+}
+export declare enum displayLabelsType {
+    displayAllLabels = "displayAllLabels",
+    hideAllCarbonLabels = "hideAllCarbonLabels",
+    hideNonTerminalCarbonLabels = "hideNonTerminalCarbonLabels"
+}
+export interface SvgExportOptions {
+    colorElements?: boolean;
+    bondLength?: number;
+    bondWidth?: number;
+    bondSpacing?: number;
+    bondShortening?: number;
+    fontFamily?: string;
+    fontSize?: number;
+    displayHydrogens?: boolean;
+    displayLabels?: displayLabelsType;
+}
+export declare const defaultSvgOptions: SvgExportOptions;
+//# sourceMappingURL=models.d.ts.map

package/dist/models.d.ts.map

@@ -0,0 +1 @@
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package/dist/models.js

@@ -0,0 +1,23 @@
+export var MoleculeDataFormat;
+(function (MoleculeDataFormat) {
+    MoleculeDataFormat["jmol"] = "jmol";
+    MoleculeDataFormat["jnmol"] = "jnmol";
+})(MoleculeDataFormat || (MoleculeDataFormat = {}));
+export var displayLabelsType;
+(function (displayLabelsType) {
+    displayLabelsType["displayAllLabels"] = "displayAllLabels";
+    displayLabelsType["hideAllCarbonLabels"] = "hideAllCarbonLabels";
+    displayLabelsType["hideNonTerminalCarbonLabels"] = "hideNonTerminalCarbonLabels";
+})(displayLabelsType || (displayLabelsType = {}));
+export const defaultSvgOptions = {
+    colorElements: true,
+    bondLength: 40,
+    bondWidth: 1,
+    bondSpacing: 0.08,
+    bondShortening: 0,
+    fontFamily: 'Helvetica, Arial, sans-serif',
+    fontSize: 14,
+    displayHydrogens: false,
+    displayLabels: displayLabelsType.hideNonTerminalCarbonLabels,
+};
+//# sourceMappingURL=models.js.map

package/dist/models.js.map

@@ -0,0 +1 @@
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package/dist/molecule.d.ts

@@ -1,11 +1,14 @@
-import { MoleculeDataFormat } from "./models";
-import { SvgExportOptions } from "./models";
-export declare class Molecule {
-    private store;
-    private readonly state;
-    getAtomCount(): number;
-    getBondCount(): number;
-    load(data: any, format?: MoleculeDataFormat): void;
-    export(format?: MoleculeDataFormat): any;
-    toSVG(options: SvgExportOptions): JSX.Element;
-}
+import type React from 'react';
+import { MoleculeDataFormat } from './models';
+import type { SvgExportOptions } from './models';
+import { type IMoleculeState } from './store';
+export declare class Molecule {
+    private store;
+    private get state();
+    getAtomCount(): number;
+    getBondCount(): number;
+    load(data: unknown, format?: MoleculeDataFormat): void;
+    export(format?: MoleculeDataFormat): IMoleculeState;
+    toSVG(options: SvgExportOptions): React.JSX.Element;
+}
+//# sourceMappingURL=molecule.d.ts.map

package/dist/molecule.d.ts.map

@@ -0,0 +1 @@
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package/dist/molecule.js

@@ -1,15 +1,27 @@
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-/*
-object-assign
-(c) Sindre Sorhus
-@license MIT
-*/var r=Object.getOwnPropertySymbols,t=Object.prototype.hasOwnProperty,s=Object.prototype.propertyIsEnumerable;o.exports=function(){try{if(!Object.assign)return!1;var o=new String("abc");if(o[5]="de","5"===Object.getOwnPropertyNames(o)[0])return!1;for(var e={},n=0;n<10;n++)e["_"+String.fromCharCode(n)]=n;if("0123456789"!==Object.getOwnPropertyNames(e).map(function(o){return e[o]}).join(""))return!1;var r={};return"abcdefghijklmnopqrst".split("").forEach(function(o){r[o]=o}),"abcdefghijklmnopqrst"===Object.keys(Object.assign({},r)).join("")}catch(o){return!1}}()?Object.assign:function(o,e){for(var n,a,l=function(o){if(null==o)throw new TypeError("Object.assign cannot be called with null or undefined");return Object(o)}(o),i=1;i<arguments.length;i++){for(var c in n=Object(arguments[i]))t.call(n,c)&&(l[c]=n[c]);if(r){a=r(n);for(var u=0;u<a.length;u++)s.call(n,a[u])&&(l[a[u]]=n[a[u]])}}return l}}])});
+import { legacy_createStore as createStore } from 'redux';
+import { MoleculeDataFormat } from './models';
+import { exportMolecule, exportToSVG, loadMolecule, reducer } from './store';
+export class Molecule {
+    constructor() {
+        this.store = createStore(reducer);
+    }
+    get state() {
+        return this.store.getState();
+    }
+    getAtomCount() {
+        return Object.keys(this.state.atoms).length;
+    }
+    getBondCount() {
+        return Object.keys(this.state.bonds).length;
+    }
+    load(data, format = MoleculeDataFormat.jnmol) {
+        this.store.dispatch(loadMolecule(data, format));
+    }
+    export(format = MoleculeDataFormat.jnmol) {
+        return exportMolecule(this.state, format);
+    }
+    toSVG(options) {
+        return exportToSVG(this.state, options);
+    }
+}
 //# sourceMappingURL=molecule.js.map