From 7a4fa760ebc9478dbbb8b21cf1330267f2c845f0 Mon Sep 17 00:00:00 2001 From: dkoes Date: Sat, 22 Jan 2022 11:37:23 -0500 Subject: [PATCH] Changes to build system. Disable amd when importing external sources so they populate the namespace as expected. Otherwise we lose access to them in request based projects (like jupyter). I'm pulling in UPNG now to support creation of animated pngs in py3Dmol. --- 3Dmol/3dmol.js | 8 + gulpfile.js | 5 +- js/disable_amd.js | 8 + package-lock.json | 5721 +++++++++++++++++++++++++++++++++-- package.json | 2 +- py3Dmol/.gitignore | 2 + py3Dmol/examples.ipynb | 377 +-- py3Dmol/py3Dmol/__init__.py | 4 +- py3Dmol/saveanim.ipynb | 141 + 9 files changed, 5831 insertions(+), 437 deletions(-) create mode 100644 js/disable_amd.js create mode 100644 py3Dmol/.gitignore create mode 100644 py3Dmol/saveanim.ipynb diff --git a/3Dmol/3dmol.js b/3Dmol/3dmol.js index 2614c3be0..9d6077f43 100644 --- a/3Dmol/3dmol.js +++ b/3Dmol/3dmol.js @@ -657,6 +657,14 @@ $3Dmol.getPropertyRange = function (atomlist, prop) { //hackish way to work with requirejs - doesn't actually work yet //since we don't use the require optimizer to combine modules +if(typeof(_3dmol_saved_define) !== 'undefined') { + /** When pulling in external sources, disable amd to ensure they + * populate the global namespace as expected. Restore it so code + * using amd still works. */ + /*global _3dmol_saved_define, _3dmol_saved_require, define:true, require:true */ + define = _3dmol_saved_define; + require = _3dmol_saved_require; +} if( typeof(define) === 'function' && define.amd) { define('$3Dmol',[], function() { return $3Dmol; }); } diff --git a/gulpfile.js b/gulpfile.js index a55a4d710..a1215d691 100644 --- a/gulpfile.js +++ b/gulpfile.js @@ -9,7 +9,7 @@ del = require('del'); jsdoc = require('gulp-jsdoc3'); coresrc = ['3Dmol/3dmol.js','3Dmol/WebGL/math.js','3Dmol/WebGL/shapes.js','3Dmol/WebGL/core.js','3Dmol/WebGL/**.js','3Dmol/**.js','!3Dmol/SurfaceWorker.js','3Dmol/SurfaceWorker.js']; -extsrc = ['js/mmtf.js','node_modules/pako/dist/pako.js','node_modules/netcdfjs/dist/netcdfjs.js','node_modules/upng-js/UPNG.js']; +extsrc = ['js/disable_amd.js','js/mmtf.js','node_modules/pako/dist/pako.js','node_modules/netcdfjs/dist/netcdfjs.js','node_modules/upng-js/UPNG.js']; uisrc = ['3Dmol/ui/ui.js', '3Dmol/ui/state.js', '3Dmol/ui/icon.js', '3Dmol/ui/form.js', '3Dmol/ui/defaultValues.js']; jqsrc = ['node_modules/jquery/dist/jquery.js']; @@ -49,7 +49,8 @@ function check() { 'MMTF': false, 'TextDecoder': false, 'FileReader': false, - 'define':false}})) + 'define':false, + 'require':false}})) .pipe(jshint.reporter('default')) .pipe(jshint.reporter('fail')); } diff --git a/js/disable_amd.js b/js/disable_amd.js new file mode 100644 index 000000000..41bbffac6 --- /dev/null +++ b/js/disable_amd.js @@ -0,0 +1,8 @@ + +if(typeof define !== 'undefined') { + // UPNG checks the existence of require, not define, so need to do both + var _3dmol_saved_define = define; + var _3dmol_saved_require = require; + define = null; + require = null; +} diff --git a/package-lock.json b/package-lock.json index 977325318..e3ef06820 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,8 +1,5436 @@ { "name": "3dmol", "version": "1.7.1", - "lockfileVersion": 1, + "lockfileVersion": 2, "requires": true, + "packages": { + "": { 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"picocolors": "^0.2.1", + "source-map": "^0.6.1" }, "dependencies": { "source-map": { @@ -3786,12 +9037,6 @@ "requires": { "is-extendable": "^0.1.0" } - }, - "is-extendable": { - "version": "0.1.1", - "resolved": "https://registry.npmjs.org/is-extendable/-/is-extendable-0.1.1.tgz", - "integrity": "sha1-YrEQ4omkcUGOPsNqYX1HLjAd/Ik=", - "dev": true } } }, @@ -4049,6 +9294,15 @@ "integrity": "sha1-1cdSgl5TZ+eG944Y5EXqIjoVWVI=", "dev": true }, + "string_decoder": { + "version": "1.0.3", + "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.0.3.tgz", + "integrity": "sha1-D8Z9fBQYJd6UKC3VNr7GubzoYKs=", + "dev": true, + "requires": { + "safe-buffer": "~5.1.0" + } + }, "string-width": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/string-width/-/string-width-1.0.2.tgz", @@ -4060,15 +9314,6 @@ "strip-ansi": "^3.0.0" } }, - "string_decoder": { - "version": "1.0.3", - "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.0.3.tgz", - "integrity": "sha1-D8Z9fBQYJd6UKC3VNr7GubzoYKs=", - "dev": true, - "requires": { - "safe-buffer": "~5.1.0" - } - }, "strip-ansi": { "version": "3.0.1", "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz", @@ -4093,15 +9338,6 @@ "integrity": "sha512-6fPc+R4ihwqP6N/aIv2f1gMH8lOVtWQHoqC4yK6oSDVVocumAsfCqjkXnqiYMhmMwS/mEHLp7Vehlt3ql6lEig==", "dev": true }, - "supports-color": { - "version": "6.1.0", - "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-6.1.0.tgz", - "integrity": "sha512-qe1jfm1Mg7Nq/NSh6XE24gPXROEVsWHxC1LIx//XNlD9iw7YZQGjZNjYN7xGaEG6iKdA8EtNFW6R0gjnVXp+wQ==", - "dev": true, - "requires": { - "has-flag": "^3.0.0" - } - }, "sver-compat": { "version": "1.5.0", "resolved": "https://registry.npmjs.org/sver-compat/-/sver-compat-1.5.0.tgz", @@ -4422,15 +9658,6 @@ "integrity": "sha1-RQ1Nyfpw3nMnYvvS1KKJgUGaDM8=", "dev": true }, - "v8flags": { - "version": "3.1.3", - "resolved": "https://registry.npmjs.org/v8flags/-/v8flags-3.1.3.tgz", - "integrity": "sha1-/J3CNSHKIMVDP4HMTrmzAzuxBdg=", - "dev": true, - "requires": { - "homedir-polyfill": "^1.0.1" - } - }, "validate-npm-package-license": { "version": "3.0.4", "resolved": "https://registry.npmjs.org/validate-npm-package-license/-/validate-npm-package-license-3.0.4.tgz", @@ -4464,7 +9691,7 @@ "vinyl-fs": { "version": "3.0.3", "resolved": "https://registry.npmjs.org/vinyl-fs/-/vinyl-fs-3.0.3.tgz", - "integrity": "sha1-yFhJQF9nQo/qu71cXb3WT0fTG8c=", + "integrity": "sha512-vIu34EkyNyJxmP0jscNzWBSygh7VWhqun6RmqVfXePrOwi9lhvRs//dOaGOTRUQr4tx7/zd26Tk5WeSVZitgng==", "dev": true, "requires": { "fs-mkdirp-stream": "^1.0.0", diff --git a/package.json b/package.json index 709e1cb31..73d4ddfb8 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "3dmol", - "version": "1.7.1", + "version": "1.8.0", "description": "Object oriented Javascript molecular visualization library", "repository": { "type": "git", diff --git a/py3Dmol/.gitignore b/py3Dmol/.gitignore new file mode 100644 index 000000000..aee7d0cba --- /dev/null +++ b/py3Dmol/.gitignore @@ -0,0 +1,2 @@ +py3Dmol.egg-info +.pypirc diff --git a/py3Dmol/examples.ipynb b/py3Dmol/examples.ipynb index 4881931ca..96c6cc399 100644 --- a/py3Dmol/examples.ipynb +++ b/py3Dmol/examples.ipynb @@ -32,7 +32,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 17, "metadata": {}, "outputs": [], "source": [ @@ -41,16 +41,16 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 18, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "'0.9.2'" + "'1.8.0'" ] }, - "execution_count": 13, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } @@ -61,17 +61,17 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 19, "metadata": { "scrolled": false }, "outputs": [ { "data": { - "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" @@ -116,10 +116,10 @@ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 3, + "execution_count": 19, "metadata": {}, "output_type": "execute_result" } @@ -132,7 +132,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 20, "metadata": {}, "outputs": [], "source": [ @@ -147,15 +147,15 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 21, "metadata": {}, "outputs": [ { "data": { - "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" ] @@ -219,15 +219,15 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 22, "metadata": {}, "outputs": [ { "data": { - "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" ] @@ -301,15 +301,15 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 23, "metadata": {}, "outputs": [ { "data": { - "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" @@ -466,15 +466,15 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 25, "metadata": {}, "outputs": [ { "data": { - "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" @@ -532,15 +532,15 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 26, "metadata": {}, "outputs": [ { "data": { - "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" @@ -586,10 +586,10 @@ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 10, + "execution_count": 26, "metadata": {}, "output_type": "execute_result" } @@ -609,17 +609,17 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 27, "metadata": {}, "outputs": [ { "data": { - "application/3dmoljs_load.v0": "\n ", + "application/3dmoljs_load.v0": "\n ", "text/html": [ - "\n", + "\n", " " ] }, @@ -634,15 +634,15 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 28, "metadata": {}, "outputs": [ { "data": { - "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" ] @@ -687,10 +687,10 @@ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 14, + "execution_count": 28, "metadata": {}, "output_type": "execute_result" } @@ -713,15 +713,15 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 29, "metadata": {}, "outputs": [ { "data": { - "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" @@ -840,10 +840,10 @@ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 16, + "execution_count": 30, "metadata": {}, "output_type": "execute_result" } @@ -856,15 +856,15 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 31, "metadata": {}, "outputs": [ { "data": { - "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", "text/html": [ - "
\n", - "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + "

\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", " jupyter labextension install jupyterlab_3dmol

\n", "
\n", "" @@ -910,10 +910,10 @@ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 17, + "execution_count": 31, "metadata": {}, "output_type": "execute_result" } @@ -932,6 +932,13 @@ " }''')" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, { "cell_type": "code", "execution_count": null, @@ -956,7 +963,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.2" + "version": "3.8.10" }, "widgets": { "state": {}, diff --git a/py3Dmol/py3Dmol/__init__.py b/py3Dmol/py3Dmol/__init__.py index 3043ce5d0..f384a0c92 100644 --- a/py3Dmol/py3Dmol/__init__.py +++ b/py3Dmol/py3Dmol/__init__.py @@ -213,8 +213,8 @@ def apng(self, nframes=1): raise AssertionError('Must instantiate viewer before generating animated image.') script = ''' '''.format(self.uniqueid,nframes) return IPython.display.publish_display_data({'application/3dmoljs_load.v0':script, 'text/html': script},metadata={}) diff --git a/py3Dmol/saveanim.ipynb b/py3Dmol/saveanim.ipynb new file mode 100644 index 000000000..4c113e9dc --- /dev/null +++ b/py3Dmol/saveanim.ipynb @@ -0,0 +1,141 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "ca494fca", + "metadata": {}, + "outputs": [], + "source": [ + "import py3Dmol" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "fc0d8521", + "metadata": {}, + "outputs": [ + { + "data": { + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "text/html": [ + "
\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + " jupyter labextension install jupyterlab_3dmol

\n", + "
\n", + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "v = py3Dmol.view(query='1ycr',js='http://localhost/3Dmol/build/3Dmol.js')\n", + "v.setStyle('cartoon')\n", + "v.zoomTo()\n", + "v.spin()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "3b0c9674", + "metadata": {}, + "outputs": [ + { + "data": { + "application/3dmoljs_load.v0": "\n ", + "text/html": [ + "\n", + " " + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "v.apng(100)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "97fb8690", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}