mirror of
https://github.com/3dmol/3Dmol.js.git
synced 2026-06-04 08:39:49 +09:00
py3dmol improvements
Don't use the CDN minified URL (it is broken for surfaces). Inspired by Issue #645 add print_to_console function prefix.
This commit is contained in:
David Koes
File diff suppressed because one or more lines are too long
@@ -33,23 +33,52 @@
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": 1,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"/home/dkoes/git/3Dmol.js/py3Dmol/build/lib\n"
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]
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}
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],
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"source": [
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"cd build/lib"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/3dmoljs_load.v0": "<div id=\"3dmolviewer_15219945140\" style=\"position: relative; width: 640px; height: 480px\">\n<script>\n\nvar loadScriptAsync = function(uri){\n return new Promise((resolve, reject) => {\n var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\n resolve();\n };\n var firstScriptTag = document.getElementsByTagName('script')[0];\n firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15219945140 = null;\n$3Dmolpromise.then(function() {\nviewer_15219945140 = $3Dmol.createViewer($(\"#3dmolviewer_15219945140\"),{backgroundColor:\"white\"});\n\tviewer_15219945140.addModel(\"\\n RDKit 3D\\n\\n 6 6 0 0 0 0 0 0 0 0999 V2000\\n -0.9517 0.7811 -0.6622 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2847 1.3329 -0.3121 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2365 0.5518 0.3512 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.9517 -0.7811 0.6644 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2847 -1.3329 0.3144 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2365 -0.5518 -0.3489 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 2 0\\n 2 3 1 0\\n 3 4 2 0\\n 4 5 1 0\\n 5 6 2 0\\n 6 1 1 0\\nM END\\n$$$$\",\"sdf\");\n\tviewer_15219945140.setStyle({\"stick\": {}});\n\tviewer_15219945140.zoomTo();\nviewer_15219945140.render();\n});\n</script><script>$(\"#left\").append($(\"#3dmolviewer_15219945140\")); </script>",
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"application/3dmoljs_load.v0": "<div id=\"3dmolviewer_1676050474639691\" style=\"position: relative; width: 640px; height: 480px\">\n <p id=\"3dmolwarning_1676050474639691\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: <br>\n <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n return new Promise((resolve, reject) => {\n //this is to ignore the existence of requirejs amd\n var savedexports, savedmodule;\n if (typeof exports !== 'undefined') savedexports = exports;\n else exports = {}\n if (typeof module !== 'undefined') savedmodule = module;\n else module = {}\n\n var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\n exports = savedexports;\n module = savedmodule;\n resolve();\n };\n var firstScriptTag = document.getElementsByTagName('script')[0];\n firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol-min.min.js');\n}\n\nvar viewer_1676050474639691 = null;\nvar warn = document.getElementById(\"3dmolwarning_1676050474639691\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_1676050474639691 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_1676050474639691\"),{backgroundColor:\"white\"});\nviewer_1676050474639691.zoomTo();\n\tviewer_1676050474639691.addModel([\"\\n RDKit 3D\\n\\n 6 6 0 0 0 0 0 0 0 0999 V2000\\n -0.9517 0.7811 -0.6622 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2847 1.3329 -0.3121 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2365 0.5518 0.3512 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.9517 -0.7811 0.6644 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2847 -1.3329 0.3144 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2365 -0.5518 -0.3489 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 2 0\\n 2 3 1 0\\n 3 4 2 0\\n 4 5 1 0\\n 5 6 2 0\\n 6 1 1 0\\nM END\\n$$$$\", \"sdf\"],{});\n\tviewer_1676050474639691.setStyle([{\"stick\": {}}],{});\n\tviewer_1676050474639691.zoomTo([],{});\nviewer_1676050474639691.render();\n});\n</script><script>document.getElementById(\"left\").append(document.getElementById(\"3dmolviewer_1676050474639691\")); </script>",
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"text/html": [
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"<div id=\"3dmolviewer_15219945140\" style=\"position: relative; width: 640px; height: 480px\">\n",
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"<div id=\"3dmolviewer_1676050474639691\" style=\"position: relative; width: 640px; height: 480px\">\n",
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" <p id=\"3dmolwarning_1676050474639691\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: <br>\n",
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" <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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" </div>\n",
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"<script>\n",
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"\n",
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"var loadScriptAsync = function(uri){\n",
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" return new Promise((resolve, reject) => {\n",
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" //this is to ignore the existence of requirejs amd\n",
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" var savedexports, savedmodule;\n",
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" if (typeof exports !== 'undefined') savedexports = exports;\n",
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" else exports = {}\n",
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" if (typeof module !== 'undefined') savedmodule = module;\n",
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" else module = {}\n",
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"\n",
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" var tag = document.createElement('script');\n",
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" tag.src = uri;\n",
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" tag.async = true;\n",
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" tag.onload = () => {\n",
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" resolve();\n",
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" exports = savedexports;\n",
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" module = savedmodule;\n",
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" resolve();\n",
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" };\n",
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" var firstScriptTag = document.getElementsByTagName('script')[0];\n",
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" firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
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@@ -58,18 +87,23 @@
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"\n",
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"if(typeof $3Dmolpromise === 'undefined') {\n",
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"$3Dmolpromise = null;\n",
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" $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n",
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" $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol-min.min.js');\n",
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"}\n",
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"\n",
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"var viewer_15219945140 = null;\n",
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"var viewer_1676050474639691 = null;\n",
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"var warn = document.getElementById(\"3dmolwarning_1676050474639691\");\n",
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"if(warn) {\n",
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" warn.parentNode.removeChild(warn);\n",
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"}\n",
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"$3Dmolpromise.then(function() {\n",
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"viewer_15219945140 = $3Dmol.createViewer($(\"#3dmolviewer_15219945140\"),{backgroundColor:\"white\"});\n",
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"\tviewer_15219945140.addModel(\"\\n RDKit 3D\\n\\n 6 6 0 0 0 0 0 0 0 0999 V2000\\n -0.9517 0.7811 -0.6622 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2847 1.3329 -0.3121 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2365 0.5518 0.3512 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.9517 -0.7811 0.6644 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2847 -1.3329 0.3144 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2365 -0.5518 -0.3489 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 2 0\\n 2 3 1 0\\n 3 4 2 0\\n 4 5 1 0\\n 5 6 2 0\\n 6 1 1 0\\nM END\\n$$$$\",\"sdf\");\n",
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"\tviewer_15219945140.setStyle({\"stick\": {}});\n",
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"\tviewer_15219945140.zoomTo();\n",
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"viewer_15219945140.render();\n",
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"viewer_1676050474639691 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_1676050474639691\"),{backgroundColor:\"white\"});\n",
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"viewer_1676050474639691.zoomTo();\n",
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"\tviewer_1676050474639691.addModel([\"\\n RDKit 3D\\n\\n 6 6 0 0 0 0 0 0 0 0999 V2000\\n -0.9517 0.7811 -0.6622 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2847 1.3329 -0.3121 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2365 0.5518 0.3512 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.9517 -0.7811 0.6644 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2847 -1.3329 0.3144 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2365 -0.5518 -0.3489 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 2 0\\n 2 3 1 0\\n 3 4 2 0\\n 4 5 1 0\\n 5 6 2 0\\n 6 1 1 0\\nM END\\n$$$$\", \"sdf\"],{});\n",
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"\tviewer_1676050474639691.setStyle([{\"stick\": {}}],{});\n",
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"\tviewer_1676050474639691.zoomTo([],{});\n",
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"viewer_1676050474639691.render();\n",
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"});\n",
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"</script><script>$(\"#left\").append($(\"#3dmolviewer_15219945140\")); </script>"
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"</script><script>document.getElementById(\"left\").append(document.getElementById(\"3dmolviewer_1676050474639691\")); </script>"
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]
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},
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"metadata": {},
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@@ -106,10 +140,32 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": []
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"source": [
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"import py3Dmol\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"u'/home/dkoes/git/3Dmol.js/py3Dmol'"
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]
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},
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"execution_count": 2,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"pwd"
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]
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},
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{
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"cell_type": "code",
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@@ -121,21 +177,21 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 2",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python2"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.14"
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"pygments_lexer": "ipython3",
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"version": "3.10.6"
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}
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},
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"nbformat": 4,
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File diff suppressed because one or more lines are too long
@@ -53,7 +53,7 @@ class view(object):
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the exception that the functions all return None.
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http://3dmol.org/doc/GLViewer.html
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'''
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def __init__(self,query='',width=640,height=480,viewergrid=None,data=None,style=None,linked=True,options=dict(),js='https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol-min.min.js'):
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def __init__(self,query='',width=640,height=480,viewergrid=None,data=None,style=None,linked=True,options=dict(),js='https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol-min.js'):
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'''Create a 3Dmol.js view.
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width -- width in pixels of container
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height -- height in pixels of container
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@@ -281,35 +281,47 @@ if(warn) {
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if name.startswith('_') or name == 'getdoc': #object to ipython canary functions
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raise AttributeError("%r object has no attribute %r" % (self.__class__, name))
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print_result = False
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if name.startswith('print_to_console_'):
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print_result = True
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name = name[17:]
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def makejs(*args,**kwargs):
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def make_viewer_cmd(vname, name, *args, **kwargs):
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cmd = '\t'
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if print_result:
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cmd += 'console.log('
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cmd += f'{vname}.{name}('
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for arg in args:
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cmd += '%s,' % tostr(arg)
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cmd = cmd.rstrip(',')
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if print_result:
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cmd += ')'
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cmd += ');\n'
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return cmd
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if self.viewergrid:
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if kwargs and 'viewer' in kwargs:
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coords = kwargs['viewer']
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if len(coords) != 2 or coords[0] >= self.viewergrid[0] or coords[1] >= self.viewergrid[1] or coords[0] < 0 or coords[1] < 0:
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raise ValueError("Incorrectly formated viewer argument. Must specify row and column",self.viewergrid)
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cmd = '\tviewergrid_UNIQUEID[%d][%d].%s(' % (coords[0],coords[1],name);
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for arg in args:
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cmd += '%s,' % tostr(arg)
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cmd = cmd.rstrip(',')
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cmd += ');\n';
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cmd = make_viewer_cmd('viewergrid_UNIQUEID[%d][%d]'%(coords[0],coords[1]),name,*args,**kwargs)
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else: #apply to every viewer
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cmd = ''
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for r in range(self.viewergrid[0]):
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for c in range(self.viewergrid[1]):
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cmd += '\tviewergrid_UNIQUEID[%d][%d].%s(' % (r,c,name);
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for arg in args:
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cmd += '%s,' % tostr(arg)
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cmd = cmd.rstrip(',')
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cmd += ');\n';
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cmd += make_viewer_cmd('viewergrid_UNIQUEID[%d][%d]'%(r,c),name,*args,**kwargs)
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else:
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cmd = '\tviewer_UNIQUEID.%s(' % name;
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for arg in args:
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cmd += '%s,' % tostr(arg)
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cmd = cmd.rstrip(',')
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cmd += ');\n';
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cmd = make_viewer_cmd('viewer_UNIQUEID',name,*args,**kwargs)
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self.startjs += cmd
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self.updatejs += cmd
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return self
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if print_result:
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self.update()
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return "Inspect the JavaScript console for your requested result."
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else:
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return self
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return makejs
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