From b3cd271c03cd2af23f0fb1e128ef09c08d098ab7 Mon Sep 17 00:00:00 2001 From: Joe Greener Date: Sun, 21 Mar 2021 17:21:26 +0000 Subject: [PATCH] line and cylinder example in tutorial --- examples/tutorial.ipynb | 878 ++++++++++++++++++++++++++++++++++++---- 1 file changed, 800 insertions(+), 78 deletions(-) diff --git a/examples/tutorial.ipynb b/examples/tutorial.ipynb index 30f4745..2f7bb40 100644 --- a/examples/tutorial.ipynb +++ b/examples/tutorial.ipynb @@ -21,7 +21,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -40,7 +40,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 2, "metadata": {}, "outputs": [ { @@ -687,7 +687,7 @@ "$3Dmol.workerString=function(){self.onmessage=function(b){b=b.data;var c=b.type;if(0>c)self.atomData=b.atoms,self.volume=b.volume,self.ps=new ProteinSurface;else{var d=self.ps;d.initparm(b.expandedExtent,1==c?!1:!0,self.volume);d.fillvoxels(self.atomData,b.extendedAtoms);d.buildboundary();if(4===c||2===c)d.fastdistancemap(),d.boundingatom(!1),d.fillvoxelswaals(self.atomData,b.extendedAtoms);d.marchingcube(c);b=d.getFacesAndVertices(b.atomsToShow);self.postMessage(b)}}}.toString().replace(/(^.*?\\{|\\}$)/g,\n", "\"\");$3Dmol.workerString+=\"; var ProteinSurface=\"+$3Dmol.ProteinSurface.toString().replace(/[a-zA-Z_$]{1}[0-9a-zA-Z_$]*.MarchingCube./g,\"MarchingCube.\");$3Dmol.workerString+=\",MarchingCube=(\"+$3Dmol.MarchingCubeInitializer.toString()+\")();\";$3Dmol.SurfaceWorker=window.URL?window.URL.createObjectURL(new Blob([$3Dmol.workerString],{type:\"text/javascript\"})):{postMessage:function(){}};$3Dmol.workerString=$3Dmol.workerString;$3Dmol.SurfaceWorker=$3Dmol.SurfaceWorker;\n", "\n", - "\n", - "
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\n", "\n" ], "text/plain": [ - "HTML{String}(\"\\n\\n\\n
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\\n\\n\")" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lines = [\n", + " Line([ 0.0, 1.0, 2.0], [2.0, 7.0, 7.0]),\n", + " Line([-3.0, -2.0, -1.0], [1.0, 4.0, 5.0])\n", + "]\n", + "cylinders = [\n", + " Cylinder([ 0.0, 1.0, 2.0], [6.0, 7.0, 7.0]),\n", + " Cylinder([-3.0, -2.0, -1.0], [3.0, 4.0, 5.0];\n", + " startcap=RoundCap, stopcap=FlatCap),\n", + "]\n", + "viewfile(\"benzene.sdf\", \"sdf\", lines=lines, cylinders=cylinders)" + ] + }, { "cell_type": "markdown", "metadata": {}, @@ -9556,7 +10278,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 12, "metadata": {}, "outputs": [ { @@ -10203,7 +10925,7 @@ "$3Dmol.workerString=function(){self.onmessage=function(b){b=b.data;var c=b.type;if(0>c)self.atomData=b.atoms,self.volume=b.volume,self.ps=new ProteinSurface;else{var d=self.ps;d.initparm(b.expandedExtent,1==c?!1:!0,self.volume);d.fillvoxels(self.atomData,b.extendedAtoms);d.buildboundary();if(4===c||2===c)d.fastdistancemap(),d.boundingatom(!1),d.fillvoxelswaals(self.atomData,b.extendedAtoms);d.marchingcube(c);b=d.getFacesAndVertices(b.atomsToShow);self.postMessage(b)}}}.toString().replace(/(^.*?\\{|\\}$)/g,\n", "\"\");$3Dmol.workerString+=\"; var ProteinSurface=\"+$3Dmol.ProteinSurface.toString().replace(/[a-zA-Z_$]{1}[0-9a-zA-Z_$]*.MarchingCube./g,\"MarchingCube.\");$3Dmol.workerString+=\",MarchingCube=(\"+$3Dmol.MarchingCubeInitializer.toString()+\")();\";$3Dmol.SurfaceWorker=window.URL?window.URL.createObjectURL(new Blob([$3Dmol.workerString],{type:\"text/javascript\"})):{postMessage:function(){}};$3Dmol.workerString=$3Dmol.workerString;$3Dmol.SurfaceWorker=$3Dmol.SurfaceWorker;\n", "\n", - "\n", - "
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\n", "\n" ], "text/plain": [ - "HTML{String}(\"\\n\\n\\n
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\n", "\n" ], "text/plain": [ - "HTML{String}(\"\\n\\n\\n
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