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Patch/cleanup 20170503 #316

Merged
merged 5 commits into from May 7, 2017
Merged

Patch/cleanup 20170503 #316

merged 5 commits into from May 7, 2017

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johnmay
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@johnmay johnmay commented May 3, 2017

Some misc cleanup. I was trying to debug the builder3d code for another patch and got annoyed with it's slowness. I still think we should deprecate it but anyways:

Currently
testModelBuilder3D_reserpine: ~27s
After Patch
testModelBuilder3D_reserpine: ~3s

Incidentally do you know where the 3D templates came from? I could get that 3 seconds down to under 1 second if I could convert to SMILES but the ringTemplateStructures.sdf.gz has some crazyness it in, lots of random isotopes and 5 valent carbons, aromatic query bonds etc. I can convert most of the structures but I worry at what the contents is, look here at these first entries, lots of Carbons with isotopes 2 or 4? Ehh?

c12c3C45C([4CH2]1)CC=CC5C(Cc3ccc2)[2CH2]CC4 |(2.02,1.67,-2.06;1.71,3,-2.28;1.47,3.66,-0.95;1.23,2.46,-0.05;1.95,1.37,-0.75;-0.24,2.07,0.05;-1.11,2.63,-1.02;-0.9,3.78,-1.61;0.29,4.6,-1.17;0.69,5.59,-2.26;0.99,4.97,-3.61;1.53,3.58,-3.52;1.86,2.79,-4.61;2.27,1.48,-4.43;2.35,0.88,-3.17;1.84,6.38,-1.79;2.98,5.44,-1.72;2.7,4.47,-0.55)|
C12(CCC3(C=C1)[4CH2]CC[4CH2]3)c4c([2CH2]C2)cccc4 |(0.48,-0.43,-1.39;0,-0,0;-0.02,1.54,0.01;1.45,2,-0;2.17,1.35,-1.15;1.76,0.28,-1.74;1.5,3.43,-0.14;2.7,3.79,0.61;2.51,2.87,1.86;2.07,1.64,1.24;0.65,-1.92,-1.46;-0.25,-2.37,-2.43;-0.95,-1.31,-2.97;-0.59,-0.13,-2.42;-0.33,-3.73,-2.73;0.5,-4.59,-2.03;1.38,-4.13,-1.07;1.48,-2.77,-0.76)|
C1=[2CH][2C@@H]2C([2CH]=C1)=[2CH]C=CC2 |(1.24,2.07,0;2.37,1.41,-0.01;2.35,0.01,-0.02;1.16,-0.67,-0.01;0,-0,0;-0.02,1.32,0.01;1.14,-2,-0.02;2.25,-2.73,-0.03;3.49,-2.11,-0.04;3.54,-0.7,-0.04)|
C1[4CH2]C23[C@H](CC1C[4CH2]2)CCCC3 |(2.02,-0,1.19;0.69,-0.48,1.15;0,-0,0;0.72,-0.48,-1.27;2.14,0.1,-1.28;2.33,0.93,0;1.24,2.01,0;-0.02,1.46,0.01;-0.04,0.04,-2.5;-1.46,-0.56,-2.46;-2.16,0.06,-1.23;-1.44,-0.52,0.01)|
C=12C(=[4C+][44C-2]3([4CH+]C1)[4C+]=C4C(=C[4CH+]3)Cc5c4cccc5)c6c(C2)cccc6 |(2.4,1.54,-0.01;2.55,0.09,-0.03;1.63,-0.74,-0.02;0,-0,0;-0.02,1.79,0.01;1.24,2.31,0;-0.79,-0.54,1.51;-1.82,-1.21,1.33;-2.38,-1.57,0.03;-1.94,-1.26,-1.24;-0.82,-0.52,-1.51;-3.6,-2.38,0.33;-3.74,-2.48,1.8;-2.68,-1.79,2.4;-2.58,-1.74,3.78;-3.53,-2.37,4.57;-4.57,-3.06,3.98;-4.68,-3.12,2.6;4.01,-0.22,-0.05;4.73,0.98,-0.04;3.78,2.1,-0.02;6.12,0.94,-0.06;6.78,-0.28,-0.08;6.07,-1.46,-0.09;4.68,-1.44,-0.07)|
c12c3c(ccc1)Cc4cc(Cc5c(c(Cc6cc(C2)ccc6)ccc5)[4CH2]CC[4CH2]CC[4CH2]CC[4CH2]CC[4CH2]3)ccc4 |(-1.9,2.53,-1.24;-1.53,2.01,-2.47;-2.02,2.61,-3.62;-2.98,3.59,-3.57;-3.4,4.07,-2.34;-2.85,3.55,-1.19;-1.42,2.28,-4.98;-0.11,3.03,-5.05;1.09,2.36,-5.23;2.28,3.04,-5.04;3.6,2.3,-4.97;4.2,2.66,-3.63;3.75,2.09,-2.45;4.22,2.58,-1.24;3.7,2.11,0.08;2.39,1.4,0.03;1.18,2.08,0;-0.02,1.38,0.01;-1.33,2.09,0.07;0,-0,0;1.2,-0.69,0.01;2.39,0.01,0.04;5.21,3.55,-1.23;5.71,4.07,-2.41;5.19,3.63,-3.61;2.85,1.09,-2.45;2.8,-0.11,-3.23;4.21,-0.68,-3.45;4.29,-1.99,-2.88;3.54,-2.87,-3.72;2.45,-3.55,-2.89;1.73,-4.47,-3.71;0.61,-3.77,-4.24;-0.5,-3.68,-3.19;-1.31,-2.53,-3.45;-0.84,-1.47,-2.61;-0.8,-0.17,-3.41;-0.7,0.96,-2.53;2.27,4.41,-4.84;1.07,5.09,-4.75;-0.12,4.4,-4.84)|
C1C[C@H]2[4CH2][C@H]1C[4CH2][183C-2]3([4CH2]C2)[2CH2][C@H]4[C@H]([2CH2]3)CCCC4 |(-2.79,3.45,-0.59;-2.39,2.1,-0.65;-1.22,2.05,0.02;-1.26,3.09,0.9;-1.87,4.05,0.18;-1.24,5.39,0.13;0.15,5.24,0.02;0.97,3.74,1.02;1.11,2.05,0;-0.01,1.21,0.01;2.84,4.3,1.84;2.29,4.67,3.2;1.22,3.73,3.75;0.02,3.44,2.89;0.72,4.26,5.1;1.93,4.27,6.07;2.93,5.3,5.51;3.47,4.72,4.19)|
C1C[4CH2][C@@H]2[2C@H](C1)CC2 |(2.71,-0.59,-1.56;3.18,0.88,-1.48;2,1.68,-1.33;1.52,1.48,-0;1.31,0.07,0.32;2.25,-0.96,-0.13;0,-0,0;-0.02,1.51,0.01)|

@egonw
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egonw commented May 7, 2017

Looks good! Would be nice to see this used again in Bioclipse... thanks for finding the time to update this code!

@egonw egonw merged commit 5c43a9f into master May 7, 2017
@johnmay johnmay deleted the patch/cleanup_20170503 branch June 17, 2017 10:13
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2 participants