On 10/5/10 10:56 AM, Geoffrey Hutchison wrote: > > On Oct 5, 2010, at 1:47 PM, Craig A. James wrote: > > That's good! Maybe we should let you generate a file of errors > over the next day or two(?), post it, and then make every > effort to fix them?
I had to kill everything this morning because of that runaway 26GB process, but here is a complete list (including stuff I reported yesterday) of what I found so far. The six jobs together processed about 1.1 million molecules. These problems fall into four categories. I don't think I've found anything new since yesterday. 1. Timeout - never canonicalizes 2. Doesn't canonicalize stereo centers 3. Doesn't canonicalize cis/trans bonds 4. Doesn't canonicalize fragments where the only difference is charge. Some of these molecules are pretty interesting looking. Craig ------------------------- Times out: C12(C)[Fe]3456789(C(C)(C3(C)C14C)C25C)C1(C)C6(C)C7(C8(C)C91C)C 716630 Tetrahedral centers not canonicalized http://www.emolecules.com/image?db=549&width=500&height=500&id=716644 [Ti]12345678(C9(C7C4C1C89)C(C)(C)C)(C1(c...@h]3[c@@H]2C61)C(C)(C)C)(Cl)Cl 716644 [Ti]12345678(C9(c...@h]4[c@@H]1C89)C(C)(C)C)(C1(C5C3C2C61)C(C)(C)C)(Cl)Cl 716644 http://www.emolecules.com/image?db=549&width=500&height=500&id=716648 C12([cu]345c1c...@h]4[c@@H]23)CC.P(c1ccccc1)(c1ccccc1)c1ccccc1 716648 C12([cu]34...@h]1[c@@H]5C4C23)CC.P(c1ccccc1)(c1ccccc1)c1ccccc1 716648 http://www.emolecules.com/image?db=549&width=500&height=500&id=475021 [C@@H]([C@@H](CO)O)([...@h](CO)O)O 475021 [...@h]([...@h](CO)O)([C@@H](CO)O)O 475021 http://www.emolecules.com/image?db=549&width=500&height=500&id=483354 C1(C2C[C@@h]3...@h]1c[c@H](C2)C3)O 483354 C1([C@@H]2C[C@@h]3cc1...@h](C2)C3)O 483354 http://www.emolecules.com/image?db=549&width=500&height=500&id=513261 [C@@H]([...@h](CO)O)([C@@H](CO)O)O 513261 [...@h]([C@@H](CO)O)([...@h](CO)O)O 513261 http://www.emolecules.com/image?db=549&width=500&height=500&id=1467237 c1(c2ccc(cc2)OCCOCCOc2ccc(cc2)c2nn(nn2)CC(=O)NCC2OCCC2)nn(nn1)CC(=O)n...@h]1occc1 1467237 c1(c2ccc(cc2)OCCOCCOc2ccc(cc2)c2nn(nn2)CC(=O)n...@h]2occc2)nn(nn1)CC(=O)NCC1OCCC1 1467237 http://www.emolecules.com/image?db=549&width=500&height=500&id=535589 c12=c3c4c(=c1cccc2)ccc1=c2c(=c(c41)cc3)cccc2 535589 c12c3c(c4c1cccc4)ccc1c3c(cc2)c2c1cccc2 535589 http://www.emolecules.com/image?db=549&width=500&height=500&id=550474 c12c3=c(c(c1c(c(c2c1ccccc1)c1ccccc1)c1ccccc1)c1ccccc1)c1c(c3c2ccccc2)c(c(c1c1ccccc1)c1ccccc1)c1ccccc1 550474 c1(c2c(c(c1c1ccccc1)c1ccccc1)c(c1c2c(c2c1c(c(c2c1ccccc1)c1ccccc1)c1ccccc1)c1ccccc1)c1ccccc1)c1ccccc1 550474 Cis/Trans not canonicalized: http://www.emolecules.com/image?db=549&width=500&height=500&id=1127873 C(C1C=CCCC1)(C(=O)N/N=C/c1ccc(cc1)C#N)C(=O)N/N=C\c1ccc(cc1)C#N 1127873 C(C1C=CCCC1)(C(=O)N/N=C\c1ccc(cc1)C#N)C(=O)N/N=C/c1ccc(cc1)C#N 1127873 http://www.emolecules.com/image?db=549&width=500&height=500&id=1127875 C(C1C=CCCC1)(C(=O)N/N=C/c1ccc(cc1)Cl)C(=O)N/N=C\c1ccc(cc1)Cl 1127875 C(C1C=CCCC1)(C(=O)N/N=C\c1ccc(cc1)Cl)C(=O)N/N=C/c1ccc(cc1)Cl 1127875 http://www.emolecules.com/image?db=549&width=500&height=500&id=2761690 C(=N\N)(/N/N=C/c1ccc(cc1)Cl)\N/N=C\c1ccc(cc1)Cl 2761690 C(=N\N)(\N/N=C\c1ccc(cc1)Cl)/N/N=C/c1ccc(cc1)Cl 2761690 Charged fragments not canonicalized: http://www.emolecules.com/image?db=549&width=500&height=500&id=502967 c12c3c(ccc1cccn2)cccn3.[N+](=O)([O-])[O-].[N+](=O)(O)O 502967 c12c3c(ccc1cccn2)cccn3.[N+](=O)(O)O.[N+](=O)([O-])[O-] 502967 http://www.emolecules.com/image?db=549&width=500&height=500&id=475076 [N+](=O)([O-])[O-].[N+](=O)(O)O 475076 [N+](=O)(O)O.[N+](=O)([O-])[O-] 475076 http://www.emolecules.com/image?db=549&width=500&height=500&id=478002 [N+](=O)([O-])[O-].[N+](=O)(O)[O-].[N+](=O)(O)O 478002 [N+](=O)([O-])[O-].[N+](=O)(O)O.[N+](=O)(O)[O-] 478002 [N+](=O)(O)[O-].[N+](=O)([O-])[O-].[N+](=O)(O)O 478002 [N+](=O)(O)[O-].[N+](=O)(O)O.[N+](=O)([O-])[O-] 478002 [N+](=O)(O)O.[N+](=O)([O-])[O-].[N+](=O)(O)[O-] 478002 [N+](=O)(O)O.[N+](=O)(O)[O-].[N+](=O)([O-])[O-] 478002 http://www.emolecules.com/image?db=549&width=500&height=500&id=480284 [N+](=O)([O-])[O-].[N+](=O)([O-])[O-].[N+](=O)(O)O.[N+](=O)(O)O 480284 [N+](=O)([O-])[O-].[N+](=O)(O)O.[N+](=O)([O-])[O-].[N+](=O)(O)O 480284 [N+](=O)([O-])[O-].[N+](=O)(O)O.[N+](=O)(O)O.[N+](=O)([O-])[O-] 480284 [N+](=O)(O)O.[N+](=O)([O-])[O-].[N+](=O)([O-])[O-].[N+](=O)(O)O 480284 [N+](=O)(O)O.[N+](=O)([O-])[O-].[N+](=O)(O)O.[N+](=O)([O-])[O-] 480284 [N+](=O)(O)O.[N+](=O)(O)O.[N+](=O)([O-])[O-].[N+](=O)([O-])[O-] 480284 http://www.emolecules.com/image?db=549&width=500&height=500&id=616088 C(c1[o+]c(C(C)(C)C)cc(c1)c1ccncc1)(C)(C)C.C(c1[o+]c(C(C)(C)C)cc(c1)c1cc[nH+]cc1)(C)(C)C 616088 C(c1[o+]c(C(C)(C)C)cc(c1)c1cc[nH+]cc1)(C)(C)C.C(c1[o+]c(C(C)(C)C)cc(c1)c1ccncc1)(C)(C)C 616088 http://www.emolecules.com/image?db=549&width=500&height=500&id=2751170 C(=O)(c1ncccc1)N(CC)CC.C(=O)(c1ncccc1)N(CC)CC.[N+](=O)([O-])[O-].[N+](=O)(O)O 2751170 C(=O)(c1ncccc1)N(CC)CC.C(=O)(c1ncccc1)N(CC)CC.[N+](=O)(O)O.[N+](=O)([O-])[O-] 2751170 http://www.emolecules.com/image?db=549&width=500&height=500&id=3047897 P(=O)(N(C)C)(N(C)C)N(C)C.[N+](=O)([O-])[O-].[N+](=O)(O)[O-].[N+](=O)(O)O 3047897 P(=O)(N(C)C)(N(C)C)N(C)C.[N+](=O)([O-])[O-].[N+](=O)(O)O.[N+](=O)(O)[O-] 3047897 P(=O)(N(C)C)(N(C)C)N(C)C.[N+](=O)(O)[O-].[N+](=O)([O-])[O-].[N+](=O)(O)O 3047897 P(=O)(N(C)C)(N(C)C)N(C)C.[N+](=O)(O)[O-].[N+](=O)(O)O.[N+](=O)([O-])[O-] 3047897 P(=O)(N(C)C)(N(C)C)N(C)C.[N+](=O)(O)O.[N+](=O)([O-])[O-].[N+](=O)(O)[O-] 3047897 P(=O)(N(C)C)(N(C)C)N(C)C.[N+](=O)(O)O.[N+](=O)(O)[O-].[N+](=O)([O-])[O-] 3047897 http://www.emolecules.com/image?db=549&width=500&height=500&id=3717553 [SiH](=O)([O-])[O-].[SiH](=O)(O)[O-].[AlH3+3] 3717553 [SiH](=O)(O)[O-].[SiH](=O)([O-])[O-].[AlH3+3] 3717553 http://www.emolecules.com/image?db=549&width=500&height=500&id=3725927 c1(c(c([N+](=O)[O-])cc(c1)[N+](=O)[O-])O)[N+](=O)[O-].c1(c(c([N+](=O)[O-])cc(c1)[N+](=O)O)[O-])[N+](=O)[O-] 3725927 c1(c(c([N+](=O)[O-])cc(c1)[N+](=O)O)[O-])[N+](=O)[O-].c1(c(c([N+](=O)[O-])cc(c1)[N+](=O)[O-])O)[N+](=O)[O-] 3725927 ------------------------------------------------------------------------------ Beautiful is writing same markup. 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