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Stricter checks for SDF sniffing #4729
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,55 @@ | ||
CHEBI:57262 | ||
RDKit 3D | ||
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0 0 0 0 0 0 0 0 0 0999 V3000 | ||
M V30 BEGIN CTAB | ||
M V30 COUNTS 22 21 0 0 0 | ||
M V30 BEGIN ATOM | ||
M V30 1 P 18.2567 -5.6825 0 0 | ||
M V30 2 O 18.0395 -6.6275 0 0 CHG=-1 | ||
M V30 3 O 18.255 -4.7415 0 0 | ||
M V30 4 O 18.9453 -6.0633 0 0 | ||
M V30 5 O 17.4245 -5.9341 0 0 | ||
M V30 6 C 15.2886 -5.4953 0 0 | ||
M V30 7 C 15.9989 -5.9147 0 0 | ||
M V30 8 C 16.7174 -5.5091 0 0 | ||
M V30 9 O 14.5702 -5.9009 0 0 | ||
M V30 10 C 13.8556 -5.4886 0 0 | ||
M V30 11 O 13.8553 -4.6636 0 0 | ||
M V30 12 O 15.9909 -6.7396 0 0 | ||
M V30 13 O 21.0888 -4.8258 0 0 | ||
M V30 14 C 21.0888 -5.6508 0 0 | ||
M V30 15 C 20.3743 -6.0633 0 0 | ||
M V30 16 N 20.3743 -6.8883 0 0 CHG=1 | ||
M V30 17 C 19.6598 -5.6508 0 0 | ||
M V30 18 O 21.8033 -6.0633 0 0 CHG=-1 | ||
M V30 19 R 13.1411 -5.9011 0 0 MASS=1 | ||
M V30 20 C 15.2764 -7.1521 0 0 | ||
M V30 21 O 15.2764 -7.9771 0 0 | ||
M V30 22 R 14.562 -6.7396 0 0 MASS=2 | ||
M V30 END ATOM | ||
M V30 BEGIN BOND | ||
M V30 1 1 1 2 | ||
M V30 2 2 1 3 | ||
M V30 3 1 1 4 | ||
M V30 4 1 6 9 | ||
M V30 5 1 7 6 CFG=3 | ||
M V30 6 1 8 7 | ||
M V30 7 1 5 8 | ||
M V30 8 1 10 9 | ||
M V30 9 2 10 11 | ||
M V30 10 1 7 12 | ||
M V30 11 1 1 5 | ||
M V30 12 1 15 14 CFG=1 | ||
M V30 13 2 14 13 | ||
M V30 14 1 15 16 | ||
M V30 15 1 15 17 | ||
M V30 16 1 17 4 | ||
M V30 17 1 18 14 | ||
M V30 18 1 10 19 | ||
M V30 19 1 12 20 | ||
M V30 20 2 20 21 | ||
M V30 21 1 20 22 | ||
M V30 END BOND | ||
M V30 END CTAB | ||
M END |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,32 @@ | ||
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Marvin 06030906502D | ||
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0 0 0 0 0 999 V3000 | ||
M V30 BEGIN CTAB | ||
M V30 COUNTS 8 8 0 0 0 | ||
M V30 BEGIN ATOM | ||
M V30 1 C 0.7476 -1.4581 0 0 | ||
M V30 2 C -0.7885 -1.4581 0 0 | ||
M V30 3 C 1.6627 -2.6967 0 0 | ||
M V30 4 O 1.6627 -0.2009 0 0 | ||
M V30 5 O -1.5659 -0.1115 0 0 | ||
M V30 6 O -1.5659 -2.786 0 0 | ||
M V30 7 C 3.1431 -2.2244 0 0 | ||
M V30 8 C 3.1431 -0.6844 0 0 | ||
M V30 END ATOM | ||
M V30 BEGIN BOND | ||
M V30 1 1 1 2 | ||
M V30 2 1 1 3 | ||
M V30 3 1 1 4 | ||
M V30 4 1 2 5 | ||
M V30 5 2 2 6 | ||
M V30 6 1 3 7 | ||
M V30 7 1 4 8 | ||
M V30 8 1 7 8 | ||
M V30 END BOND | ||
M V30 END CTAB | ||
M END | ||
> <prop1> | ||
4 | ||
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||
$$$$ |
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We really need to stop doing this - this line can consume unbounded memory on relatively sane user supplied inputs. I guess there are a lot of instances of it though and I'm not finding my previous advice on fixing it. (I believe the right thing to do is pick a maximum line size and use readlines directly instead of the iterator).
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xref. #4319