Two question about mol file conformer reading:
Looking through the .mol files included for testing, and chose
"Code/GraphMol/Depictor/test_data/7UPJ_spread.mol" at random.
When I read in this file using the RDKit::MolFileToMol function, and then
query its conformer's is3D() method, it returns true even though it is
definitely a 2D depiction in the file. I'm not totally familiar with the
MDL file specifications, so is there some flag I'm missing in the file?
Second question,
When I read in a file with a 3D conformer, and then later use
compute2DCoords, followed by WedgeMolBonds, it adds wedges to non-chiral
atoms. Is this by design? It definitely does serve to convey 3D
information from the file in the depiction, but I'd also like to know how
to disable it if possible. Would running assignStereochemistry fix the
issue.
The mol file for the second question is pasted below, and here is the
generated depiction,
[image: Inline image 2]
aspirin.mol
21 21 0 0 0
-2.2240 -1.4442 -0.4577 C 0 0 0 0 0
-2.1657 -0.0545 -0.5349 C 0 0 0 0 0
-0.9916 0.6085 -0.1694 C 0 0 0 0 0
0.1471 -0.0738 0.2764 C 0 0 0 0 0
0.0751 -1.4832 0.3390 C 0 0 0 0 0
-1.1052 -2.1532 -0.0188 C 0 0 0 0 0
1.2412 -2.2934 0.7925 C 0 0 0 0 0
2.4223 -1.7619 1.1727 O 0 0 0 0 0
1.1650 -3.5162 0.8364 O 0 0 0 0 0
1.2795 0.6233 0.5954 O 0 0 0 0 0
1.1005 1.7577 1.3258 C 0 0 0 0 0
2.4429 2.3635 1.6825 C 0 0 0 0 0
0.0255 2.2041 1.6578 O 0 0 0 0 0
-3.1430 -1.9775 -0.7500 H 0 0 0 0 0
-3.0382 0.5167 -0.8915 H 0 0 0 0 0
-0.9608 1.7083 -0.2479 H 0 0 0 0 0
-1.1740 -3.2520 0.0315 H 0 0 0 0 0
2.9869 -2.5132 1.4166 H 0 0 0 0 0
2.3142 3.3967 2.0773 H 0 0 0 0 0
3.1051 2.4141 0.7884 H 0 0 0 0 0
2.9391 1.7459 2.4657 H 0 0 0 0 0
1 2 2 0 0 0
1 6 1 0 0 0
1 14 1 0 0 0
2 3 1 0 0 0
2 15 1 0 0 0
3 4 2 0 0 0
3 16 1 0 0 0
4 5 1 0 0 0
4 10 1 0 0 0
5 6 2 0 0 0
5 7 1 0 0 0
6 17 1 0 0 0
7 8 1 0 0 0
7 9 2 0 0 0
8 18 1 0 0 0
10 11 1 1 0 0
11 12 1 0 0 0
11 13 2 0 0 0
12 19 1 0 0 0
12 20 1 6 0 0
12 21 1 1 0 0
M END
Thanks,
Jason
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