Hello all,
Regarding kekulization, should the bond type change from 4 to 1 and/or 2?
If I have the following file, what does the function
FixBondOrdersTool.kekuliseAromaticRings(IAtomContainer) change actually? I
am a bit confused. When I apply the function to the molecie MOL 1 below
after adding explicit H atoms (Not necessary in general but it's part of my
costum function), I get the molecule MOL2. The bond types remain the same.
Moreover, I was told in an earlier email that I should recreate a new
molecule after adding hydrogens (because all added hydrogens had the same
set of coordinates at 0.000). However, as you can see, thehydrogen atoms in
molecule MOL2 (even the one in MOL 1 that had non-zero x and y coordinates)
have the coordinates (0,0,0).
Thanks for your consideration.
MOL1
10 10 0 0 0 0 0 0 0 0999 V2000
-2.8875 -2.9759 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.7125 -2.9759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0625 -2.9759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8875 -3.8009 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.6500 -3.6904 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8250 -3.6904 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4125 -2.9759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8250 -2.2614 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6500 -2.2614 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4125 -2.9759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
3 5 4 0 0 0 0
3 9 4 0 0 0 0
5 6 4 0 0 0 0
6 7 4 0 0 0 0
7 8 4 0 0 0 0
8 9 4 0 0 0 0
7 10 1 0 0 0 0
M END
$$$$
MOL2
CDK 0421151530
16 16 0 0 0 0 0 0 0 0999 V2000
1.2990 -0.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 -2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5981 -0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2990 2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2990 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8971 2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5981 -3.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.1782 -1.9895 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7860 -3.6595 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.8971 3.7500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.3743 2.5105 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.4101 0.8405 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
3 5 4 0 0 0 0
3 9 4 0 0 0 0
5 6 4 0 0 0 0
6 7 4 0 0 0 0
7 8 4 0 0 0 0
8 9 4 0 0 0 0
7 10 1 0 0 0 0
2 11 1 0 0 0 0
2 12 1 0 0 0 0
2 13 1 0 0 0 0
10 14 1 0 0 0 0
10 15 1 0 0 0 0
10 16 1 0 0 0 0
M END
$$$$
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