why transform folds hydrogens by default?
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Karen Karapetyan
Mar 28, 2013, 11:29:19 AM3/28/13
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Hi,
I came across a molecule that has several explicit hydrogens and I suddenly learned that transform for some reason is folding them.
I would think that transform would only apply change that is given in smirks. Other drawback in this particular case is that transform also folded hydrogen in C=N-H that is carrying E/Z stereo.
Doesn't matter what reaction you feed into transform.
Please have transform do only transformation and not some hidden additional manupulation to the record.
input:
--------------------------
-INDIGO-03281311212D
22 22 0 0 1 0 0 0 0 0999 V2000
13.8150 -10.4071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.4656 -9.0446 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.9623 -9.7492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.2829 -9.0446 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.7974 -7.5557 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.9209 -7.9203 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.8743 -7.2227 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
12.8338 -7.9203 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
15.9579 -7.9848 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
14.8342 -8.3482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.9575 -7.5568 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
14.2046 -6.4018 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.3438 -8.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.2188 -5.5000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
10.2813 -11.6875 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.1250 -13.0938 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
7.0625 -6.6563 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.1563 -10.0938 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
13.7813 -8.6250 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
13.8125 -12.5625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.7346 -13.6182 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
12.5086 -13.3664 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
4 2 2 0 0 0 0
4 3 1 0 0 0 0
6 4 1 0 0 0 0
6 5 1 0 0 0 0
7 6 1 0 0 0 0
8 7 1 0 0 0 0
8 2 1 0 0 0 0
11 8 1 0 0 0 0
10 9 1 0 0 0 0
11 10 1 0 0 0 0
11 12 1 1 0 0 0
13 5 1 0 0 0 0
14 12 1 0 0 0 0
15 3 2 0 0 0 0
15 16 1 0 0 0 0
17 13 1 0 0 0 0
13 18 1 0 0 0 0
8 19 1 1 0 0 0
20 1 2 0 0 0 0
20 21 1 0 0 0 0
20 22 1 0 0 0 0
M END
--------------------------
after transform
-------------------
-INDIGO-03281311232D
15 15 0 0 1 0 0 0 0 0999 V2000
-0.2788 1.7601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3090 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8968 1.7601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3090 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5691 -0.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.6180 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8090 -0.5878 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-2.1100 -1.5962 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.1590 -1.2872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9511 -0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-1.6942 0.3601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.7770 -1.2872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8913 1.6555 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.1280 2.6736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
4 2 2 0 0 0 0
4 3 1 0 0 0 0
6 4 1 0 0 0 0
6 5 1 0 0 0 0
7 6 1 0 0 0 0
8 7 1 6 0 0 0
8 2 1 0 0 0 0
11 8 1 0 0 0 0
10 9 1 0 0 0 0
11 10 1 0 0 0 0
11 12 1 6 0 0 0
13 5 1 0 0 0 0
14 3 2 0 0 0 0
15 1 2 0 0 0 0
M END
----------------------
Ken
Karen Karapetyan
Mar 28, 2013, 11:36:23 AM3/28/13
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Here is smiles before: [H]/N=C/C1C(OC)O[C@H]([C@@H](O)CO)C=1C=C
smiles after: COC1O[C@H]([C@@H](O)CO)C(C=C)=C1C=N
stereo on double bond is gone
Mikhail Rybalkin
Apr 3, 2013, 4:58:05 AM4/3/13
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Hi Ken,
Thank you for this example. We simple forgot about such case.
Could you try a development build with this issue fixed: http://ggasoftware.com/download/indigo/dev#indigo-119trans
If everything works fine we will include this change in the main branch.
Best regards,
Mikhail
Karen Karapetyan
Apr 3, 2013, 3:12:22 PM4/3/13
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Yep, works fine.
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