Bugs item #3505116, was opened at 2012-03-15 03:34
Message generated for change (Tracker Item Submitted) made by baoilleach
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Category: Library Functions
Group: 2.3.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Noel O'Boyle (baoilleach)
Assigned to: Nobody/Anonymous (nobody)
Summary: genalias does not remove hydrogens in the aliased group
Initial Comment:
To create a test file use:
obabel -:C1C(CC)C1 --gen2d -h -O testfile.mol
If we generate the aliases, the ethyl will be replaced. However, none of its
hydrogens are, resulting in an incorrect molecular structure (with lots of
disconnected hydrogen radicals!):
obabel testfile.mol -omol --genalias -xA
OpenBabel03151210282D
14 11 0 0 0 0 0 0 0 0999 V2000
1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 -1.8660 0.0000 * 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
1.9266 0.5350 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7566 -0.7566 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.5335 -1.1430 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4266 -2.4010 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 -2.9360 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2927 -1.8310 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3660 -3.4360 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2927 -2.9010 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.9266 0.5350 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2769 1.0335 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 4 1 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 6 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 7 1 0 0 0 0
3 8 1 0 0 0 0
3 9 1 0 0 0 0
4 13 1 0 0 0 0
4 14 1 0 0 0 0
A 3
Et
M END
1 molecule converted
Note that there is a somewhat related problem with expanding aliases (should
the hydrogens be added or not?), but I don't think this really matters that
much. The user can always explicitly request new hydrogens.
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