[OpenBabel-Devel] [ openbabel-Bugs-3505116 ] genalias does not remove hydrogens in the aliased group

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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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