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Metals in mol2 blocks handled incorrectly #438

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greglandrum opened this issue Feb 21, 2015 · 0 comments
Closed

Metals in mol2 blocks handled incorrectly #438

greglandrum opened this issue Feb 21, 2015 · 0 comments
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In [5]: mol2="""@<TRIPOS>MOLECULE
   ...: UNK
   ...: 6 4 0 0 0
   ...: SMALL
   ...: GASTEIGER
   ...: 
   ...: @<TRIPOS>ATOM
   ...:    1   Na        0.0000    0.0000    0.0000 Na    1 UNL  1.0000
   ...:    2    C        0.0000    0.0000    0.0000 C.3   1 UNL -0.0305
   ...:    3    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
   ...:    4    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
   ...:    5    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
   ...:    6    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
   ...: @<TRIPOS>BOND
   ...:     1     2     3  1
   ...:     2     2     4  1
   ...:     3     2     5  1
   ...:     4     2     6  1
   ...: """

In [6]: mol = Chem.MolFromMol2Block(mol2)

In [7]: Chem.MolToSmiles(mol)
Out[7]: 'C.[Na-]'

Identified as part of #415

@greglandrum greglandrum added this to the 2015_03_1 milestone Feb 21, 2015
@greglandrum greglandrum self-assigned this Feb 21, 2015
mwojcikowski pushed a commit to mwojcikowski/rdkit that referenced this issue Mar 27, 2015
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