metamolecular / mx

Using d2312f3, this test passes, but it should fail.

A query containing hypervalent sulfur and nitrogen should match regardless of whether double bond or charge-separated forms are used.

Neither MolfileReader nor MolfileWriter currently support atom values (V) in the properties block. For example:

[NO NAME]
  CHEMWRIT          2D
Created with MX - http://rapodaca.github.com/mx
  6  6  0  0  0  0  0  0  0  0  0 V2000
   -8.0649    0.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1989    0.2078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3329    0.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3329    1.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1989    2.2078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0649    1.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
V    1 This is carbon 1
V    2 This is carbon 2
V    3 And this is carbon 3
M  END

A partially-implemented SMILES is not very useful and casts doubt on the completeness of other MX features. SMILESReader should be placed into a separate branch and worked on until it is fully implemented, then moved onto master and into subsequent releases.

An atom symbol of "D" should be interpreted as deuterium by MolfileReader.