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MDL Mol/SDF V2000 vs V3000

posted Dec 24, 2017, 3:29 PM by Dong Xu   [ updated Dec 24, 2017, 3:31 PM ]
Most apps: obabel, ChemAxon etc. can handle the conversion:

http://open-babel.readthedocs.io/en/latest/FileFormats/MDL_MOL_format.html
https://forum.chemaxon.com/ftopic10939.html

http://wiki.jmol.org/index.php/File_formats/Coordinates#MOL_and_SD_.28Symyx_MDL.29


1000-atom limit

alanine.2D.v3000

L-Alanine
GSMACCS-II07189510252D 1   0.00366     0.00000     0
Example taken from Symyx CTFile formats (pdf) p.83 Nov.07
  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 6 5 0 0 1
M  V30 BEGIN ATOM
M  V30 1 C -0.6622 0.5342 0 0 CFG=2
M  V30 2 C 0.6622 -0.3 0 0
M  V30 3 C -0.7207 2.0817 0 0 MASS=13
M  V30 4 N -1.8622 -0.3695 0 0 
M  V30 5 O 0.622 -1.8037 0 0
M  V30 6 O 1.9464 0.4244 0 0 
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 1 3 CFG=1
M  V30 3 1 1 4
M  V30 4 2 2 5
M  V30 5 1 2 6
M  V30 END BOND
M  V30 END CTAB
M  END 
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