Difference between revisions of "Support for stereochemistry"
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AngelHerraez (talk | contribs) (new section for stereochemistry support) |
AngelHerraez (talk | contribs) (→MOL formats) |
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''This includes all formats based on the chemical table files (CTfiles) specification from MDL/Symyx, like <code>mol</code>, <code>sdf</code>, etc.'' | ''This includes all formats based on the chemical table files (CTfiles) specification from MDL/Symyx, like <code>mol</code>, <code>sdf</code>, etc.'' | ||
| − | In the CTfile specification, stereochemistry is specified in the bond line, columns 10-12, with a numeric code (see the table). | + | In the CTfile specification, stereochemistry is specified in the bond line, columns 10-12 (the 4th number in the row), with a numeric code (see the table). |
If the model is flat (2D, all atoms have Z=0) '''and''' the <code>filter "2D"</code> switch is used in the <code>load</code> command, Jmol v.12 will use the stereo information to build a 3D model. | If the model is flat (2D, all atoms have Z=0) '''and''' the <code>filter "2D"</code> switch is used in the <code>load</code> command, Jmol v.12 will use the stereo information to build a 3D model. | ||
Revision as of 19:37, 30 April 2010
Jmol supports stereochemistry in some 2D file formats.
MOL formats
This includes all formats based on the chemical table files (CTfiles) specification from MDL/Symyx, like mol, sdf, etc.
In the CTfile specification, stereochemistry is specified in the bond line, columns 10-12 (the 4th number in the row), with a numeric code (see the table).
If the model is flat (2D, all atoms have Z=0) and the filter "2D" switch is used in the load command, Jmol v.12 will use the stereo information to build a 3D model.
JME format
This is only a 2D format, but allows specification of "up" and "down" wedge bonds (see the table). Jmol v.12 reads these and uses them when converting the model to 3D, which is done automatically upon load.
Bond codes
| stereo bond | bond code in MOL file | bond code in JME file |
|---|---|---|
| up | 1 | -1 |
| down | 6 | -2 |
