Difference between revisions of "Support for stereochemistry"
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== MOL formats == | == MOL formats == | ||
| − | ''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 |
| + | [[File_formats/Coordinates#MOL_and_SD_.28Symyx_MDL.29|<code>mol</code>, <code>sdf</code>]], 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). | 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. After that, the bonds will be assigned as single. |
== JME format == | == JME format == | ||
| − | This is only a 2D format, but allows specification of "up" and "down" wedge bonds (see the table). | + | This ([[File_formats/Coordinates#JME|Peter Ertl's JME Molecular Editor]]) 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. | + | Jmol v.12 reads these and uses them when converting the model to 3D, which is done automatically upon load. After that, the bonds will be assigned as single. |
== Bond codes == | == Bond codes == | ||
Latest revision as of 08:52, 21 May 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. After that, the bonds will be assigned as single.
JME format
This (Peter Ertl's JME Molecular Editor) 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. After that, the bonds will be assigned as single.
Bond codes
| stereo bond | bond code in MOL file | bond code in JME file |
|---|---|---|
| up | 1 | -1 |
| down | 6 | -2 |
