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Examples_of_CML

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Oliver Stueker edited this page May 5, 2015 · 2 revisions
    • WARNING**: I believe this to be old now. It should be modified or maybe eliminated.

Here are some examples of CML from the current parsers:

Table of Contents

NWChem

molecule

log file output: We use JumboReader to interpret this as a molecule. There are two clues to the identity of the atoms the "tag" and the "charge" (presumably nuclear). Without reading the manual we can't be sure which is important. Note that the default namespace is CML should be added as we have cut-and-pasted. The raw CML looks like: Note that: 

 * all atoms have unique ids
 * all elementTypes are standard IUPAC symbols
 * the coordinates are only defined for 3D cartesians in this example. (CML also supports 2D coordinates, fractional crystallographic coordinates and Z-matrices).
 * the default coordinates are Angstrom. Normally the units are required but {{{cml:molecule}}} is special - sorry. It's possible to set other coordinates for molecule. Perhaps we should always have a flag.
 * all information can be modelled in CML
 * there are no bonds as none were given - this is compchem after all.

tables

Here's an example where we need dictionaries We interpret it as a table with two columns. The semantics are not very clear and there are no labels for the columns. We make up ids for them and create the following.

This has two columns (think of them lying on their side) with the LH at the top, so is the first column and "&#10;&#10;&#10;The"></table}}}>Basis_sets_in_CML

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