1. petermr
  2. curly


curly /

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To create animated CMLReactions.

Creating snapshots
Author reaction snapshots in Chemdraw. Make sure to add new molecules in
each snapshot before deleting old ones. This will create a unique id scheme
for mapping reactants to products.

All snapshots should be labelled intermediate{0-n}.cdx. intermediate0.cdx is
always the initial starting material(s) but the final products are simlest the highest
numbered intermediate{n}.cdx.

A snapshot (other than the first and last) should contain all the products of the preceding
reaction step and all the reactants of the following one. Where a molecule is common it should
NOT be deleted and redrawn as this will foul up the ids.

Each reaction sequence should be in a separate directory. The directory structure itself can
be variable depth. Each directory will look like:

		... etc.

Processing is through lensfield2. Unfortunately it cannot yet do all steps so we also use 
crystaleye-processor. The steps are defined in build files. Each build*.lf has to be copied to build.lf

* build00.lf	// converts intermediaten.cdx to CML and then removes CDX attributes
* build0.lf	// makes directories step0, step1 ... stepn
		// writes intermediate{n}.cml to step(n-1)/product.cml
		// writes intermediate{n}.cml to step(n)/reactant.cml
		// this creates the right files in the directories except there is
		// a final directory that should be removed . lensfield cannot
		// yet do this
* build1.xml	// this merges thr reactant.cml and product.cml into a single reaction.cml
		// it's not under lensfield yet so we run crystaleye-moieties software
		// the file must be edited to point to the toplevel of the directories
		// e.g.     <outputDirectory>../curly/orgtest1</outputDirectory>
		// for each visitor
* build2.lf	// maps the atoms and bonds, adds electrons and creates CMLLite
		// more may be added here.