A simple example

Given the following graphical drawing for dimethylamine:

Let us look some sample CDX and CDXML files that can represent this structure. Note that these are not the exact files as produced by ChemDraw. When ChemDraw writes files, it stores a lot of information so that it can preserve every single state in the drawing environment exactly. In many case, much of that information can be extraneous, particularly if you are interested only in the chemical content of a file.

These files can be compared to those in the next example to see the sorts of extraneous information that ChemDraw writes. As you will see, most of it is related to graphical attributes such as bond width, or related to logical attributes such as a bounding box. The examples immediately below are good examples to study if you want to create a program that writes CDX or CDXML files; the ones in the next example are good ones to study if you want to write a program that reads CDX or CDXML files as produced by ChemDraw.

Note how little is actually specified in these files. Default values (such as treating a node as an unlabeled carbon atom unless otherwise specified) take care of most of the most-common cases. As an aside, these files could be made even shorter by omitting the coordinates of the three atoms. ChemDraw would generate reasonable coordinates automatically, but there's not much chance that ChemDraw's autogenerated coordinates would exactly match the originals.

These files can be represented schematically like this:

Objects are circled and the properties they contain radiate from them. Object nesting is represented by hierarchy. The one and only fragment (ID 8) object holds the entire molecule. Nodes 4 and 6 are the two carbon atoms; Node 5 is the nitrogen.

The CDX version

Original binary version

56 6A 43 44 30 31 30 30 04 03 02 01 00 00 00 00
00 00 00 00 00 00 00 00 00 00 00 00 01 80 01 00
00 00 03 80 08 00 00 00 04 80 05 00 00 00 00 02
08 00 00 40 A4 00 00 80 94 00 02 04 02 00 07 00
00 00 04 80 06 00 00 00 00 02 08 00 BA 03 AC 00
4F 7A B1 00 00 00 05 80 02 00 00 00 04 06 04 00
0C 00 00 00 05 06 04 00 0D 00 00 00 00 00 04 80
04 00 00 00 00 02 08 00 BA 03 AC 00 B0 85 77 00
00 00 05 80 03 00 00 00 04 06 04 00 0C 00 00 00
05 06 04 00 0F 00 00 00 00 00 00 00 00 00 00 00
 

The CDXML version

<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE CDXML SYSTEM "http://www.camsoft.com/xml/cdxml.dtd" >
<CDXML
><page
><fragment
><n
id="5"
p="148.5 164.25"
Element="7"
></n><n
id="6"
p="177.48 172.01"
/><n
id="4"
p="119.52 172.01"
/><b
B="5"
E="6"
/><b
B="5"
E="4"
/></fragment></page></CDXML>

Comparison

Here is a side-by-side listing of the two file formats to highlight how similar they are. The CDX file is byte-for-byte identical to the original listing above.

The CDXML file has been rearranged to match the order of the CDX file. Since objects and fragments can be listed in any order, this reordering produces a valid CDXML file in its own right.

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