CDX

Codename: cdx, cdxml

The cdx format of CambridgeSoft's ChemDraw is imported and exported by Marvin. The import of cdxml format is supported, but export isn't.

Import

The following node types are imported:

• Element
• Element List
• Nickname
• Fragment
• Generic Label
• Alternative Group
• Attachment Point
• Link Node
• Variable Attachment
• Multi Attachment
• Anonymous Alternative Group

We do not support these types at the moment:

• ElementListNickname

Detailed import features

Element

The 'Element' type node is read as a single atom. For the supported properties see the supported Atom properties list.

Element List

Element Lists are read as Marvin's Atom List (or not list). For the supported properties see the supported node properties list.

Label

Labels are converted to an S-group and appear contracted in the sketch.

Generic Label

Generic Labels are read as Generic query atoms. See details.

Atom properties

Following properties are supported: charge, isotope, substituents, free sites, unsaturation, reaction stereo, enhanced stereochemistry, radical, ring bond count. See details.

Attachment Points

Attachment Point is imported as atom property, unlimited number.

Bond types

Single bonds, double bonds, query bonds, topology, reaction centers are imported. See details.

Reaction arrows

All types of arrows are imported, but only one arrow per file. See details.

Bracketed groups

All groups are imported. See details.

Alternative Group

Alternative Groups are read as R-groups, up to two connections per R-group.

Anonymous Alternative Group

An Anonymous Alternative Group is imported as R-group and is assigned the R-group number n+1 where n is the largest R-group number in the file.

Link Node

Link Node is read as Link Node.

Variable Attachment and Multi-Center Attachment

These are imported as Multicenter S-groups.

Text Box

Marvin reads the position and the formatted text.

Basic Graphic Objects

Ellipses, rectangles and some of the symbols are read. See details.

Graphic Objects

Tables and TLC plate drawings are imported as graphics. See details.

Notes

• ElectronFlow is not supported.
• Only ASCII characters are imported.
• Complex graphical objects (e.g. laboratory equipment drawings, biological drawings) are not imported.
• R-logic import is supported, export not yet.

Export

• Chemical structures
• Formatted text
• R-groups
• S-groups See details.
• Atom and bond query properties See details.
• Rectangles, rounded rectangles and ellipses
• Reactions See details.