Features imported from CDX and CDXML files

On this page:

• Atoms

• Generic labels

• Bonds

• Reaction arrow

• Groups

• Symbols

• Complex graphics

Atoms

The atom features from the CDX file format import limitations are the following:

ChemBioDraw	ChemAxon	Comment
Charge
Isotope
Isotopic Abundance
Substituents up to		's<n>' query property up to 6
Substituents Exactly		's<n>' query property up to 6
Free Sites		0 is converted to 's', others are converted to 's<n>', calculated: Free Sites-number of bonds.
Unsaturation		'u' query property if set to 'Must be absent'
Reaction Change
Reaction Stereo
Translation
Abnormal Valence
Enhanced Stereochemistry
Radical
Implicit Hydrogens		If not allowed, the atom gets a 'h0' query property
Ring Bond Count
Hdot / HDash		Imported as explicit hydrogens

Generic labels

The generic labels from the CDX file format are imported to Marvin as:

Bonds

The following bond features from the CDX file format are imported to Marvin as:

ChemBioDraw	ChemAxon	Comment
Single bond
Plain		Single bond
Dashed		Single bond Down
Hashed		Hashed
Hashed Wedged		Singe bond Down
Bold		Bold bond
Bold Wedged		Single bond Up
Hollow Wedged		Single bond Up
Dative		Coordinative bond
Wavy		Single bond Up or Down
Double bonds
Plain		Double bond
Bold		Double bond
Double Either		Double bond
Tautomeric		Single or double query bond type
Aromatic		Aromatic bond
Triple bond		Triple bond
Quadruple bond		Any bond
Bond properties
Query bonds
Any		Any bond
S/D		Single or double query bond type
S/A		Single or aromatic query bond type
D/A		Double or aromatic query bond type
Topology
Ring		Bond is in ring
Chain		Bond is in chain
Ring or Chain		No topology
Reaction center
Center		The bond is a reacting center.
Make/Break		The bond is made or broken in the reaction
Change		The bond (order) has changed in the reaction
Make and Change		The bond is created and changed
Not Center		The bond is not a reacting center
Not modified		The bond is not modified in the reaction

Reaction arrow

The following reaction arrows from the CDX file format are imported to Marvin as:

ChemBioDraw	ChemAxon	Comment
Solid		Single reaction arrow type
Bold		Single reaction arrow type
Dashed		Single reaction arrow type
One-Sided		Single reaction arrow type
Hollow		Single reaction arrow type
No Go		Single reaction arrow type
Retrosynthetic		Double reaction arrow type
Resonance		Resonance arrow type
Equilibrium		Equilibrium arrow type
Degree arrows		Not yet supported, will be converted to electron flows

Note that files containing multi-step reactions are imported with graphical arrows, thus these won't be recognized as single reactions in Marvin.

Groups

The following groups from the CDX file format are imported to Marvin as:

ChemBioDraw	ChemAxon	ChemAxon
Bracket Usage
Unspecified		Generic S-group type
Anypolymer (anyp)		Any polymer S-group type
Component (c)		Component S-group type
Copolymer (co)		Copolymer S-group type
Copolymer, alternating (alt)		Copolymer S-group type with alternating polymer S-group subtype
Copolymer, block (blk)		Copolymer S-group type with block polymer S-group subtype
Copolymer, random (ran)		Copolymer S-group type with random polymer S-group subtype
Crosslink (xl)		Crosslink S-group type
Generic ()		Generic S-group type
Graft (grf)		Graft S-group type
Mer (mer)		Mer S-group type
Mixture, ordered (f)		Formulation S-group type.
Mixture, unordered (mix)		Mixture S-group type
Modification (mod)		Modification S-group type
Monomer (mon)		Monomer S-group type
Multiple Group (#)		Multiple group S-group type
SRU (n)		SRU S-group type
Repeat pattern
Head-to-Tail		Head-to-tail S-group connectivity
Head-to-Head		Head-to-head S-group connectivity
Either/Unknown		Either unknown S-group connectivity
Flip Type		Supported

Symbols

ChemBioDraw	ChemAxon	ChemAxon
Lone Pairs		Imported as lone pairs, but automatic lone pair calculation writes them over. It can be turned off e.g. in MarvinSketch at the Edit > Preferences... > Structure tab.
Abs label		If there is a label in the cdx file, the absolute stereo flag is set to the molecule.

Complex graphics

ChemBioDraw	ChemAxon	ChemAxon
Tables		Tables are imported as graphical objects. The cell size and relative positions are retained, and the cells visualized by rectangles.
TLC plates		TLC plate drawing is imported with graphical elements, keeping original positions.