Features imported from CDX and CDXML files

Atoms

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

ChemBioDraw

ChemAxon

Comment

Charge

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

 

Isotope

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

 

Isotopic Abundance

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/error.png

 

Substituents up to

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

's<n>' query property up to 6

Substituents Exactly

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

's<n>' query property up to 6

Free Sites

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

*0 is converted to 's*', others are converted to 's<n>', calculated: Free Sites-number of bonds.

Unsaturation

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

'u' query property if set to 'Must be absent'

Reaction Change

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/error.png

 

Reaction Stereo

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

 

Translation

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/error.png

 

Abnormal Valence

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/error.png

 

Enhanced Stereochemistry

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

 

Radical

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

 

Implicit Hydrogens

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

If not allowed, the atom gets a 'h0' query property

Ring Bond Count

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

 

Hdot / HDash

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Imported as explicit hydrogens

Generic labels

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

Label

ChemDraw

ChemAxon

A

Any Atom

Any atom type

M

Metal

Pseudo atom: M

Q

Non-hydrogen heteroatom

Hetero atom type

X

Halogen

Pseudo atom type

R

Unspecified

R-group atom type

Bonds

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

ChemBioDraw

ChemAxon

Comment

Single bond

Plain

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single bond

Dashed

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single bond Down

Hashed

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Hashed

Hashed Wedged

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Singe bond Down

Bold

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Bold bond

Bold Wedged

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single bond Up

Hollow Wedged

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single bond Up

Dative

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Coordinative bond

Wavy

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single bond Up or Down

Double bonds

Plain

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Double bond

Bold

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Double bond

Double Either

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Double bond

Tautomeric

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single or double query bond type

Aromatic

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Aromatic bond

Triple bond

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Triple bond

Quadruple bond

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Any bond

Bond properties

Query bonds

Any

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Any bond

S/D

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single or double query bond type

S/A

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single or aromatic query bond type

D/A

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Double or aromatic query bond type

Topology

Ring

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Bond is in ring

Chain

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Bond is in chain

Ring or Chain

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

No topology

Reaction center

Center

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

The bond is a reacting center.

Make/Break

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

The bond is made or broken in the reaction

Change

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

The bond (order) has changed in the reaction

Make and Change

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

The bond is created and changed

Not Center

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

The bond is not a reacting center

Not modified

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

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

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single reaction arrow type

Bold

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single reaction arrow type

Dashed

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single reaction arrow type

One-Sided

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single reaction arrow type

Hollow

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single reaction arrow type

No Go

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Single reaction arrow type

Retrosynthetic

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Double reaction arrow type

Resonance

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Resonance arrow type

Equilibrium

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Equilibrium arrow type

Degree arrows

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

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

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Generic S-group type

Anypolymer (anyp)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Any polymer S-group type

Component (c)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Component S-group type

Copolymer (co)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Copolymer S-group type

Copolymer, alternating (alt)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Copolymer S-group type with alternating polymer S-group subtype

Copolymer, block (blk)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Copolymer S-group type with block polymer S-group subtype

Copolymer, random (ran)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Copolymer S-group type with random polymer S-group subtype

Crosslink (xl)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Crosslink S-group type

Generic ()

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Generic S-group type

Graft (grf)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Graft S-group type

Mer (mer)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Mer S-group type

Mixture, ordered (f)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Formulation S-group type.

Mixture, unordered (mix)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Mixture S-group type

Modification (mod)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Modification S-group type

Monomer (mon)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Monomer S-group type

Multiple Group (#)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Multiple group S-group type

SRU (n)

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

SRU S-group type

Repeat pattern

Head-to-Tail

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Head-to-tail S-group connectivity

Head-to-Head

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Head-to-head S-group connectivity

Either/Unknown

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Either unknown S-group connectivity

Flip Type

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Supported

Symbols

ChemBioDraw

ChemAxon

ChemAxon

Lone Pairs

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

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

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

If there is a label in the cdx file, the absolute stereo flag is set to the molecule.

Complex graphics

ChemBioDraw

ChemAxon

ChemAxon

Tables

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

Tables are imported as graphical objects. The cell size and relative positions are retained, and the cells visualized by rectangles.

TLC plates

images/s/en_GB/6219/97b73ca06fd2a90682d80f34d4c4c163eebdd511.89/_/images/icons/emoticons/check.png

TLC plate drawing is imported with graphical elements, keeping original positions.