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_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Isotope

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Isotopic Abundance

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/error.svg

Substituents up to

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

's<n>' query property up to 6

Substituents Exactly

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

's<n>' query property up to 6

Free Sites

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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

Unsaturation

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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

Reaction Change

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/error.svg

Reaction Stereo

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Translation

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/error.svg

Abnormal Valence

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/error.svg

Enhanced Stereochemistry

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Radical

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Implicit Hydrogens

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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

Ring Bond Count

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Hdot / HDash

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single bond

Dashed

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single bond Down

Hashed

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Hashed

Hashed Wedged

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Singe bond Down

Bold

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Bold bond

Bold Wedged

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single bond Up

Hollow Wedged

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single bond Up

Dative

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Coordinative bond

Wavy

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single bond Up or Down

Double bonds

Plain

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Double bond

Bold

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Double bond

Double Either

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Double bond

Tautomeric

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single or double query bond type

Aromatic

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Aromatic bond

Triple bond

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Triple bond

Quadruple bond

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Any bond

Bond properties

Query bonds

Any

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Any bond

S/D

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single or double query bond type

S/A

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single or aromatic query bond type

D/A

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Double or aromatic query bond type

Topology

Ring

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Bond is in ring

Chain

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Bond is in chain

Ring or Chain

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

No topology

Reaction center

Center

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

The bond is a reacting center.

Make/Break

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

The bond is made or broken in the reaction

Change

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

The bond (order) has changed in the reaction

Make and Change

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

The bond is created and changed

Not Center

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

The bond is not a reacting center

Not modified

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single reaction arrow type

Bold

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single reaction arrow type

Dashed

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single reaction arrow type

One-Sided

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single reaction arrow type

Hollow

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single reaction arrow type

No Go

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Single reaction arrow type

Retrosynthetic

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Double reaction arrow type

Resonance

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Resonance arrow type

Equilibrium

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Equilibrium arrow type

Degree arrows

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Generic S-group type

Anypolymer (anyp)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Any polymer S-group type

Component (c)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Component S-group type

Copolymer (co)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Copolymer S-group type

Copolymer, alternating (alt)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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

Copolymer, block (blk)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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

Copolymer, random (ran)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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

Crosslink (xl)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Crosslink S-group type

Generic ()

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Generic S-group type

Graft (grf)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Graft S-group type

Mer (mer)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Mer S-group type

Mixture, ordered (f)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Formulation S-group type.

Mixture, unordered (mix)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Mixture S-group type

Modification (mod)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Modification S-group type

Monomer (mon)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Monomer S-group type

Multiple Group (#)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Multiple group S-group type

SRU (n)

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

SRU S-group type

Repeat pattern

Head-to-Tail

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Head-to-tail S-group connectivity

Head-to-Head

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Head-to-head S-group connectivity

Either/Unknown

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Either unknown S-group connectivity

Flip Type

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

Supported

Symbols

ChemBioDraw

ChemAxon

ChemAxon

Lone Pairs

images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg

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