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' query property up to 6
    Substituents Exactly images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg 's' 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', 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 images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/check.svg
    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.