Features imported from CDX and CDXML files
Atoms
The atom features from the CDX file format import limitations are the following:
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ChemBioDraw |
ChemAxon |
Comment |
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Charge |
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Isotope |
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Isotopic Abundance |
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Substituents up to |
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's<n>' query property up to 6 |
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Substituents Exactly |
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's<n>' query property up to 6 |
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Free Sites |
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*0 is converted to 's*', others are converted to 's<n>', calculated: Free Sites-number of bonds. |
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Unsaturation |
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'u' query property if set to 'Must be absent' |
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Reaction Change |
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Reaction Stereo |
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Translation |
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Abnormal Valence |
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Enhanced Stereochemistry |
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Radical |
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Implicit Hydrogens |
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If not allowed, the atom gets a 'h0' query property |
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Ring Bond Count |
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Hdot / HDash |
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Imported as explicit hydrogens |
Generic labels
The generic labels from the CDX file format are imported to Marvin as:
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Label |
ChemDraw |
ChemAxon |
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A |
Any Atom |
Any atom type |
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M |
Metal |
Pseudo atom: M |
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Q |
Non-hydrogen heteroatom |
Hetero atom type |
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X |
Halogen |
Pseudo atom type |
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R |
Unspecified |
R-group atom type |
Bonds
The following bond features from the CDX file format are imported to Marvin as:
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ChemBioDraw |
ChemAxon |
Comment |
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Single bond |
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Plain |
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Single bond |
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Dashed |
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Single bond Down |
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Hashed |
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Hashed |
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Hashed Wedged |
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Singe bond Down |
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Bold |
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Bold bond |
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Bold Wedged |
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Single bond Up |
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Hollow Wedged |
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Single bond Up |
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Dative |
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Coordinative bond |
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Wavy |
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Single bond Up or Down |
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Double bonds |
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Plain |
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Double bond |
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Bold |
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Double bond |
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Double Either |
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Double bond |
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Tautomeric |
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Single or double query bond type |
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Aromatic |
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Aromatic bond |
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Triple bond |
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Triple bond |
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Quadruple bond |
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Any bond |
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Bond properties |
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Query bonds |
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Any |
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Any bond |
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S/D |
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Single or double query bond type |
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S/A |
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Single or aromatic query bond type |
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D/A |
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Double or aromatic query bond type |
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Topology |
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Ring |
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Bond is in ring |
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Chain |
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Bond is in chain |
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Ring or Chain |
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No topology |
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Reaction center |
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Center |
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The bond is a reacting center. |
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Make/Break |
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The bond is made or broken in the reaction |
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Change |
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The bond (order) has changed in the reaction |
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Make and Change |
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The bond is created and changed |
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Not Center |
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The bond is not a reacting center |
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Not modified |
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The bond is not modified in the reaction |
Reaction arrow
The following reaction arrows from the CDX file format are imported to Marvin as:
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ChemBioDraw |
ChemAxon |
Comment |
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Solid |
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Single reaction arrow type |
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Bold |
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Single reaction arrow type |
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Dashed |
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Single reaction arrow type |
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One-Sided |
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Single reaction arrow type |
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Hollow |
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Single reaction arrow type |
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No Go |
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Single reaction arrow type |
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Retrosynthetic |
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Double reaction arrow type |
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Resonance |
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Resonance arrow type |
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Equilibrium |
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Equilibrium arrow type |
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Degree arrows |
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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:
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ChemBioDraw |
ChemAxon |
ChemAxon |
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Bracket Usage |
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Unspecified |
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Generic S-group type |
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Anypolymer (anyp) |
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Any polymer S-group type |
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Component (c) |
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Component S-group type |
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Copolymer (co) |
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Copolymer S-group type |
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Copolymer, alternating (alt) |
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Copolymer S-group type with alternating polymer S-group subtype |
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Copolymer, block (blk) |
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Copolymer S-group type with block polymer S-group subtype |
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Copolymer, random (ran) |
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Copolymer S-group type with random polymer S-group subtype |
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Crosslink (xl) |
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Crosslink S-group type |
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Generic () |
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Generic S-group type |
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Graft (grf) |
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Graft S-group type |
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Mer (mer) |
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Mer S-group type |
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Mixture, ordered (f) |
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Formulation S-group type. |
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Mixture, unordered (mix) |
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Mixture S-group type |
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Modification (mod) |
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Modification S-group type |
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Monomer (mon) |
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Monomer S-group type |
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Multiple Group (#) |
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Multiple group S-group type |
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SRU (n) |
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SRU S-group type |
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Repeat pattern |
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Head-to-Tail |
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Head-to-tail S-group connectivity |
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Head-to-Head |
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Head-to-head S-group connectivity |
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Either/Unknown |
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Either unknown S-group connectivity |
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Flip Type |
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Supported |
Symbols
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ChemBioDraw |
ChemAxon |
ChemAxon |
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Lone Pairs |
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Imported as lone pairs, but automatic lone pair calculation writes them over. |
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Abs label |
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If there is a label in the cdx file, the absolute stereo flag is set to the molecule. |
Complex graphics
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ChemBioDraw |
ChemAxon |
ChemAxon |
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Tables |
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Tables are imported as graphical objects. The cell size and relative positions are retained, and the cells visualized by rectangles. |
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TLC plates |
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TLC plate drawing is imported with graphical elements, keeping original positions. |