Features imported from SKC files¶

Atom features

Bond features

Reaction features

Group features

Graphical objects

Generic labels

Attach data

Chemistry

Chirality

Known Issues

Atom features¶

The following atom features from the SKC file format are imported to Marvin:

ISIS/Draw	Marvin	Comment
General properties
Type
Isotope
Charge
Radical
Valence
Hydrogen display
Atom number		imported as atom map
Number position
Value
Pseudo
Alias
Beilstein		(imported as Pseudo atom)
Map
Query properties
No Implicit Hydrogens		Imported as 'Number of implicit hydrogens=0'
Unsaturated atoms (Unsaturated bond to atom)
Exact change[reaction]
Ring bond count		r* imported as rb*
Reaction stereo
Enhanced stereo
Prevent hydrogen substituents
Allow these atoms		imported as Atom List
Prohibit these atoms		imported as Atom Not List
Font properties
Font, size, bold, italic
Underline, formula
Atom color

Bond features¶

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

ISIS/Draw	Marvin	Comment
Bond type
Single
Double
Triple
Up		(Single Up)
Down		(Single Down)
Either		(Single Up or Down)
Dbl Either		(Double Cis or Trans)
Any
Aromatic
Single/Double		(Single or Double)
Double/Aromatic		(Double or Aromatic)
Single/Aromatic		(Single or Aromatic)
Reacting center
Center
Make/Break
Change
Make/Change
Not Center
Topology
Ring
Chain
Other
Stereo search
Thickness
Color
Crossed bond

Reaction features¶

The following reaction features from the SKC file format are imported to Marvin as:

ISIS/Draw	Marvin	Comment
Reaction arrow		some types of reaction arrows are converted to single reaction arrows
Reactant
Product
Agent
Multiple step reaction		converted to graphic arrows
Reaction and R-group combination
Reaction and S-group combination
Resonance		Resonance arrow type
Equilibrium		Equilibrium arrow type
Degree arrows		converted to electron flows

Note that only one reaction arrow per file is imported because Marvin does not support multistep reactions yet.

Group features¶

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

ISIS/Draw	Marvin	Comment
S-groups
Anypolymer (anyp)		Any polymer S-group type
Component ©		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)		Mixture 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)		Label and bracket type supported, repeat pattern not yet supported
Superatom S-group
Repeating unit with repetition ranges(e.g.2,4-6)
Attached data
R-groups
R-group
Attachment points
R-Logic

Graphical objects¶

All graphical objects except for graphic arc and smooth spline are supported. Line style and Polygon Fill Color are not supported. All text box attributes are imported except for Underlined.

Generic labels¶

All generic labels are imported to Marvin:

Any atom ( A )

Any atom except carbon ( Q )

Any Metal ( M )

Any halogen ( X )

Any Generic

Acyclic

Acyclic hetero

Acyclic alkenyl

Acyclic Carbacyclic

Alkoxy

Alkyl

Alkynyl

Aryl

Cyclic

Carbocyclic

Cycloalkenyl

Cycloalkyl

Heteroaryl

Heterocyclic

Cyclic no carbon

Attach data¶

Import of Data to Atom, Data to Bond, Data to Molecule and Data to Brackets is supported.

Chemistry¶

Import of Autoname, Link node, Create Chiral Flag and residue is supported.

Chirality¶

Import of CHIRAL and AND attributes is supported.

Known Issues¶

The import of the following features has not been implemented yet:

Multicenter bond,

Position variation bond,

Hydrogen bond

Coodination bond

Variable Repeat Group