All atom attributes should be displayed as SMARTS if at least one purely SMARTS attribute exists

[vanoprenko]

Current State

Currently atom attributes are split onto two categories: General and Query Specific.

General properties represent base chemical attributes (charge, isotope mass, valence, radical) and atom alias. Each of these properties, if defined, has its own way of visualization on canvas:

Query Specific properties (ring bond count, H count, substitution count, aromaticity, chirality, etc) represent those properties used in search queries and are displayed as a simple semicolon separated list:

There are two problems with current representation of atom attributes:

1. Some query specific properties may be represented in two different notations: Ketcher (MOL-like) and SMARTS. For example s<n> vs d<n> for substitution count, rb<n> vs x<n> for ring bond count. Other properties have only SMARTS notation, e.g. chirality, aromaticity.
   Properties from the first set are always displayed in Ketcher notation and when mixed in a common list with properties from the second set, resulting set includes a mix of both notations.
2. When both general and query specific properties are defined for an atom, they may overlap when displayed on canvas, resulting in a broken image:
   

Target State (at least one SMARTS)
If at least one SMARTS specific property is defined, the whole set of atom properties (including general and query specific) should be interpreted as SMARTS properties and displayed based on the following rules:

1. No specific visualization for general properties (charge, valence, etc) should be used. Instead, general properties should be included into the common list of atom properties, together with query specific properties. E.g. instead of showing (IV) for valence, a v4 attribute should be added to the attributes list.
2. All properties in the list should be displayed in SMARTS notation (see table below).
3. Similarly, the pop-up window that appears on atom/label hover should display the full list of properties in SMARTS notation.

The list of SMARTS notations for atom properties is as follows:

Property	SMARTS notation	SMARTS Specific
Label	#<n>	N
Charge < 0	-<n>	N
Charge > 0	+<n>	N
Isotope (atomic mass)	<n>	N
Valence	v<n>	N
Radical		N
Ring bond count	x<n>	N
Substitution count	D<n>	N
Unsaturated		N
H count	H<n>	N
Implicit H count	h<n>	N
Inversion		N
Exact change		N
Atom list	#<n1>,#<n2>,...	N
Not atom list	!#<n1>,!#<n2>,...	N
Special atoms	*	N
Aromaticity aromatic	a	Y
Aromaticity aliphatic	A	Y
Ring membership	R<n>	Y
Ring size	r<n>	Y
Connectivity	X<n>	Y
Chirality clockwise	@@	Y
Chirality anticlockwise	@	Y

Target State (no SMARTS features)
If no SMARTS features defined, then Ketcher should display the properties the same way as currently (e.g. valence with I,II,III, ring bond count with rb<n>, atom list with [E1,E2,....] except the following changes

• For atom list display only 8 symbols for the label and show all other symbols on preview
• Display valence and other non-smarts features for atom-lists and special atoms (similar to default atoms)